From 3bc91df24685cfc5871a03252f82dd0c6f1844ac Mon Sep 17 00:00:00 2001 From: Barry digby Date: Mon, 12 Dec 2022 20:22:52 +0000 Subject: [PATCH 001/491] ch_versions.unique() --- workflows/circrna.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/circrna.nf b/workflows/circrna.nf index 7422dc54..d43b430e 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -208,7 +208,7 @@ workflow CIRCRNA { ch_versions = ch_versions.mix(DIFFERENTIAL_EXPRESSION.out.versions) CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique{ it.text }.collectFile(name: 'collated_versions.yml') + ch_versions.unique().collectFile(name: 'collated_versions.yml') ) // MODULE: MultiQC From b942c7eb7d30ead94d34ce2862bd8e4713035613 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Tue, 13 Dec 2022 10:28:09 +0000 Subject: [PATCH 002/491] release version --- CHANGELOG.md | 2 +- nextflow.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d24a1785..465d994c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.0.0 - [date] +## v1.0.0 - [13/12/2022] Initial release of nf-core/circrna, created with the [nf-core](https://nf-co.re/) template. diff --git a/nextflow.config b/nextflow.config index 2120cb54..c33b8ce2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -249,7 +249,7 @@ manifest { description = """Quantification, miRNA target prediction and differential expression analysis of circular RNAs""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = 'dev' + version = '1.0.0' doi = '' } From 2bc935a1b49de21b249a1d574bbde403f29785b5 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Tue, 13 Dec 2022 11:11:19 +0000 Subject: [PATCH 003/491] publishdir tweaks --- conf/modules.config | 48 ++++++++++++++----- .../deseq2/differential_expression/main.nf | 2 +- 2 files changed, 38 insertions(+), 12 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index b44dd7c1..f535f691 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -75,7 +75,7 @@ if (!params.skip_trimming) { withName: BOWTIE_BUILD { ext.when = { params.fasta && !params.bowtie && params.tool.split(',').contains('mapsplice') && params.module.split(',').contains('circrna_discovery') } publishDir = [ - path: { "${params.outdir}/genome/index/bowtie" }, + path: { "${params.outdir}/references/index/bowtie" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_reference @@ -85,7 +85,7 @@ if (!params.skip_trimming) { withName: BOWTIE2_BUILD { ext.when = { params.fasta && !params.bowtie2 && params.tool.split(',').contains('find_circ') && params.module.split(',').contains('circrna_discovery') } publishDir = [ - path: { "${params.outdir}/genome/index" }, + path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_reference @@ -95,7 +95,7 @@ if (!params.skip_trimming) { withName: BWA_INDEX { ext.when = { params.fasta && !params.bwa && params.tool.split(',').contains('ciriquant') && params.module.split(',').contains('circrna_discovery') } publishDir = [ - path: { "${params.outdir}/genome/index" }, + path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_reference @@ -105,7 +105,7 @@ if (!params.skip_trimming) { withName: HISAT2_EXTRACTSPLICESITES { ext.when = { params.fasta && params.gtf && ( params.module.split(',').contains('differential_expression') || params.tool.split(',').contains('ciriquant') ) } publishDir = [ - path: { "${params.outdir}/genome/index/hisat2" }, + path: { "${params.outdir}/references/index/hisat2" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_reference @@ -115,7 +115,7 @@ if (!params.skip_trimming) { withName: HISAT2_BUILD { ext.when = { params.fasta && params.gtf && ( params.module.split(',').contains('differential_expression') || params.tool.split(',').contains('ciriquant') ) } publishDir = [ - path: { "${params.outdir}/genome/index/hisat2" }, + path: { "${params.outdir}/references/index/hisat2" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_reference @@ -128,7 +128,7 @@ if (!params.skip_trimming) { params.sjdboverhang ? "--sjdbOverhang ${params.sjdboverhang}" : '', ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/genome/index/star" }, + path: { "${params.outdir}/references/index/star" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_reference @@ -138,7 +138,7 @@ if (!params.skip_trimming) { withName: SEGEMEHL_INDEX { ext.when = { params.fasta && !params.segemehl && params.tool.split(',').contains('segemehl') && params.module.split(',').contains('circrna_discovery') } publishDir = [ - path: { "${params.outdir}/genome/index/segemehl" }, + path: { "${params.outdir}/references/index/segemehl" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_reference @@ -231,7 +231,7 @@ if (!params.skip_trimming) { "-geneNameAsName2" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/genome/circexplorer2" }, + path: { "${params.outdir}/references/circexplorer2" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_reference @@ -344,7 +344,7 @@ if (!params.skip_trimming) { withName: CIRIQUANT_YML { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('ciriquant') } publishDir = [ - path: { "${params.outdir}/genome/ciriquant" }, + path: { "${params.outdir}/references/ciriquant" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_reference @@ -546,7 +546,7 @@ if (!params.skip_trimming) { "-geneNameAsName2" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/genome/mapsplice" }, + path: { "${params.outdir}/references/mapsplice" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_reference @@ -636,12 +636,18 @@ withName: MAPSPLICE_PARSE { path: { "${params.outdir}/circrna_discovery/" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - pattern: "*.txt" + pattern: "count_matrix.txt" ] } withName: TARGETSCAN_DATABASE { ext.when = { params.module.split(',').contains('mirna_prediction') } + publishDir = [ + path: { "${params.outdir}/references/targetscan" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + pattern: "mature.txt" + ] } withName: TARGETSCAN { @@ -685,6 +691,12 @@ withName: MAPSPLICE_PARSE { "--dta", "--no-spliced-alignment" ].join(' ').trim() + publishDir = [ + path: { "${params.outdir}/differential_expression/intermediates/hisat2/" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + enabled: params.save_intermediates, + ] } withName: SAMTOOLS_SORT { @@ -729,8 +741,22 @@ withName: MAPSPLICE_PARSE { ] } + withName: PARENT_GENE { + ext.when = { params.module.split(',').contains('differential_expression') } + publishDir = [ + path: { "${params.outdir}/differential_expression/circular_linear_ratio_test" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + withName: PREPARE_CLR_TEST { ext.when = { params.module.split(',').contains('differential_expression') } + publishDir = [ + path: { "${params.outdir}/differential_expression/circular_linear_ratio_test" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] } withName: CIRCTEST { diff --git a/modules/local/deseq2/differential_expression/main.nf b/modules/local/deseq2/differential_expression/main.nf index 83bf6bca..f9b5dacc 100644 --- a/modules/local/deseq2/differential_expression/main.nf +++ b/modules/local/deseq2/differential_expression/main.nf @@ -17,7 +17,6 @@ process DESEQ2_DIFFERENTIAL_EXPRESSION { path "circRNA" , emit: circular_results path "RNA-Seq" , emit: linear_results path "DESeq2_QC" , emit: deseq2_qc - path "*.RData" , emit: rsession path "versions.yml", emit: versions when: @@ -33,6 +32,7 @@ process DESEQ2_DIFFERENTIAL_EXPRESSION { DEA.R $gene_matrix $phenotype $circrna_matrix $species ensembl_database_map.txt mv boxplots/ circRNA/ + mv *.RData DESeq2_QC/ cat <<-END_VERSIONS > versions.yml "${task.process}": From 134217d3d41d381ac907ca7142b605c1fb6bf2a6 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 19 Dec 2022 12:04:47 +0000 Subject: [PATCH 004/491] Template update for nf-core/tools version 2.7.2 --- .github/workflows/fix-linting.yml | 4 +- .github/workflows/linting_comment.yml | 2 +- README.md | 2 +- assets/email_template.html | 2 +- lib/WorkflowMain.groovy | 2 +- modules.json | 6 +- modules/local/samplesheet_check.nf | 2 +- .../custom/dumpsoftwareversions/main.nf | 2 +- .../templates/dumpsoftwareversions.py | 99 ++++++++++--------- modules/nf-core/fastqc/main.nf | 40 +++----- modules/nf-core/multiqc/main.nf | 2 +- nextflow.config | 5 +- nextflow_schema.json | 8 +- workflows/circrna.nf | 2 +- 14 files changed, 86 insertions(+), 92 deletions(-) mode change 100644 => 100755 modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 7e2c46b3..bdf7eb2c 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -34,9 +34,9 @@ jobs: id: prettier_status run: | if prettier --check ${GITHUB_WORKSPACE}; then - echo "name=result::pass" >> $GITHUB_OUTPUT + echo "result=pass" >> $GITHUB_OUTPUT else - echo "name=result::fail" >> $GITHUB_OUTPUT + echo "result=fail" >> $GITHUB_OUTPUT fi - name: Run 'prettier --write' diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 39635186..0bbcd30f 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -18,7 +18,7 @@ jobs: - name: Get PR number id: pr_number - run: echo "name=pr_number::$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT + run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment uses: marocchino/sticky-pull-request-comment@v2 diff --git a/README.md b/README.md index f3e31f4e..75428759 100644 --- a/README.md +++ b/README.md @@ -14,7 +14,7 @@ -**nf-core/circrna** is a bioinformatics best-practice analysis pipeline for circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data. +**nf-core/circrna** is a bioinformatics best-practice analysis pipeline for Quantification, miRNA target prediction and differential expression analysis of circular RNAs. The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! diff --git a/assets/email_template.html b/assets/email_template.html index 0052d4b9..03b6ba6e 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -4,7 +4,7 @@ - + nf-core/circrna Pipeline Report diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 04b19a7d..0d7be86b 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -72,7 +72,7 @@ class WorkflowMain { NfcoreTemplate.checkConfigProvided(workflow, log) // Check that conda channels are set-up correctly - if (params.enable_conda) { + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { Utils.checkCondaChannels(log) } diff --git a/modules.json b/modules.json index 221a73c6..5b7c59e8 100644 --- a/modules.json +++ b/modules.json @@ -7,17 +7,17 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] } } diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 33f77b6e..4e85a56e 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -2,7 +2,7 @@ process SAMPLESHEET_CHECK { tag "$samplesheet" label 'process_single' - conda (params.enable_conda ? "conda-forge::python=3.8.3" : null) + conda "conda-forge::python=3.8.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/python:3.8.3' : 'quay.io/biocontainers/python:3.8.3' }" diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index cebb6e05..3df21765 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,7 +2,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) + conda "bioconda::multiqc=1.13" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py old mode 100644 new mode 100755 index 787bdb7b..e55b8d43 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -1,5 +1,9 @@ #!/usr/bin/env python + +"""Provide functions to merge multiple versions.yml files.""" + + import platform from textwrap import dedent @@ -7,6 +11,7 @@ def _make_versions_html(versions): + """Generate a tabular HTML output of all versions for MultiQC.""" html = [ dedent( """\\ @@ -45,47 +50,53 @@ def _make_versions_html(versions): return "\\n".join(html) -versions_this_module = {} -versions_this_module["${task.process}"] = { - "python": platform.python_version(), - "yaml": yaml.__version__, -} - -with open("$versions") as f: - versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module - -# aggregate versions by the module name (derived from fully-qualified process name) -versions_by_module = {} -for process, process_versions in versions_by_process.items(): - module = process.split(":")[-1] - try: - if versions_by_module[module] != process_versions: - raise AssertionError( - "We assume that software versions are the same between all modules. " - "If you see this error-message it means you discovered an edge-case " - "and should open an issue in nf-core/tools. " - ) - except KeyError: - versions_by_module[module] = process_versions - -versions_by_module["Workflow"] = { - "Nextflow": "$workflow.nextflow.version", - "$workflow.manifest.name": "$workflow.manifest.version", -} - -versions_mqc = { - "id": "software_versions", - "section_name": "${workflow.manifest.name} Software Versions", - "section_href": "https://github.com/${workflow.manifest.name}", - "plot_type": "html", - "description": "are collected at run time from the software output.", - "data": _make_versions_html(versions_by_module), -} - -with open("software_versions.yml", "w") as f: - yaml.dump(versions_by_module, f, default_flow_style=False) -with open("software_versions_mqc.yml", "w") as f: - yaml.dump(versions_mqc, f, default_flow_style=False) - -with open("versions.yml", "w") as f: - yaml.dump(versions_this_module, f, default_flow_style=False) +def main(): + """Load all version files and generate merged output.""" + versions_this_module = {} + versions_this_module["${task.process}"] = { + "python": platform.python_version(), + "yaml": yaml.__version__, + } + + with open("$versions") as f: + versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module + + # aggregate versions by the module name (derived from fully-qualified process name) + versions_by_module = {} + for process, process_versions in versions_by_process.items(): + module = process.split(":")[-1] + try: + if versions_by_module[module] != process_versions: + raise AssertionError( + "We assume that software versions are the same between all modules. " + "If you see this error-message it means you discovered an edge-case " + "and should open an issue in nf-core/tools. " + ) + except KeyError: + versions_by_module[module] = process_versions + + versions_by_module["Workflow"] = { + "Nextflow": "$workflow.nextflow.version", + "$workflow.manifest.name": "$workflow.manifest.version", + } + + versions_mqc = { + "id": "software_versions", + "section_name": "${workflow.manifest.name} Software Versions", + "section_href": "https://github.com/${workflow.manifest.name}", + "plot_type": "html", + "description": "are collected at run time from the software output.", + "data": _make_versions_html(versions_by_module), + } + + with open("software_versions.yml", "w") as f: + yaml.dump(versions_by_module, f, default_flow_style=False) + with open("software_versions_mqc.yml", "w") as f: + yaml.dump(versions_mqc, f, default_flow_style=False) + + with open("versions.yml", "w") as f: + yaml.dump(versions_this_module, f, default_flow_style=False) + + +if __name__ == "__main__": + main() diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 05730368..9ae58381 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -2,7 +2,7 @@ process FASTQC { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) + conda "bioconda::fastqc=0.11.9" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : 'quay.io/biocontainers/fastqc:0.11.9--0' }" @@ -20,30 +20,22 @@ process FASTQC { script: def args = task.ext.args ?: '' - // Add soft-links to original FastQs for consistent naming in pipeline def prefix = task.ext.prefix ?: "${meta.id}" - if (meta.single_end) { - """ - [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz - fastqc $args --threads $task.cpus ${prefix}.fastq.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) - END_VERSIONS - """ - } else { - """ - [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz - [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz - fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) - END_VERSIONS - """ - } + // Make list of old name and new name pairs to use for renaming in the bash while loop + def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } + def rename_to = old_new_pairs*.join(' ').join(' ') + def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') + """ + printf "%s %s\\n" $rename_to | while read old_name new_name; do + [ -f "\${new_name}" ] || ln -s \$old_name \$new_name + done + fastqc $args --threads $task.cpus $renamed_files + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + END_VERSIONS + """ stub: def prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index a8159a57..68f66bea 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,7 +1,7 @@ process MULTIQC { label 'process_single' - conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) + conda "bioconda::multiqc=1.13" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" diff --git a/nextflow.config b/nextflow.config index 31883ad1..eabafb20 100644 --- a/nextflow.config +++ b/nextflow.config @@ -39,7 +39,6 @@ params { validate_params = true show_hidden_params = false schema_ignore_params = 'genomes' - enable_conda = false // Config options @@ -81,7 +80,6 @@ try { profiles { debug { process.beforeScript = 'echo $HOSTNAME' } conda { - params.enable_conda = true conda.enabled = true docker.enabled = false singularity.enabled = false @@ -90,7 +88,6 @@ profiles { charliecloud.enabled = false } mamba { - params.enable_conda = true conda.enabled = true conda.useMamba = true docker.enabled = false @@ -193,7 +190,7 @@ manifest { name = 'nf-core/circrna' author = """Barry Digby""" homePage = 'https://github.com/nf-core/circrna' - description = """circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data""" + description = """Quantification, miRNA target prediction and differential expression analysis of circular RNAs""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' version = '1.0.0' diff --git a/nextflow_schema.json b/nextflow_schema.json index 45425578..b225d480 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -2,7 +2,7 @@ "$schema": "http://json-schema.org/draft-07/schema", "$id": "https://raw.githubusercontent.com/nf-core/circrna/master/nextflow_schema.json", "title": "nf-core/circrna pipeline parameters", - "description": "circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data", + "description": "Quantification, miRNA target prediction and differential expression analysis of circular RNAs", "type": "object", "definitions": { "input_output_options": { @@ -263,12 +263,6 @@ "description": "Show all params when using `--help`", "hidden": true, "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." - }, - "enable_conda": { - "type": "boolean", - "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.", - "hidden": true, - "fa_icon": "fas fa-bacon" } } } diff --git a/workflows/circrna.nf b/workflows/circrna.nf index 400c3a57..448b8fb1 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -82,7 +82,7 @@ workflow CIRCRNA { ch_versions = ch_versions.mix(FASTQC.out.versions.first()) CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique{ it.text }.collectFile(name: 'collated_versions.yml') + ch_versions.unique().collectFile(name: 'collated_versions.yml') ) // From 080056da97d8c50bd48b54da0de3be7b18ea012f Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 19 Dec 2022 12:04:47 +0000 Subject: [PATCH 005/491] Template update for nf-core/tools version 2.7.2 --- .github/workflows/fix-linting.yml | 4 ++-- .github/workflows/linting_comment.yml | 2 +- lib/WorkflowMain.groovy | 2 +- modules.json | 6 +++--- modules/local/samplesheet_check.nf | 2 +- modules/nf-core/custom/dumpsoftwareversions/main.nf | 2 +- .../dumpsoftwareversions/templates/dumpsoftwareversions.py | 3 ++- modules/nf-core/fastqc/main.nf | 2 +- modules/nf-core/multiqc/main.nf | 2 +- nextflow.config | 3 --- nextflow_schema.json | 6 ------ 11 files changed, 13 insertions(+), 21 deletions(-) diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 7e2c46b3..bdf7eb2c 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -34,9 +34,9 @@ jobs: id: prettier_status run: | if prettier --check ${GITHUB_WORKSPACE}; then - echo "name=result::pass" >> $GITHUB_OUTPUT + echo "result=pass" >> $GITHUB_OUTPUT else - echo "name=result::fail" >> $GITHUB_OUTPUT + echo "result=fail" >> $GITHUB_OUTPUT fi - name: Run 'prettier --write' diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 39635186..0bbcd30f 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -18,7 +18,7 @@ jobs: - name: Get PR number id: pr_number - run: echo "name=pr_number::$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT + run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment uses: marocchino/sticky-pull-request-comment@v2 diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 04b19a7d..0d7be86b 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -72,7 +72,7 @@ class WorkflowMain { NfcoreTemplate.checkConfigProvided(workflow, log) // Check that conda channels are set-up correctly - if (params.enable_conda) { + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { Utils.checkCondaChannels(log) } diff --git a/modules.json b/modules.json index 5e7f3bc3..d750d640 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "bowtie/build": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "bowtie2/align": { @@ -32,7 +32,7 @@ }, "cat/fastq": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "circexplorer2/annotate": { @@ -77,7 +77,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "samtools/index": { diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 33f77b6e..4e85a56e 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -2,7 +2,7 @@ process SAMPLESHEET_CHECK { tag "$samplesheet" label 'process_single' - conda (params.enable_conda ? "conda-forge::python=3.8.3" : null) + conda "conda-forge::python=3.8.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/python:3.8.3' : 'quay.io/biocontainers/python:3.8.3' }" diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index cebb6e05..3df21765 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,7 +2,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) + conda "bioconda::multiqc=1.13" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py index da033408..e55b8d43 100755 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -4,10 +4,11 @@ """Provide functions to merge multiple versions.yml files.""" -import yaml import platform from textwrap import dedent +import yaml + def _make_versions_html(versions): """Generate a tabular HTML output of all versions for MultiQC.""" diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 47fd0e58..9ae58381 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -2,7 +2,7 @@ process FASTQC { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) + conda "bioconda::fastqc=0.11.9" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : 'quay.io/biocontainers/fastqc:0.11.9--0' }" diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index a8159a57..68f66bea 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,7 +1,7 @@ process MULTIQC { label 'process_single' - conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) + conda "bioconda::multiqc=1.13" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" diff --git a/nextflow.config b/nextflow.config index c33b8ce2..e0d5c68a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -92,7 +92,6 @@ params { validate_params = true show_hidden_params = false schema_ignore_params = 'genomes' - enable_conda = false // Config options @@ -134,7 +133,6 @@ try { profiles { debug { process.beforeScript = 'echo $HOSTNAME' } conda { - params.enable_conda = true conda.enabled = true docker.enabled = false singularity.enabled = false @@ -143,7 +141,6 @@ profiles { charliecloud.enabled = false } mamba { - params.enable_conda = true conda.enabled = true conda.useMamba = true docker.enabled = false diff --git a/nextflow_schema.json b/nextflow_schema.json index 6b1deb4c..659d8f0d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -526,12 +526,6 @@ "description": "Show all params when using `--help`", "hidden": true, "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." - }, - "enable_conda": { - "type": "boolean", - "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.", - "hidden": true, - "fa_icon": "fas fa-bacon" } } } From 51abcba8d5999a213f26c3e45e439767bc08f85a Mon Sep 17 00:00:00 2001 From: Barry digby Date: Mon, 19 Dec 2022 15:30:35 +0000 Subject: [PATCH 006/491] update remote & local modules --- modules.json | 42 +++++++++---------- .../local/annotation/full_annotation/main.nf | 2 +- modules/local/annotation/parent_gene/main.nf | 2 +- modules/local/circexplorer2/reference/main.nf | 2 +- modules/local/circrna_finder/filter/main.nf | 2 +- modules/local/circtest/prepare/main.nf | 2 +- modules/local/circtest/test/main.nf | 2 +- modules/local/ciriquant/ciriquant/main.nf | 2 +- modules/local/ciriquant/yml/main.nf | 2 +- modules/local/count_matrix/combined/main.nf | 2 +- .../local/count_matrix/merge_tools/main.nf | 2 +- modules/local/count_matrix/single/main.nf | 2 +- modules/local/dcc/dcc/main.nf | 2 +- .../deseq2/differential_expression/main.nf | 2 +- modules/local/fasta/main.nf | 2 +- modules/local/find_circ/anchors/main.nf | 2 +- modules/local/find_circ/filter/main.nf | 2 +- modules/local/find_circ/find_circ/main.nf | 2 +- modules/local/mapsplice/align/main.nf | 2 +- modules/local/mirna_targets/main.nf | 2 +- modules/local/stringtie/prepde/main.nf | 2 +- modules/local/targetscan/predict/main.nf | 2 +- modules/nf-core/bowtie/align/main.nf | 2 +- modules/nf-core/bowtie/build/main.nf | 2 +- modules/nf-core/bowtie2/align/main.nf | 2 +- modules/nf-core/bowtie2/build/main.nf | 2 +- modules/nf-core/bwa/index/main.nf | 2 +- modules/nf-core/cat/fastq/main.nf | 2 +- .../nf-core/circexplorer2/annotate/main.nf | 2 +- modules/nf-core/circexplorer2/parse/main.nf | 2 +- .../templates/dumpsoftwareversions.py | 3 +- modules/nf-core/hisat2/align/main.nf | 2 +- modules/nf-core/hisat2/build/main.nf | 2 +- .../nf-core/hisat2/extractsplicesites/main.nf | 2 +- modules/nf-core/miranda/main.nf | 2 +- modules/nf-core/samtools/index/main.nf | 2 +- modules/nf-core/samtools/sort/main.nf | 2 +- modules/nf-core/samtools/view/main.nf | 2 +- modules/nf-core/segemehl/align/main.nf | 2 +- modules/nf-core/segemehl/index/main.nf | 2 +- modules/nf-core/star/align/main.nf | 2 +- modules/nf-core/star/genomegenerate/main.nf | 2 +- modules/nf-core/stringtie/stringtie/main.nf | 2 +- modules/nf-core/trimgalore/main.nf | 2 +- 44 files changed, 64 insertions(+), 65 deletions(-) diff --git a/modules.json b/modules.json index d750d640..5b501b5f 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "bowtie/align": { "branch": "master", - "git_sha": "653588be2a4aadab487b530643dbc9baf7a485c4", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "bowtie/build": { @@ -17,17 +17,17 @@ }, "bowtie2/align": { "branch": "master", - "git_sha": "1a96d72a3a5079424bc9a9ac5c2ca72902af327f", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "bowtie2/build": { "branch": "master", - "git_sha": "e797efb47b0d3b2124753beb55dc83ab9512bceb", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "bwa/index": { "branch": "master", - "git_sha": "9518fa4f65f3fb8cde24fde7d40333b39ec8fd65", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "cat/fastq": { @@ -37,42 +37,42 @@ }, "circexplorer2/annotate": { "branch": "master", - "git_sha": "e3ae75b5e54042683d5a1889fc733a4bf51f6819", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "circexplorer2/parse": { "branch": "master", - "git_sha": "e3ae75b5e54042683d5a1889fc733a4bf51f6819", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "8022c68e7403eecbd8ba9c49496f69f8c49d50f0", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "810e8f2603ec38401d49a4aaed06f6d058745552", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "hisat2/align": { "branch": "master", - "git_sha": "653588be2a4aadab487b530643dbc9baf7a485c4", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "hisat2/build": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "hisat2/extractsplicesites": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "miranda": { "branch": "master", - "git_sha": "270fc80f29c4dbb1a973ca1d7d748bdd56e97301", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "multiqc": { @@ -82,47 +82,47 @@ }, "samtools/index": { "branch": "master", - "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "samtools/sort": { "branch": "master", - "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "samtools/view": { "branch": "master", - "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "segemehl/align": { "branch": "master", - "git_sha": "a52cd7df53f3e88895362f2c8fd43cfe00fbf1a3", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "segemehl/index": { "branch": "master", - "git_sha": "a52cd7df53f3e88895362f2c8fd43cfe00fbf1a3", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "star/align": { "branch": "master", - "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "star/genomegenerate": { "branch": "master", - "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "stringtie/stringtie": { "branch": "master", - "git_sha": "d0e6f468af1d51ce3ea4ac4fb5e58723eac3938c", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "trimgalore": { "branch": "master", - "git_sha": "b51a69e30973c71950225c817ad07a3337d22c40", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] } } diff --git a/modules/local/annotation/full_annotation/main.nf b/modules/local/annotation/full_annotation/main.nf index 87e4e435..c47bd561 100644 --- a/modules/local/annotation/full_annotation/main.nf +++ b/modules/local/annotation/full_annotation/main.nf @@ -2,7 +2,7 @@ process ANNOTATION { tag "${meta.id}:${meta.tool}" label 'process_high' - conda (params.enable_conda ? "bioconda::ucsc-gtftogenepred=377 bioconda::ucsc-genepredtobed=377 bioconda::bedtools=2.27.0" : null) + conda "bioconda::ucsc-gtftogenepred=377 bioconda::ucsc-genepredtobed=377 bioconda::bedtools=2.27.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-d7ee3552d06d8acebbc660507b48487c7369e221:07daadbfe8182aa3c974c7b78924d5c8730b922d-0' : 'quay.io/biocontainers/mulled-v2-d7ee3552d06d8acebbc660507b48487c7369e221:07daadbfe8182aa3c974c7b78924d5c8730b922d-0' }" diff --git a/modules/local/annotation/parent_gene/main.nf b/modules/local/annotation/parent_gene/main.nf index 4edefbdd..c412ab8d 100644 --- a/modules/local/annotation/parent_gene/main.nf +++ b/modules/local/annotation/parent_gene/main.nf @@ -1,7 +1,7 @@ process PARENT_GENE { label 'process_high' - conda (params.enable_conda ? "bioconda::ucsc-gtftogenepred=377 bioconda::ucsc-genepredtobed=377 bioconda::bedtools=2.27.0" : null) + conda "bioconda::ucsc-gtftogenepred=377 bioconda::ucsc-genepredtobed=377 bioconda::bedtools=2.27.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-d7ee3552d06d8acebbc660507b48487c7369e221:07daadbfe8182aa3c974c7b78924d5c8730b922d-0' : 'quay.io/biocontainers/mulled-v2-d7ee3552d06d8acebbc660507b48487c7369e221:07daadbfe8182aa3c974c7b78924d5c8730b922d-0' }" diff --git a/modules/local/circexplorer2/reference/main.nf b/modules/local/circexplorer2/reference/main.nf index c3097860..ed2b3537 100644 --- a/modules/local/circexplorer2/reference/main.nf +++ b/modules/local/circexplorer2/reference/main.nf @@ -2,7 +2,7 @@ process CIRCEXPLORER2_REFERENCE { tag "$gtf" label 'process_single' - conda (params.enable_conda ? "bioconda::ucsc-gtftogenepred=377 bioconda::ucsc-genepredtobed=377 bioconda::bedtools=2.27.0" : null) + conda "bioconda::ucsc-gtftogenepred=377 bioconda::ucsc-genepredtobed=377 bioconda::bedtools=2.27.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-d7ee3552d06d8acebbc660507b48487c7369e221:07daadbfe8182aa3c974c7b78924d5c8730b922d-0' : 'quay.io/biocontainers/mulled-v2-d7ee3552d06d8acebbc660507b48487c7369e221:07daadbfe8182aa3c974c7b78924d5c8730b922d-0' }" diff --git a/modules/local/circrna_finder/filter/main.nf b/modules/local/circrna_finder/filter/main.nf index 423dee85..06d7cf5c 100644 --- a/modules/local/circrna_finder/filter/main.nf +++ b/modules/local/circrna_finder/filter/main.nf @@ -2,7 +2,7 @@ process CIRCRNA_FINDER_FILTER { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::circrna_finder=1.2" : null) + conda "bioconda::circrna_finder=1.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/circrna_finder%3A1.2--pl5321hdfd78af_1' : 'quay.io/biocontainers/circrna_finder:1.2--pl5321hdfd78af_1' }" diff --git a/modules/local/circtest/prepare/main.nf b/modules/local/circtest/prepare/main.nf index 3b92e52d..47d74346 100644 --- a/modules/local/circtest/prepare/main.nf +++ b/modules/local/circtest/prepare/main.nf @@ -1,7 +1,7 @@ process PREPARE_CLR_TEST { label 'process_medium' - conda (params.enable_conda ? "r-base r-aod r-ggplot2 r-plyr" : null) + conda "r-base r-aod r-ggplot2 r-plyr" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c79b00aa4647c739dbe7e8480789d3ba67988f2e:0' : 'quay.io/biocontainers/mulled-v2-c79b00aa4647c739dbe7e8480789d3ba67988f2e:0' }" diff --git a/modules/local/circtest/test/main.nf b/modules/local/circtest/test/main.nf index 5999ddaa..43b23083 100644 --- a/modules/local/circtest/test/main.nf +++ b/modules/local/circtest/test/main.nf @@ -1,7 +1,7 @@ process CIRCTEST { label 'process_medium' - conda (params.enable_conda ? "r-base r-aod r-ggplot2 r-plyr" : null) + conda "r-base r-aod r-ggplot2 r-plyr" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c79b00aa4647c739dbe7e8480789d3ba67988f2e:0' : 'quay.io/biocontainers/mulled-v2-c79b00aa4647c739dbe7e8480789d3ba67988f2e:0' }" diff --git a/modules/local/ciriquant/ciriquant/main.nf b/modules/local/ciriquant/ciriquant/main.nf index 8e358aef..3ad0c34a 100644 --- a/modules/local/ciriquant/ciriquant/main.nf +++ b/modules/local/ciriquant/ciriquant/main.nf @@ -2,7 +2,7 @@ process CIRIQUANT { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? "bioconda::ciriquant=1.1.2" : null) + conda "bioconda::ciriquant=1.1.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ciriquant:1.1.2--pyhdfd78af_2' : 'quay.io/biocontainers/ciriquant:1.1.2--pyhdfd78af_2' }" diff --git a/modules/local/ciriquant/yml/main.nf b/modules/local/ciriquant/yml/main.nf index 3489a219..6718df4b 100644 --- a/modules/local/ciriquant/yml/main.nf +++ b/modules/local/ciriquant/yml/main.nf @@ -1,7 +1,7 @@ process CIRIQUANT_YML { label 'process_single' - conda (params.enable_conda ? "bioconda::ciriquant=1.1.2" : null) + conda "bioconda::ciriquant=1.1.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ciriquant:1.1.2--pyhdfd78af_2' : 'quay.io/biocontainers/ciriquant:1.1.2--pyhdfd78af_2' }" diff --git a/modules/local/count_matrix/combined/main.nf b/modules/local/count_matrix/combined/main.nf index 1d27dfd2..65f430b5 100644 --- a/modules/local/count_matrix/combined/main.nf +++ b/modules/local/count_matrix/combined/main.nf @@ -1,7 +1,7 @@ process COUNTS_COMBINED { label 'process_low' - conda (params.enable_conda ? "r-base=3.6.3 python=2.7.15 r-argparser=0.6 r-dplyr=1.0.5" : null) + conda "r-base=3.6.3 python=2.7.15 r-argparser=0.6 r-dplyr=1.0.5" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-5fbffedf7f529cf3c5093b976deb4290f5e1267a:3456f1432b1c9dad42815275abe2d6cb6f26fd94-0' : 'quay.io/biocontainers/mulled-v2-5fbffedf7f529cf3c5093b976deb4290f5e1267a:3456f1432b1c9dad42815275abe2d6cb6f26fd94-0' }" diff --git a/modules/local/count_matrix/merge_tools/main.nf b/modules/local/count_matrix/merge_tools/main.nf index 4bbe7192..fd3feb89 100644 --- a/modules/local/count_matrix/merge_tools/main.nf +++ b/modules/local/count_matrix/merge_tools/main.nf @@ -2,7 +2,7 @@ process MERGE_TOOLS { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "r-base=3.6.3 python=2.7.15 r-argparser=0.6 r-dplyr=1.0.5" : null) + conda "r-base=3.6.3 python=2.7.15 r-argparser=0.6 r-dplyr=1.0.5" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-5fbffedf7f529cf3c5093b976deb4290f5e1267a:3456f1432b1c9dad42815275abe2d6cb6f26fd94-0' : 'quay.io/biocontainers/mulled-v2-5fbffedf7f529cf3c5093b976deb4290f5e1267a:3456f1432b1c9dad42815275abe2d6cb6f26fd94-0' }" diff --git a/modules/local/count_matrix/single/main.nf b/modules/local/count_matrix/single/main.nf index bf6976db..8ce82da8 100644 --- a/modules/local/count_matrix/single/main.nf +++ b/modules/local/count_matrix/single/main.nf @@ -2,7 +2,7 @@ process COUNTS_SINGLE { tag "${meta.tool}" label 'process_low' - conda (params.enable_conda ? "r-base=3.6.3 python=2.7.15 r-argparser=0.6 r-dplyr=1.0.5" : null) + conda "r-base=3.6.3 python=2.7.15 r-argparser=0.6 r-dplyr=1.0.5" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-5fbffedf7f529cf3c5093b976deb4290f5e1267a:3456f1432b1c9dad42815275abe2d6cb6f26fd94-0' : 'quay.io/biocontainers/mulled-v2-5fbffedf7f529cf3c5093b976deb4290f5e1267a:3456f1432b1c9dad42815275abe2d6cb6f26fd94-0' }" diff --git a/modules/local/dcc/dcc/main.nf b/modules/local/dcc/dcc/main.nf index 60cb8b71..b8db483f 100644 --- a/modules/local/dcc/dcc/main.nf +++ b/modules/local/dcc/dcc/main.nf @@ -2,7 +2,7 @@ process DCC { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? "bioconda::circtools=1.2.1" : null) + conda "bioconda::circtools=1.2.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/circtools:1.2.1--pyh7cba7a3_0' : 'quay.io/biocontainers/circtools:1.2.1--pyh7cba7a3_0' }" diff --git a/modules/local/deseq2/differential_expression/main.nf b/modules/local/deseq2/differential_expression/main.nf index f9b5dacc..67631ed5 100644 --- a/modules/local/deseq2/differential_expression/main.nf +++ b/modules/local/deseq2/differential_expression/main.nf @@ -1,7 +1,7 @@ process DESEQ2_DIFFERENTIAL_EXPRESSION { label 'process_medium' - conda (params.enable_conda ? "r-base=3.6.3 conda-forge::r-argparser=0.6 conda-forge::r-dplyr=1.0.5 conda-forge::r-ggplot2=3.3.3 r-ggpubr=0.4.0 conda-forge::r-gplots=3.1.1 conda-forge::r-pheatmap=1.0.12 r-plyr=1.8.6 r-pvclust=2.2_0 r-rcolorbrewer=1.1_2 conda-forge::r-circlize=0.4.12 bioconductor-biomart=2.42.0 bioconductor-complexheatmap=2.2.0 bioconductor-deseq2=1.26.0 bioconductor-enhancedvolcano=1.4.0 bioconductor-ihw=1.14.0 bioconductor-org.hs.eg.db=3.10.0 bioconductor-pcatools=1.2.0 bioconductor-tximport=1.14.0" : null) + conda "r-base=3.6.3 conda-forge::r-argparser=0.6 conda-forge::r-dplyr=1.0.5 conda-forge::r-ggplot2=3.3.3 r-ggpubr=0.4.0 conda-forge::r-gplots=3.1.1 conda-forge::r-pheatmap=1.0.12 r-plyr=1.8.6 r-pvclust=2.2_0 r-rcolorbrewer=1.1_2 conda-forge::r-circlize=0.4.12 bioconductor-biomart=2.42.0 bioconductor-complexheatmap=2.2.0 bioconductor-deseq2=1.26.0 bioconductor-enhancedvolcano=1.4.0 bioconductor-ihw=1.14.0 bioconductor-org.hs.eg.db=3.10.0 bioconductor-pcatools=1.2.0 bioconductor-tximport=1.14.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-04b2ef814c9c6ab8c196c3e372521b88160dc260:e0cb4046baee3fd35fdbf883ba8af34e3e8af2e8-0' : 'quay.io/biocontainers/mulled-v2-04b2ef814c9c6ab8c196c3e372521b88160dc260:e0cb4046baee3fd35fdbf883ba8af34e3e8af2e8-0' }" diff --git a/modules/local/fasta/main.nf b/modules/local/fasta/main.nf index 58c3f506..c2cd5ada 100644 --- a/modules/local/fasta/main.nf +++ b/modules/local/fasta/main.nf @@ -2,7 +2,7 @@ process FASTA { tag "${meta.id}:${meta.tool}" label 'process_single' - conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) + conda "bioconda::bedtools=2.30.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h7d7f7ad_2': 'quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_2' }" diff --git a/modules/local/find_circ/anchors/main.nf b/modules/local/find_circ/anchors/main.nf index d357c45e..15b0650a 100644 --- a/modules/local/find_circ/anchors/main.nf +++ b/modules/local/find_circ/anchors/main.nf @@ -2,7 +2,7 @@ process FIND_CIRC_ANCHORS { tag "$meta.id" label "process_high" - conda (params.enable_conda ? "find_circ=1.2" : null) + conda "find_circ=1.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/find_circ%3A1.2--hdfd78af_0' : 'quay.io/biocontainers/find_circ:1.2--hdfd78af_0' }" diff --git a/modules/local/find_circ/filter/main.nf b/modules/local/find_circ/filter/main.nf index c2220884..7be0de57 100644 --- a/modules/local/find_circ/filter/main.nf +++ b/modules/local/find_circ/filter/main.nf @@ -2,7 +2,7 @@ process FIND_CIRC_FILTER { tag "$meta.id" label "process_low" - conda (params.enable_conda ? "find_circ=1.2" : null) + conda "find_circ=1.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/find_circ%3A1.2--hdfd78af_0' : 'quay.io/biocontainers/find_circ:1.2--hdfd78af_0' }" diff --git a/modules/local/find_circ/find_circ/main.nf b/modules/local/find_circ/find_circ/main.nf index 970c87e5..57bf656c 100644 --- a/modules/local/find_circ/find_circ/main.nf +++ b/modules/local/find_circ/find_circ/main.nf @@ -2,7 +2,7 @@ process FIND_CIRC { tag "$meta.id" label "process_high" - conda (params.enable_conda ? "find_circ=1.2 bowtie2" : null) + conda "find_circ=1.2 bowtie2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c27e472038a09e49d9147bc52903e12836302c12:60ffb3b15a2c40c669f8d38382b1e6e4b065f5e4-0' : 'quay.io/biocontainers/mulled-v2-c27e472038a09e49d9147bc52903e12836302c12:60ffb3b15a2c40c669f8d38382b1e6e4b065f5e4-0' }" diff --git a/modules/local/mapsplice/align/main.nf b/modules/local/mapsplice/align/main.nf index 4aa91035..44c64d97 100644 --- a/modules/local/mapsplice/align/main.nf +++ b/modules/local/mapsplice/align/main.nf @@ -2,7 +2,7 @@ process MAPSPLICE_ALIGN { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? "bioconda::mapsplice=2.2.1" : null) + conda "bioconda::mapsplice=2.2.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mapsplice:2.2.1--py27h07887db_0': 'quay.io/biocontainers/mapsplice:2.2.1--py27h07887db_0' }" diff --git a/modules/local/mirna_targets/main.nf b/modules/local/mirna_targets/main.nf index 7a9c0666..c6beaeff 100644 --- a/modules/local/mirna_targets/main.nf +++ b/modules/local/mirna_targets/main.nf @@ -2,7 +2,7 @@ process MIRNA_TARGETS { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) + conda "bioconda::bedtools=2.30.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h7d7f7ad_2': 'quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_2' }" diff --git a/modules/local/stringtie/prepde/main.nf b/modules/local/stringtie/prepde/main.nf index e069cddd..da20b1a8 100644 --- a/modules/local/stringtie/prepde/main.nf +++ b/modules/local/stringtie/prepde/main.nf @@ -1,7 +1,7 @@ process STRINGTIE_PREPDE { label 'process_low' - conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) + conda "bioconda::stringtie=2.2.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : 'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }" diff --git a/modules/local/targetscan/predict/main.nf b/modules/local/targetscan/predict/main.nf index ae3de117..f6b37cb0 100644 --- a/modules/local/targetscan/predict/main.nf +++ b/modules/local/targetscan/predict/main.nf @@ -2,7 +2,7 @@ process TARGETSCAN { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::targetscan=7.0" : null) + conda "bioconda::targetscan=7.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/targetscan:7.0--pl5321hdfd78af_0' : 'quay.io/biocontainers/targetscan:7.0--pl5321hdfd78af_0' }" diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index 950c495e..4cb6ca7a 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -2,7 +2,7 @@ process BOWTIE_ALIGN { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.16.1' : null) + conda "bioconda::bowtie=1.3.0 bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:c84c7c55c45af231883d9ff4fe706ac44c479c36-0' : 'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:c84c7c55c45af231883d9ff4fe706ac44c479c36-0' }" diff --git a/modules/nf-core/bowtie/build/main.nf b/modules/nf-core/bowtie/build/main.nf index e01d9855..85314ec7 100644 --- a/modules/nf-core/bowtie/build/main.nf +++ b/modules/nf-core/bowtie/build/main.nf @@ -2,7 +2,7 @@ process BOWTIE_BUILD { tag "$fasta" label 'process_high' - conda (params.enable_conda ? 'bioconda::bowtie=1.3.0' : null) + conda "bioconda::bowtie=1.3.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1' : 'quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1' }" diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf index 983a3ad3..3d851866 100644 --- a/modules/nf-core/bowtie2/align/main.nf +++ b/modules/nf-core/bowtie2/align/main.nf @@ -2,7 +2,7 @@ process BOWTIE2_ALIGN { tag "$meta.id" label "process_high" - conda (params.enable_conda ? "bioconda::bowtie2=2.4.4 bioconda::samtools=1.16.1 conda-forge::pigz=2.6" : null) + conda "bioconda::bowtie2=2.4.4 bioconda::samtools=1.16.1 conda-forge::pigz=2.6" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' : 'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' }" diff --git a/modules/nf-core/bowtie2/build/main.nf b/modules/nf-core/bowtie2/build/main.nf index 218c174a..551893af 100644 --- a/modules/nf-core/bowtie2/build/main.nf +++ b/modules/nf-core/bowtie2/build/main.nf @@ -2,7 +2,7 @@ process BOWTIE2_BUILD { tag "$fasta" label 'process_high' - conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null) + conda "bioconda::bowtie2=2.4.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' : 'quay.io/biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }" diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf index 6d70fc15..7ccf3110 100644 --- a/modules/nf-core/bwa/index/main.nf +++ b/modules/nf-core/bwa/index/main.nf @@ -2,7 +2,7 @@ process BWA_INDEX { tag "$fasta" label 'process_single' - conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) + conda "bioconda::bwa=0.7.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7' : 'quay.io/biocontainers/bwa:0.7.17--hed695b0_7' }" diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 4fa365d3..8a0b5600 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -2,7 +2,7 @@ process CAT_FASTQ { tag "$meta.id" label 'process_single' - conda (params.enable_conda ? "conda-forge::sed=4.7" : null) + conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'ubuntu:20.04' }" diff --git a/modules/nf-core/circexplorer2/annotate/main.nf b/modules/nf-core/circexplorer2/annotate/main.nf index bf836bbf..335723a8 100644 --- a/modules/nf-core/circexplorer2/annotate/main.nf +++ b/modules/nf-core/circexplorer2/annotate/main.nf @@ -2,7 +2,7 @@ process CIRCEXPLORER2_ANNOTATE { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::circexplorer2=2.3.8" : null) + conda "bioconda::circexplorer2=2.3.8" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/circexplorer2:2.3.8--pyh864c0ab_1': 'quay.io/biocontainers/circexplorer2:2.3.8--pyh864c0ab_1' }" diff --git a/modules/nf-core/circexplorer2/parse/main.nf b/modules/nf-core/circexplorer2/parse/main.nf index 8d9dbb80..147a73f3 100644 --- a/modules/nf-core/circexplorer2/parse/main.nf +++ b/modules/nf-core/circexplorer2/parse/main.nf @@ -2,7 +2,7 @@ process CIRCEXPLORER2_PARSE { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::circexplorer2=2.3.8" : null) + conda "bioconda::circexplorer2=2.3.8" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/circexplorer2:2.3.8--pyh864c0ab_1': 'quay.io/biocontainers/circexplorer2:2.3.8--pyh864c0ab_1' }" diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py index e55b8d43..da033408 100755 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -4,11 +4,10 @@ """Provide functions to merge multiple versions.yml files.""" +import yaml import platform from textwrap import dedent -import yaml - def _make_versions_html(versions): """Generate a tabular HTML output of all versions for MultiQC.""" diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf index 69717729..eefb5819 100644 --- a/modules/nf-core/hisat2/align/main.nf +++ b/modules/nf-core/hisat2/align/main.nf @@ -3,7 +3,7 @@ process HISAT2_ALIGN { label 'process_high' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda (params.enable_conda ? "bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1" : null) + conda "bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2cdf6bf1e92acbeb9b2834b1c58754167173a410-0' : 'quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2cdf6bf1e92acbeb9b2834b1c58754167173a410-0' }" diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf index fee4064c..e0a7f652 100644 --- a/modules/nf-core/hisat2/build/main.nf +++ b/modules/nf-core/hisat2/build/main.nf @@ -4,7 +4,7 @@ process HISAT2_BUILD { label 'process_high_memory' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null) + conda "bioconda::hisat2=2.2.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' : 'quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3' }" diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf index 1423f25c..db6cbe6a 100644 --- a/modules/nf-core/hisat2/extractsplicesites/main.nf +++ b/modules/nf-core/hisat2/extractsplicesites/main.nf @@ -3,7 +3,7 @@ process HISAT2_EXTRACTSPLICESITES { label 'process_medium' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null) + conda "bioconda::hisat2=2.2.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' : 'quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3' }" diff --git a/modules/nf-core/miranda/main.nf b/modules/nf-core/miranda/main.nf index a050c4b6..2f32f788 100644 --- a/modules/nf-core/miranda/main.nf +++ b/modules/nf-core/miranda/main.nf @@ -2,7 +2,7 @@ process MIRANDA { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::miranda=3.3a" : null) + conda "bioconda::miranda=3.3a" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/miranda:3.3a--h779adbc_3': 'quay.io/biocontainers/miranda:3.3a--h779adbc_3' }" diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 8577dc9d..8b95687a 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_INDEX { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.16.1" : null) + conda "bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index ac43e67a..84c167cd 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_SORT { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::samtools=1.16.1" : null) + conda "bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index 314c8b72..729c85e5 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_VIEW { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::samtools=1.16.1" : null) + conda "bioconda::samtools=1.16.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" diff --git a/modules/nf-core/segemehl/align/main.nf b/modules/nf-core/segemehl/align/main.nf index 2253efac..3e7fe4c7 100644 --- a/modules/nf-core/segemehl/align/main.nf +++ b/modules/nf-core/segemehl/align/main.nf @@ -2,7 +2,7 @@ process SEGEMEHL_ALIGN { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? "bioconda::segemehl=0.3.4" : null) + conda "bioconda::segemehl=0.3.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/segemehl:0.3.4--hc2ea5fd_5': 'quay.io/biocontainers/segemehl:0.3.4--hc2ea5fd_5' }" diff --git a/modules/nf-core/segemehl/index/main.nf b/modules/nf-core/segemehl/index/main.nf index 07cac955..f545c448 100644 --- a/modules/nf-core/segemehl/index/main.nf +++ b/modules/nf-core/segemehl/index/main.nf @@ -2,7 +2,7 @@ process SEGEMEHL_INDEX { tag "$fasta" label 'process_high' - conda (params.enable_conda ? "bioconda::segemehl=0.3.4" : null) + conda "bioconda::segemehl=0.3.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/segemehl:0.3.4--hc2ea5fd_5': 'quay.io/biocontainers/segemehl:0.3.4--hc2ea5fd_5' }" diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index 8b0f9d89..0e3bd713 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -2,7 +2,7 @@ process STAR_ALIGN { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0" : null) + conda "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' : 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }" diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index 0fe88cbf..91462489 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -2,7 +2,7 @@ process STAR_GENOMEGENERATE { tag "$fasta" label 'process_high' - conda (params.enable_conda ? "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0" : null) + conda "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' : 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }" diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf index b403edee..2d5b035f 100644 --- a/modules/nf-core/stringtie/stringtie/main.nf +++ b/modules/nf-core/stringtie/stringtie/main.nf @@ -2,7 +2,7 @@ process STRINGTIE_STRINGTIE { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null) + conda "bioconda::stringtie=2.2.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : 'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }" diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 5b45e4d7..ab8bb14e 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -2,7 +2,7 @@ process TRIMGALORE { tag "$meta.id" label 'process_high' - conda (params.enable_conda ? 'bioconda::trim-galore=0.6.7' : null) + conda "bioconda::trim-galore=0.6.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0' : 'quay.io/biocontainers/trim-galore:0.6.7--hdfd78af_0' }" From 61967557df5fd23ff7609e3372fd71fa9ff2efbf Mon Sep 17 00:00:00 2001 From: Barry digby Date: Fri, 27 Jan 2023 09:10:16 +0000 Subject: [PATCH 007/491] publication info --- README.md | 11 +++++++++-- docs/images/Genomics-Data-Science-original.png | Bin 0 -> 33528 bytes 2 files changed, 9 insertions(+), 2 deletions(-) create mode 100644 docs/images/Genomics-Data-Science-original.png diff --git a/README.md b/README.md index 7ca6d3b5..48a7c220 100644 --- a/README.md +++ b/README.md @@ -76,7 +76,9 @@ The nf-core/circrna pipeline comes with documentation about the pipeline [usage] nf-core/circrna was originally written by Barry Digby. -We thank the following people for their extensive assistance in the development of this pipeline: +## Acknowledgements + +![SFI](./docs/images/Genomics-Data-Science-original.png) ## Contributions and Support @@ -86,8 +88,13 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations - +> **nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs.** +> +> Barry Digby, Stephen P. Finn, & Pilib Ó Broin +> +> [BMC Bioinformatics 24, 27 (2023)](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-022-05125-8) +> doi: [10.1186/s12859-022-05125-8](https://doi.org/10.1186/s12859-022-05125-8) An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/docs/images/Genomics-Data-Science-original.png b/docs/images/Genomics-Data-Science-original.png new file mode 100644 index 0000000000000000000000000000000000000000..50e9c02b733a2aceebc40726576b4a7e8718b217 GIT binary patch literal 33528 zcmaI7WmKF&vn~n*cPF?8cX#*T?(Q%Q?h@RB6Fj(t!QB}wNN@-?xCDZ`+a=%L`<(mZ z?mKJEn)mIgs;=&?uC9K%Iz~-J4h@+I843ytO+j8-0}2ZI^!-bM2>)IJt*k5k{zK>? zqvxRswDIsZce93)umW0GQz!t;ZLKw|&8>W0N3DgSpgw%E*V6OQQ&tkR1Oiyi|Ix7e z09@X=p`e7td|b>e9j!emEUazqokgh5I>A&F_EsWPx;)D4$}UpYcJ}gqZq}N9Dq5C) zj+O#eRAQnO!ajoU0sz(?<`g~vCues-9}%km$Q68l{#VRKMe!dJ4@VKI|58d%S&c#p z=w?m9%gWAT$UPBgn%p$i+|b-yf>?+T5&c 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zh0>vLL%*P$AtqT$Dd1Qu2(ZGph>4bm8}_gX`2Aj>{G9U7%69viepY$-IQMIn@<=gL zGXy~pxjj%%5Lfv~K$JG>W*=z1bgy!;@-Zmnohw79`G*Oea5aT5fEyGZb1YoRVY zK)b(+Db3lToMo-?(@OQG?HqTT%EcS=EEOOy)(*3!5oq4)F*3e&| z+u9+FnksJgaRxlYXb<=4anyuB%At{<7*+&uRS<3CwU)HYoFaBX8Q8t&yI zEaN3I#wZ_qi5T}dK@bEj?mPg+K9-1ar7zk?8wmKP#LS%n?-5gJtYqeq4>GE}Pxp2x z+p$(zw>$ORZr$!tcBoa^qvw0Dujiv9Slqahqt`>$x=P)z(X+L>ZBz@iN&noe`;+zD z6y3JyH6r`4xJ#iPw~mv4g=g{tp@EpCFK#XXS$i}Nl^SbP^)D?C%gku2j+%2&nA zcQ3bA;Rlu9SH7)G#|DwvhguRN14(iat$sU)f*^=|Ai^QoFSaR{DNk3nSS$Qq0YQv6N#Hr4XcGiM;VuTWiHRs*VnzHkYgzqAOo>n| z8^bcQbHpq=nlB~?`rkQpWiQw_DjV&#k3&Kb1ckf!fGNr+#njJ6fEt3S-X~`5G!lFu z^uUOekf-7*gLFcPD`ycfGH2G z9zekwtRP^eOM)OM+!G8>D?e#1w@Z|db4ZE~aED`+z$`IS9)IJI5ClQtCVH%OeukKw z=+}ywD<{Se2rfiTb|iuMf@E27jUWhu!aebT%w)F;@@*R{51HKlEp*Ek0xOl*D5r{9 z&WCJz9*2b>h++d1uoN#~<=t-CY{leUG0V+bI6Pwl#3CTG8P?{%#^E3cg2GLV6;P7$ zZcF5xM0rvKN}Z`ZRawg+$_fYs{D<;E%Z(fof*>f|M7{yH`7@SSj#O!d90HD{Fi83` zgTpic6#4k4n0ae#lN=I)ASm3#cw3PxEJGky`f--Wh{@u1_yiaWB)EA_`IH?G#0Tu) zSA-x43O7;gSZ8@(#<@epB!odOb*v+AwOfdMyaewNmh&1hsb&#aw#tfj2S0v-ASm2K zIp9sp<-^V+@NJHmf+mUko?6v!_kaycY sz^%RAa*KV?z&S35BM5@9_`d)H08KnE8O(p7>Hq)$07*qoM6N<$g1=kGOaK4? literal 0 HcmV?d00001 From 3b37a582285a55ccc7731b821958c03cd4ff6895 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Fri, 27 Jan 2023 09:13:22 +0000 Subject: [PATCH 008/491] prettier -_- --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 48a7c220..6e8ee225 100644 --- a/README.md +++ b/README.md @@ -89,6 +89,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations + > **nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs.** > > Barry Digby, Stephen P. Finn, & Pilib Ó Broin From ecfea066439195ade06c9df5f476b5b3f589c847 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Tue, 31 Jan 2023 13:07:47 +0000 Subject: [PATCH 009/491] first pass reviewer comments --- .github/workflows/ci.yml | 3 +- CITATIONS.md | 122 ++++++++++++---- README.md | 44 +++--- bin/DEA.R | 39 +---- bin/ID_to_BED.sh | 15 -- bin/annotate_outputs.sh | 7 +- bin/backsplice_gen.sh | 4 + bin/check_empty.sh | 2 + bin/check_samplesheet.py | 29 ---- bin/circRNA_counts_matrix.py | 9 +- bin/circ_test.R | 17 +-- bin/consolidate_algorithms_intersection.R | 8 +- bin/prepare_circ_test.R | 3 + bin/reformat_count_matrix.R | 4 + bin/targetscan_format.sh | 8 +- conf/modules.config | 64 ++++----- conf/test.config | 2 +- docs/output.md | 135 +++++++----------- docs/usage.md | 116 +++++---------- .../local/annotation/full_annotation/main.nf | 3 +- modules/local/annotation/parent_gene/main.nf | 12 +- modules/local/circexplorer2/filter/main.nf | 11 ++ modules/local/circexplorer2/reference/main.nf | 1 + modules/local/circrna_finder/filter/main.nf | 2 + modules/local/circtest/prepare/main.nf | 2 +- modules/local/circtest/test/main.nf | 2 +- modules/local/ciriquant/filter/main.nf | 11 ++ modules/local/count_matrix/combined/main.nf | 5 +- .../local/count_matrix/merge_tools/main.nf | 4 +- modules/local/count_matrix/single/main.nf | 5 +- modules/local/dcc/filter/main.nf | 11 ++ modules/local/fasta/main.nf | 1 + modules/local/mapsplice/align/main.nf | 12 +- modules/local/mirna_targets/main.nf | 1 + modules/local/segemehl/filter/main.nf | 14 +- modules/local/star/sjdb/main.nf | 11 ++ modules/local/stringtie/prepde/main.nf | 6 + modules/local/targetscan/database/main.nf | 2 +- modules/local/targetscan/predict/main.nf | 1 + nextflow.config | 2 +- nextflow_schema.json | 11 +- subworkflows/local/circrna_discovery.nf | 30 +++- subworkflows/local/differential_expression.nf | 1 + subworkflows/local/prepare_genome.nf | 32 +---- workflows/circrna.nf | 4 - 45 files changed, 418 insertions(+), 410 deletions(-) delete mode 100755 bin/ID_to_BED.sh diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 98016682..181b2aea 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -26,8 +26,7 @@ jobs: NXF_VER: - "22.10.1" - "latest-everything" - profile: - - "test" + steps: - name: Check out pipeline code uses: actions/checkout@v3 diff --git a/CITATIONS.md b/CITATIONS.md index 9b05020c..d0b737d9 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,73 +10,135 @@ ## Pipeline tools -- **bedtools** Quinlan, A.R. & Hall, I.M., (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics , 26(6), pp.841–842. Available at: [http://dx.doi.org/10.1093/bioinformatics/btq033](http://dx.doi.org/10.1093/bioinformatics/btq033). Download: [https://github.com/arq5x/bedtools2/releases](https://github.com/arq5x/bedtools2/) +- [BEDTools](https://pubmed.ncbi.nlm.nih.gov/20110278/) -- **Bowite** Langmead, B., Trapnell, C., Pop, M. et al., (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25. Availabe at: [https://doi.org/10.1186/gb-2009-10-3-r25](https://doi.org/10.1186/gb-2009-10-3-r25). Download: [https://sourceforge.net/projects/bowtie-bio/](https://sourceforge.net/projects/bowtie-bio/) + > Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PubMed PMID: 20110278; PubMed Central PMCID: PMC2832824. -- **Bowtie2** Langmead, B. & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), p. 357–359. Available at: [10.1038/nmeth.1923](https:/dx.doi.org/10.1038/nmeth.1923). Download: [http://bowtie-bio.sourceforge.net/bowtie2/index.shtml](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) +- [Bowtie](https://doi.org/10.1186/gb-2009-10-3-r25) -- **bwa** Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics , 25(14), 1754–1760. Available at: [https://doi.org/10.1093/bioinformatics/btp324](https://doi.org/10.1093/bioinformatics/btp324). Download: [http://bio-bwa.sourceforge.net/bwa.shtml](http://bio-bwa.sourceforge.net/bwa.shtml). + > Langmead, B., Trapnell, C., Pop, M. et al., 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25. doi: 10.1186/gb-2009-10-3-r25 -- **CIRCexplorer2** Zhang XO, Dong R, Zhang Y, Zhang JL, Luo Z, Zhang J, Chen LL, Yang L. (2016). Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res. 2016 Sep;26(9):1277-87. Available at: [https://doi.org/10.1101/gr.202895.115](https://doi.org/10.1101/gr.202895.115). Download: [https://circexplorer2.readthedocs.io/en/latest/tutorial/setup/](https://circexplorer2.readthedocs.io/en/latest/tutorial/setup/) +- [Bowtie2](https:/dx.doi.org/10.1038/nmeth.1923) -- **circRNA finder** Westholm, J.O., Lai, E.C., et al. (2016). Genome-wide Analysis of Drosophila Circular RNAs Reveals Their Structural and Sequence Properties and Age-Dependent Neural Accumulation Westholm et al. Cell Reports. Available at: [https://doi.org/10.1016/j.celrep.2014.10.062](https://doi.org/10.1016/j.celrep.2014.10.062). Download: [https://github.com/orzechoj/circRNA_finder](https://github.com/orzechoj/circRNA_finder) + > Langmead, B. and Salzberg, S. L. 2012 Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), p. 357–359. doi: 10.1038/nmeth.1923. -- **CIRIquant** Zhang, J., Chen, S., Yang, J. et al. (2020). Accurate quantification of circular RNAs identifies extensive circular isoform switching events. Nat Commun 11, 90. Available at: [https://doi.org/10.1038/s41467-019-13840-9](https://doi.org/10.1038/s41467-019-13840-9). Download: [https://github.com/bioinfo-biols/CIRIquant](https://github.com/bioinfo-biols/CIRIquant) +- [BWA](https://www.ncbi.nlm.nih.gov/pubmed/19451168/) -- **DCC** Jun Cheng, Franziska Metge, Christoph Dieterich, (2016). Specific identification and quantification of circular RNAs from sequencing data, Bioinformatics, 32(7), 1094–1096. Available at: [https://doi.org/10.1093/bioinformatics/btv656](https://doi.org/10.1093/bioinformatics/btv656). Download: [https://github.com/dieterich-lab/DCC](https://github.com/dieterich-lab/DCC) + > Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18. PubMed PMID: 19451168; PubMed Central PMCID: PMC2705234. + +- [CIRCexplorer2](https://doi.org/10.1101/gr.202895.115) + + > Zhang XO, Dong R, Zhang Y, Zhang JL, Luo Z, Zhang J, Chen LL, Yang L. (2016). Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res. 2016 Sep;26(9):1277-87. + +- [circRNA finder](https://doi.org/10.1016/j.celrep.2014.10.062) + + > Westholm, J.O., Lai, E.C., et al. (2016). Genome-wide Analysis of Drosophila Circular RNAs Reveals Their Structural and Sequence Properties and Age-Dependent Neural Accumulation Westholm et al. Cell Reports. + +- [CIRIquant](https://doi.org/10.1038/s41467-019-13840-9) + + > Zhang, J., Chen, S., Yang, J. et al. (2020). Accurate quantification of circular RNAs identifies extensive circular isoform switching events. Nat Commun 11, 90. + +- [DCC](https://doi.org/10.1093/bioinformatics/btv656) + + > Jun Cheng, Franziska Metge, Christoph Dieterich, (2016). Specific identification and quantification of circular RNAs from sequencing data, Bioinformatics, 32(7), 1094–1096. - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) -- **find circ** Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., Maier, L., Mackowiak, S. D., Gregersen, L. H., Munschauer, M., Loewer, A., Ziebold, U., Landthaler, M., Kocks, C., le Noble, F., & Rajewsky, N. (2013). Circular RNAs are a large class of animal RNAs with regulatory potency. Nature, 495(7441), 333–338. Available at: [https://doi.org/10.1038/nature11928](https://doi.org/10.1038/nature11928). Download: [https://github.com/marvin-jens/find_circ](https://github.com/marvin-jens/find_circ) +- [find circ](https://doi.org/10.1038/nature11928) -- **HISAT2** Kim, D., Paggi, J.M., Park, C. et al. (2019). Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915 (2019). Available at: [https://doi.org/10.1038/s41587-019-0201-4](https://doi.org/10.1038/s41587-019-0201-4). Download: [http://daehwankimlab.github.io/hisat2/download/](http://daehwankimlab.github.io/hisat2/download/) + > Memczak, S., Jens, M., Elefsinioti, A., Torti, F., Krueger, J., Rybak, A., Maier, L., Mackowiak, S. D., Gregersen, L. H., Munschauer, M., Loewer, A., Ziebold, U., Landthaler, M., Kocks, C., le Noble, F., & Rajewsky, N. (2013). Circular RNAs are a large class of animal RNAs with regulatory potency. Nature, 495(7441), 333–338. -- **MapSplice2** Wang, K., Liu J., et al. (2010) MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery, Nucleic Acids Research, 38(18), 178. Avaialable at: [https://doi.org/10.1093/nar/gkq622](https://doi.org/10.1093/nar/gkq622). Download: [http://www.netlab.uky.edu/p/bioinfo/MapSplice2Download](http://www.netlab.uky.edu/p/bioinfo/MapSplice2Download) +- [GATK](https://pubmed.ncbi.nlm.nih.gov/20644199/) -- **miRanda** Enright, A.J., John, B., Gaul, U. et al. (2003). MicroRNA targets in Drosophila. Genome Biol 5, R1. Available at: [https://doi.org/10.1186/gb-2003-5-1-r1](https://doi.org/10.1186/gb-2003-5-1-r1). Download: [http://cbio.mskcc.org/miRNA2003/miranda.html](http://cbio.mskcc.org/miRNA2003/miranda.html). + > McKenna A, Hanna M, Banks E, et al.: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010 Sep;20(9):1297-303. doi: 10.1101/gr.107524.110. Epub 2010 Jul 19. PubMed PMID: 20644199; PubMed Central PMCID: PMC2928508. + +- [HISAT2](https://pubmed.ncbi.nlm.nih.gov/31375807/) + + > Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4. Epub 2019 Aug 2. PubMed PMID: 31375807. + +- [MapSplice2](https://doi.org/10.1093/nar/gkq622) + + > Wang, K., Liu J., et al. (2010) MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery, Nucleic Acids Research, 38(18), 178. + +- [miRanda](https://doi.org/10.1186/gb-2003-5-1-r1) + + > Enright, A.J., John, B., Gaul, U. et al. (2003). MicroRNA targets in Drosophila. Genome Biol 5, R1. - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. -- **R**: R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Download: [https://www.R-project.org/](https://www.R-project.org/). +- [R](https://www.R-project.org/) + + > R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. + + - [biomaRt](https://doi.org/10.1038/nprot.2009.97) + + > Durinck S, Spellman PT, Birney E, Huber W. (2009). Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat Protoc. 4(8):1184-91. + + - [circlize](https://doi.org/10.1093/bioinformatics/btu393) + + > Zuguang Gu, Lei Gu, Roland Eils, Matthias Schlesner, Benedikt Brors (2014). circlize implements and enhances circular visualization in R , Bioinformatics, 30,(19) 2811–2812. + + - [DESeq2](https://doi.org/10.1186/s13059-014-0550-8) + + > Love, M.I., Huber, W. & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550. + + - [EnhancedVolcano](https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html) + + > Blighe K, Rana S, Lewis M (2020). EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling. + + - [ggplot2](https://ggplot2.tidyverse.org) + + > Wickham H (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4. + + - [ggpubr](https://rpkgs.datanovia.com/ggpubr/) + + > Kassambara A. (2020). ggpubr: 'ggplot2' Based Publication Ready Plots. + + - [ihw](https://doi.org/10.1038/nmeth.3885) + + > Ignatiadis, N., Klaus, B., Zaugg, J. et al. (2016). Data-driven hypothesis weighting increases detection power in genome-scale multiple testing. Nat Methods 13, 577–580. + + - [PCAtools](https://bioconductor.org/packages/release/bioc/html/PCAtools.html) + + > Blighe K, Lun A (2020). PCAtools: PCAtools: Everything Principal Components Analysis. - - **biomaRt** Durinck S, Spellman PT, Birney E, Huber W. (2009). Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nat Protoc. 4(8):1184-91. Available at: [https://doi.org/10.1038/nprot.2009.97](https://doi.org/10.1038/nprot.2009.97). Download: [https://bioconductor.org/packages/release/bioc/html/biomaRt.html](https://bioconductor.org/packages/release/bioc/html/biomaRt.html) + - [pheatmap](https://cran.r-project.org/package=pheatmap) - - **circlize** Zuguang Gu, Lei Gu, Roland Eils, Matthias Schlesner, Benedikt Brors (2014). circlize implements and enhances circular visualization in R , Bioinformatics, 30,(19) 2811–2812. Available at: [https://doi.org/10.1093/bioinformatics/btu393](https://doi.org/10.1093/bioinformatics/btu393). Download: [https://cran.r-project.org/web/packages/circlize/index.html](https://cran.r-project.org/web/packages/circlize/index.html) + > Kolde, R. (2019) Pretty Heatmaps. - - **DESeq2** Love, M.I., Huber, W. & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15, 550. Available at: [https://doi.org/10.1186/s13059-014-0550-8](https://doi.org/10.1186/s13059-014-0550-8). Download: [https://bioconductor.org/packages/release/bioc/html/DESeq2.html](https://bioconductor.org/packages/release/bioc/html/DESeq2.html) + - [pvclust](https://doi.org/10.1093/bioinformatics/btl117) - - **EnhancedVolcano** Blighe K, Rana S, Lewis M (2020). EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling. Download: [https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html](https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html) + > Suzuki R., Shimodaira H., (2006). Pvclust: an R package for assessing the uncertainty in hierarchical clustering, Bioinformatics, 22(12), 1540–1542. - - **ggplot2** Wickham H (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4, Download: [https://ggplot2.tidyverse.org](https://ggplot2.tidyverse.org). +- [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/) - - **ggpubr** Kassambara A. (2020). ggpubr: 'ggplot2' Based Publication Ready Plots. Download: [https://rpkgs.datanovia.com/ggpubr/](https://rpkgs.datanovia.com/ggpubr/) + > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002. - - **ihw** Ignatiadis, N., Klaus, B., Zaugg, J. et al. (2016). Data-driven hypothesis weighting increases detection power in genome-scale multiple testing. Nat Methods 13, 577–580. Available at: [https://doi.org/10.1038/nmeth.3885](https://doi.org/10.1038/nmeth.3885). Download: [https://bioconductor.org/packages/release/bioc/html/IHW.html](https://bioconductor.org/packages/release/bioc/html/IHW.html) +- [Segemehl](https://doi.org/10.1371/journal.pcbi.1000502) - - **PCAtools** Blighe K, Lun A (2020). PCAtools: PCAtools: Everything Principal Components Analysis. Download: [https://bioconductor.org/packages/release/bioc/html/PCAtools.html](https://bioconductor.org/packages/release/bioc/html/PCAtools.html) + > Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermueller J: "Fast mapping of short sequences with mismatches, insertions and deletions using index structures", PLoS Comput Biol (2009) vol. 5 (9) pp. e1000502. - - **pheatmap** Kolde, R. (2019) Pretty Heatmaps. Download: [https://cran.r-project.org/package=pheatmap](https://cran.r-project.org/package=pheatmap) +- [STAR](https://pubmed.ncbi.nlm.nih.gov/23104886/) - - **pvclust** Suzuki R., Shimodaira H., (2006). Pvclust: an R package for assessing the uncertainty in hierarchical clustering, Bioinformatics, 22(12), 1540–1542. Available at: [https://doi.org/10.1093/bioinformatics/btl117](https://doi.org/10.1093/bioinformatics/btl117). Download: [https://cran.r-project.org/web/packages/pvclust/index.html](https://cran.r-project.org/web/packages/pvclust/index.html) + > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905. -- **SAMtools** Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., … 1000 Genome Project Data Processing Subgroup. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics , 25(16), 2078–2079. [https://doi.org/10.1093/bioinformatics/btp352](https://doi.org/10.1093/bioinformatics/btp352). Download: [http://www.htslib.org/](http://www.htslib.org/) +- [StringTie2](https://pubmed.ncbi.nlm.nih.gov/31842956/) -- **Segemehl** Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermueller J: "Fast mapping of short sequences with mismatches, insertions and deletions using index structures", PLoS Comput Biol (2009) vol. 5 (9) pp. e1000502. Available at: [https://doi.org/10.1371/journal.pcbi.1000502](https://doi.org/10.1371/journal.pcbi.1000502). Download: [https://www.bioinf.uni-leipzig.de/Software/segemehl/](https://www.bioinf.uni-leipzig.de/Software/segemehl/) + > Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2 Genome Biol. 2019 Dec 16;20(1):278. doi: 10.1186/s13059-019-1910-1. PubMed PMID: 31842956; PubMed Central PMCID: PMC6912988. -- **STAR** Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics (Oxford, England), 29(1), 15–21. Available at: [https://doi.org/10.1093/bioinformatics/bts635](https://doi.org/10.1093/bioinformatics/bts635). Download: [https://github.com/alexdobin/STAR](https://github.com/alexdobin/STAR) +- [TargetScan](https://doi.org/10.7554/elife.05005) -- **StringTie** Pertea, M., Pertea, G., Antonescu, C. et al. (2015). StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol 33, 290–295. Available at: [https://doi.org/10.1038/nbt.3122](https://doi.org/10.1038/nbt.3122). Download: [https://ccb.jhu.edu/software/stringtie/](https://ccb.jhu.edu/software/stringtie/) + > Agarwal V, Bell GW, Nam JW, Bartel DP. (2015). Predicting effective microRNA target sites in mammalian mRNAs. Elife, 4:e05005. -- **TargetScan** Agarwal V, Bell GW, Nam JW, Bartel DP. (2015). Predicting effective microRNA target sites in mammalian mRNAs. Elife, 4:e05005. Available at: [https://doi.org/10.7554/elife.05005](https://doi.org/10.7554/elife.05005). Download: [http://www.targetscan.org/cgi-bin/targetscan/data_download.vert72.cgi](http://www.targetscan.org/cgi-bin/targetscan/data_download.vert72.cgi) +- [ViennaRNA](https://doi.org/10.1186/1748-7188-6-26) -- **ViennaRNA** Lorenz, R., Bernhart, S.H., Höner zu Siederdissen, C. et al. (2011). ViennaRNA Package 2.0. Algorithms Mol Biol 6, 26. Available at: [https://doi.org/10.1186/1748-7188-6-26](https://doi.org/10.1186/1748-7188-6-26). Download: [https://www.tbi.univie.ac.at/RNA/#download](https://www.tbi.univie.ac.at/RNA/#download) + > Lorenz, R., Bernhart, S.H., Höner zu Siederdissen, C. et al. (2011). ViennaRNA Package 2.0. Algorithms Mol Biol 6, 26. ## Test data References -Dong Cao (2021). An autoregulation loop in fust-1 for circular RNA regulation in Caenorhabditis elegans. Biorxiv. Available at: [https://doi.org/10.1101/2021.03.22.436400](https://doi.org/10.1101/2021.03.22.436400). + > Cao D. An autoregulation loop in fust-1 for circular RNA regulation in Caenorhabditis elegans. Genetics. 2021 Nov 5;219(3):iyab145. doi: 10.1093/genetics/iyab145. PMID: 34740247; PMCID: PMC8570788. ## Software packaging/containerisation tools diff --git a/README.md b/README.md index 6e8ee225..bd2c7b02 100644 --- a/README.md +++ b/README.md @@ -20,28 +20,28 @@ On release, automated continuous integration tests run the pipeline on a full-si ## Pipeline summary -1. Raw read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) -2. Adapter trimming ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)) -3. circRNA quantification - 1. [`CIRIquant`](https://github.com/Kevinzjy/CIRIquant) - 2. [`STAR 2-Pass mode`](https://github.com/alexdobin/STAR) - 1. [`CIRCexplorer2`](https://circexplorer2.readthedocs.io/en/latest/) - 2. [`circRNA finder`](https://github.com/orzechoj/circRNA_finder) - 3. [`DCC`](https://github.com/dieterich-lab/DCC) - 3. [`find circ`](https://github.com/marvin-jens/find_circ) - 4. [`MapSplice`](http://www.netlab.uky.edu/p/bioinfo/MapSplice2) - 5. [`Segemehl`](https://www.bioinf.uni-leipzig.de/Software/segemehl/) -4. circRNA annotation -5. Export mature spliced length as FASTA file -6. Annotate parent gene, underlying transcripts. -7. circRNA count matrix -8. miRNA target prediction - 1. [`miRanda`](http://cbio.mskcc.org/miRNA2003/miranda.html) - 2. [`TargetScan`](http://www.targetscan.org/cgi-bin/targetscan/data_download.vert72.cgi) - 3. Filter results, miRNAs must be called by both tools -9. Differential expression analysis [`DESeq2`](https://bioconductor.org/packages/release/bioc/html/DESeq2.html) -10. Circular - Linear ratio tests ['CircTest'](https://github.com/dieterich-lab/CircTest) -11. MultiQC report [`MultiQC`](http://multiqc.info/) +- Raw read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) +- Adapter trimming ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)) +- circRNA quantification +- [`CIRIquant`](https://github.com/Kevinzjy/CIRIquant) +- [`STAR 2-Pass mode`](https://github.com/alexdobin/STAR) + - [`CIRCexplorer2`](https://circexplorer2.readthedocs.io/en/latest/) + - [`circRNA finder`](https://github.com/orzechoj/circRNA_finder) + - [`DCC`](https://github.com/dieterich-lab/DCC) +- [`find circ`](https://github.com/marvin-jens/find_circ) +- [`MapSplice`](http://www.netlab.uky.edu/p/bioinfo/MapSplice2) +- [`Segemehl`](https://www.bioinf.uni-leipzig.de/Software/segemehl/) +- circRNA annotation +- Export mature spliced length as FASTA file +- Annotate parent gene, underlying transcripts. +- circRNA count matrix +- miRNA target prediction + - [`miRanda`](http://cbio.mskcc.org/miRNA2003/miranda.html) + - [`TargetScan`](http://www.targetscan.org/cgi-bin/targetscan/data_download.vert72.cgi) + - Filter results, miRNAs must be called by both tools +- Differential expression analysis [`DESeq2`](https://bioconductor.org/packages/release/bioc/html/DESeq2.html) +- Circular - Linear ratio tests ['CircTest'](https://github.com/dieterich-lab/CircTest) +- MultiQC report [`MultiQC`](http://multiqc.info/) ## Quick Start diff --git a/bin/DEA.R b/bin/DEA.R index 5e1658f7..83f3cccf 100755 --- a/bin/DEA.R +++ b/bin/DEA.R @@ -1,8 +1,7 @@ #!/usr/bin/env Rscript -# Automated differential expression analysis script for nf-core/circrna -# Relies on Stirngtie prepde.py outputs -# Would be fun to adapt to STAR + Kallisto for own use in future. +## Author: Barry Digby +## License: MIT get_args <- function(){ @@ -121,20 +120,6 @@ checkinputdata <- function(phenotype){ giveError("Not enough samples per condition to perform DE analysis!") } - # Rename sex to gender.. - if("sex" %in% names(pheno)){ - print("Renaming sex to gender in phenotype file") - rename <- gsub("sex", "gender", names(pheno)) - names(pheno) <- rename - } - - # Check gender is only male, female, unknown - if ("gender" %in% names(pheno)) { - if (! all(unique(pheno$gender) %in% c("m", "f", "u"))) { - giveError("SAMPLEINFO ERROR:\nOnly the values m [male], f [female] and u [unknown] are supported in field .\n") - } - } - ## check if all columns are factors. If numeric, convert to factor. factor_cols <- sapply(pheno, is.factor) if(all(factor_cols) == TRUE){ @@ -175,8 +160,6 @@ ens2symbol <- function(mat, inputdata){ ## designed to work on input gene_count_matrix.csv file ## everything else downstream no longer needs to be converted - ## figure out if working with ENS, or ENS IDs - mat <- as.data.frame(mat) map <- inputdata$map species <- inputdata$species @@ -367,12 +350,6 @@ getDESeqDEAbyContrast <- function(dds, contrast, reference, var, outdir, inputda res_df <- as.data.frame(res) - #if(outdir == "RNA-Seq/"){ - # ann_res <- ens2symbol(res_df, inputdata) - #}else{ - # ann_res <- res_df - #} - volcano_plot(res_df, contrast, outdir) pdf(file.path(dir, paste("DESeq2", contrast, "fold_change_distribution.pdf", sep="_")), width=8, height=8) @@ -623,29 +600,17 @@ make_boxplots <- function(de, cts, contrast){ options(error=function()traceback(2)) suppressPackageStartupMessages(library("argparser")) -#suppressPackageStartupMessages(library("BiocParallel")) suppressPackageStartupMessages(library("biomaRt")) suppressPackageStartupMessages(library("DESeq2")) suppressPackageStartupMessages(library("dplyr")) -#suppressPackageStartupMessages(library("edgeR")) suppressPackageStartupMessages(library("EnhancedVolcano")) -#suppressPackageStartupMessages(library("EnsDb.Hsapiens.v86")) -#suppressPackageStartupMessages(library("genefilter")) #for rowVars suppressPackageStartupMessages(library("ggplot2")) suppressPackageStartupMessages(library("ggpubr")) -#suppressPackageStartupMessages(library("ggrepel")) -#suppressPackageStartupMessages(library("ggfortify")) suppressPackageStartupMessages(library("gplots")) suppressPackageStartupMessages(library("IHW")) -#suppressPackageStartupMessages(library("limma")) -#suppressPackageStartupMessages(library("parallel")) suppressPackageStartupMessages(library("PCAtools")) suppressPackageStartupMessages(library("pheatmap")) suppressPackageStartupMessages(library("RColorBrewer")) -#suppressPackageStartupMessages(library("readr")) -#suppressPackageStartupMessages(library("Rsubread")) -#suppressPackageStartupMessages(library("tximport")) -#suppressPackageStartupMessages(library("VennDiagram")) arg <- get_args() diff --git a/bin/ID_to_BED.sh b/bin/ID_to_BED.sh deleted file mode 100755 index 432ef3b8..00000000 --- a/bin/ID_to_BED.sh +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env bash - -file=$1 - -while IFS='' read -r line; do - - name=$(echo $line) - chr=$(echo $line | cut -d: -f1) - start=$(echo $line | cut -d- -f1 | cut -d: -f2) - stop=$(echo $line | cut -d- -f2 | cut -d: -f1) - sign=$(echo $line | cut -d: -f3) - - echo -e "$chr\t$start\t$stop\t$name\t0\t$sign" >> ${name}.bed - -done < $file diff --git a/bin/annotate_outputs.sh b/bin/annotate_outputs.sh index 92abc21b..3c2054f2 100755 --- a/bin/annotate_outputs.sh +++ b/bin/annotate_outputs.sh @@ -1,14 +1,11 @@ #!/usr/bin/env bash -## -## Expected Input: -## Chr Start Stop name count strand -## name= chr":"start"-"stop":"strand - echo "====================================================================================" echo "[nf-core/circrna]: circRNA annotation script " echo "[nf-core/circrna]: Author: Barry Digby " echo "[nf-core/circrna]: Institution: National University of Ireland, Galway " +echo "[nf-core/circrna]: " +echo "[nf-core/circrna]: MIT license " echo "====================================================================================" mkdir -p bed12 diff --git a/bin/backsplice_gen.sh b/bin/backsplice_gen.sh index 2801c52b..3134046b 100755 --- a/bin/backsplice_gen.sh +++ b/bin/backsplice_gen.sh @@ -1,5 +1,9 @@ #!/usr/bin/env bash +## Shell script to generate backsplice sequence from circRNA sequence. +## Author: Barry Digby +## License: MIT + ## .fa = backsplice .fasta = canonical to publish file_prefix=$(basename $1 .fa) diff --git a/bin/check_empty.sh b/bin/check_empty.sh index f45532d0..2f54d6da 100755 --- a/bin/check_empty.sh +++ b/bin/check_empty.sh @@ -2,6 +2,8 @@ ## When consolidating tool outputs for a sample, check if any are empty. ## This will prevent R from throwing errors +## Author: Barry Digby +## License: MIT for i in *bed; do diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index aea3b88b..339900f2 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -58,7 +58,6 @@ def check_samplesheet(file_in, file_out): ## Check header MIN_COLS = 2 ## edit by BDigby as not using strandedness yet. - # HEADER = ["sample", "fastq_1", "fastq_2", "strandedness"] HEADER = ["sample", "fastq_1", "fastq_2"] header = [x.strip('"') for x in fin.readline().strip().split(",")] if header[: len(HEADER)] != HEADER: @@ -87,7 +86,6 @@ def check_samplesheet(file_in, file_out): ) ## Check sample name entries - # sample, fastq_1, fastq_2, strandedness = lspl[: len(HEADER)] sample, fastq_1, fastq_2 = lspl[: len(HEADER)] if sample.find(" ") != -1: print(f"WARNING: Spaces have been replaced by underscores for sample: {sample}") @@ -107,29 +105,11 @@ def check_samplesheet(file_in, file_out): line, ) - ## Check strandedness - # strandednesses = ["unstranded", "forward", "reverse"] - # if strandedness: - # if strandedness not in strandednesses: - # print_error( - # f"Strandedness must be one of '{', '.join(strandednesses)}'!", - # "Line", - # line, - # ) - # else: - # print_error( - # f"Strandedness has not been specified! Must be one of {', '.join(strandednesses)}.", - # "Line", - # line, - # ) - ## Auto-detect paired-end/single-end sample_info = [] ## [single_end, fastq_1, fastq_2, strandedness] if sample and fastq_1 and fastq_2: ## Paired-end short reads - # sample_info = ["0", fastq_1, fastq_2, strandedness] sample_info = ["0", fastq_1, fastq_2] elif sample and fastq_1 and not fastq_2: ## Single-end short reads - # sample_info = ["1", fastq_1, fastq_2, strandedness] sample_info = ["1", fastq_1, fastq_2] else: print_error("Invalid combination of columns provided!", "Line", line) @@ -148,7 +128,6 @@ def check_samplesheet(file_in, file_out): out_dir = os.path.dirname(file_out) make_dir(out_dir) with open(file_out, "w") as fout: - # fout.write(",".join(["sample", "single_end", "fastq_1", "fastq_2", "strandedness"]) + "\n") fout.write(",".join(["sample", "single_end", "fastq_1", "fastq_2"]) + "\n") for sample in sorted(sample_mapping_dict.keys()): @@ -160,14 +139,6 @@ def check_samplesheet(file_in, file_out): sample, ) - ## Check that multiple runs of the same sample are of the same strandedness - # if not all(x[-1] == sample_mapping_dict[sample][0][-1] for x in sample_mapping_dict[sample]): - # print_error( - # f"Multiple runs of a sample must have the same strandedness!", - # "Sample", - # sample, - # ) - for idx, val in enumerate(sample_mapping_dict[sample]): fout.write(",".join([f"{sample}_T{idx+1}"] + val) + "\n") else: diff --git a/bin/circRNA_counts_matrix.py b/bin/circRNA_counts_matrix.py index bcd6ff96..07999b23 100755 --- a/bin/circRNA_counts_matrix.py +++ b/bin/circRNA_counts_matrix.py @@ -1,6 +1,14 @@ import sys, glob from collections import defaultdict +""" +Script to parse circRNA quantification bed files, creating a count matrix suitable for statistical analyses +requires python 2.7 +Author: Declan Bennett @declan93 +License: MIT +""" + + par = sys.argv hld = defaultdict(list) samps = defaultdict(list) @@ -31,7 +39,6 @@ def Diff(list1, list2): disj = Diff(tmp, [a_tuple[0] for a_tuple in v]) for val in disj: v.append((val, "0")) - # print(" ".join(k.split("_")),v) li = [] for h in tmp: for x in v: diff --git a/bin/circ_test.R b/bin/circ_test.R index 96a4f81e..3e9ea6af 100755 --- a/bin/circ_test.R +++ b/bin/circ_test.R @@ -4,7 +4,11 @@ require(aod) require(plyr) require(ggplot2) -# The CircTest devs never had containers in mind for their code. It is not published on any R channels, nor are there any stable releases on their github page. I have decided to take their source functions and roll with it instead. +## CircTest functions +## Package: CircTest (https://github.com/dieterich-lab/CircTest) +## Version: 0.1.1 +## Author(s): Jun Cheng, Tobias Jakobi +## License: GPL ## SUMMMARY @@ -140,7 +144,6 @@ Circ.ratioplot <- function(Circ,Linear,CircCoordinates = None,plotrow='1',size=2 theme(legend.text=element_text(size=size)) + theme(plot.title = element_text(size=size)) + theme(axis.text.y = element_text(margin=margin(5,5,10,5,"pt")))+ - #labs(list(title=paste("Annotation: ", genename, "\nChr ", toString(Circ[plotrow,circle_description]),sep=""),x=x,y=y)) + ggtitle(paste("Annotation: ", genename, "\nChr ", toString(Circ[plotrow,circle_description]),sep="")) + ylab("circRNA/(circRNA + Linear RNA)") + xlab("Sample") + @@ -179,7 +182,6 @@ Circ.ratioplot <- function(Circ,Linear,CircCoordinates = None,plotrow='1',size=2 Circ.lineplot <- function(Circ,Linear,CircCoordinates = None,plotrow='1',size=18,ncol=2,groupindicator1=NULL,groupindicator2=NULL,x='Conditions',y='Counts', circle_description = c(1:3), gene_column = None){ require(ggplot2) - #require(Rmisc) if( !is.null(groupindicator1) & length(groupindicator1) != ncol(Circ)-length(circle_description) ){ stop("If provided, the length of groupindicator1 should be equal to the number of samples.") @@ -376,21 +378,16 @@ Circ.test <- function(Circ, Linear, CircCoordinates=None, group, alpha=0.05, plo # test models a <- anova(fitNull,fitAlt) p.value <- a@anova.table[,11][2] - # print(predict(fitAlt,testdat, se.fit=T)) p.val <- c( p.val, p.value ) - # dir <- 1 # fitAlt@param[2][["group2"]] - # direction <- c(direction, dir) } message(paste(counter, "candidates processed in total")) Circ$direction <- direction - #names(Circ$direction ) <- c("direction") p.adj <- p.adjust(p.val,n=sum(!is.na(p.val)),'BH') # select significant ones sig_dat <- Circ[p.adj<=alpha & !is.na(p.adj),] sig_ratios <- tmp_df[p.adj<=alpha & !is.na(p.adj),] sig_p <- p.adj[p.adj<=alpha & !is.na(p.adj)] - # direction <- direction[p.adj<=alpha & !is.na(p.adj)] # sort by p-val sig_dat <- sig_dat[order(sig_p),] @@ -404,9 +401,6 @@ Circ.test <- function(Circ, Linear, CircCoordinates=None, group, alpha=0.05, plo rownames(summary_table) <- rownames(sig_dat) names(summary_table) <- c(names(sig_dat)[circle_description],"sig_p",names(sig_ratios)[circle_description]) } else { - # summary_table <- cbind(CircCoordinates[rownames(sig_dat),],sig_p,sig_dat$direction) - # colnames(summary_table) <- c(colnames(CircCoordinates),"sig_p","direction") - summary_table <- cbind(CircCoordinates[rownames(sig_dat),],sig_p,sig_ratios) colnames(summary_table) <- c(colnames(CircCoordinates),"sig_p",colnames(sig_ratios)) } @@ -420,7 +414,6 @@ Circ.test <- function(Circ, Linear, CircCoordinates=None, group, alpha=0.05, plo p.adj=p.adj, sig_p=sig_p, ratios=sig_ratios - # direction=direction ) ) } diff --git a/bin/consolidate_algorithms_intersection.R b/bin/consolidate_algorithms_intersection.R index a147c105..1fbd27b4 100755 --- a/bin/consolidate_algorithms_intersection.R +++ b/bin/consolidate_algorithms_intersection.R @@ -1,4 +1,10 @@ -#!/usr/bin/Rscript +#!/usr/bin/env Rscript + +## Script to consolidate circRNAs across multiple tools. Allow user +## to apply 'max' or 'mean' aggregate function to those called by multiple +## tools. +## Author: Barry Digby +## License: MIT get_args <- function(){ diff --git a/bin/prepare_circ_test.R b/bin/prepare_circ_test.R index 065119d5..f95b8f9c 100755 --- a/bin/prepare_circ_test.R +++ b/bin/prepare_circ_test.R @@ -1,5 +1,8 @@ #!/usr/bin/env Rscript +## Author: Barry Digby +## License: MIT + circ_mat = read.table("count_matrix.txt", header=T, sep="\t", check.names = FALSE, stringsAsFactors = F, row.names = "ID") gene_mat = read.table("gene_count_matrix.csv", sep=",", header=T, row.names="gene_id", stringsAsFactors = F) map = read.table("circrna_host-gene.txt", header = F, sep="\t", stringsAsFactors = F) diff --git a/bin/reformat_count_matrix.R b/bin/reformat_count_matrix.R index c78b48d7..8afabe6f 100755 --- a/bin/reformat_count_matrix.R +++ b/bin/reformat_count_matrix.R @@ -1,4 +1,8 @@ #!/usr/bin/env Rscript + +## Author: Barry Digby +## License: MIT + library(dplyr) mat <- read.table("circRNA_matrix.txt", sep="\t", header=T, stringsAsFactors=F) mat$ID <- with(mat, paste0(Chr, sep=":", Start, sep="-", Stop, sep=":", Strand)) diff --git a/bin/targetscan_format.sh b/bin/targetscan_format.sh index 2a23c9f6..9321221b 100755 --- a/bin/targetscan_format.sh +++ b/bin/targetscan_format.sh @@ -1,4 +1,7 @@ -#!/usr/bin/env +#!/usr/bin/env bash + +## Author: Barry Digby +## License: MIT ## Script that converts miRbase (mature.fa) file to ## TargetScan compatability. The motivation for doing @@ -15,7 +18,6 @@ ## Stage input mature.fa file, species MATURE="$1" -#GENOME_ID="$2" ## Uncompress if necessary if [ ${MATURE: -3} == ".gz" ]; then @@ -35,7 +37,7 @@ paste miR_ID seed_sequence > targetscan_tmp.txt ## Correct delimiter, add dummy species awk -v OFS="\t" '{print $1, $2, "0000"}' targetscan_tmp.txt > mature.txt -## Tidy the work dir (uncomment these for debugging scratch dirs) +## Tidy the work dir (comment these for debugging scratch dirs) rm -rf mature_sequence rm -rf miR_ID rm -rf targetscan_tmp.txt diff --git a/conf/modules.config b/conf/modules.config index f535f691..21b50e7e 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -38,7 +38,7 @@ process { ] } - // TRIMMING couresy of nf-core/rnaseq + // TRIMMING courtesy of nf-core/rnaseq if (!params.skip_trimming) { process { @@ -180,9 +180,9 @@ if (!params.skip_trimming) { "--outFilterType BySJout", "--outReadsUnmapped None", "--readFilesCommand zcat", - params.alignSJDBoverhangMin ? "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}" : "", - params.chimJunctionOverhangMin ? "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}" : "", - params.chimSegmentMin ? "--chimSegmentMin ${params.chimSegmentMin}" : "" + "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}", + "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}", + "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ path: { "${params.outdir}/circrna_discovery/star/1st_pass" }, @@ -205,16 +205,15 @@ if (!params.skip_trimming) { withName: STAR_2ND_PASS { ext.when = { params.module.split(',').contains('circrna_discovery') && ( params.tool.split(',').contains('circexplorer2') || params.tool.split(',').contains('circrna_finder') ) } ext.args = [ "", - // TODO: is this valid when both tools are run? params.tool.split(',').contains('circrna_finder') ? "--chimOutType Junctions SeparateSAMold" : "--chimOutType Junctions WithinBAM", "--outSAMunmapped Within", "--outFilterType BySJout", "--outReadsUnmapped None", "--readFilesCommand zcat", "--sjdbFileChrStartEnd dataset.SJ.out.tab", - params.alignSJDBoverhangMin ? "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}" : "--alignSJDBoverhangMin 10", - params.chimJunctionOverhangMin ? "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}" : "--chimJunctionOverhangMin 10", - params.chimSegmentMin ? "--chimSegmentMin ${params.chimSegmentMin}" : "--chimSegmentMin 10" + "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}", + "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}", + "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ path: { "${params.outdir}/circrna_discovery/star/2nd_pass" }, @@ -240,7 +239,6 @@ if (!params.skip_trimming) { withName: CIRCEXPLORER2_PARSE { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('circexplorer2') } - publishDir = [ path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates" }, mode: params.publish_dir_mode, @@ -380,9 +378,9 @@ if (!params.skip_trimming) { "--outFilterType BySJout", "--outReadsUnmapped None", "--readFilesCommand zcat", - params.alignSJDBoverhangMin ? "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}" : "", - params.chimJunctionOverhangMin ? "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}" : "", - params.chimSegmentMin ? "--chimSegmentMin ${params.chimSegmentMin}" : "" + "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}", + "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}", + "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ path: { "${params.outdir}/circrna_discovery/dcc/intermediates/align/1st_pass" }, @@ -411,9 +409,9 @@ if (!params.skip_trimming) { "--outReadsUnmapped None", "--readFilesCommand zcat", "--sjdbFileChrStartEnd dataset.SJ.out.tab", - params.alignSJDBoverhangMin ? "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}" : "--alignSJDBoverhangMin 10", - params.chimJunctionOverhangMin ? "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}" : "--chimJunctionOverhangMin 10", - params.chimSegmentMin ? "--chimSegmentMin ${params.chimSegmentMin}" : "--chimSegmentMin 10" + "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}", + "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}", + "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ path: { "${params.outdir}/circrna_discovery/dcc/intermediates/align/2nd_pass" }, @@ -432,9 +430,9 @@ if (!params.skip_trimming) { "--outFilterType BySJout", "--outReadsUnmapped None", "--readFilesCommand zcat", - params.alignSJDBoverhangMin ? "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}" : "", - params.chimJunctionOverhangMin ? "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}" : "", - params.chimSegmentMin ? "--chimSegmentMin ${params.chimSegmentMin}" : "" + "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}", + "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}", + "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ path: { "${params.outdir}/circrna_discovery/dcc/intermediates/mate1/1st_pass" }, @@ -464,9 +462,9 @@ if (!params.skip_trimming) { "--outReadsUnmapped None", "--readFilesCommand zcat", "--sjdbFileChrStartEnd dataset.SJ.out.tab", - params.alignSJDBoverhangMin ? "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}" : "--alignSJDBoverhangMin 10", - params.chimJunctionOverhangMin ? "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}" : "--chimJunctionOverhangMin 10", - params.chimSegmentMin ? "--chimSegmentMin ${params.chimSegmentMin}" : "--chimSegmentMin 10" + "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}", + "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}", + "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ path: { "${params.outdir}/circrna_discovery/dcc/intermediates/mate1/2nd_pass" }, @@ -485,9 +483,9 @@ if (!params.skip_trimming) { "--outFilterType BySJout", "--outReadsUnmapped None", "--readFilesCommand zcat", - params.alignSJDBoverhangMin ? "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}" : "", - params.chimJunctionOverhangMin ? "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}" : "", - params.chimSegmentMin ? "--chimSegmentMin ${params.chimSegmentMin}" : "" + "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}", + "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}", + "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ path: { "${params.outdir}/circrna_discovery/dcc/intermediates/mate2/1st_pass" }, @@ -517,9 +515,9 @@ if (!params.skip_trimming) { "--outReadsUnmapped None", "--readFilesCommand zcat", "--sjdbFileChrStartEnd dataset.SJ.out.tab", - params.alignSJDBoverhangMin ? "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}" : "--alignSJDBoverhangMin 10", - params.chimJunctionOverhangMin ? "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}" : "--chimJunctionOverhangMin 10", - params.chimSegmentMin ? "--chimSegmentMin ${params.chimSegmentMin}" : "--chimSegmentMin 10" + "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}", + "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}", + "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ path: { "${params.outdir}/circrna_discovery/dcc/intermediates/mate2/2nd_pass" }, @@ -556,11 +554,11 @@ if (!params.skip_trimming) { withName: MAPSPLICE_ALIGN { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('mapsplice') } ext.args = [ "", - params.seglen ? "--seglen ${params.seglen}" : "--seglen 25", - params.min_intron ? "--min-intron ${params.min_intron}" : "--min-intron 20", - params.max_intron ? "--max-intron ${params.max_intron}" : "--max-intron 1000000", - params.min_map_len ? "--min-map-len ${params.min_map_len}" : "--min-map-len 40", - params.min_fusion_distance ? "--min-fusion-distance ${params.min_fusion_distance}" : "--min-fusion-distance 200", + "--seglen ${params.seglen}", + "--min-intron ${params.min_intron}", + "--max-intron ${params.max_intron}", + "--min-map-len ${params.min_map_len}", + "--min-fusion-distance ${params.min_fusion_distance}", "--fusion-non-canonical" ].join(' ').trim() publishDir = [ @@ -571,7 +569,7 @@ if (!params.skip_trimming) { ] } -withName: MAPSPLICE_PARSE { + withName: MAPSPLICE_PARSE { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('mapsplice') } publishDir = [ path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates" }, diff --git a/conf/test.config b/conf/test.config index d778abc1..10095fa6 100644 --- a/conf/test.config +++ b/conf/test.config @@ -17,7 +17,7 @@ params { // Limit resources so that this can run on GitHub Actions max_cpus = 2 max_memory = 6.GB - max_time = 48.h + max_time = 6.h // Input data for test data input = 'https://raw.githubusercontent.com/nf-core/test-datasets/circrna/samples.csv' diff --git a/docs/output.md b/docs/output.md index a3ed45d6..27dd215f 100644 --- a/docs/output.md +++ b/docs/output.md @@ -20,60 +20,71 @@ A full run of the workflow will produce the following directory output structure The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: -- [nf-core/circrna: Output](#nf-corecircrna-output) - - [Introduction](#introduction) - - [Pipeline Overview](#pipeline-overview) - - [Quality Control](#quality-control) - - [Sam to Fastq](#sam-to-fastq) - - [BBDUK](#bbduk) - - [DESeq2](#deseq2) - - [MultiQC](#multiqc) - - [Genome Index Files](#genome-index-files) - - [circRNA Quantification](#circrna-quantification) - - [CIRCexplorer2](#circexplorer2) - - [circRNA finder](#circrna-finder) - - [CIRIquant](#ciriquant) - - [DCC](#dcc) - - [Find circ](#find-circ) - - [MapSplice](#mapsplice) - - [STAR](#star) - - [Segemehl](#segemehl) - - [Count Matrix](#count-matrix) - - [miRNA Prediction](#mirna-prediction) - - [miRanda](#miranda) - - [TargetScan](#targetscan) - - [miRNA targets](#mirna-targets) - - [Circos Plot](#circos-plot) - - [Differential Expression Analysis](#differential-expression-analysis) - - [circRNA](#circrna) - - [Boxplots](#boxplots) - - [RNA-Seq](#rna-seq) +- Raw read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) +- Adapter trimming ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)) +- MultiQC report [`MultiQC`](http://multiqc.info/) +- circRNA quantification +- [`CIRIquant`](https://github.com/Kevinzjy/CIRIquant) +- [`STAR 2-Pass mode`](https://github.com/alexdobin/STAR) + - [`CIRCexplorer2`](https://circexplorer2.readthedocs.io/en/latest/) + - [`circRNA finder`](https://github.com/orzechoj/circRNA_finder) + - [`DCC`](https://github.com/dieterich-lab/DCC) +- [`find circ`](https://github.com/marvin-jens/find_circ) +- [`MapSplice`](http://www.netlab.uky.edu/p/bioinfo/MapSplice2) +- [`Segemehl`](https://www.bioinf.uni-leipzig.de/Software/segemehl/) +- circRNA annotation +- Export mature spliced length as FASTA file +- Annotate parent gene, underlying transcripts. +- circRNA count matrix +- miRNA target prediction + - [`miRanda`](http://cbio.mskcc.org/miRNA2003/miranda.html) + - [`TargetScan`](http://www.targetscan.org/cgi-bin/targetscan/data_download.vert72.cgi) + - Filter results, miRNAs must be called by both tools +- Differential expression analysis [`DESeq2`](https://bioconductor.org/packages/release/bioc/html/DESeq2.html) +- Circular - Linear ratio tests ['CircTest'](https://github.com/dieterich-lab/CircTest) ## Quality Control -### Sam to Fastq +### FastQC
Output files -- `quality_control/SamToFastq` - - `*_R{1,2}.fq.gz`: Paired end fastq files, generated using `VALIDATION_STRINGENCY=LENIENT`. +- `fastqc/` + - `*_fastqc.html`: FastQC report containing quality metrics. + - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. + +> **NB:** The FastQC plots in this directory are generated relative to the raw, input reads. They may contain adapter sequence and regions of low quality. To see how your reads look after adapter and quality trimming please refer to the FastQC reports in the `trimgalore/fastqc/` directory.
-`nf-core/circrna` can accept input BAM files generated from paired end sequencing reads (e.g `TCGA`) by invoking [picard](https://broadinstitute.github.io/picard/) `SamToFastq`, converting BAM files to paired end fastq files. +[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). + +![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png) + +![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png) + +![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png) -### BBDUK +### TrimGalore
Output files -- `quality_control/BBDUK/` - - `*_r{1,2}.trim.fq.gz`: Processed paired end fastq files. +- `trimgalore/` + - `*.fq.gz`: If `--save_trimmed` is specified, FastQ files **after** adapter trimming will be placed in this directory. + - `*_trimming_report.txt`: Log file generated by Trim Galore!. +- `trimgalore/fastqc/` + - `*_fastqc.html`: FastQC report containing quality metrics for read 1 (_and read2 if paired-end_) **after** adapter trimming. + - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
-[BBDUK](https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/) (DUK - "Decontamination Using Kmers") is capable of performing adapter trimming, quality trimming/filtering and read length filtering (refer to BBDUK [parameter documentation](https://nf-co.re/circrna/dev/parameters#read-trimming--adapter-removal)) for the quality control of sequencing reads. `nf-core/circrna` will automatically output gzipped fastq files from `BBDUK` to minimise data usage. +[Trim Galore!](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) is a wrapper tool around Cutadapt and FastQC to peform quality and adapter trimming on FastQ files. By default, Trim Galore! will automatically detect and trim the appropriate adapter sequence. + +> **NB:** TrimGalore! will only run using multiple cores if you are able to use more than > 5 and > 6 CPUs for single- and paired-end data, respectively. The total cores available to TrimGalore! will also be capped at 4 (7 and 8 CPUs in total for single- and paired-end data, respectively) because there is no longer a run-time benefit. See [release notes](https://github.com/FelixKrueger/TrimGalore/blob/master/Changelog.md#version-060-release-on-1-mar-2019) and [discussion whilst adding this logic to the nf-core/atacseq pipeline](https://github.com/nf-core/atacseq/pull/65). + +![MultiQC - cutadapt trimmed sequence length plot](images/mqc_cutadapt_trimmed.png) ### DESeq2 @@ -81,46 +92,36 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d Output files - `quality_control/DESeq2_QC` - - `circRNA/` - - `DESeq2_condition_PCA.pdf`: PCA plot of PC1 vs. PC2 displaying the highest amount of variation within the response variable `condition`.

circRNA PCA

- - `DESeq2_dispersion.pdf`: Plot of re-fitted genes + gene outliers after shrinkage estimation performed by gene-wide maximum likelihood estimates (red curve) & maximum a posteriori estimates of dispersion.

circRNA dispersion

- - `DESeq2_sample_dendogram.pdf`: Dendogram displaying sample distances using [pvclust](https://cran.r-project.org/web/packages/pvclust/index.html).

circRNA dendo

- - `DESeq2_sample_heatmap.pdf`: Heatmap displaying Manhattan distance between samples.

circRNA samplehm

- - `RNA-Seq/` - - `DESeq2_condition_PCA.pdf`: PCA plot of PC1 vs. PC2 displaying the highest amount of variation within the response variable `condition`.

circRNA PCA

- - `DESeq2_dispersion.pdf`: Plot of re-fitted genes + gene outliers after shrinkage estimation performed by gene-wide maximum likelihood estimates (red curve) & maximum a posteriori estimates of dispersion.

circRNA dispersion

- - `DESeq2_sample_dendogram.pdf`: Dendogram displaying sample distances using [pvclust](https://cran.r-project.org/web/packages/pvclust/index.html).

circRNA dendo

- - `DESeq2_sample_heatmap.pdf`: Heatmap displaying Manhattan distance between samples.

circRNA samplehm @@ -159,7 +160,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d -`nf-core/circrna` will save genome indices when `--save_reference true`. This is highly encouraged to reduce runtimes on redeployment of the workflow. +`nf-core/circrna` will save genome indices when `--save_reference true`. This is highly encouraged to reduce runtimes on redeployment of the workflow, as you can supply them to aligner in question via the aligner flag (for example `--star '/path/to/STAR/'`. Available: `bowtie`, `bowtie2`, `bwa`, `hisat2`, `star`, `segemehl`). Make sure to move the saved genome indicies to a different location before doing so. ## circRNA Quantification @@ -169,10 +170,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d

Output files - `circrna_discovery/CIRCexplorer2/intermediates/${sample_id}/` - - `*.STAR.junction.bed`: Intermediate file generated by `CIRCexplorer2 parse` module, identifying STAR fusion junctions for downstream annotation. - `*.txt`: Output files generated by `CIRCexplorer2 annotate` module, based on BED 12 format containing circRNA genomic location information, exon cassette composition and an additional 6 columns specifying circRNA annotations. Full descriptions of the 18 columns can be found in the `CIRCexplorer2` [documentation](https://circexplorer2.readthedocs.io/en/latest/modules/annotate/#output). - - `circrna_discovery/CIRCexplorer2/${sample_id}/` - `${sample_id}.bed`: Filtered, annotated circRNAs in customised BED12 format. - `fasta/`: Mature spliced length circRNA FASTA sequences. @@ -187,7 +186,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d Output files - `circrna_discovery/circRNA_Finder/intermediates/${sample_id}/` - - `*.Aligned.sortedByCoord.out.bam`: Coordinate sorted bam file containing aligned reads and chimeric reads. - `*.Chimeric.out.junction`: Each line contains the details of chimerically aligned reads. Full descriptions of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 5.4). - `*.Chimeric.out.sam`: Chimeric alignments in SAM format. @@ -199,8 +197,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - `*.filteredJunctions.bed`: A bed file with **all** circular junctions found by the pipeline. The score column indicates the number reads spanning each junction. - `*.s_filteredJunctions.bed`: A bed file with those junctions in `*.filteredJunctions.bed` that are flanked by GT-AG splice sites. The score column indicates the number reads spanning each junction. - `*.s_filteredJunctions_fw.bed`: A bed file with the same circular junctions as in file (b), but here the score column gives the average number of forward spliced reads at both splice sites around each circular junction. - -- `circrna_discovery/circRNA_Finder/${sample_id}/ +- `circrna_discovery/circRNA_Finder/${sample_id}/` - `${sample_id}.bed`: Filtered, annotated circRNAs in customised BED12 format. - `fasta/`: Mature spliced length circRNA FASTA sequences. @@ -214,7 +211,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d Output files - `circrna_discovery/CIRIquant/intermediates/${sample_id}/` - - `*.log`: A `CIRIerror.log` file which should be empty, and a `${sample_id}.log` file which contains the output log of `CIRIquant`. - `*.bed`: `CIRI2` output file in BED 6 format. - `*.gtf`: Output file from `CIRIquant` in GTF format. Full description of the columns available in the `CIRIquant` [documentation](https://ciriquant-cookbook.readthedocs.io/en/latest/quantification.html#output-format). @@ -225,7 +221,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - `*_denovo.sorted.{bam, bam.bai}`: (Sorted and indexed) bam file from `BWA` alignment of candidate circular reads to the pseudo reference. - `*_index.*.ht2`: `BWA` index files of the pseudo reference. - `*_index.fa`: Reference FASTA file of candidate circular reads. - - `circrna_discovery/CIRIquant/${sample_id}/`` - `${sample_id}.bed`: Filtered, annotated circRNAs in customised BED12 format. - `fasta/`: Mature spliced length circRNA FASTA sequences. @@ -268,13 +263,11 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d Output files - `circrna_discovery/find_circ/intermediates/${sample_id}/` - - `*_anchors.qfa.gz`: 20mer anchors extracted from unmapped reads. - `*_unmapped.bam`: Unmapped RNA-Seq reads to reference genome. - `*.sites.bed`: Output from `find_circ`, first six columns are in standard BED format. A description of the remaining columns is available in the `find_circ` [documentation](https://github.com/marvin-jens/find_circ#output-format). - `*.sites.log`: Summary statistics of candidate circular reads in the sample. - `*.sites.reads`: Tab delimited file containing circRNA ID & sequence. - - `circrna_discovery/find_circ/${sample_id}/` - `${sample_id}.bed`: Filtered, annotated circRNAs in customised BED12 format. - `fasta/`: Mature spliced length circRNA FASTA sequences. @@ -295,7 +288,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d Output files - `circrna_discovery/MapSplice/intermediates/${sample_id}/` - - `alignments.bam`: Bam file containing aligned reads and fusion alignments. - `deletions.txt`: Report of deletions. - `Fusion output files`: @@ -307,7 +299,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - `insertions.txt`: Report of Insertions. - `junctions.txt`: Reported splice junctions. - `stats.txt`: Read alignment, Junction statistics. - - `circrna_discovery/MapSplice/${sample_id}/` - `${sample_id}.bed`: Filtered, annotated circRNAs in customised BED12 format. - `fasta/`: Mature spliced length circRNA FASTA sequences. @@ -330,9 +321,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - `*.Log.out`: Main log file with a lot of detailed information about the run. This file is most useful for troubleshooting and debugging. - `*.Log.progress.out`: Reports job progress statistics, such as the number of processed reads, % of mapped reads etc. - `*.SJ.out.tab`: High confidence collapsed splice junctions in tab-delimited form. Full description of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 4.4). - - `circrna_discovery/STAR/2nd_Pass/${sample_id}/` - - `*.Aligned.sortedByCoord.out.bam`: Coordinate sorted bam file containing aligned reads and chimeric reads. - `*.Chimeric.out.junction`: Each line contains the details of chimerically aligned reads. Full descriptions of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 5.4). - `*.Chimeric.out.sam`: Chimeric alignments in SAM format. @@ -340,7 +329,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - `*.Log.out`: Main log file with a lot of detailed information about the run. This file is most useful for troubleshooting and debugging. - `*.Log.progress.out`: Reports job progress statistics, such as the number of processed reads, % of mapped reads etc. - `*.SJ.out.tab`: High confidence collapsed splice junctions in tab-delimited form. Full description of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 4.4). - - `circrna_discovery/STAR/SJFile/` - `*.SJFile.tab`: Chromosome, start, end & strand coordinates of novel splice junctions. @@ -463,42 +451,31 @@ _N.B:_ In the phenotype file the response variable must be called `condition`, t Output files - `differential_expression/circRNA/` - - `DESeq2_log2_transformed_counts.txt`: _log2(Normalised counts + 1)_ - - `DESeq2_normalized_counts.txt`: Normalised circRNA counts. - - `control_vs_lung/` - - `DESeq2_{control_vs_lung}_Adj_pvalue_distribution.pdf`: Histogram of Adj pvalues from `results(dds)` displaying the distribution of circRNAs that reject the null hypothesis (padj <= 0.05).

circRNA adj-p histogram

- - `DESeq2_{control_vs_lung}_down_regulated_differential_expression.txt`: DESeq2 `results()` output filtered to include down regulated circRNAs (fold change <= -1, pvalue <= 0.05) in `condition` with respect to `control`. - - `DESeq2_{control_vs_lung}_fold_change_distribution.pdf`: Histogram of fold-change values for differentially expressed circRNAs.

circRNA FC histogram

- - `DESeq2_{control_vs_lung}_heatmap.pdf`: Heatmap of all differentially expressed circRNAs.

circRNA heatmap

- - `DESeq2_{control_vs_lung}_MA_plot.pdf`: Plot of the relationship between intensity and difference between the contrast made by `DESeq2`.

circRNA heatmap

- - `DESeq2_{control_vs_lung}_pvalue_distribution.pdf`: Histogram of pvalues from `results(dds)` displaying the distribution of circRNAs that reject the null hypothesis (pvalue <= 0.05).

circRNA pval dist

- - `DESeq2_{condition_vs_lung}_up_regulated_differential_expression.txt`: DEseq2 `results()` ouput filtered to include up regulated circRNAs (fold change >= 1, pvalue <= 0.05) in `condition` with respect to `control`. - - `DESeq2_{condition_vs_lung}_volcano_plot.pdf`: Volcano plot of differentially expressed circRNAs from DESeq2 `results()` using [EnhancedVolcano](https://www.bioconductor.org/packages/release/bioc/vignettes/EnhancedVolcano/inst/doc/EnhancedVolcano.html).

circRNA volcano @@ -516,14 +493,11 @@ _Note:_ The test dataset produces sparsely populated plots due to aggressive sub

Output files - `differential_expression/boxplots/` - - `control_vs_lung` - - `*boxplot.pdf`: Boxplot of differentially expressed circRNAs in `control_vs_lung`.

circRNA boxplot

- - `control_vs_lung` - `*boxplot.pdf`: Boxplot of differentially expressed circRNAs in `control_vs_melanoma`.

@@ -542,42 +516,31 @@ _Note:_ The output files give examples for `control_vs_lung` and `control_vs_mel

Output files - `differential_expression/RNA-Seq/` - - `DESeq2_log2_transformed_counts.txt`: _log2(Normalised counts + 1)_ - - `DESeq2_normalized_counts.txt`: Normalised RNA-Seq counts. - - `control_vs_lung/` - - `DESeq2_{control_vs_lung}_Adj_pvalue_distribution.pdf`: Histogram of Adj pvalues from `results(dds)` displaying the distribution of genes that reject the null hypothesis (padj <= 0.05).

circRNA adj-p histogram

- - `DESeq2_{control_vs_lung}_down_regulated_differential_expression.txt`: DESeq2 `results()` output filtered to include down regulated genes (fold change <= -1, pvalue <= 0.05) in `condition` with respect to `control`. - - `DESeq2_{control_vs_lung}_fold_change_distribution.pdf`: Histogram of fold-change values for differentially expressed genes.

circRNA FC histogram

- - `DESeq2_{control_vs_lung}_heatmap.pdf`: Heatmap of all differentially expressed genes.

circRNA heatmap

- - `DESeq2_{control_vs_lung}_MA_plot.pdf`: Plot of the relationship between intensity and difference between the contrast made by `DESeq2`.

circRNA heatmap

- - `DESeq2_{control_vs_lung}_pvalue_distribution.pdf`: Histogram of pvalues from `results(dds)` displaying the distribution of genes that reject the null hypothesis (pvalue <= 0.05).

circRNA pval dist

- - `DESeq2_{condition_vs_lung}_up_regulated_differential_expression.txt`: DEseq2 `results()` ouput filtered to include up regulated genes (fold change >= 1, pvalue <= 0.05) in `condition` with respect to `control`. - - `DESeq2_{condition_vs_lung}_volcano_plot.pdf`: Volcano plot of differentially expressed genes from DESeq2 `results()` using [EnhancedVolcano](https://www.bioconductor.org/packages/release/bioc/vignettes/EnhancedVolcano/inst/doc/EnhancedVolcano.html).

circRNA volcano diff --git a/docs/usage.md b/docs/usage.md index 953fb337..f1f0ab39 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -2,29 +2,28 @@ It is recommended that first time users run `nf-core/circrna` with the minimal test dataset either locally or on a HPC, referring to the [output documentation](https://nf-co.re/circrna/dev/output) before running a full analysis. -```console +```bash nextflow run nf-core/circrna -profile test, ``` -## Running the pipeline +# Running the pipeline A typical command for running the pipeline is as follows: -```console +```bash nextflow run nf-core/circrna \ -profile \ --genome 'GRCh37' \ - --input 'samples.csv' \ - --input_type 'fastq' + --input 'samples.csv' ``` By default, `nf-core/circrna` runs the circRNA discovery analysis module using `CIRCexplorer2`. The above command will perform circRNA quantification using these tools on ENSEMBL GRCh37 reference annotation files as defined in the iGenomes config. -### Updating the pipeline +## Updating the pipeline To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: -```console +```bash nextflow pull nf-core/circrna ``` @@ -38,63 +37,28 @@ First, go to the [nf-core/circrna releases page](https://github.com/nf-core/circ This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. -## Input specifications - -Input data can be passed to `nf-core/circrna` in two possible ways using the `--input` parameter. - -### `--input ""` - -The simplest way to pass input data to `nf-core/circrna` is by providing the path to the input data with a suitable wildcard glob pattern: - -#### fastq - -```console ---input "/data/*_r{1,2}.fastq.gz" -``` - -##### bam - -```console ---input "/data/*.bam" -``` +# Input specifications -> Beware that providing a path to input data will result in samples being named according to the common tuple key based on the glob pattern supplied. Take this into consideration when designing your phenotype file for differential expression analysis. +Input data can be passed to `nf-core/circrna` using a CSV file containing the absolute paths to input fastq files. -### `--input samples.csv` +The headers of the CSV file must be: `sample,fastq_1,fastq_2`. -Alternatively, the user may wish to provide a CSV file containing the absolute paths to input fastq/bam files. +Valid examples for fastq input data in a CSV file is given below: -The headers of the CSV file must be: `Sample_ID,Read1,Read2,Bam`. - -> This approach is recommended for most real life situations, where in-house sequencing facilities file naming convention requires the user to manually match file names to metadata. The below input files use `TCGA` identifiers as proof of concept. - -Valid examples for fastq/bam input data in a CSV file is given below: - -| Sample_ID | Read1 | Read2 | Bam | -| ---------------- | :---------------------------------------------------------------------- | ----------------------------------------------------------------------- | --- | -| TCGA-EJ-7783-11A | /data/f4c1b2b1-ba1f-4355-a1ac-3e952cf351a5_gdc_realn_rehead_R1.fastq.gz | /data/f4c1b2b1-ba1f-4355-a1ac-3e952cf351a5_gdc_realn_rehead_R2.fastq.gz | NA | -| TCGA-G9-6365-11A | /data/8a36555b-9e27-40ee-a8df-4b15d6580a02_gdc_realn_rehead_R1.fastq.gz | /data/8a36555b-9e27-40ee-a8df-4b15d6580a02_gdc_realn_rehead_R2.fastq.gz | NA | -| TCGA-EJ-7782-11A | /data/8b3d4a3d-2bfa-48f8-b31f-901f49a5bf6b_gdc_realn_rehead_R1.fastq.gz | /data/8b3d4a3d-2bfa-48f8-b31f-901f49a5bf6b_gdc_realn_rehead_R2.fastq.gz | NA | -| TCGA-CH-5772-01A | /data/b6546f66-3c13-4390-9643-d1fb3d660a2f_gdc_realn_rehead_R1.fastq.gz | /data/b6546f66-3c13-4390-9643-d1fb3d660a2f_gdc_realn_rehead_R2.fastq.gz | NA | -| TCGA-EJ-5518-01A | /data/afbbc370-5970-43d3-b9f8-f40f8e649bb6_gdc_realn_rehead_R1.fastq.gz | /data/afbbc370-5970-43d3-b9f8-f40f8e649bb6_gdc_realn_rehead_R2.fastq.gz | NA | -| TCGA-KK-A8I4-01A | /data/81254692-ee1e-4985-bd0a-4929eed4c620_gdc_realn_rehead_R1.fastq.gz | /data/81254692-ee1e-4985-bd0a-4929eed4c620_gdc_realn_rehead_R2.fastq.gz | NA | - ---- - -| Sample_ID | Read1 | Read2 | Bam | -| :--------------- | ----- | ----- | :-------------------------------------------------------------- | -| TCGA-EJ-7783-11A | NA | NA | /data/f4c1b2b1-ba1f-4355-a1ac-3e952cf351a5_gdc_realn_rehead.bam | -| TCGA-G9-6365-11A | NA | NA | /data/8a36555b-9e27-40ee-a8df-4b15d6580a02_gdc_realn_rehead.bam | -| TCGA-EJ-7782-11A | NA | NA | /data/8b3d4a3d-2bfa-48f8-b31f-901f49a5bf6b_gdc_realn_rehead.bam | -| TCGA-CH-5772-01A | NA | NA | /data/b6546f66-3c13-4390-9643-d1fb3d660a2f_gdc_realn_rehead.bam | -| TCGA-EJ-5518-01A | NA | NA | /data/afbbc370-5970-43d3-b9f8-f40f8e649bb6_gdc_realn_rehead.bam | -| TCGA-KK-A8I4-01A | NA | NA | /data/81254692-ee1e-4985-bd0a-4929eed4c620_gdc_realn_rehead.bam | +| sample | fastq_1 | fastq_2 | +| ---------------- | :---------------------------------------------------------------------- | ----------------------------------------------------------------------- | +| TCGA-EJ-7783-11A | /data/f4c1b2b1-ba1f-4355-a1ac-3e952cf351a5_gdc_realn_rehead_R1.fastq.gz | /data/f4c1b2b1-ba1f-4355-a1ac-3e952cf351a5_gdc_realn_rehead_R2.fastq.gz | +| TCGA-G9-6365-11A | /data/8a36555b-9e27-40ee-a8df-4b15d6580a02_gdc_realn_rehead_R1.fastq.gz | /data/8a36555b-9e27-40ee-a8df-4b15d6580a02_gdc_realn_rehead_R2.fastq.gz | +| TCGA-EJ-7782-11A | /data/8b3d4a3d-2bfa-48f8-b31f-901f49a5bf6b_gdc_realn_rehead_R1.fastq.gz | /data/8b3d4a3d-2bfa-48f8-b31f-901f49a5bf6b_gdc_realn_rehead_R2.fastq.gz | +| TCGA-CH-5772-01A | /data/b6546f66-3c13-4390-9643-d1fb3d660a2f_gdc_realn_rehead_R1.fastq.gz | /data/b6546f66-3c13-4390-9643-d1fb3d660a2f_gdc_realn_rehead_R2.fastq.gz | +| TCGA-EJ-5518-01A | /data/afbbc370-5970-43d3-b9f8-f40f8e649bb6_gdc_realn_rehead_R1.fastq.gz | /data/afbbc370-5970-43d3-b9f8-f40f8e649bb6_gdc_realn_rehead_R2.fastq.gz | +| TCGA-KK-A8I4-01A | /data/81254692-ee1e-4985-bd0a-4929eed4c620_gdc_realn_rehead_R1.fastq.gz | /data/81254692-ee1e-4985-bd0a-4929eed4c620_gdc_realn_rehead_R2.fastq.gz | > Do not leave any cell empty in the CSV file. -### `--phenotype` +## Phenotype file -When running the differential expression analysis module, an input `phenotype.csv` file is required to specify levels for `DESeq2`. At a minimum, the user must supply one column of levels for `DESeq2` which **must be called condition**. This should be the primary contrast of interest in your experiment (e.g case vs. control). If additional columns are supplied to the phenotype file, they will be controlled for in the linear mixed model. A brief proof of concept is given below in R notation: +When running the differential expression analysis module via the `--module differential_expression` parameter, an input `phenotype.csv` file is required to specify levels for `DESeq2`. At a minimum, the user must supply one column of levels for `DESeq2` which **must be called condition**. This should be the primary contrast of interest in your experiment (e.g case vs. control). If additional columns are supplied to the phenotype file, they will be controlled for in the linear mixed model. A brief proof of concept is given below in R notation: ```R colnames(phenotype) @@ -112,9 +76,9 @@ print(dds$design) [1] ' ~ location + replicates + condition' ``` -It is recommended to use an input CSV file in conjunction with your phenotype file as the `Sample_ID` column **must match** the first column of the `phenotype.csv` file. +It is recommended to construct your input CSV file in conjunction with your phenotype file as the first column denoting sample names **must match** the first column of the `phenotype.csv` file. -A valid example of a `phenotype.csv` file (matching the TCGA example input CSV file above) is given below: +A valid example of a `phenotype.csv` file (matching the TCGA example input CSV file above) is given: | Sample_ID | condition | | ---------------- | --------- | @@ -125,7 +89,7 @@ A valid example of a `phenotype.csv` file (matching the TCGA example input CSV f | TCGA-EJ-5518-01A | tumor | | TCGA-KK-A8I4-01A | tumor | -## Analysis modules +# Analysis modules `nf-core/circrna` provides 3 analysis modules to the user: @@ -133,18 +97,17 @@ A valid example of a `phenotype.csv` file (matching the TCGA example input CSV f 2. miRNA target prediction. 3. Differential circRNA expression analysis. -### circRNA discovery +## circRNA discovery The core module of `nf-core/circrna`, a user can utilise up to seven circRNA quantification tools to fully characterise the circRNA profile in samples. Currently, supported tools include `CIRCexplorer2`, `circRNA finder`, `CIRIquant`, `DCC`, `find circ` , `MapSplice` & `Segemehl` however, the authors of `nf-core/circrna` welcome contributions from authors of novel quantification tools to keep the workflow current. By default, `nf-core/circrna` runs the circRNA discovery analysis module. -```console +```bash nextflow run nf-core/circrna \ -profile \ --genome 'GRCh37' \ --input 'samples.csv' \ - --input_type 'fastq' \ --module 'circrna_discovery' ``` @@ -152,38 +115,36 @@ To view the outputs of the module, please see the output [documentation](https:/ > Please note that this module must be included for every run of the workflow -#### Tool selection +### Tool selection The user may use one, all or any combination of circRNA quantification tools listed above in the analysis. To select which tools to use for the analysis, specify the `--tool` parameter in the configuration profile or pass it via the command line when running the workflow: -```console +```bash nextflow run nf-core/circrna \ -profile \ --genome 'GRCh37' \ --input 'samples.csv' \ - --input_type 'fastq' \ --module 'circrna_discovery' \ --tool 'ciriquant,dcc,find_circ' ``` > When providing multiple tools, separate each entry with a comma. -#### circRNA filtering +### circRNA filtering `nf-core/circrna` offers robust filtering of each called circRNA to reduce the number of spurious calls within the dataset. -##### BSJ reads +#### BSJ reads The user can specify the minimum number of reads spanning the back-splice junction site required for a circRNA to be considered for further analysis. circRNAs with counts below this value will be filtered to remove from the results. To apply this filtering method, specify the `--bsj_reads` parameter in the configuration profile or pass it via the command line when running the workflow: -```console +```bash nextflow run nf-core/circrna \ -profile \ --genome 'GRCh37' \ --input 'samples.csv' \ - --input_type 'fastq' \ --phenotype 'phenotype.csv' \ --module 'circrna_discovery' \ --tool 'ciriquant, dcc, find_circ' \ @@ -192,7 +153,7 @@ nextflow run nf-core/circrna \ Disable the filter by setting the value to 0. -##### Multiple tool filtering +#### Multiple tool filtering When more than one tool has been provided using the `--tool` parameter, the user can specify the minimum number of tools circRNAs must be called by using `--tool_filter`. Setting this parameter to 0 or 1 will result in the union being output, i.e no filtering is applied. Setting this parameter to 2 will output circRNAs that have been called by at least 2 quantification tools and so on. @@ -200,12 +161,11 @@ When more than one tool has been provided using the `--tool` parameter, the user To apply this filtering method, specify the `--tool_filter` parameter in the configuration profile or pass it via the command line when running the workflow: -```console +```bash nextflow run nf-core/circrna \ -profile \ --genome 'GRCh37' \ --input 'samples.csv' \ - --input_type 'fastq' \ --module 'circrna_discovery' \ --tool 'ciriquant, dcc, find_circ' \ --bsj_reads 2 \ @@ -214,39 +174,37 @@ nextflow run nf-core/circrna \ > This filtering method is reflected in the circRNA count matrix. Per tool circRNA annotations are subject to back-splice read filtering only. -##### Handling duplicate circRNAs +#### Handling duplicate circRNAs In the event a circRNA has been called by more than one quantification tool, the user can specify which aggregate function to apply to the duplicated circRNA. The accepted values are 'mean' and 'max', which are passed to the workflow using the `--duplicates_fun` parameter. -### miRNA prediction +## miRNA prediction The second module of `nf-core/circrna`, `mirna_prediction` analyses the mature spliced sequences of circRNAs to test for the presence of miRNA response elements using both `miRanda` and `TargetScan`. Results from both tools are consolidated and filtering methods are applied to produce robust miRNA target predictions of circRNAs in the dataset. To invoke the module, specify the `--module` parameter via the configuration profile or pass it via the command line when running the workflow: -```console +```bash nextflow run nf-core/circrna \ -profile \ --genome 'GRCh37' \ --input 'samples.csv' \ - --input_type 'fastq' \ --module 'circrna_discovery, mirna_prediction' ``` To view the outputs of the module, please see the output [documentation](https://nf-co.re/circrna/dev/output#mirna-prediction). -### Differential circRNA analysis +## Differential circRNA analysis The third and final module of `nf-core/circrna` performs differential expression analysis of circRNAs, returning `DESeq2` result outputs, plots and diagnostic plots for the user. In order to run this module, it is essential that your `phenotype.csv` file is in the correct format - please refer to the input [specifications](https://nf-co.re/circrna/dev/usage#differential-expression-analysis). To invoke the module, specify the `--module` parameter via the configuration profile or pass it via the command line when running the workflow: -```console +```bash nextflow run nf-core/circrna \ -profile \ --genome 'GRCh37' \ --input 'samples.csv' \ - --input_type 'fastq' \ --phenotype 'phenotype.csv' \ --module 'circrna_discovery, differential_expression' ``` diff --git a/modules/local/annotation/full_annotation/main.nf b/modules/local/annotation/full_annotation/main.nf index c47bd561..4d751d66 100644 --- a/modules/local/annotation/full_annotation/main.nf +++ b/modules/local/annotation/full_annotation/main.nf @@ -25,7 +25,7 @@ process ANNOTATION { prefix = task.ext.prefix ?: "${meta.id}" def VERSION = '377' """ - grep -vf ${workflow.projectDir}/bin/unwanted_biotypes.txt $gtf > filt.gtf + grep -vf unwanted_biotypes.txt $gtf > filt.gtf mv $bed circs.bed annotate_outputs.sh $exon_boundary &> ${prefix}.log @@ -38,6 +38,7 @@ process ANNOTATION { cat <<-END_VERSIONS > versions.yml "${task.process}": + awk: \$(awk --version | head -n1 | cut -d' ' -f3 | sed 's/,//g' ) bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") ucsc: $VERSION END_VERSIONS diff --git a/modules/local/annotation/parent_gene/main.nf b/modules/local/annotation/parent_gene/main.nf index c412ab8d..023bed74 100644 --- a/modules/local/annotation/parent_gene/main.nf +++ b/modules/local/annotation/parent_gene/main.nf @@ -26,7 +26,17 @@ process PARENT_GENE { # generate circrna BED file. tail -n +2 $circrna_matrix | awk '{print \$1}' > IDs.txt - ID_to_BED.sh IDs.txt + + # ID_to_BED + while IFS='' read -r line; do + name=\$(echo \$line) + chr=\$(echo \$line | cut -d: -f1) + start=\$(echo \$line | cut -d- -f1 | cut -d: -f2) + stop=\$(echo \$line | cut -d- -f2 | cut -d: -f1) + sign=\$(echo \$line | cut -d: -f3) + echo -e "\$chr\t\$start\t\$stop\t\$name\t0\t\$sign" >> \${name}.bed + done < IDs.txt + cat *.bed > merged.txt && rm IDs.txt && rm *.bed && mv merged.txt circs.bed # Re-use annotation script to identify the host gene. diff --git a/modules/local/circexplorer2/filter/main.nf b/modules/local/circexplorer2/filter/main.nf index 3594ac95..fece7a46 100644 --- a/modules/local/circexplorer2/filter/main.nf +++ b/modules/local/circexplorer2/filter/main.nf @@ -2,6 +2,11 @@ process CIRCEXPLORER2_FILTER { tag "$meta.id" label 'process_single' + conda "bioconda::gawk=5.1.0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gawk%3A5.1.0' : + 'quay.io/biocontainers/gawk:5.1.0' }" + input: tuple val(meta), path(txt) val(bsj_reads) @@ -9,6 +14,7 @@ process CIRCEXPLORER2_FILTER { output: tuple val(meta), path("${prefix}_${meta.tool}_circs.bed"), emit: results tuple val(meta), path("${prefix}_${meta.tool}.bed") , emit: matrix + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -20,5 +26,10 @@ process CIRCEXPLORER2_FILTER { awk '{if(\$13 >= ${bsj_reads}) print \$0}' ${prefix}.txt | awk -v OFS="\t" '{print \$1,\$2,\$3,\$6,\$13}' > ${prefix}_${meta.tool}.bed awk -v OFS="\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_${meta.tool}.bed > ${prefix}_${meta.tool}_circs.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + awk: \$(awk --version | head -n1 | cut -d' ' -f3 | sed 's/,//g' ) + END_VERSIONS """ } diff --git a/modules/local/circexplorer2/reference/main.nf b/modules/local/circexplorer2/reference/main.nf index ed2b3537..6bb46f78 100644 --- a/modules/local/circexplorer2/reference/main.nf +++ b/modules/local/circexplorer2/reference/main.nf @@ -31,6 +31,7 @@ process CIRCEXPLORER2_REFERENCE { cat <<-END_VERSIONS > versions.yml "${task.process}": + awk: \$(awk --version | head -n1 | cut -d' ' -f3 | sed 's/,//g' ) ucsc: $VERSION END_VERSIONS """ diff --git a/modules/local/circrna_finder/filter/main.nf b/modules/local/circrna_finder/filter/main.nf index 06d7cf5c..e5198cfb 100644 --- a/modules/local/circrna_finder/filter/main.nf +++ b/modules/local/circrna_finder/filter/main.nf @@ -34,6 +34,8 @@ process CIRCRNA_FINDER_FILTER { cat <<-END_VERSIONS > versions.yml "${task.process}": + awk: \$(awk --version | head -n1 | cut -d' ' -f3 | sed 's/,//g' ) + cat: \$(cat --version | head -n 1 | sed -e 's/cat (GNU coreutils) //') circRNA_finder: $VERSION END_VERSIONS """ diff --git a/modules/local/circtest/prepare/main.nf b/modules/local/circtest/prepare/main.nf index 47d74346..2fecd7b0 100644 --- a/modules/local/circtest/prepare/main.nf +++ b/modules/local/circtest/prepare/main.nf @@ -1,7 +1,7 @@ process PREPARE_CLR_TEST { label 'process_medium' - conda "r-base r-aod r-ggplot2 r-plyr" + conda "conda-forge::r-base=4.2.2 conda-forge::r-aod=1.3.2 conda-forge::r-ggplot2=3.4.0 conda-forge::r-plyr=1.8.8" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c79b00aa4647c739dbe7e8480789d3ba67988f2e:0' : 'quay.io/biocontainers/mulled-v2-c79b00aa4647c739dbe7e8480789d3ba67988f2e:0' }" diff --git a/modules/local/circtest/test/main.nf b/modules/local/circtest/test/main.nf index 43b23083..1d1e4df3 100644 --- a/modules/local/circtest/test/main.nf +++ b/modules/local/circtest/test/main.nf @@ -1,7 +1,7 @@ process CIRCTEST { label 'process_medium' - conda "r-base r-aod r-ggplot2 r-plyr" + conda "conda-forge::r-base=4.2.2 conda-forge::r-aod=1.3.2 conda-forge::r-ggplot2=3.4.0 conda-forge::r-plyr=1.8.8" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c79b00aa4647c739dbe7e8480789d3ba67988f2e:0' : 'quay.io/biocontainers/mulled-v2-c79b00aa4647c739dbe7e8480789d3ba67988f2e:0' }" diff --git a/modules/local/ciriquant/filter/main.nf b/modules/local/ciriquant/filter/main.nf index a1341a94..253d6d2b 100644 --- a/modules/local/ciriquant/filter/main.nf +++ b/modules/local/ciriquant/filter/main.nf @@ -2,6 +2,11 @@ process CIRIQUANT_FILTER { tag "$meta.id" label 'process_single' + conda "bioconda::gawk=5.1.0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gawk%3A5.1.0' : + 'quay.io/biocontainers/gawk:5.1.0' }" + input: tuple val(meta), path(gtf) val bsj_reads @@ -9,6 +14,7 @@ process CIRIQUANT_FILTER { output: tuple val(meta), path("${prefix}_ciriquant_circs.bed"), emit: results tuple val(meta), path("${prefix}_ciriquant.bed") , emit: matrix + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -27,5 +33,10 @@ process CIRIQUANT_FILTER { rm ${prefix}.gtf awk -v OFS="\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_ciriquant.bed > ${prefix}_ciriquant_circs.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + awk: \$(awk --version | head -n1 | cut -d' ' -f3 | sed 's/,//g' ) + END_VERSIONS """ } diff --git a/modules/local/count_matrix/combined/main.nf b/modules/local/count_matrix/combined/main.nf index 65f430b5..e277ffff 100644 --- a/modules/local/count_matrix/combined/main.nf +++ b/modules/local/count_matrix/combined/main.nf @@ -1,7 +1,7 @@ process COUNTS_COMBINED { label 'process_low' - conda "r-base=3.6.3 python=2.7.15 r-argparser=0.6 r-dplyr=1.0.5" + conda "conda-forge::r-base=3.6.3 conda-forge::python=2.7.15 conda-forge::r-argparser=0.6 conda-forge::r-dplyr=1.0.5" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-5fbffedf7f529cf3c5093b976deb4290f5e1267a:3456f1432b1c9dad42815275abe2d6cb6f26fd94-0' : 'quay.io/biocontainers/mulled-v2-5fbffedf7f529cf3c5093b976deb4290f5e1267a:3456f1432b1c9dad42815275abe2d6cb6f26fd94-0' }" @@ -12,6 +12,7 @@ process COUNTS_COMBINED { output: path("circRNA_matrix.txt"), emit: dea_matrix path("count_matrix.txt") , emit: clr_matrix + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -28,9 +29,11 @@ process COUNTS_COMBINED { cat <<-END_VERSIONS > versions.yml "${task.process}": + awk: \$(awk --version | head -n 1 | cut -d' ' -f3 | sed 's/,//g') r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//') argparser: \$(Rscript -e "library(arparser); cat(as.character(packageVersion('argparser')))") dplyr: \$(Rscript -e "library(dplyr); cat(as.character(packageVersion('dplyr')))") + python: \$(python --version | sed -e 's/Python //g') END_VERSIONS """ } diff --git a/modules/local/count_matrix/merge_tools/main.nf b/modules/local/count_matrix/merge_tools/main.nf index fd3feb89..e2ee4b11 100644 --- a/modules/local/count_matrix/merge_tools/main.nf +++ b/modules/local/count_matrix/merge_tools/main.nf @@ -2,7 +2,7 @@ process MERGE_TOOLS { tag "$meta.id" label 'process_low' - conda "r-base=3.6.3 python=2.7.15 r-argparser=0.6 r-dplyr=1.0.5" + conda "conda-forge::r-base=3.6.3 conda-forge::python=2.7.15 conda-forge::r-argparser=0.6 conda-forge::r-dplyr=1.0.5" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-5fbffedf7f529cf3c5093b976deb4290f5e1267a:3456f1432b1c9dad42815275abe2d6cb6f26fd94-0' : 'quay.io/biocontainers/mulled-v2-5fbffedf7f529cf3c5093b976deb4290f5e1267a:3456f1432b1c9dad42815275abe2d6cb6f26fd94-0' }" @@ -14,6 +14,7 @@ process MERGE_TOOLS { output: tuple val(meta), path("${prefix}.bed"), emit: merged + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -38,6 +39,7 @@ process MERGE_TOOLS { r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//') argparser: \$(Rscript -e "library(arparser); cat(as.character(packageVersion('argparser')))") dplyr: \$(Rscript -e "library(dplyr); cat(as.character(packageVersion('dplyr')))") + python: \$(python --version | sed -e 's/Python //g') END_VERSIONS """ } diff --git a/modules/local/count_matrix/single/main.nf b/modules/local/count_matrix/single/main.nf index 8ce82da8..59f628c8 100644 --- a/modules/local/count_matrix/single/main.nf +++ b/modules/local/count_matrix/single/main.nf @@ -2,7 +2,7 @@ process COUNTS_SINGLE { tag "${meta.tool}" label 'process_low' - conda "r-base=3.6.3 python=2.7.15 r-argparser=0.6 r-dplyr=1.0.5" + conda "conda-forge::r-base=3.6.3 conda-forge::python=2.7.15 conda-forge::r-argparser=0.6 conda-forge::r-dplyr=1.0.5" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-5fbffedf7f529cf3c5093b976deb4290f5e1267a:3456f1432b1c9dad42815275abe2d6cb6f26fd94-0' : 'quay.io/biocontainers/mulled-v2-5fbffedf7f529cf3c5093b976deb4290f5e1267a:3456f1432b1c9dad42815275abe2d6cb6f26fd94-0' }" @@ -13,6 +13,7 @@ process COUNTS_SINGLE { output: path("circRNA_matrix.txt"), emit: dea_matrix path("count_matrix.txt") , emit: clr_matrix + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -37,9 +38,11 @@ process COUNTS_SINGLE { cat <<-END_VERSIONS > versions.yml "${task.process}": + awk: \$(awk --version | head -n 1 | cut -d' ' -f3 | sed 's/,//g') r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//') argparser: \$(Rscript -e "library(arparser); cat(as.character(packageVersion('argparser')))") dplyr: \$(Rscript -e "library(dplyr); cat(as.character(packageVersion('dplyr')))") + python: \$(python --version | sed -e 's/Python //g') END_VERSIONS """ } diff --git a/modules/local/dcc/filter/main.nf b/modules/local/dcc/filter/main.nf index b9bcca46..1fcd3ef7 100644 --- a/modules/local/dcc/filter/main.nf +++ b/modules/local/dcc/filter/main.nf @@ -2,6 +2,11 @@ process DCC_FILTER { tag "$meta.id" label 'process_single' + conda "bioconda::gawk=5.1.0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gawk%3A5.1.0' : + 'quay.io/biocontainers/gawk:5.1.0' }" + input: tuple val(meta), path(txt) val bsj_reads @@ -9,6 +14,7 @@ process DCC_FILTER { output: tuple val(meta), path("${prefix}_dcc_circs.bed"), emit: results tuple val(meta), path("${prefix}_dcc.bed") , emit: matrix + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -19,5 +25,10 @@ process DCC_FILTER { awk '{if(\$5 >= ${bsj_reads}) print \$0}' ${prefix}.txt > ${prefix}_dcc.filtered awk -v OFS="\t" '{\$2-=1;print}' ${prefix}_dcc.filtered > ${prefix}_dcc.bed awk -v OFS="\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_dcc.bed > ${prefix}_dcc_circs.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + awk: \$(awk --version | head -n1 | cut -d' ' -f3 | sed 's/,//g' ) + END_VERSIONS """ } diff --git a/modules/local/fasta/main.nf b/modules/local/fasta/main.nf index c2cd5ada..f43543d8 100644 --- a/modules/local/fasta/main.nf +++ b/modules/local/fasta/main.nf @@ -38,6 +38,7 @@ process FASTA { cat <<-END_VERSIONS > versions.yml "${task.process}": bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + cut: \$(cut --version | head -n 1 | cut -d' ' -f4) END_VERSIONS """ } diff --git a/modules/local/mapsplice/align/main.nf b/modules/local/mapsplice/align/main.nf index 44c64d97..b62e4db2 100644 --- a/modules/local/mapsplice/align/main.nf +++ b/modules/local/mapsplice/align/main.nf @@ -26,8 +26,8 @@ process MAPSPLICE_ALIGN { def VERSION = 'v2.2.1' def gtf_prefix = gtf.toString() - ~/.gtf/ if(meta.single_end){ - def handleGzip_R1 = reads[0].toString().endsWith('.gz') ? "gzip -d -f ${reads[0]}" : '' - def read1 = reads[0].toString().endsWith('.gz') ? reads[0].toString() - ~/.gz/ : reads[0] + def handleGzip_R1 = reads[0].getExtension() == 'gz' ? "gzip -d -f ${reads[0]}" : '' + def read1 = reads[0].getExtension() == 'gz' ? reads[0].toString() - ~/.gz/ : reads[0] """ $handleGzip_R1 @@ -47,10 +47,10 @@ process MAPSPLICE_ALIGN { END_VERSIONS """ }else{ - def handleGzip_R1 = reads[0].toString().endsWith('.gz') ? "gzip -d -f ${reads[0]}" : '' - def handleGzip_R2 = reads[1].toString().endsWith('.gz') ? "gzip -d -f ${reads[1]}" : '' - def read1 = reads[0].toString().endsWith('.gz') ? reads[0].toString() - ~/.gz/ : reads[0] - def read2 = reads[1].toString().endsWith('.gz') ? reads[1].toString() - ~/.gz/ : reads[1] + def handleGzip_R1 = reads[0].getExtension() == 'gz' ? "gzip -d -f ${reads[0]}" : '' + def handleGzip_R2 = reads[1].getExtension() == 'gz' ? "gzip -d -f ${reads[1]}" : '' + def read1 = reads[0].getExtension() == 'gz' ? reads[0].toString() - ~/.gz/ : reads[0] + def read2 = reads[1].getExtension() == 'gz' ? reads[1].toString() - ~/.gz/ : reads[1] """ $handleGzip_R1 $handleGzip_R2 diff --git a/modules/local/mirna_targets/main.nf b/modules/local/mirna_targets/main.nf index c6beaeff..4f70ca03 100644 --- a/modules/local/mirna_targets/main.nf +++ b/modules/local/mirna_targets/main.nf @@ -37,6 +37,7 @@ process MIRNA_TARGETS { cat <<-END_VERSIONS > versions.yml "${task.process}": + awk: \$(awk --version | head -n1 | cut -d' ' -f3 | sed 's/,//g' ) bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") END_VERSIONS """ diff --git a/modules/local/segemehl/filter/main.nf b/modules/local/segemehl/filter/main.nf index 8ea15603..5ca86cca 100644 --- a/modules/local/segemehl/filter/main.nf +++ b/modules/local/segemehl/filter/main.nf @@ -1,7 +1,12 @@ -process SEGEMEHL_FILTER{ +process SEGEMEHL_FILTER { tag "$meta.id" label 'process_single' + conda "bioconda::gawk=5.1.0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gawk%3A5.1.0' : + 'quay.io/biocontainers/gawk:5.1.0' }" + input: tuple val(meta), path(results) val(bsj_reads) @@ -9,6 +14,7 @@ process SEGEMEHL_FILTER{ output: tuple val(meta), path("${prefix}_segemehl_circs.bed"), emit: results tuple val(meta), path("${prefix}_segemehl.bed") , emit: matrix + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -22,5 +28,11 @@ process SEGEMEHL_FILTER{ awk -v OFS="\t" -v BSJ=${bsj_reads} '{if(\$5>=BSJ) print \$0}' ${prefix}_collapsed.bed > ${prefix}_segemehl.bed awk -v OFS="\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_segemehl.bed > ${prefix}_segemehl_circs.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + awk: \$(awk --version | head -n1 | cut -d' ' -f3 | sed 's/,//g' ) + sort: \$(sort --version | sed -e 's/sort (GNU coreutils) //g') + END_VERSIONS """ } diff --git a/modules/local/star/sjdb/main.nf b/modules/local/star/sjdb/main.nf index 602d0da9..60b81849 100644 --- a/modules/local/star/sjdb/main.nf +++ b/modules/local/star/sjdb/main.nf @@ -1,12 +1,18 @@ process SJDB { label 'process_single' + conda "bioconda::gawk=5.1.0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gawk%3A5.1.0' : + 'quay.io/biocontainers/gawk:5.1.0' }" + input: path(sjdb) val(bsj_reads) output: path("dataset.SJ.out.tab"), emit: sjtab + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -14,5 +20,10 @@ process SJDB { script: """ cat *.tab | awk -v BSJ=${bsj_reads} '(\$7 >= BSJ && \$6==0)' | cut -f1-6 | sort | uniq > dataset.SJ.out.tab + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + awk: \$(awk --version | head -n1 | cut -d' ' -f3 | sed 's/,//g' ) + END_VERSIONS """ } diff --git a/modules/local/stringtie/prepde/main.nf b/modules/local/stringtie/prepde/main.nf index da20b1a8..c5700673 100644 --- a/modules/local/stringtie/prepde/main.nf +++ b/modules/local/stringtie/prepde/main.nf @@ -12,6 +12,7 @@ process STRINGTIE_PREPDE { output: path "transcript_count_matrix.csv" , emit: transcript_matrix path "gene_count_matrix.csv" , emit: gene_matrix + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -21,5 +22,10 @@ process STRINGTIE_PREPDE { for file in \$(ls *.gtf); do sample_id=\${file%".transcripts.gtf"}; touch samples.txt; printf "\$sample_id\t\$file\n" >> samples.txt ; done prepDE.py -i samples.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed -e "s/Python //g") + END_VERSIONS """ } diff --git a/modules/local/targetscan/database/main.nf b/modules/local/targetscan/database/main.nf index 0581aa4c..75657365 100644 --- a/modules/local/targetscan/database/main.nf +++ b/modules/local/targetscan/database/main.nf @@ -13,6 +13,6 @@ process TARGETSCAN_DATABASE { script: """ - bash ${workflow.projectDir}/bin/targetscan_format.sh $mature + targetscan_format.sh $mature """ } diff --git a/modules/local/targetscan/predict/main.nf b/modules/local/targetscan/predict/main.nf index f6b37cb0..62599ab8 100644 --- a/modules/local/targetscan/predict/main.nf +++ b/modules/local/targetscan/predict/main.nf @@ -31,6 +31,7 @@ process TARGETSCAN { cat <<-END_VERSIONS > versions.yml "${task.process}": + awk: \$(awk --version | head -n1 | cut -d' ' -f3 | sed 's/,//g' ) targetscan: $VERSION END_VERSIONS """ diff --git a/nextflow.config b/nextflow.config index e0d5c68a..14f1455c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -22,7 +22,7 @@ params { tool_filter = 0 duplicates_fun = 'mean' exon_boundary = 200 - save_intermediates = true + save_intermediates = false // reference genome options genome = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 659d8f0d..5eda7888 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -88,7 +88,7 @@ "save_intermediates": { "type": "boolean", "description": "Save intermediate alignment/circRNA files.", - "default": true, + "default": false, "fa_icon": "fas fa-save" }, "exon_boundary": { @@ -443,11 +443,10 @@ }, "email": { "type": "string", - "description": "Phenotype CSV file specifying the experimental design for DESeq2.", - "fa_icon": "fas fa-journal-whills", - "mimetype": "text/csv", - "help_text": "The response variable containing the phenotype of primary interest in the experiment must have the column name condition. An example phenotype file is given below:\n\n| Sample_ID | condition | replicates |\n|---------|-----------|------------|\n| control_rep1 | control | 1 |\n| control_rep2 | control | 2 |\n| control_rep3 | control | 3 |\n| lung_rep1 | lung | 1 |\n| lung_rep2 | lung | 2 |\n| lung_rep3 | lung | 3 |\n| melanoma_rep1 | melanoma | 1 |\n| melanoma_rep2 | melanoma | 2 |\n| melanoma_rep3 | melanoma | 3 |\n\nThis will produce the DESeq2 design formula '~ replicates + condition' i.e all columns not named condition will be controlled for in the linear mixed model.", - "pattern": "\\.csv$" + "description": "Email address for completion summary.", + "fa_icon": "fas fa-envelope", + "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.", + "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$" }, "email_on_fail": { "type": "string", diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index e6f6571a..7a85eaa0 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -69,6 +69,7 @@ workflow CIRCRNA_DISCOVERY { SEGEMEHL_FILTER( segemehl_filter, bsj_reads ) ch_versions = ch_versions.mix(SEGEMEHL_ALIGN.out.versions) + ch_versions = ch_versions.mix(SEGEMEHL_FILTER.out.versions) // // STAR WORFKLOW: @@ -80,6 +81,7 @@ workflow CIRCRNA_DISCOVERY { STAR_2ND_PASS( reads, star_index, STAR_SJDB.out.sjtab, true, '', '' ) ch_versions = ch_versions.mix(STAR_1ST_PASS.out.versions) + ch_versions = ch_versions.mix(STAR_2ND_PASS.out.versions) // // CIRCEXPLORER2 WORKFLOW: @@ -94,6 +96,7 @@ workflow CIRCRNA_DISCOVERY { ch_versions = ch_versions.mix(CIRCEXPLORER2_REFERENCE.out.versions) ch_versions = ch_versions.mix(CIRCEXPLORER2_PARSE.out.versions) ch_versions = ch_versions.mix(CIRCEXPLORER2_ANNOTATE.out.versions) + ch_versions = ch_versions.mix(CIRCEXPLORER2_FILTER.out.versions) // // CIRCRNA_FINDER WORKFLOW: @@ -121,6 +124,7 @@ workflow CIRCRNA_DISCOVERY { ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions) ch_versions = ch_versions.mix(FIND_CIRC_ANCHORS.out.versions) + ch_versions = ch_versions.mix(FIND_CIRC.out.versions) ch_versions = ch_versions.mix(FIND_CIRC_FILTER.out.versions) // @@ -132,6 +136,7 @@ workflow CIRCRNA_DISCOVERY { CIRIQUANT_FILTER( CIRIQUANT.out.gtf.map{ meta, gtf -> meta.tool = "ciriquant"; return [ meta, gtf ] }, bsj_reads ) ch_versions = ch_versions.mix(CIRIQUANT.out.versions) + ch_versions = ch_versions.mix(CIRIQUANT_FILTER.out.versions) // // DCC WORKFLOW @@ -157,7 +162,13 @@ workflow CIRCRNA_DISCOVERY { DCC_FILTER( DCC.out.txt.map{ meta, txt -> meta.tool = "dcc"; return [ meta, txt ] }, bsj_reads ) ch_versions = ch_versions.mix(DCC_MATE1_1ST_PASS.out.versions) + ch_versions = ch_versions.mix(DCC_MATE1_SJDB.out.versions) + ch_versions = ch_versions.mix(DCC_MATE1_2ND_PASS.out.versions) + ch_versions = ch_versions.mix(DCC_MATE2_1ST_PASS.out.versions) + ch_versions = ch_versions.mix(DCC_MATE2_SJDB.out.versions) + ch_versions = ch_versions.mix(DCC_MATE2_2ND_PASS.out.versions) ch_versions = ch_versions.mix(DCC.out.versions) + ch_versions = ch_versions.mix(DCC_FILTER.out.versions) // // MAPSPLICE WORKFLOW: @@ -179,7 +190,12 @@ workflow CIRCRNA_DISCOVERY { // ANNOTATION WORKFLOW: // - circrna_filtered = CIRCEXPLORER2_FILTER.out.results.mix(SEGEMEHL_FILTER.out.results, CIRCRNA_FINDER_FILTER.out.results, FIND_CIRC_FILTER.out.results, CIRIQUANT_FILTER.out.results, DCC_FILTER.out.results, MAPSPLICE_FILTER.out.results ) + circrna_filtered = CIRCEXPLORER2_FILTER.out.results.mix(SEGEMEHL_FILTER.out.results, + CIRCRNA_FINDER_FILTER.out.results, + FIND_CIRC_FILTER.out.results, + CIRIQUANT_FILTER.out.results, + DCC_FILTER.out.results, + MAPSPLICE_FILTER.out.results) ANNOTATION( circrna_filtered, gtf, exon_boundary ) ch_versions = ch_versions.mix(ANNOTATION.out.versions) @@ -196,7 +212,13 @@ workflow CIRCRNA_DISCOVERY { // COUNT MATRIX WORKFLOW: // - ch_matrix = CIRCEXPLORER2_FILTER.out.matrix.mix(SEGEMEHL_FILTER.out.matrix, CIRCRNA_FINDER_FILTER.out.matrix, FIND_CIRC_FILTER.out.matrix, CIRIQUANT_FILTER.out.matrix, DCC_FILTER.out.matrix, MAPSPLICE_FILTER.out.matrix ) + ch_matrix = CIRCEXPLORER2_FILTER.out.matrix.mix(SEGEMEHL_FILTER.out.matrix, + CIRCRNA_FINDER_FILTER.out.matrix, + FIND_CIRC_FILTER.out.matrix, + CIRIQUANT_FILTER.out.matrix, + DCC_FILTER.out.matrix, + MAPSPLICE_FILTER.out.matrix) + tools_selected = params.tool.split(',').collect{it.trim().toLowerCase()} if( tools_selected.size() > 1){ @@ -207,14 +229,16 @@ workflow CIRCRNA_DISCOVERY { dea_matrix = COUNTS_COMBINED.out.dea_matrix clr_matrix = COUNTS_COMBINED.out.clr_matrix + ch_versions = ch_versions.mix(MERGE_TOOLS.out.versions) + ch_versions = ch_versions.mix(COUNTS_COMBINED.out.versions) }else{ - // TODO: concerned that this does not wait for all files? COUNTS_SINGLE( ch_matrix.map{ meta, bed -> var = [:]; var.tool = meta.tool; return [ var, bed ] }.groupTuple() ) dea_matrix = COUNTS_SINGLE.out.dea_matrix clr_matrix = COUNTS_SINGLE.out.clr_matrix + ch_versions = ch_versions.mix(COUNTS_SINGLE.out.versions) } diff --git a/subworkflows/local/differential_expression.nf b/subworkflows/local/differential_expression.nf index ef9c4c59..d6b22ab2 100644 --- a/subworkflows/local/differential_expression.nf +++ b/subworkflows/local/differential_expression.nf @@ -51,6 +51,7 @@ workflow DIFFERENTIAL_EXPRESSION { ch_versions = ch_versions.mix(HISAT2_ALIGN.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions) ch_versions = ch_versions.mix(STRINGTIE_STRINGTIE.out.versions) + ch_versions = ch_versions.mix(STRINGTIE_PREPDE.out.versions) ch_versions = ch_versions.mix(DESEQ2_DIFFERENTIAL_EXPRESSION.out.versions) ch_versions = ch_versions.mix(PARENT_GENE.out.versions) ch_versions = ch_versions.mix(PREPARE_CLR_TEST.out.versions) diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 516b3fae..b49a4e83 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -31,43 +31,25 @@ workflow PREPARE_GENOME { stage_chromosomes = Channel.value("${workflow.launchDir}/${params.outdir}/genome/chromosomes") } - // some index procs use tuple, some dont -_- ch_fasta.map{ it -> meta = [:] meta.id = it.simpleName return [ meta, [it] ] }.set{ fasta_tuple } - BOWTIE_BUILD( - fasta - ) + BOWTIE_BUILD(fasta) - BOWTIE2_BUILD( - fasta_tuple - ) + BOWTIE2_BUILD(fasta_tuple) - BWA_INDEX ( - fasta_tuple - ) + BWA_INDEX (fasta_tuple) - HISAT2_EXTRACTSPLICESITES( - gtf - ) + HISAT2_EXTRACTSPLICESITES(gtf) - HISAT2_BUILD( - fasta, - gtf, - HISAT2_EXTRACTSPLICESITES.out.txt - ) + HISAT2_BUILD(fasta, gtf, HISAT2_EXTRACTSPLICESITES.out.txt) - STAR_GENOMEGENERATE( - fasta, - gtf - ) + STAR_GENOMEGENERATE(fasta, gtf) - SEGEMEHL_INDEX( - fasta - ) + SEGEMEHL_INDEX(fasta) // Collect versions ch_versions = ch_versions.mix(BOWTIE_BUILD.out.versions) diff --git a/workflows/circrna.nf b/workflows/circrna.nf index d43b430e..34ff6947 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -49,8 +49,6 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// MODULES: - // SUBWORKFLOWS: include { INPUT_CHECK } from '../subworkflows/local/input_check' include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome' @@ -100,9 +98,7 @@ workflow CIRCRNA { meta, fastq -> meta.id = meta.id.split('_')[0..-2].join('_') [ meta, fastq ] } - .dump(tag: 'map') .groupTuple(by: [0]) - .dump(tag: 'group') .branch { meta, fastq -> single : fastq.size() == 1 From 575f732b5c6186dccd0213415ba24b17a3d40e61 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Tue, 31 Jan 2023 13:23:22 +0000 Subject: [PATCH 010/491] stage bin/biotypes file --- modules/local/annotation/full_annotation/main.nf | 4 +++- modules/local/annotation/parent_gene/main.nf | 3 ++- subworkflows/local/circrna_discovery.nf | 4 +++- subworkflows/local/differential_expression.nf | 4 +++- 4 files changed, 11 insertions(+), 4 deletions(-) diff --git a/modules/local/annotation/full_annotation/main.nf b/modules/local/annotation/full_annotation/main.nf index 4d751d66..a8954311 100644 --- a/modules/local/annotation/full_annotation/main.nf +++ b/modules/local/annotation/full_annotation/main.nf @@ -10,8 +10,10 @@ process ANNOTATION { input: tuple val(meta), path(bed) path gtf + path biotypes val exon_boundary + output: tuple val(meta), path("${prefix}.bed"), emit: bed path("*.log") , emit: log @@ -25,7 +27,7 @@ process ANNOTATION { prefix = task.ext.prefix ?: "${meta.id}" def VERSION = '377' """ - grep -vf unwanted_biotypes.txt $gtf > filt.gtf + grep -vf $biotypes $gtf > filt.gtf mv $bed circs.bed annotate_outputs.sh $exon_boundary &> ${prefix}.log diff --git a/modules/local/annotation/parent_gene/main.nf b/modules/local/annotation/parent_gene/main.nf index 023bed74..ed035527 100644 --- a/modules/local/annotation/parent_gene/main.nf +++ b/modules/local/annotation/parent_gene/main.nf @@ -9,6 +9,7 @@ process PARENT_GENE { input: path circrna_matrix path gtf + path biotypes val exon_boundary output: @@ -22,7 +23,7 @@ process PARENT_GENE { def VERSION = '377' """ # remove redundant biotypes from GTF. - grep -vf ${workflow.projectDir}/bin/unwanted_biotypes.txt $gtf > filt.gtf + grep -vf $biotypes $gtf > filt.gtf # generate circrna BED file. tail -n +2 $circrna_matrix | awk '{print \$1}' > IDs.txt diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 7a85eaa0..89d4df68 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -190,13 +190,15 @@ workflow CIRCRNA_DISCOVERY { // ANNOTATION WORKFLOW: // + ch_biotypes = Channel.fromPath("${projectDir}/bin/unwanted_biotypes.txt") + circrna_filtered = CIRCEXPLORER2_FILTER.out.results.mix(SEGEMEHL_FILTER.out.results, CIRCRNA_FINDER_FILTER.out.results, FIND_CIRC_FILTER.out.results, CIRIQUANT_FILTER.out.results, DCC_FILTER.out.results, MAPSPLICE_FILTER.out.results) - ANNOTATION( circrna_filtered, gtf, exon_boundary ) + ANNOTATION( circrna_filtered, gtf, ch_biotypes, exon_boundary ) ch_versions = ch_versions.mix(ANNOTATION.out.versions) diff --git a/subworkflows/local/differential_expression.nf b/subworkflows/local/differential_expression.nf index d6b22ab2..1d442a80 100644 --- a/subworkflows/local/differential_expression.nf +++ b/subworkflows/local/differential_expression.nf @@ -44,7 +44,9 @@ workflow DIFFERENTIAL_EXPRESSION { // CircRNA - Host Gene Ratio tests // - PARENT_GENE( clr_matrix, gtf, exon_boundary ) + ch_biotypes = Channel.fromPath("${projectDir}/bin/unwanted_biotypes.txt") + + PARENT_GENE( clr_matrix, gtf, ch_biotypes, exon_boundary ) PREPARE_CLR_TEST( STRINGTIE_PREPDE.out.gene_matrix, clr_matrix, PARENT_GENE.out.circ_host_map, gtf ) CIRCTEST( PREPARE_CLR_TEST.out.circular, PREPARE_CLR_TEST.out.linear, phenotype ) From d1230f28006c5e59ff87381f4fd96d0b32190691 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Tue, 31 Jan 2023 13:46:20 +0000 Subject: [PATCH 011/491] versions indentation --- modules/local/stringtie/prepde/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/stringtie/prepde/main.nf b/modules/local/stringtie/prepde/main.nf index c5700673..189cea1e 100644 --- a/modules/local/stringtie/prepde/main.nf +++ b/modules/local/stringtie/prepde/main.nf @@ -25,7 +25,7 @@ process STRINGTIE_PREPDE { cat <<-END_VERSIONS > versions.yml "${task.process}": - python: \$(python --version | sed -e "s/Python //g") + python: \$(python --version | sed -e 's/Python //g') END_VERSIONS """ } From 1c7bf5c5043dbb7e76987f34bd53d11a0307ae99 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Tue, 31 Jan 2023 14:02:02 +0000 Subject: [PATCH 012/491] use stringtie version for stringtie script --- modules/local/stringtie/prepde/main.nf | 2 +- subworkflows/local/circrna_discovery.nf | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/local/stringtie/prepde/main.nf b/modules/local/stringtie/prepde/main.nf index 189cea1e..07ff052e 100644 --- a/modules/local/stringtie/prepde/main.nf +++ b/modules/local/stringtie/prepde/main.nf @@ -25,7 +25,7 @@ process STRINGTIE_PREPDE { cat <<-END_VERSIONS > versions.yml "${task.process}": - python: \$(python --version | sed -e 's/Python //g') + stringtie: \$(stringtie --version 2>&1) END_VERSIONS """ } diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 89d4df68..651427e1 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -198,6 +198,7 @@ workflow CIRCRNA_DISCOVERY { CIRIQUANT_FILTER.out.results, DCC_FILTER.out.results, MAPSPLICE_FILTER.out.results) + ANNOTATION( circrna_filtered, gtf, ch_biotypes, exon_boundary ) ch_versions = ch_versions.mix(ANNOTATION.out.versions) From 2dabe07171e37a210be79f425be28d2ef3e46271 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Tue, 31 Jan 2023 14:17:23 +0000 Subject: [PATCH 013/491] collect biotypes chan --- subworkflows/local/circrna_discovery.nf | 4 ++-- subworkflows/local/differential_expression.nf | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 651427e1..a253959c 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -198,8 +198,8 @@ workflow CIRCRNA_DISCOVERY { CIRIQUANT_FILTER.out.results, DCC_FILTER.out.results, MAPSPLICE_FILTER.out.results) - - ANNOTATION( circrna_filtered, gtf, ch_biotypes, exon_boundary ) + + ANNOTATION( circrna_filtered, gtf, ch_biotypes.collect(), exon_boundary ) ch_versions = ch_versions.mix(ANNOTATION.out.versions) diff --git a/subworkflows/local/differential_expression.nf b/subworkflows/local/differential_expression.nf index 1d442a80..85e33af0 100644 --- a/subworkflows/local/differential_expression.nf +++ b/subworkflows/local/differential_expression.nf @@ -46,7 +46,7 @@ workflow DIFFERENTIAL_EXPRESSION { ch_biotypes = Channel.fromPath("${projectDir}/bin/unwanted_biotypes.txt") - PARENT_GENE( clr_matrix, gtf, ch_biotypes, exon_boundary ) + PARENT_GENE( clr_matrix, gtf, ch_biotypes.collect(), exon_boundary ) PREPARE_CLR_TEST( STRINGTIE_PREPDE.out.gene_matrix, clr_matrix, PARENT_GENE.out.circ_host_map, gtf ) CIRCTEST( PREPARE_CLR_TEST.out.circular, PREPARE_CLR_TEST.out.linear, phenotype ) From 7727fa7006773acff493c661f1c6bbb854313db9 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Tue, 31 Jan 2023 15:03:59 +0000 Subject: [PATCH 014/491] mawk not gawk, ubuntu20.04 container --- modules/local/circexplorer2/filter/main.nf | 9 +++++---- modules/local/ciriquant/filter/main.nf | 9 +++++---- modules/local/dcc/filter/main.nf | 9 +++++---- modules/local/segemehl/filter/main.nf | 11 ++++++----- modules/local/star/sjdb/main.nf | 9 +++++---- modules/local/targetscan/database/main.nf | 14 +++++++++++++- subworkflows/local/mirna_prediction.nf | 1 + 7 files changed, 40 insertions(+), 22 deletions(-) diff --git a/modules/local/circexplorer2/filter/main.nf b/modules/local/circexplorer2/filter/main.nf index fece7a46..4b246961 100644 --- a/modules/local/circexplorer2/filter/main.nf +++ b/modules/local/circexplorer2/filter/main.nf @@ -2,10 +2,10 @@ process CIRCEXPLORER2_FILTER { tag "$meta.id" label 'process_single' - conda "bioconda::gawk=5.1.0" + conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gawk%3A5.1.0' : - 'quay.io/biocontainers/gawk:5.1.0' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'ubuntu:20.04' }" input: tuple val(meta), path(txt) @@ -22,6 +22,7 @@ process CIRCEXPLORER2_FILTER { script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '1.3.4' """ awk '{if(\$13 >= ${bsj_reads}) print \$0}' ${prefix}.txt | awk -v OFS="\t" '{print \$1,\$2,\$3,\$6,\$13}' > ${prefix}_${meta.tool}.bed @@ -29,7 +30,7 @@ process CIRCEXPLORER2_FILTER { cat <<-END_VERSIONS > versions.yml "${task.process}": - awk: \$(awk --version | head -n1 | cut -d' ' -f3 | sed 's/,//g' ) + mawk: $VERSION END_VERSIONS """ } diff --git a/modules/local/ciriquant/filter/main.nf b/modules/local/ciriquant/filter/main.nf index 253d6d2b..38520091 100644 --- a/modules/local/ciriquant/filter/main.nf +++ b/modules/local/ciriquant/filter/main.nf @@ -2,10 +2,10 @@ process CIRIQUANT_FILTER { tag "$meta.id" label 'process_single' - conda "bioconda::gawk=5.1.0" + conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gawk%3A5.1.0' : - 'quay.io/biocontainers/gawk:5.1.0' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'ubuntu:20.04' }" input: tuple val(meta), path(gtf) @@ -21,6 +21,7 @@ process CIRIQUANT_FILTER { script: prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '1.3.4' """ grep -v "#" ${prefix}.gtf | awk '{print \$14}' | cut -d '.' -f1 > counts grep -v "#" ${prefix}.gtf | awk -v OFS="\t" '{print \$1,\$4,\$5,\$7}' > ${prefix}.tmp @@ -36,7 +37,7 @@ process CIRIQUANT_FILTER { cat <<-END_VERSIONS > versions.yml "${task.process}": - awk: \$(awk --version | head -n1 | cut -d' ' -f3 | sed 's/,//g' ) + mawk: $VERSION END_VERSIONS """ } diff --git a/modules/local/dcc/filter/main.nf b/modules/local/dcc/filter/main.nf index 1fcd3ef7..d7bc3c54 100644 --- a/modules/local/dcc/filter/main.nf +++ b/modules/local/dcc/filter/main.nf @@ -2,10 +2,10 @@ process DCC_FILTER { tag "$meta.id" label 'process_single' - conda "bioconda::gawk=5.1.0" + conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gawk%3A5.1.0' : - 'quay.io/biocontainers/gawk:5.1.0' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'ubuntu:20.04' }" input: tuple val(meta), path(txt) @@ -21,6 +21,7 @@ process DCC_FILTER { script: prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '1.3.4' """ awk '{if(\$5 >= ${bsj_reads}) print \$0}' ${prefix}.txt > ${prefix}_dcc.filtered awk -v OFS="\t" '{\$2-=1;print}' ${prefix}_dcc.filtered > ${prefix}_dcc.bed @@ -28,7 +29,7 @@ process DCC_FILTER { cat <<-END_VERSIONS > versions.yml "${task.process}": - awk: \$(awk --version | head -n1 | cut -d' ' -f3 | sed 's/,//g' ) + mawk: $VERSION END_VERSIONS """ } diff --git a/modules/local/segemehl/filter/main.nf b/modules/local/segemehl/filter/main.nf index 5ca86cca..40c895ff 100644 --- a/modules/local/segemehl/filter/main.nf +++ b/modules/local/segemehl/filter/main.nf @@ -2,10 +2,10 @@ process SEGEMEHL_FILTER { tag "$meta.id" label 'process_single' - conda "bioconda::gawk=5.1.0" + conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gawk%3A5.1.0' : - 'quay.io/biocontainers/gawk:5.1.0' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'ubuntu:20.04' }" input: tuple val(meta), path(results) @@ -22,6 +22,7 @@ process SEGEMEHL_FILTER { script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '1.3.4' """ grep ';C;' ${prefix}.sngl.bed | awk -v OFS="\t" '{print \$1,\$2,\$3,\$6}' | sort | uniq -c | awk -v OFS="\t" '{print \$2,\$3,\$4,\$5,\$1}' > ${prefix}_collapsed.bed @@ -31,8 +32,8 @@ process SEGEMEHL_FILTER { cat <<-END_VERSIONS > versions.yml "${task.process}": - awk: \$(awk --version | head -n1 | cut -d' ' -f3 | sed 's/,//g' ) - sort: \$(sort --version | sed -e 's/sort (GNU coreutils) //g') + mawk: $VERSION + sort: \$(sort --version | head -n 1 | sed -e 's/sort (GNU coreutils) //g') END_VERSIONS """ } diff --git a/modules/local/star/sjdb/main.nf b/modules/local/star/sjdb/main.nf index 60b81849..3a09d91a 100644 --- a/modules/local/star/sjdb/main.nf +++ b/modules/local/star/sjdb/main.nf @@ -1,10 +1,10 @@ process SJDB { label 'process_single' - conda "bioconda::gawk=5.1.0" + conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gawk%3A5.1.0' : - 'quay.io/biocontainers/gawk:5.1.0' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'ubuntu:20.04' }" input: path(sjdb) @@ -18,12 +18,13 @@ process SJDB { task.ext.when == null || task.ext.when script: + def VERSION = '1.3.4' """ cat *.tab | awk -v BSJ=${bsj_reads} '(\$7 >= BSJ && \$6==0)' | cut -f1-6 | sort | uniq > dataset.SJ.out.tab cat <<-END_VERSIONS > versions.yml "${task.process}": - awk: \$(awk --version | head -n1 | cut -d' ' -f3 | sed 's/,//g' ) + mawk: $VERSION END_VERSIONS """ } diff --git a/modules/local/targetscan/database/main.nf b/modules/local/targetscan/database/main.nf index 75657365..030ffe9b 100644 --- a/modules/local/targetscan/database/main.nf +++ b/modules/local/targetscan/database/main.nf @@ -2,17 +2,29 @@ process TARGETSCAN_DATABASE { tag "$mature" label 'process_low' + conda "conda-forge::sed=4.7" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'ubuntu:20.04' }" + input: path(mature) output: - path("mature.txt"), emit: mature_txt + path("mature.txt") , emit: mature_txt + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: + def VERSION = '1.3.4' """ targetscan_format.sh $mature + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mawk: $VERSION + END_VERSIONS """ } diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index 953c794e..b9a4cfc7 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -20,6 +20,7 @@ workflow MIRNA_PREDICTION{ TARGETSCAN_DATABASE( mature ) TARGETSCAN( circrna_fasta, TARGETSCAN_DATABASE.out.mature_txt ) + ch_versions = ch_versions.mix(TARGETSCAN_DATABASE.out.versions) ch_versions = ch_versions.mix(TARGETSCAN.out.versions) // From 77e7b4adf85091a7e54924349c2e35937effa35d Mon Sep 17 00:00:00 2001 From: Barry digby Date: Tue, 31 Jan 2023 15:45:21 +0000 Subject: [PATCH 015/491] update outputs.md --- docs/output.md | 30 +++++++++---------------- subworkflows/local/circrna_discovery.nf | 2 +- 2 files changed, 12 insertions(+), 20 deletions(-) diff --git a/docs/output.md b/docs/output.md index 27dd215f..80185914 100644 --- a/docs/output.md +++ b/docs/output.md @@ -164,6 +164,17 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d ## circRNA Quantification +## Common Outputs + +The workflow is designed to output three files per quantification tool selected in the `circrna_discovery` directory. By design, the workflow standardises the outputs of each quantification tool. + +- `quantification_tool/`: + - `${sample_id}.bed`: A customised BED 12 file containing filtered, annotated circRNAs. Columns: chromosome, start, end, name, read counts, strand, start, end, RGB, number of exon blocks, size of exon blocks, start positions (within sequence) of exon blocks, parent gene ID(s), parent transcript ID(s), mature spliced length. + - `${sample_id}.log`: Script detailing the decisions made by `annotate_outputs.sh` when annotating each circRNA. + - `${sample_id}.fasta`: Mature spliced sequence of circRNA in FASTA format. Includes splice junction site (+-20bp). + +Intermediate files generated by each quantification tool are described in depth below. + ### CIRCexplorer2

@@ -172,9 +183,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - `circrna_discovery/CIRCexplorer2/intermediates/${sample_id}/` - `*.STAR.junction.bed`: Intermediate file generated by `CIRCexplorer2 parse` module, identifying STAR fusion junctions for downstream annotation. - `*.txt`: Output files generated by `CIRCexplorer2 annotate` module, based on BED 12 format containing circRNA genomic location information, exon cassette composition and an additional 6 columns specifying circRNA annotations. Full descriptions of the 18 columns can be found in the `CIRCexplorer2` [documentation](https://circexplorer2.readthedocs.io/en/latest/modules/annotate/#output). -- `circrna_discovery/CIRCexplorer2/${sample_id}/` - - `${sample_id}.bed`: Filtered, annotated circRNAs in customised BED12 format. - - `fasta/`: Mature spliced length circRNA FASTA sequences.
@@ -197,9 +205,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - `*.filteredJunctions.bed`: A bed file with **all** circular junctions found by the pipeline. The score column indicates the number reads spanning each junction. - `*.s_filteredJunctions.bed`: A bed file with those junctions in `*.filteredJunctions.bed` that are flanked by GT-AG splice sites. The score column indicates the number reads spanning each junction. - `*.s_filteredJunctions_fw.bed`: A bed file with the same circular junctions as in file (b), but here the score column gives the average number of forward spliced reads at both splice sites around each circular junction. -- `circrna_discovery/circRNA_Finder/${sample_id}/` - - `${sample_id}.bed`: Filtered, annotated circRNAs in customised BED12 format. - - `fasta/`: Mature spliced length circRNA FASTA sequences. @@ -221,9 +226,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - `*_denovo.sorted.{bam, bam.bai}`: (Sorted and indexed) bam file from `BWA` alignment of candidate circular reads to the pseudo reference. - `*_index.*.ht2`: `BWA` index files of the pseudo reference. - `*_index.fa`: Reference FASTA file of candidate circular reads. -- `circrna_discovery/CIRIquant/${sample_id}/`` - - `${sample_id}.bed`: Filtered, annotated circRNAs in customised BED12 format. - - `fasta/`: Mature spliced length circRNA FASTA sequences. @@ -241,10 +243,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - `mate1/`: Output directory of STAR 2nd pass alignment for R1. - `mate2/`: Output directory of STAR 2nd pass alignment for R2. -- `circrna_discovery/DCC/${sample_id}/` - - `${sample_id}.bed`: Filtered, annotated circRNAs in customised BED12 format. - - `fasta/`: Mature spliced length circRNA FASTA sequences. - [DCC](https://github.com/dieterich-lab/DCC) identifies back-splice junction sites from `*Chimeric.out.junction`, `*SJ.out.tab` & `*Aligned.sortedByCoord.out.bam` files generated by `STAR` 2 pass mode, mapping the paired end reads both jointly and separately (`STAR` does not output read pairs that contain more than one chimeric junction thus a more granular approach is taken by `DCC` to fully characterise back-splice junctions in reads). @@ -268,9 +266,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - `*.sites.bed`: Output from `find_circ`, first six columns are in standard BED format. A description of the remaining columns is available in the `find_circ` [documentation](https://github.com/marvin-jens/find_circ#output-format). - `*.sites.log`: Summary statistics of candidate circular reads in the sample. - `*.sites.reads`: Tab delimited file containing circRNA ID & sequence. -- `circrna_discovery/find_circ/${sample_id}/` - - `${sample_id}.bed`: Filtered, annotated circRNAs in customised BED12 format. - - `fasta/`: Mature spliced length circRNA FASTA sequences. @@ -299,9 +294,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - `insertions.txt`: Report of Insertions. - `junctions.txt`: Reported splice junctions. - `stats.txt`: Read alignment, Junction statistics. -- `circrna_discovery/MapSplice/${sample_id}/` - - `${sample_id}.bed`: Filtered, annotated circRNAs in customised BED12 format. - - `fasta/`: Mature spliced length circRNA FASTA sequences. diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index a253959c..213c6eeb 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -157,7 +157,7 @@ workflow CIRCRNA_DISCOVERY { DCC_MATE2_2ND_PASS( mate2, star_index, DCC_MATE2_SJDB.out.sjtab, true, '', '' ) dcc_stage = DCC_2ND_PASS.out.junction.join( DCC_MATE1_2ND_PASS.out.junction, remainder: true ).join( DCC_MATE2_2ND_PASS.out.junction, remainder: true ) - dcc = dcc_stage.map{ it -> def meta = it[0]; if( meta.single_end ){ return [ it[0], it[1], [], [] ] } else { return it } }.view() + dcc = dcc_stage.map{ it -> def meta = it[0]; if( meta.single_end ){ return [ it[0], it[1], [], [] ] } else { return it } } DCC( dcc, fasta, gtf ) DCC_FILTER( DCC.out.txt.map{ meta, txt -> meta.tool = "dcc"; return [ meta, txt ] }, bsj_reads ) From dab98acf20384648f50608bf4529936d25a76785 Mon Sep 17 00:00:00 2001 From: BarryDigby Date: Tue, 31 Jan 2023 15:57:55 +0000 Subject: [PATCH 016/491] Update CHANGELOG.md Co-authored-by: James A. Fellows Yates --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 465d994c..a1b80afd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.0.0 - [13/12/2022] +## v1.0.0 - [27/01/2023] Initial release of nf-core/circrna, created with the [nf-core](https://nf-co.re/) template. From d1387ba29406c28f6119bdf884f889c798e7a6e8 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Tue, 31 Jan 2023 16:03:48 +0000 Subject: [PATCH 017/491] credits to contributors. --- README.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/README.md b/README.md index bd2c7b02..027e8d10 100644 --- a/README.md +++ b/README.md @@ -76,6 +76,14 @@ The nf-core/circrna pipeline comes with documentation about the pipeline [usage] nf-core/circrna was originally written by Barry Digby. +We thank the following people for their extensive assistance in the development of this pipeline: + +- @apeltzer +- @ewels +- @maxulysse +- @KevinMenden +- @bj-w + ## Acknowledgements ![SFI](./docs/images/Genomics-Data-Science-original.png) From 5922ef22068b8daf2736c1751b9074394cc0368c Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 1 Feb 2023 10:52:24 +0000 Subject: [PATCH 018/491] collect on ref genome paths ? ? : : [] --- README.md | 2 +- bin/check_empty.sh | 2 +- conf/modules.config | 4 --- .../local/count_matrix/merge_tools/main.nf | 2 +- modules/local/fasta/main.nf | 1 - modules/local/find_circ/anchors/main.nf | 2 +- modules/local/find_circ/filter/main.nf | 2 +- modules/local/find_circ/find_circ/main.nf | 2 +- modules/local/mirna_targets/main.nf | 2 +- nextflow.config | 3 +- nextflow_schema.json | 10 +++---- subworkflows/local/circrna_discovery.nf | 29 +++++++++++-------- subworkflows/local/differential_expression.nf | 2 +- subworkflows/local/input_check.nf | 1 - subworkflows/local/prepare_genome.nf | 6 ++-- workflows/circrna.nf | 11 ++++--- 16 files changed, 39 insertions(+), 42 deletions(-) diff --git a/README.md b/README.md index 027e8d10..8f1d2970 100644 --- a/README.md +++ b/README.md @@ -22,6 +22,7 @@ On release, automated continuous integration tests run the pipeline on a full-si - Raw read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) - Adapter trimming ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)) +- MultiQC report [`MultiQC`](http://multiqc.info/) - circRNA quantification - [`CIRIquant`](https://github.com/Kevinzjy/CIRIquant) - [`STAR 2-Pass mode`](https://github.com/alexdobin/STAR) @@ -41,7 +42,6 @@ On release, automated continuous integration tests run the pipeline on a full-si - Filter results, miRNAs must be called by both tools - Differential expression analysis [`DESeq2`](https://bioconductor.org/packages/release/bioc/html/DESeq2.html) - Circular - Linear ratio tests ['CircTest'](https://github.com/dieterich-lab/CircTest) -- MultiQC report [`MultiQC`](http://multiqc.info/) ## Quick Start diff --git a/bin/check_empty.sh b/bin/check_empty.sh index 2f54d6da..8f28e88c 100755 --- a/bin/check_empty.sh +++ b/bin/check_empty.sh @@ -1,4 +1,4 @@ -#!/usr/bin/bash +#!/usr/bin/env bash ## When consolidating tool outputs for a sample, check if any are empty. ## This will prevent R from throwing errors diff --git a/conf/modules.config b/conf/modules.config index 21b50e7e..3c6f41b1 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -26,10 +26,6 @@ process { ] } - withName: FASTQC { - ext.args = '--quiet' - } - withName: CUSTOM_DUMPSOFTWAREVERSIONS { publishDir = [ path: { "${params.outdir}/pipeline_info" }, diff --git a/modules/local/count_matrix/merge_tools/main.nf b/modules/local/count_matrix/merge_tools/main.nf index e2ee4b11..cc6818dd 100644 --- a/modules/local/count_matrix/merge_tools/main.nf +++ b/modules/local/count_matrix/merge_tools/main.nf @@ -27,7 +27,7 @@ process MERGE_TOOLS { ls *.bed > samples.csv ## Add catch for empty bed file and delete - bash ${workflow.projectDir}/bin/check_empty.sh + check_empty.sh ## Use intersection of "n" (params.tool_filter) circRNAs called by tools ## remove duplicate IDs, keep highest count. diff --git a/modules/local/fasta/main.nf b/modules/local/fasta/main.nf index f43543d8..e33edeed 100644 --- a/modules/local/fasta/main.nf +++ b/modules/local/fasta/main.nf @@ -22,7 +22,6 @@ process FASTA { script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '377' """ ## FASTA sequences (bedtools does not like the extra annotation info - split will not work properly) cut -d\$'\t' -f1-12 ${prefix}.bed > bed12.tmp diff --git a/modules/local/find_circ/anchors/main.nf b/modules/local/find_circ/anchors/main.nf index 15b0650a..5359497d 100644 --- a/modules/local/find_circ/anchors/main.nf +++ b/modules/local/find_circ/anchors/main.nf @@ -2,7 +2,7 @@ process FIND_CIRC_ANCHORS { tag "$meta.id" label "process_high" - conda "find_circ=1.2" + conda "bioconda::find_circ=1.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/find_circ%3A1.2--hdfd78af_0' : 'quay.io/biocontainers/find_circ:1.2--hdfd78af_0' }" diff --git a/modules/local/find_circ/filter/main.nf b/modules/local/find_circ/filter/main.nf index 7be0de57..a12c15ba 100644 --- a/modules/local/find_circ/filter/main.nf +++ b/modules/local/find_circ/filter/main.nf @@ -2,7 +2,7 @@ process FIND_CIRC_FILTER { tag "$meta.id" label "process_low" - conda "find_circ=1.2" + conda "bioconda::find_circ=1.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/find_circ%3A1.2--hdfd78af_0' : 'quay.io/biocontainers/find_circ:1.2--hdfd78af_0' }" diff --git a/modules/local/find_circ/find_circ/main.nf b/modules/local/find_circ/find_circ/main.nf index 57bf656c..242e195f 100644 --- a/modules/local/find_circ/find_circ/main.nf +++ b/modules/local/find_circ/find_circ/main.nf @@ -2,7 +2,7 @@ process FIND_CIRC { tag "$meta.id" label "process_high" - conda "find_circ=1.2 bowtie2" + conda "bioconda::find_circ=1.2 bioconda::bowtie2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c27e472038a09e49d9147bc52903e12836302c12:60ffb3b15a2c40c669f8d38382b1e6e4b065f5e4-0' : 'quay.io/biocontainers/mulled-v2-c27e472038a09e49d9147bc52903e12836302c12:60ffb3b15a2c40c669f8d38382b1e6e4b065f5e4-0' }" diff --git a/modules/local/mirna_targets/main.nf b/modules/local/mirna_targets/main.nf index 4f70ca03..0891e6e4 100644 --- a/modules/local/mirna_targets/main.nf +++ b/modules/local/mirna_targets/main.nf @@ -12,7 +12,7 @@ process MIRNA_TARGETS { output: tuple val(meta), path("${prefix}.mirna_targets.txt"), emit: results - path "versions.yml" , emit: versions + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/nextflow.config b/nextflow.config index 14f1455c..a2828498 100644 --- a/nextflow.config +++ b/nextflow.config @@ -7,7 +7,6 @@ */ // Global default params, used in configs -// TODO: tidy up after workflow is running smoothly params { // Input options @@ -246,7 +245,7 @@ manifest { description = """Quantification, miRNA target prediction and differential expression analysis of circular RNAs""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '1.0.0' + version = '1.0.0' doi = '' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 5eda7888..5b61d7d8 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -291,6 +291,11 @@ "help_text": "By default, trimmed FastQ files will not be saved to the results directory. Specify this flag (or set to true in your config file) to copy these files to the results directory when complete.", "fa_icon": "fas fa-save" }, + "skip_fastqc": { + "type": "boolean", + "description": "Skip FastQC quality control of the sequencing reads.", + "fa_icon": "fas fa-terminal" + }, "clip_r1": { "type": "integer", "description": "Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads).", @@ -415,11 +420,6 @@ "description": "Less common options for the pipeline, typically set in a config file.", "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", "properties": { - "skip_fastqc": { - "type": "boolean", - "description": "Skip FastQC quality control of the sequencing reads.", - "fa_icon": "fas fa-terminal" - }, "help": { "type": "boolean", "description": "Display help text.", diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 213c6eeb..22b5c11c 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -30,15 +30,15 @@ include { STAR_ALIGN as DCC_MATE2_2ND_PASS } from '../../modules/nf-core/star/al include { SJDB as DCC_MATE2_SJDB } from '../../modules/local/star/sjdb/main' include { DCC } from '../../modules/local/dcc/dcc/main' include { DCC_FILTER } from '../../modules/local/dcc/filter/main' -include { CIRCEXPLORER2_REFERENCE as MAPSPLICE_REFERENCE } from '../../modules/local/circexplorer2/reference/main' include { MAPSPLICE_ALIGN } from '../../modules/local/mapsplice/align/main' -include { CIRCEXPLORER2_PARSE as MAPSPLICE_PARSE } from '../../modules/nf-core/circexplorer2/parse/main' -include { CIRCEXPLORER2_ANNOTATE as MAPSPLICE_ANNOTATE } from '../../modules/nf-core/circexplorer2/annotate/main' -include { CIRCEXPLORER2_FILTER as MAPSPLICE_FILTER } from '../../modules/local/circexplorer2/filter/main' include { FASTA } from '../../modules/local/fasta/main' include { MERGE_TOOLS } from '../../modules/local/count_matrix/merge_tools/main' include { COUNTS_COMBINED } from '../../modules/local/count_matrix/combined/main' include { COUNTS_SINGLE } from '../../modules/local/count_matrix/single/main' +include { CIRCEXPLORER2_REFERENCE as MAPSPLICE_REFERENCE } from '../../modules/local/circexplorer2/reference/main' +include { CIRCEXPLORER2_PARSE as MAPSPLICE_PARSE } from '../../modules/nf-core/circexplorer2/parse/main' +include { CIRCEXPLORER2_ANNOTATE as MAPSPLICE_ANNOTATE } from '../../modules/nf-core/circexplorer2/annotate/main' +include { CIRCEXPLORER2_FILTER as MAPSPLICE_FILTER } from '../../modules/local/circexplorer2/filter/main' workflow CIRCRNA_DISCOVERY { @@ -75,10 +75,15 @@ workflow CIRCRNA_DISCOVERY { // STAR WORFKLOW: // - STAR_1ST_PASS( reads, star_index, gtf, true, '', '' ) + // Define variables here, star_ignore_sjdbgtf not supposed to be toggled by user. + star_ignore_sjdbgtf = true + seq_center = params.seq_center ?: '' + seq_platform = '' + + STAR_1ST_PASS( reads, star_index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center) sjdb = STAR_1ST_PASS.out.tab.map{ meta, tab -> return [ tab ] }.collect() STAR_SJDB( sjdb, bsj_reads ) - STAR_2ND_PASS( reads, star_index, STAR_SJDB.out.sjtab, true, '', '' ) + STAR_2ND_PASS( reads, star_index, STAR_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) ch_versions = ch_versions.mix(STAR_1ST_PASS.out.versions) ch_versions = ch_versions.mix(STAR_2ND_PASS.out.versions) @@ -142,19 +147,19 @@ workflow CIRCRNA_DISCOVERY { // DCC WORKFLOW // - DCC_1ST_PASS( reads, star_index, gtf, true, '', '' ) + DCC_1ST_PASS( reads, star_index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center ) DCC_SJDB( DCC_1ST_PASS.out.tab.map{ meta, tab -> return [ tab ] }.collect(), bsj_reads ) - DCC_2ND_PASS( reads, star_index, DCC_SJDB.out.sjtab, true, '', '' ) + DCC_2ND_PASS( reads, star_index, DCC_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) mate1 = reads.map{ meta, reads -> return [meta, reads[0] ] } - DCC_MATE1_1ST_PASS( mate1, star_index, gtf, true, '', '' ) + DCC_MATE1_1ST_PASS( mate1, star_index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center ) DCC_MATE1_SJDB( DCC_MATE1_1ST_PASS.out.tab.map{ meta, tab -> return [ tab ] }.collect(), bsj_reads ) - DCC_MATE1_2ND_PASS( mate1, star_index, DCC_MATE1_SJDB.out.sjtab, true, '', '' ) + DCC_MATE1_2ND_PASS( mate1, star_index, DCC_MATE1_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) mate2 = reads.map{ meta, reads -> return [ meta, reads[1] ] } - DCC_MATE2_1ST_PASS( mate2, star_index, gtf, true, '', '' ) + DCC_MATE2_1ST_PASS( mate2, star_index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center ) DCC_MATE2_SJDB( DCC_MATE2_1ST_PASS.out.tab.map{ meta, tab -> return [ tab ] }.collect(), bsj_reads ) - DCC_MATE2_2ND_PASS( mate2, star_index, DCC_MATE2_SJDB.out.sjtab, true, '', '' ) + DCC_MATE2_2ND_PASS( mate2, star_index, DCC_MATE2_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) dcc_stage = DCC_2ND_PASS.out.junction.join( DCC_MATE1_2ND_PASS.out.junction, remainder: true ).join( DCC_MATE2_2ND_PASS.out.junction, remainder: true ) dcc = dcc_stage.map{ it -> def meta = it[0]; if( meta.single_end ){ return [ it[0], it[1], [], [] ] } else { return it } } diff --git a/subworkflows/local/differential_expression.nf b/subworkflows/local/differential_expression.nf index 85e33af0..8bf83bda 100644 --- a/subworkflows/local/differential_expression.nf +++ b/subworkflows/local/differential_expression.nf @@ -2,10 +2,10 @@ include { HISAT2_ALIGN } from '../../modules/nf-core/hisat2/align/m include { SAMTOOLS_SORT } from '../../modules/nf-core/samtools/sort/main' include { STRINGTIE_STRINGTIE } from '../../modules/nf-core/stringtie/stringtie/main' include { STRINGTIE_PREPDE } from '../../modules/local/stringtie/prepde/main' -include { DESEQ2_DIFFERENTIAL_EXPRESSION } from '../../modules/local/deseq2/differential_expression/main' include { PARENT_GENE } from '../../modules/local/annotation/parent_gene/main' include { PREPARE_CLR_TEST } from '../../modules/local/circtest/prepare/main' include { CIRCTEST } from '../../modules/local/circtest/test/main' +include { DESEQ2_DIFFERENTIAL_EXPRESSION } from '../../modules/local/deseq2/differential_expression/main' workflow DIFFERENTIAL_EXPRESSION { diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf index 753a2838..faf7c5b2 100644 --- a/subworkflows/local/input_check.nf +++ b/subworkflows/local/input_check.nf @@ -24,7 +24,6 @@ workflow INPUT_CHECK { versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ] } -// Function to get list of [ meta, [ fastq_1, fastq_2 ] ] // Function to get list of [ meta, [ fastq_1, fastq_2 ] ] def create_fastq_channel(LinkedHashMap row) { // create meta map diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index b49a4e83..e3b1b5e2 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -20,15 +20,15 @@ workflow PREPARE_GENOME { // MapSplice & find_circ requires reference genome to be split per chromosome: if( ( params.tool.contains('mapsplice') || params.tool.contains('find_circ') ) && params.module.contains('circrna_discovery') ){ - file("${params.outdir}/genome/chromosomes").mkdirs() + file("${params.outdir}/reference/chromosomes").mkdirs() ch_fasta.splitFasta( record: [id:true] ) .map{ record -> record.id.toString() } .set{ ID } ch_fasta.splitFasta( file: true ) - .merge( ID ).map{ file, id -> file.copyTo("${params.outdir}/genome/chromosomes/${id}.fa") } + .merge( ID ).map{ file, id -> file.copyTo("${params.outdir}/reference/chromosomes/${id}.fa") } - stage_chromosomes = Channel.value("${workflow.launchDir}/${params.outdir}/genome/chromosomes") + stage_chromosomes = Channel.value("${workflow.launchDir}/${params.outdir}/reference/chromosomes") } ch_fasta.map{ it -> diff --git a/workflows/circrna.nf b/workflows/circrna.nf index 34ff6947..f165519a 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -63,7 +63,6 @@ include { DIFFERENTIAL_EXPRESSION } from '../subworkflows/local/differential_exp */ // MODULES: -include { FASTQC } from '../modules/nf-core/fastqc/main' include { MULTIQC } from '../modules/nf-core/multiqc/main' include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' include { CAT_FASTQ } from '../modules/nf-core/cat/fastq/main' @@ -127,13 +126,13 @@ workflow CIRCRNA { ) // Stage the indices via newly created indices, iGenomes or empty list if tool not selected. - bowtie_index = params.fasta ? params.bowtie ? Channel.fromPath(params.bowtie) : PREPARE_GENOME.out.bowtie : [] - bowtie2_index = params.fasta ? params.bowtie2 ? Channel.fromPath(params.bowtie2) : PREPARE_GENOME.out.bowtie2 : [] - bwa_index = params.fasta ? params.bwa ? Channel.fromPath(params.bwa) : PREPARE_GENOME.out.bwa : [] + bowtie_index = params.fasta ? params.bowtie ? Channel.fromPath(params.bowtie).collect() : PREPARE_GENOME.out.bowtie : [] + bowtie2_index = params.fasta ? params.bowtie2 ? Channel.fromPath(params.bowtie2).collect() : PREPARE_GENOME.out.bowtie2 : [] + bwa_index = params.fasta ? params.bwa ? Channel.fromPath(params.bwa).collect() : PREPARE_GENOME.out.bwa : [] chromosomes = ( params.tool.contains('mapsplice') || params.tool.contains('find_circ') ) ? PREPARE_GENOME.out.chromosomes : [] hisat2_index = ( params.tool.contains('ciriquant') || params.module.contains('differential_expression') ) ? PREPARE_GENOME.out.hisat2 : [] - star_index = params.fasta ? params.star ? Channel.fromPath(params.star) : PREPARE_GENOME.out.star : [] - segemehl_index = params.fasta ? params.segemehl ? Channel.fromPath(params.segemehl) : PREPARE_GENOME.out.segemehl : [] + star_index = params.fasta ? params.star ? Channel.fromPath(params.star).collect() : PREPARE_GENOME.out.star : [] + segemehl_index = params.fasta ? params.segemehl ? Channel.fromPath(params.segemehl).collect() : PREPARE_GENOME.out.segemehl : [] ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) // MODULE: Run FastQC, trimgalore! From 3e6fe7350feb4cde59a6243869f442a6f4a16328 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 1 Feb 2023 11:04:46 +0000 Subject: [PATCH 019/491] bwa test --- subworkflows/local/prepare_genome.nf | 6 +++--- workflows/circrna.nf | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index e3b1b5e2..0cdf0c38 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -32,9 +32,9 @@ workflow PREPARE_GENOME { } ch_fasta.map{ it -> - meta = [:] - meta.id = it.simpleName - return [ meta, [it] ] + meta = [:] + meta.id = it.simpleName + return [ meta, [it] ] }.set{ fasta_tuple } BOWTIE_BUILD(fasta) diff --git a/workflows/circrna.nf b/workflows/circrna.nf index f165519a..d8c277f2 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -128,7 +128,7 @@ workflow CIRCRNA { // Stage the indices via newly created indices, iGenomes or empty list if tool not selected. bowtie_index = params.fasta ? params.bowtie ? Channel.fromPath(params.bowtie).collect() : PREPARE_GENOME.out.bowtie : [] bowtie2_index = params.fasta ? params.bowtie2 ? Channel.fromPath(params.bowtie2).collect() : PREPARE_GENOME.out.bowtie2 : [] - bwa_index = params.fasta ? params.bwa ? Channel.fromPath(params.bwa).collect() : PREPARE_GENOME.out.bwa : [] + bwa_index = params.fasta ? params.bwa ? Channel.fromPath(params.bwa).collect().map{ it -> [[id:it[0].baseName], it] }, sort : PREPARE_GENOME.out.bwa : [] chromosomes = ( params.tool.contains('mapsplice') || params.tool.contains('find_circ') ) ? PREPARE_GENOME.out.chromosomes : [] hisat2_index = ( params.tool.contains('ciriquant') || params.module.contains('differential_expression') ) ? PREPARE_GENOME.out.hisat2 : [] star_index = params.fasta ? params.star ? Channel.fromPath(params.star).collect() : PREPARE_GENOME.out.star : [] From 9b979d0f99d78fad7fdf8b4200324dcf8a51c0cb Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 1 Feb 2023 11:05:32 +0000 Subject: [PATCH 020/491] s --- workflows/circrna.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/circrna.nf b/workflows/circrna.nf index d8c277f2..dc9de65e 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -128,7 +128,7 @@ workflow CIRCRNA { // Stage the indices via newly created indices, iGenomes or empty list if tool not selected. bowtie_index = params.fasta ? params.bowtie ? Channel.fromPath(params.bowtie).collect() : PREPARE_GENOME.out.bowtie : [] bowtie2_index = params.fasta ? params.bowtie2 ? Channel.fromPath(params.bowtie2).collect() : PREPARE_GENOME.out.bowtie2 : [] - bwa_index = params.fasta ? params.bwa ? Channel.fromPath(params.bwa).collect().map{ it -> [[id:it[0].baseName], it] }, sort : PREPARE_GENOME.out.bwa : [] + bwa_index = params.fasta ? params.bwa ? Channel.fromPath(params.bwa).collect().map{ it -> [[id:it[0].baseName], it] }, sort } : PREPARE_GENOME.out.bwa : [] chromosomes = ( params.tool.contains('mapsplice') || params.tool.contains('find_circ') ) ? PREPARE_GENOME.out.chromosomes : [] hisat2_index = ( params.tool.contains('ciriquant') || params.module.contains('differential_expression') ) ? PREPARE_GENOME.out.hisat2 : [] star_index = params.fasta ? params.star ? Channel.fromPath(params.star).collect() : PREPARE_GENOME.out.star : [] From ccd8d7251bd6e3edda1174624e52f8d2644ef598 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 1 Feb 2023 11:38:16 +0000 Subject: [PATCH 021/491] bwa index fix --- workflows/circrna.nf | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/workflows/circrna.nf b/workflows/circrna.nf index dc9de65e..7f0a9da3 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -126,13 +126,13 @@ workflow CIRCRNA { ) // Stage the indices via newly created indices, iGenomes or empty list if tool not selected. - bowtie_index = params.fasta ? params.bowtie ? Channel.fromPath(params.bowtie).collect() : PREPARE_GENOME.out.bowtie : [] - bowtie2_index = params.fasta ? params.bowtie2 ? Channel.fromPath(params.bowtie2).collect() : PREPARE_GENOME.out.bowtie2 : [] - bwa_index = params.fasta ? params.bwa ? Channel.fromPath(params.bwa).collect().map{ it -> [[id:it[0].baseName], it] }, sort } : PREPARE_GENOME.out.bwa : [] + bowtie_index = params.fasta ? params.bowtie ? Channel.fromPath(params.bowtie) : PREPARE_GENOME.out.bowtie : [] + bowtie2_index = params.fasta ? params.bowtie2 ? Channel.fromPath(params.bowtie2) : PREPARE_GENOME.out.bowtie2 : [] + bwa_index = params.fasta ? params.bwa ? Channel.fromPath(params.bwa).map{ it -> [[id:it[0].baseName], it] }.view() : PREPARE_GENOME.out.bwa : [] chromosomes = ( params.tool.contains('mapsplice') || params.tool.contains('find_circ') ) ? PREPARE_GENOME.out.chromosomes : [] hisat2_index = ( params.tool.contains('ciriquant') || params.module.contains('differential_expression') ) ? PREPARE_GENOME.out.hisat2 : [] - star_index = params.fasta ? params.star ? Channel.fromPath(params.star).collect() : PREPARE_GENOME.out.star : [] - segemehl_index = params.fasta ? params.segemehl ? Channel.fromPath(params.segemehl).collect() : PREPARE_GENOME.out.segemehl : [] + star_index = params.fasta ? params.star ? Channel.fromPath(params.star): PREPARE_GENOME.out.star : [] + segemehl_index = params.fasta ? params.segemehl ? Channel.fromPath(params.segemehl) : PREPARE_GENOME.out.segemehl : [] ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) // MODULE: Run FastQC, trimgalore! From 487102c11f211c7c5f4a105875121d0ed9488be5 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 1 Feb 2023 11:47:43 +0000 Subject: [PATCH 022/491] testing collect --- workflows/circrna.nf | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/workflows/circrna.nf b/workflows/circrna.nf index 7f0a9da3..462de2f3 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -126,11 +126,11 @@ workflow CIRCRNA { ) // Stage the indices via newly created indices, iGenomes or empty list if tool not selected. - bowtie_index = params.fasta ? params.bowtie ? Channel.fromPath(params.bowtie) : PREPARE_GENOME.out.bowtie : [] - bowtie2_index = params.fasta ? params.bowtie2 ? Channel.fromPath(params.bowtie2) : PREPARE_GENOME.out.bowtie2 : [] - bwa_index = params.fasta ? params.bwa ? Channel.fromPath(params.bwa).map{ it -> [[id:it[0].baseName], it] }.view() : PREPARE_GENOME.out.bwa : [] - chromosomes = ( params.tool.contains('mapsplice') || params.tool.contains('find_circ') ) ? PREPARE_GENOME.out.chromosomes : [] - hisat2_index = ( params.tool.contains('ciriquant') || params.module.contains('differential_expression') ) ? PREPARE_GENOME.out.hisat2 : [] + bowtie_index = params.fasta ? params.bowtie ? Channel.fromPath(params.bowtie).collect() : PREPARE_GENOME.out.bowtie : [] + bowtie2_index = params.fasta ? params.bowtie2 ? Channel.fromPath(params.bowtie2).collect() : PREPARE_GENOME.out.bowtie2 : [] + bwa_index = params.fasta ? params.bwa ? Channel.fromPath(params.bwa).collect().map{ it -> [[id:it[0].baseName], it] }.view() : PREPARE_GENOME.out.bwa : [] + chromosomes = params.fasta && ( params.tool.contains('mapsplice') || params.tool.contains('find_circ') ) ? PREPARE_GENOME.out.chromosomes : [] + hisat2_index = params.fasta ? params.hisat2 && ( params.tool.contains('ciriquant') || params.module.contains('differential_expression') ) ? Channel.fromPath(params.hisat2).collect() : PREPARE_GENOME.out.hisat2 : [] star_index = params.fasta ? params.star ? Channel.fromPath(params.star): PREPARE_GENOME.out.star : [] segemehl_index = params.fasta ? params.segemehl ? Channel.fromPath(params.segemehl) : PREPARE_GENOME.out.segemehl : [] ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) From 513e594bb439bb8902dc98c7468fbdc05d868abc Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 1 Feb 2023 11:51:52 +0000 Subject: [PATCH 023/491] yaml stuff --- subworkflows/local/circrna_discovery.nf | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 22b5c11c..8f39b3a3 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -136,7 +136,9 @@ workflow CIRCRNA_DISCOVERY { // CIRIQUANT WORKFLOW: // - CIRIQUANT_YML( gtf, fasta, bwa_index.map{ meta, index -> return index }, hisat2_index ) + // only need path to bwa, only need path to hisat2. + // do not want to upset the collect declr for all indices just for this. + CIRIQUANT_YML( gtf, fasta, bwa_index.map{ meta, index -> return index[0].getPath() }, hisat2_index.map{ it -> return it[0].getPath() } ) CIRIQUANT( reads, CIRIQUANT_YML.out.yml.collect() ) CIRIQUANT_FILTER( CIRIQUANT.out.gtf.map{ meta, gtf -> meta.tool = "ciriquant"; return [ meta, gtf ] }, bsj_reads ) From f070228dbdc554bfea9ad41232550ae097b3f9bd Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 1 Feb 2023 12:23:50 +0000 Subject: [PATCH 024/491] user paths fix --- subworkflows/local/circrna_discovery.nf | 2 +- subworkflows/local/prepare_genome.nf | 6 +++--- workflows/circrna.nf | 6 +++--- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 8f39b3a3..054b34d6 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -138,7 +138,7 @@ workflow CIRCRNA_DISCOVERY { // only need path to bwa, only need path to hisat2. // do not want to upset the collect declr for all indices just for this. - CIRIQUANT_YML( gtf, fasta, bwa_index.map{ meta, index -> return index[0].getPath() }, hisat2_index.map{ it -> return it[0].getPath() } ) + CIRIQUANT_YML( gtf, fasta, bwa_index.map{ meta, index -> return index }, hisat2_index ) CIRIQUANT( reads, CIRIQUANT_YML.out.yml.collect() ) CIRIQUANT_FILTER( CIRIQUANT.out.gtf.map{ meta, gtf -> meta.tool = "ciriquant"; return [ meta, gtf ] }, bsj_reads ) diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 0cdf0c38..e4ec459e 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -20,15 +20,15 @@ workflow PREPARE_GENOME { // MapSplice & find_circ requires reference genome to be split per chromosome: if( ( params.tool.contains('mapsplice') || params.tool.contains('find_circ') ) && params.module.contains('circrna_discovery') ){ - file("${params.outdir}/reference/chromosomes").mkdirs() + file("${params.outdir}/references/chromosomes").mkdirs() ch_fasta.splitFasta( record: [id:true] ) .map{ record -> record.id.toString() } .set{ ID } ch_fasta.splitFasta( file: true ) - .merge( ID ).map{ file, id -> file.copyTo("${params.outdir}/reference/chromosomes/${id}.fa") } + .merge( ID ).map{ file, id -> file.copyTo("${params.outdir}/references/chromosomes/${id}.fa") } - stage_chromosomes = Channel.value("${workflow.launchDir}/${params.outdir}/reference/chromosomes") + stage_chromosomes = Channel.value("${workflow.launchDir}/${params.outdir}/references/chromosomes") } ch_fasta.map{ it -> diff --git a/workflows/circrna.nf b/workflows/circrna.nf index 462de2f3..4f5e7056 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -126,9 +126,9 @@ workflow CIRCRNA { ) // Stage the indices via newly created indices, iGenomes or empty list if tool not selected. - bowtie_index = params.fasta ? params.bowtie ? Channel.fromPath(params.bowtie).collect() : PREPARE_GENOME.out.bowtie : [] - bowtie2_index = params.fasta ? params.bowtie2 ? Channel.fromPath(params.bowtie2).collect() : PREPARE_GENOME.out.bowtie2 : [] - bwa_index = params.fasta ? params.bwa ? Channel.fromPath(params.bwa).collect().map{ it -> [[id:it[0].baseName], it] }.view() : PREPARE_GENOME.out.bwa : [] + bowtie_index = params.fasta ? params.bowtie ? Channel.fromPath(params.bowtie) : PREPARE_GENOME.out.bowtie : [] + bowtie2_index = params.fasta ? params.bowtie2 ? Channel.fromPath(params.bowtie2).map{ it -> [[id:'bowtie2'], it] } : PREPARE_GENOME.out.bowtie2 : [] + bwa_index = params.fasta ? params.bwa ? Channel.fromPath(params.bwa).map{ it -> [[id:'bwa'], it] } : PREPARE_GENOME.out.bwa : [] chromosomes = params.fasta && ( params.tool.contains('mapsplice') || params.tool.contains('find_circ') ) ? PREPARE_GENOME.out.chromosomes : [] hisat2_index = params.fasta ? params.hisat2 && ( params.tool.contains('ciriquant') || params.module.contains('differential_expression') ) ? Channel.fromPath(params.hisat2).collect() : PREPARE_GENOME.out.hisat2 : [] star_index = params.fasta ? params.star ? Channel.fromPath(params.star): PREPARE_GENOME.out.star : [] From a6e64237110d2bf1bdcd430a647d6bc249e8cefc Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 1 Feb 2023 12:27:38 +0000 Subject: [PATCH 025/491] star ref output path --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 3c6f41b1..57de9f9b 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -124,7 +124,7 @@ if (!params.skip_trimming) { params.sjdboverhang ? "--sjdbOverhang ${params.sjdboverhang}" : '', ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/references/index/star" }, + path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_reference From 3f1709380cb27587ec72437d51a949bceb5b2244 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 1 Feb 2023 12:57:40 +0000 Subject: [PATCH 026/491] star collect user path --- conf/modules.config | 4 ++-- subworkflows/local/circrna_discovery.nf | 16 ++++++++-------- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 57de9f9b..75584759 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -71,7 +71,7 @@ if (!params.skip_trimming) { withName: BOWTIE_BUILD { ext.when = { params.fasta && !params.bowtie && params.tool.split(',').contains('mapsplice') && params.module.split(',').contains('circrna_discovery') } publishDir = [ - path: { "${params.outdir}/references/index/bowtie" }, + path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_reference @@ -111,7 +111,7 @@ if (!params.skip_trimming) { withName: HISAT2_BUILD { ext.when = { params.fasta && params.gtf && ( params.module.split(',').contains('differential_expression') || params.tool.split(',').contains('ciriquant') ) } publishDir = [ - path: { "${params.outdir}/references/index/hisat2" }, + path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_reference diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 054b34d6..c7612946 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -80,10 +80,10 @@ workflow CIRCRNA_DISCOVERY { seq_center = params.seq_center ?: '' seq_platform = '' - STAR_1ST_PASS( reads, star_index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center) + STAR_1ST_PASS( reads, star_index.collect(), gtf, star_ignore_sjdbgtf, seq_platform, seq_center) sjdb = STAR_1ST_PASS.out.tab.map{ meta, tab -> return [ tab ] }.collect() STAR_SJDB( sjdb, bsj_reads ) - STAR_2ND_PASS( reads, star_index, STAR_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) + STAR_2ND_PASS( reads, star_index.collect(), STAR_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) ch_versions = ch_versions.mix(STAR_1ST_PASS.out.versions) ch_versions = ch_versions.mix(STAR_2ND_PASS.out.versions) @@ -149,19 +149,19 @@ workflow CIRCRNA_DISCOVERY { // DCC WORKFLOW // - DCC_1ST_PASS( reads, star_index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center ) + DCC_1ST_PASS( reads, star_index.collect(), gtf, star_ignore_sjdbgtf, seq_platform, seq_center ) DCC_SJDB( DCC_1ST_PASS.out.tab.map{ meta, tab -> return [ tab ] }.collect(), bsj_reads ) - DCC_2ND_PASS( reads, star_index, DCC_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) + DCC_2ND_PASS( reads, star_index.collect(), DCC_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) mate1 = reads.map{ meta, reads -> return [meta, reads[0] ] } - DCC_MATE1_1ST_PASS( mate1, star_index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center ) + DCC_MATE1_1ST_PASS( mate1, star_index.collect(), gtf, star_ignore_sjdbgtf, seq_platform, seq_center ) DCC_MATE1_SJDB( DCC_MATE1_1ST_PASS.out.tab.map{ meta, tab -> return [ tab ] }.collect(), bsj_reads ) - DCC_MATE1_2ND_PASS( mate1, star_index, DCC_MATE1_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) + DCC_MATE1_2ND_PASS( mate1, star_index.collect(), DCC_MATE1_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) mate2 = reads.map{ meta, reads -> return [ meta, reads[1] ] } - DCC_MATE2_1ST_PASS( mate2, star_index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center ) + DCC_MATE2_1ST_PASS( mate2, star_index.collect(), gtf, star_ignore_sjdbgtf, seq_platform, seq_center ) DCC_MATE2_SJDB( DCC_MATE2_1ST_PASS.out.tab.map{ meta, tab -> return [ tab ] }.collect(), bsj_reads ) - DCC_MATE2_2ND_PASS( mate2, star_index, DCC_MATE2_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) + DCC_MATE2_2ND_PASS( mate2, star_index.collect(), DCC_MATE2_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) dcc_stage = DCC_2ND_PASS.out.junction.join( DCC_MATE1_2ND_PASS.out.junction, remainder: true ).join( DCC_MATE2_2ND_PASS.out.junction, remainder: true ) dcc = dcc_stage.map{ it -> def meta = it[0]; if( meta.single_end ){ return [ it[0], it[1], [], [] ] } else { return it } } From e6bd4d8e2f67b392f53ebef72a77ff6825ea012e Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 1 Feb 2023 13:40:30 +0000 Subject: [PATCH 027/491] segemehl usr path collect --- subworkflows/local/circrna_discovery.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index c7612946..3dd50135 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -64,7 +64,7 @@ workflow CIRCRNA_DISCOVERY { // // SEGEMEHL WORKFLOW: // - SEGEMEHL_ALIGN( reads, fasta, segemehl_index ) + SEGEMEHL_ALIGN( reads, fasta, segemehl_index.collect() ) segemehl_filter = SEGEMEHL_ALIGN.out.results.map{ meta, results -> meta.tool = "segemehl"; return [ meta, results ] } SEGEMEHL_FILTER( segemehl_filter, bsj_reads ) From a46f123269b155ee53cd4c793aadc3b53969abf9 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 1 Feb 2023 14:04:41 +0000 Subject: [PATCH 028/491] segemehl path file() --- workflows/circrna.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/circrna.nf b/workflows/circrna.nf index 4f5e7056..0adea651 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -132,7 +132,7 @@ workflow CIRCRNA { chromosomes = params.fasta && ( params.tool.contains('mapsplice') || params.tool.contains('find_circ') ) ? PREPARE_GENOME.out.chromosomes : [] hisat2_index = params.fasta ? params.hisat2 && ( params.tool.contains('ciriquant') || params.module.contains('differential_expression') ) ? Channel.fromPath(params.hisat2).collect() : PREPARE_GENOME.out.hisat2 : [] star_index = params.fasta ? params.star ? Channel.fromPath(params.star): PREPARE_GENOME.out.star : [] - segemehl_index = params.fasta ? params.segemehl ? Channel.fromPath(params.segemehl) : PREPARE_GENOME.out.segemehl : [] + segemehl_index = params.fasta ? params.segemehl ? Channel.fromPath(file(params.segemehl)) : PREPARE_GENOME.out.segemehl : [] ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) // MODULE: Run FastQC, trimgalore! From 4d986aee7d53a4f7e8e0cb5b27b049884e0cf929 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 1 Feb 2023 14:38:16 +0000 Subject: [PATCH 029/491] modules config fix for segemehl align --- conf/modules.config | 2 +- subworkflows/local/circrna_discovery.nf | 2 +- workflows/circrna.nf | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 75584759..b46f3b52 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -144,7 +144,7 @@ if (!params.skip_trimming) { // circRNA withName: SEGEMEHL_ALIGN { - ext.when = { params.fasta && !params.segemehl && params.tool.split(',').contains('segemehl') && params.module.split(',').contains('circrna_discovery') } + ext.when = { params.fasta && params.tool.split(',').contains('segemehl') && params.module.split(',').contains('circrna_discovery') } ext.args = [ "", "-b", "-S" diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 3dd50135..c7612946 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -64,7 +64,7 @@ workflow CIRCRNA_DISCOVERY { // // SEGEMEHL WORKFLOW: // - SEGEMEHL_ALIGN( reads, fasta, segemehl_index.collect() ) + SEGEMEHL_ALIGN( reads, fasta, segemehl_index ) segemehl_filter = SEGEMEHL_ALIGN.out.results.map{ meta, results -> meta.tool = "segemehl"; return [ meta, results ] } SEGEMEHL_FILTER( segemehl_filter, bsj_reads ) diff --git a/workflows/circrna.nf b/workflows/circrna.nf index 0adea651..4f5e7056 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -132,7 +132,7 @@ workflow CIRCRNA { chromosomes = params.fasta && ( params.tool.contains('mapsplice') || params.tool.contains('find_circ') ) ? PREPARE_GENOME.out.chromosomes : [] hisat2_index = params.fasta ? params.hisat2 && ( params.tool.contains('ciriquant') || params.module.contains('differential_expression') ) ? Channel.fromPath(params.hisat2).collect() : PREPARE_GENOME.out.hisat2 : [] star_index = params.fasta ? params.star ? Channel.fromPath(params.star): PREPARE_GENOME.out.star : [] - segemehl_index = params.fasta ? params.segemehl ? Channel.fromPath(file(params.segemehl)) : PREPARE_GENOME.out.segemehl : [] + segemehl_index = params.fasta ? params.segemehl ? Channel.fromPath(params.segemehl) : PREPARE_GENOME.out.segemehl : [] ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) // MODULE: Run FastQC, trimgalore! From 5c494b69b03898b69bdd78d90dfb84dd2d60d2a8 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 1 Feb 2023 15:53:47 +0000 Subject: [PATCH 030/491] DCC: ditch remainder, use groupTuple instead. --- conf/test.config | 2 +- nextflow_schema.json | 26 ++++++++++++------------- subworkflows/local/circrna_discovery.nf | 2 +- 3 files changed, 15 insertions(+), 15 deletions(-) diff --git a/conf/test.config b/conf/test.config index 10095fa6..aad536a2 100644 --- a/conf/test.config +++ b/conf/test.config @@ -28,7 +28,7 @@ params { phenotype = 'https://raw.githubusercontent.com/nf-core/test-datasets/circrna/phenotype.csv' skip_trimming = false module = 'circrna_discovery,mirna_prediction,differential_expression' - outdir = 'test_outdir/' + outdir = 'results/' bsj_reads = 2 species = 'cel' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 5b61d7d8..f7b22160 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -188,7 +188,7 @@ "mimetype": "text/plain", "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$", "description": "Path to FASTA genome file.", - "help_text": "Must be provided if --genome null", + "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\n\nThis parameter is *mandatory* if `--genome` is not specified.", "fa_icon": "fas fa-book" }, "gtf": { @@ -204,38 +204,38 @@ "mimetype": "text/plain", "help_text": "Typically this will be the `mature.fa` file from miRBase. Can be given either as a plain text `.fa` file or a compressed `.gz` file.", "fa_icon": "fas fa-wheelchair", - "default": "null" + "default": null }, "species": { "type": "string", "fa_icon": "fas fa-dog", "description": "String identifying species.", "help_text": "Check the igenomes.config file for species configured to work with nf-core/circrna", - "default": "null" + "default": null }, "bowtie": { "type": "string", "fa_icon": "fas fa-bold", - "description": "Path to Bowtie index files.", - "default": "null" + "description": "Path to Bowtie index files, surrounded by quotes. No glob pattern required.", + "default": null }, "bowtie2": { "type": "string", "fa_icon": "fas fa-bold", - "description": "Path to Bowtie2 index files.", - "default": "null" + "description": "Path to Bowtie2 index files, surrounded by quotes. No glob pattern required.", + "default": null }, "bwa": { "type": "string", "fa_icon": "fas fa-bold", - "description": "Path to BWA index directory.", - "default": "null" + "description": "Path to BWA index directory, surrounded by quotes. No glob pattern required.", + "default": null }, "hisat2": { "type": "string", - "description": "The title to use in the MultiQC report.", + "description": "Path to Hisat2 index directory, surrounded by quotes. No glob pattern required.", "default": null, - "fa_icon": "fab fa-redhat" + "fa_icon": "fab fa-bold" }, "hisat2_build_memory": { "type": "string", @@ -249,12 +249,12 @@ "type": "string", "default": "None", "fa_icon": "fab fa-stripe-s", - "description": "Path to Segemehl Index file" + "description": "Path to Segemehl Index **file**." }, "star": { "type": "string", "fa_icon": "far fa-star", - "description": "Path to STAR index directory." + "description": "Path to STAR index directory, surrounded by quotes. No glob pattern required." }, "igenomes_base": { "type": "string", diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index c7612946..6df5e63a 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -163,7 +163,7 @@ workflow CIRCRNA_DISCOVERY { DCC_MATE2_SJDB( DCC_MATE2_1ST_PASS.out.tab.map{ meta, tab -> return [ tab ] }.collect(), bsj_reads ) DCC_MATE2_2ND_PASS( mate2, star_index.collect(), DCC_MATE2_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) - dcc_stage = DCC_2ND_PASS.out.junction.join( DCC_MATE1_2ND_PASS.out.junction, remainder: true ).join( DCC_MATE2_2ND_PASS.out.junction, remainder: true ) + dcc_stage = DCC_2ND_PASS.out.junction.join( DCC_MATE1_2ND_PASS.out.junction).join( DCC_MATE2_2ND_PASS.out.junction ).groupTuple() dcc = dcc_stage.map{ it -> def meta = it[0]; if( meta.single_end ){ return [ it[0], it[1], [], [] ] } else { return it } } DCC( dcc, fasta, gtf ) DCC_FILTER( DCC.out.txt.map{ meta, txt -> meta.tool = "dcc"; return [ meta, txt ] }, bsj_reads ) From c9c5c00d6cf86aee9ba846392e6322bf4bec7e38 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 1 Feb 2023 16:13:18 +0000 Subject: [PATCH 031/491] alias circexplorer2 modules avoid mapslice mixups --- subworkflows/local/circrna_discovery.nf | 30 ++++++++++++------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 6df5e63a..1cd897b1 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -9,10 +9,6 @@ include { FIND_CIRC_FILTER } from '../../modules/local/find_circ include { CIRIQUANT_YML } from '../../modules/local/ciriquant/yml/main' include { CIRIQUANT } from '../../modules/local/ciriquant/ciriquant/main' include { CIRIQUANT_FILTER } from '../../modules/local/ciriquant/filter/main' -include { CIRCEXPLORER2_REFERENCE } from '../../modules/local/circexplorer2/reference/main' -include { CIRCEXPLORER2_PARSE } from '../../modules/nf-core/circexplorer2/parse/main' -include { CIRCEXPLORER2_ANNOTATE } from '../../modules/nf-core/circexplorer2/annotate/main' -include { CIRCEXPLORER2_FILTER } from '../../modules/local/circexplorer2/filter/main' include { CIRCRNA_FINDER_FILTER } from '../../modules/local/circrna_finder/filter/main' include { SEGEMEHL_ALIGN } from '../../modules/nf-core/segemehl/align/main' include { SEGEMEHL_FILTER } from '../../modules/local/segemehl/filter/main' @@ -35,6 +31,10 @@ include { FASTA } from '../../modules/local/fasta/mai include { MERGE_TOOLS } from '../../modules/local/count_matrix/merge_tools/main' include { COUNTS_COMBINED } from '../../modules/local/count_matrix/combined/main' include { COUNTS_SINGLE } from '../../modules/local/count_matrix/single/main' +include { CIRCEXPLORER2_REFERENCE as CIRCEXPLORER2_REF } from '../../modules/local/circexplorer2/reference/main' +include { CIRCEXPLORER2_PARSE as CIRCEXPLORER2_PAR } from '../../modules/nf-core/circexplorer2/parse/main' +include { CIRCEXPLORER2_ANNOTATE as CIRCEXPLORER2_ANN } from '../../modules/nf-core/circexplorer2/annotate/main' +include { CIRCEXPLORER2_FILTER as CIRCEXPLORER2_FLT } from '../../modules/local/circexplorer2/filter/main' include { CIRCEXPLORER2_REFERENCE as MAPSPLICE_REFERENCE } from '../../modules/local/circexplorer2/reference/main' include { CIRCEXPLORER2_PARSE as MAPSPLICE_PARSE } from '../../modules/nf-core/circexplorer2/parse/main' include { CIRCEXPLORER2_ANNOTATE as MAPSPLICE_ANNOTATE } from '../../modules/nf-core/circexplorer2/annotate/main' @@ -92,16 +92,16 @@ workflow CIRCRNA_DISCOVERY { // CIRCEXPLORER2 WORKFLOW: // - CIRCEXPLORER2_REFERENCE( gtf ) - CIRCEXPLORER2_PARSE( STAR_2ND_PASS.out.junction ) - CIRCEXPLORER2_ANNOTATE( CIRCEXPLORER2_PARSE.out.junction, fasta, CIRCEXPLORER2_REFERENCE.out.txt ) - circexplorer2_filter = CIRCEXPLORER2_ANNOTATE.out.txt.map{ meta, txt -> meta.tool = "circexplorer2"; return [ meta, txt ] } - CIRCEXPLORER2_FILTER( circexplorer2_filter, bsj_reads ) + CIRCEXPLORER2_REF( gtf ) + CIRCEXPLORER2_PAR( STAR_2ND_PASS.out.junction ) + CIRCEXPLORER2_ANN( CIRCEXPLORER2_PAR.out.junction, fasta, CIRCEXPLORER2_REF.out.txt ) + circexplorer2_filter = CIRCEXPLORER2_ANN.out.txt.map{ meta, txt -> meta.tool = "circexplorer2"; return [ meta, txt ] } + CIRCEXPLORER2_FLT( circexplorer2_filter, bsj_reads ) - ch_versions = ch_versions.mix(CIRCEXPLORER2_REFERENCE.out.versions) - ch_versions = ch_versions.mix(CIRCEXPLORER2_PARSE.out.versions) - ch_versions = ch_versions.mix(CIRCEXPLORER2_ANNOTATE.out.versions) - ch_versions = ch_versions.mix(CIRCEXPLORER2_FILTER.out.versions) + ch_versions = ch_versions.mix(CIRCEXPLORER2_REF.out.versions) + ch_versions = ch_versions.mix(CIRCEXPLORER2_PAR.out.versions) + ch_versions = ch_versions.mix(CIRCEXPLORER2_ANN.out.versions) + ch_versions = ch_versions.mix(CIRCEXPLORER2_FLT.out.versions) // // CIRCRNA_FINDER WORKFLOW: @@ -199,7 +199,7 @@ workflow CIRCRNA_DISCOVERY { ch_biotypes = Channel.fromPath("${projectDir}/bin/unwanted_biotypes.txt") - circrna_filtered = CIRCEXPLORER2_FILTER.out.results.mix(SEGEMEHL_FILTER.out.results, + circrna_filtered = CIRCEXPLORER2_FLT.out.results.mix(SEGEMEHL_FILTER.out.results, CIRCRNA_FINDER_FILTER.out.results, FIND_CIRC_FILTER.out.results, CIRIQUANT_FILTER.out.results, @@ -222,7 +222,7 @@ workflow CIRCRNA_DISCOVERY { // COUNT MATRIX WORKFLOW: // - ch_matrix = CIRCEXPLORER2_FILTER.out.matrix.mix(SEGEMEHL_FILTER.out.matrix, + ch_matrix = CIRCEXPLORER2_FLT.out.matrix.mix(SEGEMEHL_FILTER.out.matrix, CIRCRNA_FINDER_FILTER.out.matrix, FIND_CIRC_FILTER.out.matrix, CIRIQUANT_FILTER.out.matrix, From ec3217c6c092927fb0e11bd3f7b802c0943c76b7 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 1 Feb 2023 16:29:16 +0000 Subject: [PATCH 032/491] apply to modules conf too! --- conf/modules.config | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index b46f3b52..f3b96c6d 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -219,7 +219,7 @@ if (!params.skip_trimming) { ] } - withName: CIRCEXPLORER2_REFERENCE { + withName: CIRCEXPLORER2_REF { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('circexplorer2') } ext.args = [ "", "-genePredExt", @@ -233,7 +233,7 @@ if (!params.skip_trimming) { ] } - withName: CIRCEXPLORER2_PARSE { + withName: CIRCEXPLORER2_PAR { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('circexplorer2') } publishDir = [ path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates" }, @@ -243,7 +243,7 @@ if (!params.skip_trimming) { ] } - withName: CIRCEXPLORER2_ANNOTATE { + withName: CIRCEXPLORER2_ANN { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('circexplorer2') } publishDir = [ path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates" }, @@ -253,7 +253,7 @@ if (!params.skip_trimming) { ] } - withName: CIRCEXPLORER2_FILTER { + withName: CIRCEXPLORER2_FLT { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('circexplorer2') } publishDir = [ path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates" }, From 2028b1596e09d84a3fdbc5e0fb480ac8f71a98df Mon Sep 17 00:00:00 2001 From: Barry digby Date: Tue, 7 Feb 2023 10:58:29 +0000 Subject: [PATCH 033/491] prettier --- CITATIONS.md | 2 +- docs/output.md | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CITATIONS.md b/CITATIONS.md index d0b737d9..7c7df82a 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -138,7 +138,7 @@ ## Test data References - > Cao D. An autoregulation loop in fust-1 for circular RNA regulation in Caenorhabditis elegans. Genetics. 2021 Nov 5;219(3):iyab145. doi: 10.1093/genetics/iyab145. PMID: 34740247; PMCID: PMC8570788. +> Cao D. An autoregulation loop in fust-1 for circular RNA regulation in Caenorhabditis elegans. Genetics. 2021 Nov 5;219(3):iyab145. doi: 10.1093/genetics/iyab145. PMID: 34740247; PMCID: PMC8570788. ## Software packaging/containerisation tools diff --git a/docs/output.md b/docs/output.md index 80185914..398f958e 100644 --- a/docs/output.md +++ b/docs/output.md @@ -313,6 +313,7 @@ Intermediate files generated by each quantification tool are described in depth - `*.Log.out`: Main log file with a lot of detailed information about the run. This file is most useful for troubleshooting and debugging. - `*.Log.progress.out`: Reports job progress statistics, such as the number of processed reads, % of mapped reads etc. - `*.SJ.out.tab`: High confidence collapsed splice junctions in tab-delimited form. Full description of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 4.4). + - `circrna_discovery/STAR/2nd_Pass/${sample_id}/` - `*.Aligned.sortedByCoord.out.bam`: Coordinate sorted bam file containing aligned reads and chimeric reads. - `*.Chimeric.out.junction`: Each line contains the details of chimerically aligned reads. Full descriptions of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 5.4). From 1edbfd6323d72dd6fcb654e550fb3bcfa8a79a50 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Tue, 7 Feb 2023 11:03:11 +0000 Subject: [PATCH 034/491] implement James ci.yml suggestion properly --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 181b2aea..9245777e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -38,4 +38,4 @@ jobs: - name: Run pipeline with test data run: | - nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results From 3ac54c5166644ae56a67cd781b92ea77954c71a1 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Tue, 7 Feb 2023 12:35:51 +0000 Subject: [PATCH 035/491] robust '--module' checks --- workflows/circrna.nf | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/workflows/circrna.nf b/workflows/circrna.nf index 4f5e7056..477badf3 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -9,6 +9,34 @@ def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params) // Validate input parameters WorkflowCircrna.initialise(params, log) +// Check modules paramater +def checkParameterExistence(it, list) { + if (!list.contains(it)) { + log.warn "Unknown parameter: ${it}" + return false + } + return true +} + +def checkParameterList(list, realList) { + return list.every{ checkParameterExistence(it, realList) } +} + +def defineModuleList() { + return [ + 'circrna_discovery', + 'mirna_prediction', + 'differential_expression' + ] +} + +moduleList = defineModuleList() +module = params.module ? params.module.split(',').collect{it.trim().toLowerCase()} : [] +if(!checkParameterList(module, moduleList)) { + log.error "error: Unknown module selected, please choose one of the following:\n\n circrna_discovery\n\n mirna_prediction\n\n differential_expression\n\nPlease refer to the help documentation for a description of each module." + System.exit(1) +} + // Check input path parameters to see if they exist def checkPathParamList = [ params.input, params.multiqc_config ] for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } } From e26c3c256baa0ea21764899e86207446fbaed67f Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 8 Feb 2023 09:21:27 +0000 Subject: [PATCH 036/491] BAM QC --- modules.json | 33 +++++++++- modules/nf-core/samtools/flagstat/main.nf | 35 ++++++++++ modules/nf-core/samtools/flagstat/meta.yml | 49 ++++++++++++++ modules/nf-core/samtools/idxstats/main.nf | 36 ++++++++++ modules/nf-core/samtools/idxstats/meta.yml | 50 ++++++++++++++ modules/nf-core/samtools/stats/main.nf | 49 ++++++++++++++ modules/nf-core/samtools/stats/meta.yml | 53 +++++++++++++++ subworkflows/local/differential_expression.nf | 15 ++++- .../nf-core/bam_sort_stats_samtools/main.nf | 50 ++++++++++++++ .../nf-core/bam_sort_stats_samtools/meta.yml | 65 +++++++++++++++++++ .../nf-core/bam_stats_samtools/main.nf | 32 +++++++++ .../nf-core/bam_stats_samtools/meta.yml | 54 +++++++++++++++ workflows/circrna.nf | 5 ++ 13 files changed, 521 insertions(+), 5 deletions(-) create mode 100644 modules/nf-core/samtools/flagstat/main.nf create mode 100644 modules/nf-core/samtools/flagstat/meta.yml create mode 100644 modules/nf-core/samtools/idxstats/main.nf create mode 100644 modules/nf-core/samtools/idxstats/meta.yml create mode 100644 modules/nf-core/samtools/stats/main.nf create mode 100644 modules/nf-core/samtools/stats/meta.yml create mode 100644 subworkflows/nf-core/bam_sort_stats_samtools/main.nf create mode 100644 subworkflows/nf-core/bam_sort_stats_samtools/meta.yml create mode 100644 subworkflows/nf-core/bam_stats_samtools/main.nf create mode 100644 subworkflows/nf-core/bam_stats_samtools/meta.yml diff --git a/modules.json b/modules.json index 5b501b5f..4471d3e7 100644 --- a/modules.json +++ b/modules.json @@ -80,15 +80,30 @@ "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, + "samtools/flagstat": { + "branch": "master", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "installed_by": ["bam_stats_samtools"] + }, + "samtools/idxstats": { + "branch": "master", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "installed_by": ["bam_stats_samtools"] + }, "samtools/index": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": ["bam_sort_stats_samtools", "modules"] }, "samtools/sort": { "branch": "master", "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "installed_by": ["bam_sort_stats_samtools", "modules"] + }, + "samtools/stats": { + "branch": "master", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "installed_by": ["bam_stats_samtools"] }, "samtools/view": { "branch": "master", @@ -126,6 +141,20 @@ "installed_by": ["modules"] } } + }, + "subworkflows": { + "nf-core": { + "bam_sort_stats_samtools": { + "branch": "master", + "git_sha": "3911652a6b24249358f79e8b8466338d63efb2a2", + "installed_by": ["subworkflows"] + }, + "bam_stats_samtools": { + "branch": "master", + "git_sha": "92eb5091ae5368a60cda58b3a0ced8b36d715b0f", + "installed_by": ["bam_sort_stats_samtools"] + } + } } } } diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf new file mode 100644 index 00000000..2120cd7d --- /dev/null +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -0,0 +1,35 @@ +process SAMTOOLS_FLAGSTAT { + tag "$meta.id" + label 'process_single' + + conda "bioconda::samtools=1.16.1" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : + 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + + input: + tuple val(meta), path(bam), path(bai) + + output: + tuple val(meta), path("*.flagstat"), emit: flagstat + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + samtools \\ + flagstat \\ + --threads ${task.cpus} \\ + $bam \\ + > ${prefix}.flagstat + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/samtools/flagstat/meta.yml b/modules/nf-core/samtools/flagstat/meta.yml new file mode 100644 index 00000000..95269063 --- /dev/null +++ b/modules/nf-core/samtools/flagstat/meta.yml @@ -0,0 +1,49 @@ +name: samtools_flagstat +description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type +keywords: + - stats + - mapping + - counts + - bam + - sam + - cram +tools: + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index for BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - flagstat: + type: file + description: File containing samtools flagstat output + pattern: "*.{flagstat}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@drpatelh" diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf new file mode 100644 index 00000000..a7b87d8b --- /dev/null +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -0,0 +1,36 @@ +process SAMTOOLS_IDXSTATS { + tag "$meta.id" + label 'process_single' + + conda "bioconda::samtools=1.16.1" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : + 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + + input: + tuple val(meta), path(bam), path(bai) + + output: + tuple val(meta), path("*.idxstats"), emit: idxstats + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + samtools \\ + idxstats \\ + --threads ${task.cpus-1} \\ + $bam \\ + > ${prefix}.idxstats + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/samtools/idxstats/meta.yml b/modules/nf-core/samtools/idxstats/meta.yml new file mode 100644 index 00000000..3710ab88 --- /dev/null +++ b/modules/nf-core/samtools/idxstats/meta.yml @@ -0,0 +1,50 @@ +name: samtools_idxstats +description: Reports alignment summary statistics for a BAM/CRAM/SAM file +keywords: + - stats + - mapping + - counts + - chromosome + - bam + - sam + - cram +tools: + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index for BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - idxstats: + type: file + description: File containing samtools idxstats output + pattern: "*.{idxstats}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@drpatelh" diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf new file mode 100644 index 00000000..0a2a3640 --- /dev/null +++ b/modules/nf-core/samtools/stats/main.nf @@ -0,0 +1,49 @@ +process SAMTOOLS_STATS { + tag "$meta.id" + label 'process_single' + + conda "bioconda::samtools=1.16.1" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : + 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + + input: + tuple val(meta), path(input), path(input_index) + path fasta + + output: + tuple val(meta), path("*.stats"), emit: stats + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def reference = fasta ? "--reference ${fasta}" : "" + """ + samtools \\ + stats \\ + --threads ${task.cpus} \\ + ${reference} \\ + ${input} \\ + > ${prefix}.stats + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.stats + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml new file mode 100644 index 00000000..cac50b1c --- /dev/null +++ b/modules/nf-core/samtools/stats/meta.yml @@ -0,0 +1,53 @@ +name: samtools_stats +description: Produces comprehensive statistics from SAM/BAM/CRAM file +keywords: + - statistics + - counts + - bam + - sam + - cram +tools: + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - fasta: + type: optional file + description: Reference file the CRAM was created with + pattern: "*.{fasta,fa}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - stats: + type: file + description: File containing samtools stats output + pattern: "*.{stats}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@drpatelh" + - "@FriederikeHanssen" diff --git a/subworkflows/local/differential_expression.nf b/subworkflows/local/differential_expression.nf index 8bf83bda..82107038 100644 --- a/subworkflows/local/differential_expression.nf +++ b/subworkflows/local/differential_expression.nf @@ -6,6 +6,7 @@ include { PARENT_GENE } from '../../modules/local/annotation/paren include { PREPARE_CLR_TEST } from '../../modules/local/circtest/prepare/main' include { CIRCTEST } from '../../modules/local/circtest/test/main' include { DESEQ2_DIFFERENTIAL_EXPRESSION } from '../../modules/local/deseq2/differential_expression/main' +include { BAM_SORT_STATS_SAMTOOLS } from '../nf-core/bam_sort_stats_samtools/main' workflow DIFFERENTIAL_EXPRESSION { @@ -24,16 +25,23 @@ workflow DIFFERENTIAL_EXPRESSION { main: ch_versions = Channel.empty() + qc_reports = Channel.empty() // // LINEAR RNA ALIGNEMT WORKFLOW: // HISAT2_ALIGN( reads, hisat2_index, splice_sites ) - SAMTOOLS_SORT( HISAT2_ALIGN.out.bam ) - STRINGTIE_STRINGTIE( SAMTOOLS_SORT.out.bam, gtf ) + BAM_SORT_STATS_SAMTOOLS( HISAT2_ALIGN.out.bam, fasta ) + STRINGTIE_STRINGTIE( BAM_SORT_STATS_SAMTOOLS.out.bam, gtf ) STRINGTIE_PREPDE( STRINGTIE_STRINGTIE.out.transcript_gtf.map{ meta, gtf -> return [ gtf ] }.collect() ) + qc_reports = qc_reports.mix(HISAT2_ALIGN.out.summary.map{ meta, log -> log}) + qc_reports = qc_reports.mix(BAM_SORT_STATS_SAMTOOLS.out.stats.map{ meta, stats -> stats}) + qc_reports = qc_reports.mix(BAM_SORT_STATS_SAMTOOLS.out.flagstat.map{ meta, flagstat -> flagstat}) + qc_reports = qc_reports.mix(BAM_SORT_STATS_SAMTOOLS.out.idxstats.map{ meta, idxstats -> idxstats}) + + // // Circular, Linear Differential Expression // @@ -51,7 +59,7 @@ workflow DIFFERENTIAL_EXPRESSION { CIRCTEST( PREPARE_CLR_TEST.out.circular, PREPARE_CLR_TEST.out.linear, phenotype ) ch_versions = ch_versions.mix(HISAT2_ALIGN.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions) + ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS.out.versions) ch_versions = ch_versions.mix(STRINGTIE_STRINGTIE.out.versions) ch_versions = ch_versions.mix(STRINGTIE_PREPDE.out.versions) ch_versions = ch_versions.mix(DESEQ2_DIFFERENTIAL_EXPRESSION.out.versions) @@ -61,4 +69,5 @@ workflow DIFFERENTIAL_EXPRESSION { emit: versions = ch_versions + reports = qc_reports } diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf new file mode 100644 index 00000000..617871fe --- /dev/null +++ b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf @@ -0,0 +1,50 @@ +// +// Sort, index BAM file and run samtools stats, flagstat and idxstats +// + +include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' +include { BAM_STATS_SAMTOOLS } from '../bam_stats_samtools/main' + +workflow BAM_SORT_STATS_SAMTOOLS { + take: + ch_bam // channel: [ val(meta), [ bam ] ] + ch_fasta // channel: [ fasta ] + + main: + + ch_versions = Channel.empty() + + SAMTOOLS_SORT ( ch_bam ) + ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions.first()) + + SAMTOOLS_INDEX ( SAMTOOLS_SORT.out.bam ) + ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) + + SAMTOOLS_SORT.out.bam + .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) + .join(SAMTOOLS_INDEX.out.csi, by: [0], remainder: true) + .map { + meta, bam, bai, csi -> + if (bai) { + [ meta, bam, bai ] + } else { + [ meta, bam, csi ] + } + } + .set { ch_bam_bai } + + BAM_STATS_SAMTOOLS ( ch_bam_bai, ch_fasta ) + ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions) + + emit: + bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), [ bam ] ] + bai = SAMTOOLS_INDEX.out.bai // channel: [ val(meta), [ bai ] ] + csi = SAMTOOLS_INDEX.out.csi // channel: [ val(meta), [ csi ] ] + + stats = BAM_STATS_SAMTOOLS.out.stats // channel: [ val(meta), [ stats ] ] + flagstat = BAM_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), [ flagstat ] ] + idxstats = BAM_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), [ idxstats ] ] + + versions = ch_versions // channel: [ versions.yml ] +} diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml b/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml new file mode 100644 index 00000000..131065be --- /dev/null +++ b/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml @@ -0,0 +1,65 @@ +name: bam_sort_stats_samtools +description: Sort SAM/BAM/CRAM file +keywords: + - sort + - bam + - sam + - cram +modules: + - samtools/sort + - samtools/index + - samtools/stats + - samtools/idxstats + - samtools/flagstat +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - fasta: + type: file + description: Reference genome fasta file + pattern: "*.{fasta,fa}" +# TODO Update when we decide on a standard for subworkflow docs +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - crai: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - stats: + type: file + description: File containing samtools stats output + pattern: "*.{stats}" + - flagstat: + type: file + description: File containing samtools flagstat output + pattern: "*.{flagstat}" + - idxstats: + type: file + description: File containing samtools idxstats output + pattern: "*.{idxstats}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@drpatelh" + - "@ewels" diff --git a/subworkflows/nf-core/bam_stats_samtools/main.nf b/subworkflows/nf-core/bam_stats_samtools/main.nf new file mode 100644 index 00000000..cfcc48dd --- /dev/null +++ b/subworkflows/nf-core/bam_stats_samtools/main.nf @@ -0,0 +1,32 @@ +// +// Run SAMtools stats, flagstat and idxstats +// + +include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' +include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/main' +include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main' + +workflow BAM_STATS_SAMTOOLS { + take: + bam_bai // channel: [ val(meta), [ bam/cram ], [bai/csi] ] + fasta // channel: [ fasta ] + + main: + ch_versions = Channel.empty() + + SAMTOOLS_STATS ( bam_bai, fasta ) + ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions) + + SAMTOOLS_FLAGSTAT ( bam_bai ) + ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions) + + SAMTOOLS_IDXSTATS ( bam_bai ) + ch_versions = ch_versions.mix(SAMTOOLS_IDXSTATS.out.versions) + + emit: + stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), [ stats ] ] + flagstat = SAMTOOLS_FLAGSTAT.out.flagstat // channel: [ val(meta), [ flagstat ] ] + idxstats = SAMTOOLS_IDXSTATS.out.idxstats // channel: [ val(meta), [ idxstats ] ] + + versions = ch_versions // channel: [ versions.yml ] +} diff --git a/subworkflows/nf-core/bam_stats_samtools/meta.yml b/subworkflows/nf-core/bam_stats_samtools/meta.yml new file mode 100644 index 00000000..5252b0e4 --- /dev/null +++ b/subworkflows/nf-core/bam_stats_samtools/meta.yml @@ -0,0 +1,54 @@ +name: bam_stats_samtools +description: Produces comprehensive statistics from SAM/BAM/CRAM file +keywords: + - statistics + - counts + - bam + - sam + - cram +modules: + - samtools/stats + - samtools/idxstats + - samtools/flagstat +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index for BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" + - fasta: + type: file + description: Reference genome fasta file + pattern: "*.{fasta,fa}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - stats: + type: file + description: File containing samtools stats output + pattern: "*.{stats}" + - flagstat: + type: file + description: File containing samtools flagstat output + pattern: "*.{flagstat}" + - idxstats: + type: file + description: File containing samtools idxstats output + pattern: "*.{idxstats}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@drpatelh" diff --git a/workflows/circrna.nf b/workflows/circrna.nf index 477badf3..0101bc67 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -108,6 +108,7 @@ def multiqc_report = [] workflow CIRCRNA { + ch_reports = Channel.empty() ch_versions = Channel.empty() // @@ -170,6 +171,8 @@ workflow CIRCRNA { params.skip_trimming ) ch_versions = ch_versions.mix(FASTQC_TRIMGALORE.out.versions) + ch_reports = ch_reports.mix(FASTQC_TRIMGALORE.out.trim_zip.collect{it[1]}.ifEmpty([])) + ch_reports = ch_reports.mix(FASTQC_TRIMGALORE.out.trim_log.collect{it[1]}.ifEmpty([])) reads_for_circrna = FASTQC_TRIMGALORE.out.reads reads_for_diff_exp = FASTQC_TRIMGALORE.out.reads @@ -229,6 +232,7 @@ workflow CIRCRNA { ) ch_versions = ch_versions.mix(DIFFERENTIAL_EXPRESSION.out.versions) + ch_reports = ch_reports.mix(DIFFERENTIAL_EXPRESSION.out.reports) CUSTOM_DUMPSOFTWAREVERSIONS ( ch_versions.unique().collectFile(name: 'collated_versions.yml') @@ -246,6 +250,7 @@ workflow CIRCRNA { ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) ch_multiqc_files = ch_multiqc_files.mix(FASTQC_TRIMGALORE.out.fastqc_zip.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(ch_reports.collect().ifEmpty([])) MULTIQC ( ch_multiqc_files.collect(), From 1caf535541067c4bc6f2845d22530f594fd66dc9 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Wed, 8 Feb 2023 09:39:17 +0000 Subject: [PATCH 037/491] black, 23.1.0 --- bin/check_samplesheet.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index 339900f2..0a5041b0 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -55,7 +55,6 @@ def check_samplesheet(file_in, file_out): sample_mapping_dict = {} with open(file_in, "r", encoding="utf-8-sig") as fin: - ## Check header MIN_COLS = 2 ## edit by BDigby as not using strandedness yet. HEADER = ["sample", "fastq_1", "fastq_2"] @@ -130,7 +129,6 @@ def check_samplesheet(file_in, file_out): with open(file_out, "w") as fout: fout.write(",".join(["sample", "single_end", "fastq_1", "fastq_2"]) + "\n") for sample in sorted(sample_mapping_dict.keys()): - ## Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end if not all(x[0] == sample_mapping_dict[sample][0][0] for x in sample_mapping_dict[sample]): print_error( From 0bc397f07231c4233cb732a394e228bbe52636a6 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Thu, 9 Feb 2023 15:19:15 +0000 Subject: [PATCH 038/491] tidy circrna outdirs + corresponding output.md doc --- conf/modules.config | 46 +++--- docs/output.md | 154 +++++++++++--------- modules/local/circrna_finder/filter/main.nf | 1 + 3 files changed, 109 insertions(+), 92 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index f3b96c6d..e90eb069 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -47,18 +47,18 @@ if (!params.skip_trimming) { } publishDir = [ [ - path: { "${params.outdir}/trimgalore/fastqc" }, + path: { "${params.outdir}/quality_control/trimgalore/fastqc" }, mode: params.publish_dir_mode, pattern: "*.{html,zip}" ], [ - path: { "${params.outdir}/trimgalore" }, + path: { "${params.outdir}/quality_control/trimgalore" }, mode: params.publish_dir_mode, pattern: "*.fq.gz", enabled: params.save_trimmed ], [ - path: { "${params.outdir}/trimgalore" }, + path: { "${params.outdir}/quality_control/trimgalore" }, mode: params.publish_dir_mode, pattern: "*.txt" ] @@ -150,7 +150,7 @@ if (!params.skip_trimming) { "-S" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/circrna_discovery/segemehl/intermediates" }, + path: { "${params.outdir}/circrna_discovery/segemehl/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates @@ -160,7 +160,7 @@ if (!params.skip_trimming) { withName: SEGEMEHL_FILTER { ext.when = { params.tool.split(',').contains('segemehl') && params.module.split(',').contains('circrna_discovery') } publishDir = [ - path: { "${params.outdir}/circrna_discovery/segemehl/intermediates" }, + path: { "${params.outdir}/circrna_discovery/segemehl/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates, @@ -236,7 +236,7 @@ if (!params.skip_trimming) { withName: CIRCEXPLORER2_PAR { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('circexplorer2') } publishDir = [ - path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates" }, + path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates @@ -246,7 +246,7 @@ if (!params.skip_trimming) { withName: CIRCEXPLORER2_ANN { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('circexplorer2') } publishDir = [ - path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates" }, + path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates @@ -256,7 +256,7 @@ if (!params.skip_trimming) { withName: CIRCEXPLORER2_FLT { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('circexplorer2') } publishDir = [ - path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates" }, + path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates, @@ -267,7 +267,7 @@ if (!params.skip_trimming) { withName: CIRCRNA_FINDER_FILTER { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('circrna_finder') } publishDir = [ - path: { "${params.outdir}/circrna_discovery/circrna_finder/intermediates" }, + path: { "${params.outdir}/circrna_discovery/circrna_finder/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates, @@ -285,7 +285,7 @@ if (!params.skip_trimming) { "-q" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/circrna_discovery/find_circ/intermediates" }, + path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates @@ -297,7 +297,7 @@ if (!params.skip_trimming) { ext.prefix = { "${meta.id}_unmapped" } ext.args = "-hf 4" publishDir = [ - path: { "${params.outdir}/circrna_discovery/find_circ/intermediates" }, + path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates @@ -307,7 +307,7 @@ if (!params.skip_trimming) { withName: FIND_CIRC_ANCHORS { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('find_circ') } publishDir = [ - path: { "${params.outdir}/circrna_discovery/find_circ/intermediates" }, + path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates @@ -317,7 +317,7 @@ if (!params.skip_trimming) { withName: FIND_CIRC { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('find_circ') } publishDir = [ - path: { "${params.outdir}/circrna_discovery/find_circ/intermediates" }, + path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates @@ -327,7 +327,7 @@ if (!params.skip_trimming) { withName: FIND_CIRC_FILTER { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('find_circ') } publishDir = [ - path: { "${params.outdir}/circrna_discovery/find_circ/intermediates" }, + path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates, @@ -348,7 +348,7 @@ if (!params.skip_trimming) { withName: CIRIQUANT { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('ciriquant') } publishDir = [ - path: { "${params.outdir}/circrna_discovery/ciriquant/intermediates" }, + path: { "${params.outdir}/circrna_discovery/ciriquant/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates @@ -358,7 +358,7 @@ if (!params.skip_trimming) { withName: CIRIQUANT_FILTER { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('ciriquant') } publishDir = [ - path: { "${params.outdir}/circrna_discovery/ciriquant/intermediates" }, + path: { "${params.outdir}/circrna_discovery/ciriquant/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates, @@ -526,7 +526,7 @@ if (!params.skip_trimming) { withName: DCC { ext.when = { params.tool.split(',').contains('dcc') && params.module.split(',').contains('circrna_discovery') } publishDir = [ - path: { "${params.outdir}/circrna_discovery/dcc/intermediates/" }, + path: { "${params.outdir}/circrna_discovery/dcc/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates @@ -558,7 +558,7 @@ if (!params.skip_trimming) { "--fusion-non-canonical" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates" }, + path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates @@ -568,7 +568,7 @@ if (!params.skip_trimming) { withName: MAPSPLICE_PARSE { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('mapsplice') } publishDir = [ - path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates" }, + path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates @@ -578,7 +578,7 @@ if (!params.skip_trimming) { withName: MAPSPLICE_ANNOTATE { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('mapsplice') } publishDir = [ - path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates" }, + path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates @@ -588,7 +588,7 @@ if (!params.skip_trimming) { withName: MAPSPLICE_FILTER { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('mapsplice') } publishDir = [ - path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates" }, + path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates, @@ -598,7 +598,7 @@ if (!params.skip_trimming) { withName: ANNOTATION { publishDir = [ - path: { "${params.outdir}/circrna_discovery/${meta.tool}" }, + path: { "${params.outdir}/circrna_discovery/${meta.tool}/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -607,7 +607,7 @@ if (!params.skip_trimming) { withName: FASTA { ext.when = { params.module.split(',').contains('circrna_discovery') } publishDir = [ - path: { "${params.outdir}/circrna_discovery/${meta.tool}" }, + path: { "${params.outdir}/circrna_discovery/${meta.tool}/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.fasta" diff --git a/docs/output.md b/docs/output.md index 398f958e..0264fb06 100644 --- a/docs/output.md +++ b/docs/output.md @@ -11,9 +11,10 @@ A full run of the workflow will produce the following directory output structure |-- circrna_discovery |-- differential_expression |-- mirna_prediction + |-- multiqc |-- pipeline_info |-- quality_control - |-- reference_genome + |-- references ``` ## Pipeline Overview @@ -166,12 +167,45 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d ## Common Outputs -The workflow is designed to output three files per quantification tool selected in the `circrna_discovery` directory. By design, the workflow standardises the outputs of each quantification tool. +The workflow is designed to output three files _per sample_, _per quantification tool_ in the `circrna_discovery` directory. Using the test dataset as an example, the directory structure for the `fust_1` sample is: -- `quantification_tool/`: - - `${sample_id}.bed`: A customised BED 12 file containing filtered, annotated circRNAs. Columns: chromosome, start, end, name, read counts, strand, start, end, RGB, number of exon blocks, size of exon blocks, start positions (within sequence) of exon blocks, parent gene ID(s), parent transcript ID(s), mature spliced length. - - `${sample_id}.log`: Script detailing the decisions made by `annotate_outputs.sh` when annotating each circRNA. - - `${sample_id}.fasta`: Mature spliced sequence of circRNA in FASTA format. Includes splice junction site (+-20bp). +```console +|-- results/ + |-- circrna_discovery/ + |-- circexplorer2/ + | -- fust_1/ + | -- fust_1.bed + | -- fust_1.fasta + | -- fust_1.log + + +- `${sample_id}.bed`: A customised BED 12 file containing filtered, annotated circRNAs. Columns: chromosome, start, end, name, read counts, strand, start, end, RGB, number of exon blocks, size of exon blocks, start positions (within sequence) of exon blocks, parent gene ID(s), parent transcript ID(s), mature spliced length. +- `${sample_id}.log`: Script detailing the decisions made by `annotate_outputs.sh` when annotating each circRNA. +- `${sample_id}.fasta`: Mature spliced sequence of circRNA in FASTA format. Includes splice junction site (+-20bp). + +Sample outputs for the corresponding `.log`, `.bed` and `.fasta` entry are given below for a circRNA called by `CIRCexplorer2`: + +```console +[nf-core/circrna]: Starting analysis for: chrI:1140805-1147588:- +[nf-core/circrna]: chrI:1140805-1147588:- overlaps features in GTF file +[nf-core/circrna]: Inspecting Genes... +[nf-core/circrna]: Overlapping Gene IDs: Y48G8AL.10 +[nf-core/circrna]: Converting to BED12 +[nf-core/circrna]: Attempting to fit circRNA to gene exon boundaries +[nf-core/circrna]: chrI:1140805-1147588:- fits gene exons, is a circRNA +[nf-core/circrna]: cleaning up intermediate files +``` + +```console +chrI 1140805 1147588 chrI:1140805-1147588:- 2 - 1140805 1147588 0 5 229,214,191,141,499 0,1282,2546,4912,6284 circRNA Y48G8AL.10 NM_001306296,NM_001306297,NM_001306298,NM_001306299 1274 +``` + +```console +>chrI:1087252-1088602:- +CATGAAGTCTCGAGATCTCGTTTATAAGCACCAATATCCACGTTCAGCATTATTGATTGataaaattaatttataaattcgaaaataaaatttaaatttttCTTTAGAAATTATCGATTTATCGACTTCCACGTAATTCCACACCACGCTAAAATTCCATATCAATCTCGCGTTGTTTGGCTTCTCGTTGGGTGTCCGCCGCGTGGGAGTAGTATCTGCAAAAAAAAATTTGAGAATAAAAAATGTAAAATTGtttttcctattttctattgccgaaatttgagatttccggcaaatcggcaaattgccggaattgaaatttgcggcaaatcggcaaactgccgcaattgaaatttcgggtaaatcggcaaatttccggcaaatcggcatattgccggaatttaaatttccggcaaggcggccaatcggaaaattggcaaattgccgcaattgaaatttgcggcaaatcggcaattgtcgactattttcgacaacttctcgctttgcacttttttgtacatttcagattttttttcaatttcaatcggcaaaaacatttccggcaaatcggtaaattgccagaattgaaatttccggcaaatcggcaaattgccggaattgaaatttcccgcaaatcggcaaatttctttaattgaaatttccggcaaatcggtaaattgccggaatttaaatttccggcaactcggcaaactgccccaattgaaatttccggtaaatcggtaaaatgccgaaatttaaatttccggcaaggtggcaaatcggaaaattggcaaattgccggaattcaaatatccggcaaatcggcaagttgctggaattgaaatttccggcaaggcggcaaatttccggcaaatcggcaattGTCTTATattttcgacaacttctcgttttgcacttttttttgtacatttcaggttttttttcaatttcaatcggcaaaaacatttccggcaaatctgatatccggcaaacggcaaatcggcaatttgccgaaaataaaaaattcaagcaactcggcaaaccggcaaattTTATAGAGCACATTTGACCCACCTATTGAGAATAAACAATTGCGAGATAAAAATCTTGATGTAAATTCCGGCGAATGCGATCAAAATTGCTTTTCGATCTGAAAAAAATCCAATTTTGCTCAGCCAATAAATGGACGGAGCTAAAAACAAGGCGCTACTCACGAGAAATCCACTCATACGGGTCTTCTGTCACATTTTCCTGCTCGGATTTCGATTTTGGCGTATCTTCGGTCGGATTTCCGTGGTAATCGGACAACCAGGCAATCACTACAATTATTGCGCAAATGAATCGGGCAAC +``` + +The workflow's manual annotation process is designed to mimick annotation performed by `CIRCexplorer2` to standardise the annotation process for all circRNA quantification tools. Intermediate files generated by each quantification tool are described in depth below. @@ -180,10 +214,29 @@ Intermediate files generated by each quantification tool are described in depth
Output files -- `circrna_discovery/CIRCexplorer2/intermediates/${sample_id}/` - - `*.STAR.junction.bed`: Intermediate file generated by `CIRCexplorer2 parse` module, identifying STAR fusion junctions for downstream annotation. +- `circrna_discovery/circexplorer2/intermediates/${sample_id}/` + - `*.bed`: Intermediate file generated by `CIRCexplorer2 parse` module, identifying STAR fusion junctions for downstream annotation. + - `*_circexplorer2_circs.bed`: Filtered BED6 file containing circRNA counts used for count matrix generation. - `*.txt`: Output files generated by `CIRCexplorer2 annotate` module, based on BED 12 format containing circRNA genomic location information, exon cassette composition and an additional 6 columns specifying circRNA annotations. Full descriptions of the 18 columns can be found in the `CIRCexplorer2` [documentation](https://circexplorer2.readthedocs.io/en/latest/modules/annotate/#output). +- `circrna_discovery/star` + - `1st_pass` + - `*.Aligned.out.bam`: Coordinate sorted bam file containing aligned reads and chimeric reads. + - `*.Chimeric.out.junction`: Each line contains the details of chimerically aligned reads. Full descriptions of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 5.4). + - `*.Log.final.out`: Summary mapping statistics after mapping job is complete, useful for quality control. The statistics are calculated for each read (single- or paired-end) and then summed or averaged over all reads. + - `*.Log.out`: Main log file with a lot of detailed information about the run. This file is most useful for troubleshooting and debugging. + - `*.Log.progress.out`: Reports job progress statistics, such as the number of processed reads, % of mapped reads etc. + - `*.SJ.out.tab`: High confidence collapsed splice junctions in tab-delimited form. Full description of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 4.4). + - `2nd_pass` + - `*.Aligned.out.bam`: Coordinate sorted bam file containing aligned reads and chimeric reads. + - `*.Chimeric.out.junction`: Each line contains the details of chimerically aligned reads. Full descriptions of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 5.4). + - `*.Log.final.out`: Summary mapping statistics after mapping job is complete, useful for quality control. The statistics are calculated for each read (single- or paired-end) and then summed or averaged over all reads. + - `*.Log.out`: Main log file with a lot of detailed information about the run. This file is most useful for troubleshooting and debugging. + - `*.Log.progress.out`: Reports job progress statistics, such as the number of processed reads, % of mapped reads etc. + - `*.SJ.out.tab`: High confidence collapsed splice junctions in tab-delimited form. Full description of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 4.4). + - `sjdb` + - `dataset.SJ.out.tab`: Chromosome, start, end & strand coordinates of novel splice junctions for **all samples** aligned using STAR 1st pass. +
[CIRCexplorer2](https://circexplorer2.readthedocs.io/en/latest/) uses `*.Chimeric.out.junction` files generated from `STAR` 2 pass mode to extract back-splice junction sites using the `CIRCexplorer2 parse` module. Following this, `CIRCexplorer2 annotate` performs re-alignment of reads to the back-splice junction sites to determine the precise positions of downstream donor and upstream acceptor splice sites. Back-splice junction sites are subsequently updated and annotated using the customised annotation text file. @@ -193,29 +246,40 @@ Intermediate files generated by each quantification tool are described in depth
Output files -- `circrna_discovery/circRNA_Finder/intermediates/${sample_id}/` - - `*.Aligned.sortedByCoord.out.bam`: Coordinate sorted bam file containing aligned reads and chimeric reads. - - `*.Chimeric.out.junction`: Each line contains the details of chimerically aligned reads. Full descriptions of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 5.4). - - `*.Chimeric.out.sam`: Chimeric alignments in SAM format. - - `*.Log.final.out`: Summary mapping statistics after mapping job is complete, useful for quality control. The statistics are calculated for each read (single- or paired-end) and then summed or averaged over all reads. - - `*.Log.out`: Main log file with a lot of detailed information about the run. This file is most useful for troubleshooting and debugging. - - `*.Log.progress.out`: Reports job progress statistics, such as the number of processed reads, % of mapped reads etc. - - `*.SJ.out.tab`: High confidence collapsed splice junctions in tab-delimited form. Full description of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 4.4). - - `*.Chimeric.out.sorted.{bam,bam.bai}`: (Sorted and indexed) bam file with all chimeric reads identified by STAR. The circRNA junction spanning reads are a subset of these. +- `circrna_discovery/circrna_finder/intermediates/${sample_id}/` - `*.filteredJunctions.bed`: A bed file with **all** circular junctions found by the pipeline. The score column indicates the number reads spanning each junction. - `*.s_filteredJunctions.bed`: A bed file with those junctions in `*.filteredJunctions.bed` that are flanked by GT-AG splice sites. The score column indicates the number reads spanning each junction. - `*.s_filteredJunctions_fw.bed`: A bed file with the same circular junctions as in file (b), but here the score column gives the average number of forward spliced reads at both splice sites around each circular junction. +- `circrna_discovery/star` + - `1st_pass` + - `*.Aligned.out.bam`: Coordinate sorted bam file containing aligned reads and chimeric reads. + - `*.Chimeric.out.junction`: Each line contains the details of chimerically aligned reads. Full descriptions of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 5.4). + - `*.Log.final.out`: Summary mapping statistics after mapping job is complete, useful for quality control. The statistics are calculated for each read (single- or paired-end) and then summed or averaged over all reads. + - `*.Log.out`: Main log file with a lot of detailed information about the run. This file is most useful for troubleshooting and debugging. + - `*.Log.progress.out`: Reports job progress statistics, such as the number of processed reads, % of mapped reads etc. + - `*.SJ.out.tab`: High confidence collapsed splice junctions in tab-delimited form. Full description of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 4.4). + - `2nd_pass` + - `*.Aligned.out.bam`: Coordinate sorted bam file containing aligned reads and chimeric reads. + - `*.Chimeric.out.junction`: Each line contains the details of chimerically aligned reads. Full descriptions of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 5.4). + - `*.Chimeric.out.sam`: Chimeric alignments in SAM format. + - `*.Log.final.out`: Summary mapping statistics after mapping job is complete, useful for quality control. The statistics are calculated for each read (single- or paired-end) and then summed or averaged over all reads. + - `*.Log.out`: Main log file with a lot of detailed information about the run. This file is most useful for troubleshooting and debugging. + - `*.Log.progress.out`: Reports job progress statistics, such as the number of processed reads, % of mapped reads etc. + - `*.SJ.out.tab`: High confidence collapsed splice junctions in tab-delimited form. Full description of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 4.4). + - `sjdb` + - `dataset.SJ.out.tab`: Chromosome, start, end & strand coordinates of novel splice junctions for **all samples** aligned using STAR 1st pass. +
-[circRNA finder](https://github.com/orzechoj/circRNA_finder) uses `*.Chimeric.out.sam`, `*.Chimeric.out.junction` & `*.SJ.out.tab` files to identify circular RNAs in RNA-Seq data. +[circRNA finder](https://github.com/orzechoj/circRNA_finder) uses `*.Chimeric.out.sam`, `*.Chimeric.out.junction` & `*.SJ.out.tab` from STAR 2nd pass files to identify circular RNAs in RNA-Seq data. ### CIRIquant
Output files -- `circrna_discovery/CIRIquant/intermediates/${sample_id}/` +- `circrna_discovery/ciriquant/intermediates/${sample_id}/` - `*.log`: A `CIRIerror.log` file which should be empty, and a `${sample_id}.log` file which contains the output log of `CIRIquant`. - `*.bed`: `CIRI2` output file in BED 6 format. - `*.gtf`: Output file from `CIRIquant` in GTF format. Full description of the columns available in the `CIRIquant` [documentation](https://ciriquant-cookbook.readthedocs.io/en/latest/quantification.html#output-format). @@ -282,7 +346,7 @@ Intermediate files generated by each quantification tool are described in depth
Output files -- `circrna_discovery/MapSplice/intermediates/${sample_id}/` +- `circrna_discovery/mapsplice/intermediates/${sample_id}/` - `alignments.bam`: Bam file containing aligned reads and fusion alignments. - `deletions.txt`: Report of deletions. - `Fusion output files`: @@ -299,46 +363,13 @@ Intermediate files generated by each quantification tool are described in depth [MapSplice](http://www.netlab.uky.edu/p/bioinfo/MapSplice2) first splits reads into segments, and maps them to reference genome by using `Bowtie`. `MapSplice` attempts to fix unmapped segments as gapped alignments, with each gap corresponding to a splice junction. Finally a remapping step is used to identify back-spliced alignments that are in the presence of small exons. -### STAR - -
-Output files - -- `circrna_discovery/STAR/1st_Pass/${sample_id}/` - - - `*.Aligned.sortedByCoord.out.bam`: Coordinate sorted bam file containing aligned reads and chimeric reads. - - `*.Chimeric.out.junction`: Each line contains the details of chimerically aligned reads. Full descriptions of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 5.4). - - `*.Chimeric.out.sam`: Chimeric alignments in SAM format. - - `*.Log.final.out`: Summary mapping statistics after mapping job is complete, useful for quality control. The statistics are calculated for each read (single- or paired-end) and then summed or averaged over all reads. - - `*.Log.out`: Main log file with a lot of detailed information about the run. This file is most useful for troubleshooting and debugging. - - `*.Log.progress.out`: Reports job progress statistics, such as the number of processed reads, % of mapped reads etc. - - `*.SJ.out.tab`: High confidence collapsed splice junctions in tab-delimited form. Full description of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 4.4). - -- `circrna_discovery/STAR/2nd_Pass/${sample_id}/` - - `*.Aligned.sortedByCoord.out.bam`: Coordinate sorted bam file containing aligned reads and chimeric reads. - - `*.Chimeric.out.junction`: Each line contains the details of chimerically aligned reads. Full descriptions of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 5.4). - - `*.Chimeric.out.sam`: Chimeric alignments in SAM format. - - `*.Log.final.out`: Summary mapping statistics after mapping job is complete, useful for quality control. The statistics are calculated for each read (single- or paired-end) and then summed or averaged over all reads. - - `*.Log.out`: Main log file with a lot of detailed information about the run. This file is most useful for troubleshooting and debugging. - - `*.Log.progress.out`: Reports job progress statistics, such as the number of processed reads, % of mapped reads etc. - - `*.SJ.out.tab`: High confidence collapsed splice junctions in tab-delimited form. Full description of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 4.4). -- `circrna_discovery/STAR/SJFile/` - - `*.SJFile.tab`: Chromosome, start, end & strand coordinates of novel splice junctions. - -
- -[STAR](https://github.com/alexdobin/STAR) can characterise novel splice junctions in RNA-Seq data by specifying `--ChimOutType Junctions`, with reported novel junctions written to a `*SJ.out.tab` file (per sample). Following the initial `STAR` alignment, a 2nd pass strategy is employed whereby **all** `*SJ.out.tab` files from RNA-Seq samples are converted to `*SJFile.tab` files of novel junction coordinates and provided during the 2nd alignment step via `--sjdbFileChrStartEnd`. - -This achieves the highest sensitivity for novel junction alignment. For instance, if there is a novel junction that's highly expressed (many reads, confident detection) in the wild-type, but only weakly expressed (few reads) in the experimental group, by using junctions detected in all samples for the 2nd pass, `STAR` will detect lowly expressed spliced reads in the experimental group. - ### Segemehl
Output files -- `circrna_discovery/Segemehl/intermediates/${sample_id}/` +- `circrna_discovery/segemehl/intermediates/${sample_id}/` - `*.bam`: Aligned reads in BAM format - - `*_collapsed.bed`: Segemehl circRNA counts in minimal BED 6 format - `*.mult.bed`: Thus, this bed file contains all splice events of a read. The start and end positions indicate the nucleotide after the first split (i.e. the beginning of the first intron) and the nucleotide before the last split (i.e. the end of the last intron), respectively. The name and score are equivalent to the one in the \*.sngl file described above. The following fields 7 & 8 (thickStart and thickEnd) should be the identical to fields 2 & 3. Field 9 holds the color information for the item in RGB encoding (itemRGB). Field 10 (blockCount) indicates the number of splits represented by the BED item. Field 11 is a comma separated list of the intron sizes (blockSizes). Field 12 is the comma separated list of intron starts (blockStarts). - `*.sngl.bed`: The bed file contains all single splice events predicted in the split read alignments. - `*.trns.bed`: The custom text file contains all single split alignments predicted to be in trans, i.e. split alignments that are located on different chromosomes and/or different strands. @@ -403,21 +434,6 @@ This achieves the highest sensitivity for novel junction alignment. For instance 1. miRNA must be called by both `miRanda` and `TargetScan`. 2. If a site within the circRNA mature sequence shares duplicate miRNA ID's overlapping the same coordinates, the miRNA with the highest score is kept. -### Circos Plot - -
-Output files - -- `mirna_prediction/${sample_id}/` - - `*_miRNA_Plot.pdf`: Circos plot of mature spliced circRNA sequence with exon boundaries where applicable, displaying miRNA binding sites. -

- circRNA - miRNA circos plot -

- -
- -`nf-core/circrna` plots the filtered miRNA targets given using a circos plot, displaying the miRNA response elements along the mature circRNA sequence. Please note this plot becomes overcrowded when plotting `EIciRNAs` due to their highly variable sequence length (in contrast to `circRNAs` and `ciRNAs` which typically fall within the range of 100 - 1000nt). Therefore `EIciRNAs` with large mature spliced lengths should be considered as potentially spurious calls. - ## Differential Expression Analysis `nf-core/circrna` will perform differential expression analysis by contrasting every variable within the `condition` column i.e the response variable. diff --git a/modules/local/circrna_finder/filter/main.nf b/modules/local/circrna_finder/filter/main.nf index e5198cfb..0cda828e 100644 --- a/modules/local/circrna_finder/filter/main.nf +++ b/modules/local/circrna_finder/filter/main.nf @@ -15,6 +15,7 @@ process CIRCRNA_FINDER_FILTER { output: tuple val(meta), path("${prefix}_circrna_finder_circs.bed"), emit: results tuple val(meta), path("${prefix}_circrna_finder.bed") , emit: matrix + tuple val(meta), path("*filteredJunctions*") , emit: intermediates path "versions.yml" , emit: versions when: From ffdf7966ace420050257d0f67a1a98ea860aecb0 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Thu, 9 Feb 2023 15:28:42 +0000 Subject: [PATCH 039/491] pre-commit --- .pre-commit-config.yaml | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 .pre-commit-config.yaml diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 00000000..aa6b011a --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,10 @@ +repos: + - repo: https://github.com/pre-commit/mirrors-prettier + rev: "v2.6.2" + hooks: + - id: prettier + - repo: https://github.com/psf/black + rev: 23.1.0 + hooks: + - id: black + From adece2df10d8395f41575cf37f4421d445497ed1 Mon Sep 17 00:00:00 2001 From: Barry digby Date: Thu, 9 Feb 2023 15:34:23 +0000 Subject: [PATCH 040/491] pre-commit run? --- .pre-commit-config.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index aa6b011a..1ec7576e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,4 +7,3 @@ repos: rev: 23.1.0 hooks: - id: black - From 60cbad737a7db28ddd0399bf48d399d076ec5e3d Mon Sep 17 00:00:00 2001 From: Barry digby Date: Thu, 9 Feb 2023 15:34:39 +0000 Subject: [PATCH 041/491] pre-commit :) --- docs/output.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/output.md b/docs/output.md index 0264fb06..e661bf63 100644 --- a/docs/output.md +++ b/docs/output.md @@ -169,7 +169,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d The workflow is designed to output three files _per sample_, _per quantification tool_ in the `circrna_discovery` directory. Using the test dataset as an example, the directory structure for the `fust_1` sample is: -```console +````console |-- results/ |-- circrna_discovery/ |-- circexplorer2/ @@ -194,7 +194,7 @@ Sample outputs for the corresponding `.log`, `.bed` and `.fasta` entry are given [nf-core/circrna]: Attempting to fit circRNA to gene exon boundaries [nf-core/circrna]: chrI:1140805-1147588:- fits gene exons, is a circRNA [nf-core/circrna]: cleaning up intermediate files -``` +```` ```console chrI 1140805 1147588 chrI:1140805-1147588:- 2 - 1140805 1147588 0 5 229,214,191,141,499 0,1282,2546,4912,6284 circRNA Y48G8AL.10 NM_001306296,NM_001306297,NM_001306298,NM_001306299 1274 @@ -215,6 +215,7 @@ Intermediate files generated by each quantification tool are described in depth Output files - `circrna_discovery/circexplorer2/intermediates/${sample_id}/` + - `*.bed`: Intermediate file generated by `CIRCexplorer2 parse` module, identifying STAR fusion junctions for downstream annotation. - `*_circexplorer2_circs.bed`: Filtered BED6 file containing circRNA counts used for count matrix generation. - `*.txt`: Output files generated by `CIRCexplorer2 annotate` module, based on BED 12 format containing circRNA genomic location information, exon cassette composition and an additional 6 columns specifying circRNA annotations. Full descriptions of the 18 columns can be found in the `CIRCexplorer2` [documentation](https://circexplorer2.readthedocs.io/en/latest/modules/annotate/#output). @@ -247,6 +248,7 @@ Intermediate files generated by each quantification tool are described in depth Output files - `circrna_discovery/circrna_finder/intermediates/${sample_id}/` + - `*.filteredJunctions.bed`: A bed file with **all** circular junctions found by the pipeline. The score column indicates the number reads spanning each junction. - `*.s_filteredJunctions.bed`: A bed file with those junctions in `*.filteredJunctions.bed` that are flanked by GT-AG splice sites. The score column indicates the number reads spanning each junction. - `*.s_filteredJunctions_fw.bed`: A bed file with the same circular junctions as in file (b), but here the score column gives the average number of forward spliced reads at both splice sites around each circular junction. From b969146ba24502018d13b0f0a1c4cfa40e24a2e4 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 28 Apr 2023 14:19:44 +0000 Subject: [PATCH 042/491] Template update for nf-core/tools version 2.8 --- .editorconfig | 2 +- .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/PULL_REQUEST_TEMPLATE.md | 3 +- .github/workflows/awsfulltest.yml | 2 +- .github/workflows/awstest.yml | 2 +- .github/workflows/branch.yml | 2 +- .github/workflows/clean-up.yml | 24 ++++ .github/workflows/linting.yml | 2 +- .pre-commit-config.yaml | 5 + README.md | 74 ++++++---- bin/check_samplesheet.py | 3 - conf/base.config | 2 +- conf/igenomes.config | 8 ++ conf/test_full.config | 2 + docs/usage.md | 130 +++++------------- lib/NfcoreSchema.groovy | 4 +- lib/WorkflowCircrna.groovy | 12 +- lib/WorkflowMain.groovy | 13 +- main.nf | 1 - modules.json | 4 +- modules/local/samplesheet_check.nf | 2 +- .../custom/dumpsoftwareversions/main.nf | 6 +- .../custom/dumpsoftwareversions/meta.yml | 2 + modules/nf-core/multiqc/main.nf | 6 +- modules/nf-core/multiqc/meta.yml | 3 +- nextflow.config | 29 +++- tower.yml | 5 + 27 files changed, 193 insertions(+), 157 deletions(-) create mode 100644 .github/workflows/clean-up.yml create mode 100644 .pre-commit-config.yaml create mode 100644 tower.yml diff --git a/.editorconfig b/.editorconfig index b78de6e6..b6b31907 100644 --- a/.editorconfig +++ b/.editorconfig @@ -8,7 +8,7 @@ trim_trailing_whitespace = true indent_size = 4 indent_style = space -[*.{md,yml,yaml,html,css,scss,js,cff}] +[*.{md,yml,yaml,html,css,scss,js}] indent_size = 2 # These files are edited and tested upstream in nf-core/modules diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index d0232664..485ce3a4 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -45,6 +45,6 @@ body: * Nextflow version _(eg. 22.10.1)_ * Hardware _(eg. HPC, Desktop, Cloud)_ * Executor _(eg. slurm, local, awsbatch)_ - * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_ + * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ * OS _(eg. CentOS Linux, macOS, Linux Mint)_ * Version of nf-core/circrna _(eg. 1.1, 1.5, 1.8.2)_ diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 8e964d35..fcb76164 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -15,7 +15,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/circ - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! -- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/circrna/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/circrna _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/circrna/tree/master/.github/CONTRIBUTING.md) +- [ ] If necessary, also make a PR on the nf-core/circrna _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 96940e16..ec111638 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: nf-core/tower-action@v3 + uses: seqeralabs/action-tower-launch@v1 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 6677bb32..31933f32 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: nf-core/tower-action@v3 + uses: seqeralabs/action-tower-launch@v1 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 10173ce4..343d881e 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -13,7 +13,7 @@ jobs: - name: Check PRs if: github.repository == 'nf-core/circrna' run: | - { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/circrna ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] + { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/circrna ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] # If the above check failed, post a comment on the PR explaining the failure # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml new file mode 100644 index 00000000..694e90ec --- /dev/null +++ b/.github/workflows/clean-up.yml @@ -0,0 +1,24 @@ +name: "Close user-tagged issues and PRs" +on: + schedule: + - cron: "0 0 * * 0" # Once a week + +jobs: + clean-up: + runs-on: ubuntu-latest + permissions: + issues: write + pull-requests: write + steps: + - uses: actions/stale@v7 + with: + stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." + stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." + close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity." + days-before-stale: 30 + days-before-close: 20 + days-before-pr-close: -1 + any-of-labels: "awaiting-changes,awaiting-feedback" + exempt-issue-labels: "WIP" + exempt-pr-labels: "WIP" + repo-token: "${{ secrets.GITHUB_TOKEN }}" diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 858d622e..888cb4bc 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -78,7 +78,7 @@ jobs: - uses: actions/setup-python@v4 with: - python-version: "3.7" + python-version: "3.8" architecture: "x64" - name: Install dependencies diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 00000000..0c31cdb9 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,5 @@ +repos: + - repo: https://github.com/pre-commit/mirrors-prettier + rev: "v2.7.1" + hooks: + - id: prettier diff --git a/README.md b/README.md index 75428759..c4c1179b 100644 --- a/README.md +++ b/README.md @@ -8,57 +8,71 @@ [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/circrna) -[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23circrna-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/circrna)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) +[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23circrna-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/circrna)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) ## Introduction - +**nf-core/circrna** is a bioinformatics pipeline that ... -**nf-core/circrna** is a bioinformatics best-practice analysis pipeline for Quantification, miRNA target prediction and differential expression analysis of circular RNAs. - -The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! - - - -On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/circrna/results). - -## Pipeline summary + + 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) 2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) -## Quick Start +## Usage + +> **Note** +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how +> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) +> with `-profile test` before running the workflow on actual data. + + - Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string. +Now, you can run the pipeline using: - > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`. - > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. - > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. - > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. + -4. Start running your own analysis! +```bash +nextflow run nf-core/circrna \ + -profile \ + --input samplesheet.csv \ + --outdir +``` - +> **Warning:** +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those +> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; +> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). - ```bash - nextflow run nf-core/circrna --input samplesheet.csv --outdir --genome GRCh37 -profile - ``` +For more details, please refer to the [usage documentation](https://nf-co.re/circrna/usage) and the [parameter documentation](https://nf-co.re/circrna/parameters). -## Documentation +## Pipeline output -The nf-core/circrna pipeline comes with documentation about the pipeline [usage](https://nf-co.re/circrna/usage), [parameters](https://nf-co.re/circrna/parameters) and [output](https://nf-co.re/circrna/output). +To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/circrna/results) tab on the nf-core website pipeline page. +For more details about the output files and reports, please refer to the +[output documentation](https://nf-co.re/circrna/output). ## Credits diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index 11b15572..4a758fe0 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -158,9 +158,6 @@ def sniff_format(handle): peek = read_head(handle) handle.seek(0) sniffer = csv.Sniffer() - if not sniffer.has_header(peek): - logger.critical("The given sample sheet does not appear to contain a header.") - sys.exit(1) dialect = sniffer.sniff(peek) return dialect diff --git a/conf/base.config b/conf/base.config index 5e4a442d..307e9381 100644 --- a/conf/base.config +++ b/conf/base.config @@ -15,7 +15,7 @@ process { memory = { check_max( 6.GB * task.attempt, 'memory' ) } time = { check_max( 4.h * task.attempt, 'time' ) } - errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 maxErrors = '-1' diff --git a/conf/igenomes.config b/conf/igenomes.config index 7a1b3ac6..3f114377 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -36,6 +36,14 @@ params { macs_gsize = "2.7e9" blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" } + 'CHM13' { + fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/" + bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/" + gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf" + gff = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz" + mito_name = "chrM" + } 'GRCm38' { fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" diff --git a/conf/test_full.config b/conf/test_full.config index a3b229ad..7a280c2a 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -10,6 +10,8 @@ ---------------------------------------------------------------------------------------- */ +cleanup = true + params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' diff --git a/docs/usage.md b/docs/usage.md index ab73d14e..6b8b01f5 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -71,6 +71,29 @@ work # Directory containing the nextflow working files # Other nextflow hidden files, eg. history of pipeline runs and old logs. ``` +If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file. + +Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. + +> ⚠️ Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). +> The above pipeline run specified with a params file in yaml format: + +```bash +nextflow run nf-core/circrna -profile docker -params-file params.yaml +``` + +with `params.yaml` containing: + +```yaml +input: './samplesheet.csv' +outdir: './results/' +genome: 'GRCh37' +input: 'data' +<...> +``` + +You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). + ### Updating the pipeline When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: @@ -87,6 +110,10 @@ First, go to the [nf-core/circrna releases page](https://github.com/nf-core/circ This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. +To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. + +> 💡 If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. + ## Core Nextflow arguments > **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen). @@ -95,7 +122,7 @@ This version number will be logged in reports when you run the pipeline, so that Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments. -Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Conda) - see below. +Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below. > We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. @@ -119,8 +146,10 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) - `charliecloud` - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) +- `apptainer` + - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) - `conda` - - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud. + - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. ### `-resume` @@ -138,102 +167,19 @@ Specify the path to a specific config file (this is a core Nextflow command). Se Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. -For example, if the nf-core/rnaseq pipeline is failing after multiple re-submissions of the `STAR_ALIGN` process due to an exit code of `137` this would indicate that there is an out of memory issue: - -```console -[62/149eb0] NOTE: Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) -- Execution is retried (1) -Error executing process > 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)' - -Caused by: - Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) - -Command executed: - STAR \ - --genomeDir star \ - --readFilesIn WT_REP1_trimmed.fq.gz \ - --runThreadN 2 \ - --outFileNamePrefix WT_REP1. \ - - -Command exit status: - 137 - -Command output: - (empty) - -Command error: - .command.sh: line 9: 30 Killed STAR --genomeDir star --readFilesIn WT_REP1_trimmed.fq.gz --runThreadN 2 --outFileNamePrefix WT_REP1. -Work dir: - /home/pipelinetest/work/9d/172ca5881234073e8d76f2a19c88fb - -Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` -``` - -#### For beginners - -A first step to bypass this error, you could try to increase the amount of CPUs, memory, and time for the whole pipeline. Therefor you can try to increase the resource for the parameters `--max_cpus`, `--max_memory`, and `--max_time`. Based on the error above, you have to increase the amount of memory. Therefore you can go to the [parameter documentation of rnaseq](https://nf-co.re/rnaseq/3.9/parameters) and scroll down to the `show hidden parameter` button to get the default value for `--max_memory`. In this case 128GB, you than can try to run your pipeline again with `--max_memory 200GB -resume` to skip all process, that were already calculated. If you can not increase the resource of the complete pipeline, you can try to adapt the resource for a single process as mentioned below. - -#### Advanced option on process level - -To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN). -We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/star/align/main.nf`. -If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9). -The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. -The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB. -Providing you haven't set any other standard nf-core parameters to **cap** the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB. -The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections. - -```nextflow -process { - withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN' { - memory = 100.GB - } -} -``` - -> **NB:** We specify the full process name i.e. `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN` in the config file because this takes priority over the short name (`STAR_ALIGN`) and allows existing configuration using the full process name to be correctly overridden. -> -> If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly. - -### Updating containers (advanced users) - -The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`. - -1. Check the default version used by the pipeline in the module file for [Pangolin](https://github.com/nf-core/viralrecon/blob/a85d5969f9025409e3618d6c280ef15ce417df65/modules/nf-core/software/pangolin/main.nf#L14-L19) -2. Find the latest version of the Biocontainer available on [Quay.io](https://quay.io/repository/biocontainers/pangolin?tag=latest&tab=tags) -3. Create the custom config accordingly: - - - For Docker: +To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website. - ```nextflow - process { - withName: PANGOLIN { - container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0' - } - } - ``` +### Custom Containers - - For Singularity: +In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date. - ```nextflow - process { - withName: PANGOLIN { - container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0' - } - } - ``` +To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. - - For Conda: +### Custom Tool Arguments - ```nextflow - process { - withName: PANGOLIN { - conda = 'bioconda::pangolin=3.0.5' - } - } - ``` +A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default. -> **NB:** If you wish to periodically update individual tool-specific results (e.g. Pangolin) generated by the pipeline then you must ensure to keep the `work/` directory otherwise the `-resume` ability of the pipeline will be compromised and it will restart from scratch. +To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website. ### nf-core/configs diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy index 33cd4f6e..9b34804d 100755 --- a/lib/NfcoreSchema.groovy +++ b/lib/NfcoreSchema.groovy @@ -2,6 +2,7 @@ // This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template. // +import nextflow.Nextflow import org.everit.json.schema.Schema import org.everit.json.schema.loader.SchemaLoader import org.everit.json.schema.ValidationException @@ -83,6 +84,7 @@ class NfcoreSchema { 'stub-run', 'test', 'w', + 'with-apptainer', 'with-charliecloud', 'with-conda', 'with-dag', @@ -177,7 +179,7 @@ class NfcoreSchema { } if (has_error) { - System.exit(1) + Nextflow.error('Exiting!') } } diff --git a/lib/WorkflowCircrna.groovy b/lib/WorkflowCircrna.groovy index 7833ed4a..f990810a 100755 --- a/lib/WorkflowCircrna.groovy +++ b/lib/WorkflowCircrna.groovy @@ -2,6 +2,7 @@ // This file holds several functions specific to the workflow/circrna.nf in the nf-core/circrna pipeline // +import nextflow.Nextflow import groovy.text.SimpleTemplateEngine class WorkflowCircrna { @@ -14,8 +15,7 @@ class WorkflowCircrna { if (!params.fasta) { - log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." - System.exit(1) + Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." } } @@ -61,17 +61,19 @@ class WorkflowCircrna { def description_html = engine.createTemplate(methods_text).make(meta) return description_html - }// + } + + // // Exit pipeline if incorrect --genome key provided // private static void genomeExistsError(params, log) { if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { - log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + " Currently, the available genome keys are:\n" + " ${params.genomes.keySet().join(", ")}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - System.exit(1) + Nextflow.error(error_string) } } } diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 0d7be86b..328c2764 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -2,6 +2,8 @@ // This file holds several functions specific to the main.nf workflow in the nf-core/circrna pipeline // +import nextflow.Nextflow + class WorkflowMain { // @@ -21,7 +23,7 @@ class WorkflowMain { // // Generate help string // - public static String help(workflow, params, log) { + public static String help(workflow, params) { def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" def help_string = '' help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs) @@ -34,7 +36,7 @@ class WorkflowMain { // // Generate parameter summary log string // - public static String paramsSummaryLog(workflow, params, log) { + public static String paramsSummaryLog(workflow, params) { def summary_log = '' summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs) summary_log += NfcoreSchema.paramsSummaryLog(workflow, params) @@ -49,7 +51,7 @@ class WorkflowMain { public static void initialise(workflow, params, log) { // Print help to screen if required if (params.help) { - log.info help(workflow, params, log) + log.info help(workflow, params) System.exit(0) } @@ -61,7 +63,7 @@ class WorkflowMain { } // Print parameter summary log to screen - log.info paramsSummaryLog(workflow, params, log) + log.info paramsSummaryLog(workflow, params) // Validate workflow parameters via the JSON schema if (params.validate_params) { @@ -81,8 +83,7 @@ class WorkflowMain { // Check input has been provided if (!params.input) { - log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'" - System.exit(1) + Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'") } } // diff --git a/main.nf b/main.nf index 526c619d..1c002ad4 100644 --- a/main.nf +++ b/main.nf @@ -4,7 +4,6 @@ nf-core/circrna ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Github : https://github.com/nf-core/circrna - Website: https://nf-co.re/circrna Slack : https://nfcore.slack.com/channels/circrna ---------------------------------------------------------------------------------------- diff --git a/modules.json b/modules.json index 5b7c59e8..11cb5db3 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543", "installed_by": ["modules"] }, "fastqc": { @@ -17,7 +17,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7", "installed_by": ["modules"] } } diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 4e85a56e..e102f46d 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -5,7 +5,7 @@ process SAMPLESHEET_CHECK { conda "conda-forge::python=3.8.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'quay.io/biocontainers/python:3.8.3' }" + 'biocontainers/python:3.8.3' }" input: path samplesheet diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index 3df21765..800a6099 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.13" + conda "bioconda::multiqc=1.14" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index 60b546a0..c32657de 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,7 +1,9 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: - custom + - dump - version tools: - custom: diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 68f66bea..4b604749 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.13" + conda "bioconda::multiqc=1.14" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index ebc29b27..f93b5ee5 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,3 +1,4 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: MultiQC description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: @@ -37,7 +38,7 @@ output: description: MultiQC report file pattern: "multiqc_report.html" - data: - type: dir + type: directory description: MultiQC data dir pattern: "multiqc_data" - plots: diff --git a/nextflow.config b/nextflow.config index eabafb20..8ab54444 100644 --- a/nextflow.config +++ b/nextflow.config @@ -78,7 +78,11 @@ try { profiles { - debug { process.beforeScript = 'echo $HOSTNAME' } + debug { + dumpHashes = true + process.beforeScript = 'echo $HOSTNAME' + cleanup = false + } conda { conda.enabled = true docker.enabled = false @@ -86,6 +90,7 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } mamba { conda.enabled = true @@ -95,14 +100,18 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } docker { docker.enabled = true + docker.registry = 'quay.io' docker.userEmulation = true + conda.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' @@ -110,31 +119,49 @@ profiles { singularity { singularity.enabled = true singularity.autoMounts = true + conda.enabled = false docker.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } podman { podman.enabled = true + podman.registry = 'quay.io' + conda.enabled = false docker.enabled = false singularity.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } shifter { shifter.enabled = true + conda.enabled = false docker.enabled = false singularity.enabled = false podman.enabled = false charliecloud.enabled = false + apptainer.enabled = false } charliecloud { charliecloud.enabled = true + conda.enabled = false docker.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false + apptainer.enabled = false + } + apptainer { + apptainer.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false } gitpod { executor.name = 'local' diff --git a/tower.yml b/tower.yml new file mode 100644 index 00000000..787aedfe --- /dev/null +++ b/tower.yml @@ -0,0 +1,5 @@ +reports: + multiqc_report.html: + display: "MultiQC HTML report" + samplesheet.csv: + display: "Auto-created samplesheet with collated metadata and FASTQ paths" From ab234c96d00ca5e54133420e08ae737657385694 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 30 Jun 2023 16:12:56 +0000 Subject: [PATCH 043/491] Template update for nf-core/tools version 2.9 --- .github/CONTRIBUTING.md | 1 - .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/workflows/awsfulltest.yml | 11 +- .github/workflows/awstest.yml | 10 +- .github/workflows/ci.yml | 2 +- .gitpod.yml | 5 + CITATIONS.md | 6 + README.md | 6 +- assets/methods_description_template.yml | 12 +- assets/multiqc_config.yml | 4 +- assets/nf-core-circrna_logo_light.png | Bin 9946 -> 64214 bytes assets/slackreport.json | 2 +- conf/test_full.config | 2 - docs/usage.md | 6 +- lib/NfcoreSchema.groovy | 530 ------------------------ lib/NfcoreTemplate.groovy | 2 +- lib/WorkflowCircrna.groovy | 45 +- lib/WorkflowMain.groovy | 37 -- main.nf | 16 + nextflow.config | 52 ++- nextflow_schema.json | 36 +- workflows/circrna.nf | 25 +- 22 files changed, 175 insertions(+), 637 deletions(-) delete mode 100755 lib/NfcoreSchema.groovy diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 6566cc5d..c173003a 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -116,4 +116,3 @@ To get started: Devcontainer specs: - [DevContainer config](.devcontainer/devcontainer.json) -- [Dockerfile](.devcontainer/Dockerfile) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 485ce3a4..42e95fff 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -42,7 +42,7 @@ body: attributes: label: System information description: | - * Nextflow version _(eg. 22.10.1)_ + * Nextflow version _(eg. 23.04.0)_ * Hardware _(eg. HPC, Desktop, Cloud)_ * Executor _(eg. slurm, local, awsbatch)_ * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index ec111638..552540b6 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 + uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -22,13 +22,18 @@ jobs: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/circrna/work-${{ github.sha }} parameters: | { + "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/circrna/results-${{ github.sha }}" } - profiles: test_full,aws_tower + profiles: test_full + - uses: actions/upload-artifact@v3 with: name: Tower debug log file - path: tower_action_*.log + path: | + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 31933f32..75cde376 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,18 +12,22 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 + uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/circrna/work-${{ github.sha }} parameters: | { "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/circrna/results-test-${{ github.sha }}" } - profiles: test,aws_tower + profiles: test + - uses: actions/upload-artifact@v3 with: name: Tower debug log file - path: tower_action_*.log + path: | + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7c650441..735ec12e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -24,7 +24,7 @@ jobs: strategy: matrix: NXF_VER: - - "22.10.1" + - "23.04.0" - "latest-everything" steps: - name: Check out pipeline code diff --git a/.gitpod.yml b/.gitpod.yml index 85d95ecc..25488dcc 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,4 +1,9 @@ image: nfcore/gitpod:latest +tasks: + - name: Update Nextflow and setup pre-commit + command: | + pre-commit install --install-hooks + nextflow self-update vscode: extensions: # based on nf-core.nf-core-extensionpack diff --git a/CITATIONS.md b/CITATIONS.md index a90e70da..c3be1aad 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,7 +12,10 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) + > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. + - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) + > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools @@ -31,5 +34,8 @@ - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241) + > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241. + - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) + > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. diff --git a/README.md b/README.md index c4c1179b..12e662ff 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/circrna/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -66,11 +66,11 @@ nextflow run nf-core/circrna \ > provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; > see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). -For more details, please refer to the [usage documentation](https://nf-co.re/circrna/usage) and the [parameter documentation](https://nf-co.re/circrna/parameters). +For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/circrna/usage) and the [parameter documentation](https://nf-co.re/circrna/parameters). ## Pipeline output -To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/circrna/results) tab on the nf-core website pipeline page. +To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/circrna/results) tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/circrna/output). diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index 32e39806..3affe6b5 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -3,17 +3,21 @@ description: "Suggested text and references to use when describing pipeline usag section_name: "nf-core/circrna Methods Description" section_href: "https://github.com/nf-core/circrna" plot_type: "html" -## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline +## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline ## You inject any metadata in the Nextflow '${workflow}' object data: |

Methods

-

Data was processed using nf-core/circrna v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020).

+

Data was processed using nf-core/circrna v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

${workflow.commandLine}
+

${tool_citations}

References

    -
  • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. https://doi.org/10.1038/nbt.3820
    • -
  • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. https://doi.org/10.1038/s41587-020-0439-x
    • +
  • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
    • +
  • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
    • +
  • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
    • +
  • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
    • + ${tool_bibliography}
Notes:
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index ecd398c2..82a8c2de 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/circrna + This report has been generated by the nf-core/circrna analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-circrna-methods-description": order: -1000 diff --git a/assets/nf-core-circrna_logo_light.png b/assets/nf-core-circrna_logo_light.png index b1316cff22fe2008894af4a6d7f86a09dec8ebcf..d3cd49c1fffb4c615ab9d6e96f131be71830d2b2 100644 GIT binary patch literal 64214 zcmeEt`9IX_`~RRQS?ZKSWhn*~p=96c5GGq9OZHNfecuPCQz(&w!1jG0qM))u18{N;szxKLnntC7*Z0~7*=;B1!jv^4p5Gb_^hQ29NgTYTSd@O|5 zS3HI44fR<@BwC_WweNAg^K`t?ay|Ua^`zuS;o*5X;p5j0nLR_3TdTw-*C$<<{Vk$; z9`%au>-b1%=CCl=x~!Jp!Br{RFpzjKp!3X+Tb;*QRKss@Kb){h^c+@seV?p-3zMBT zv9)Zlu({<`v3Pc z_~QTk@G~L)&kz6ShyTBGp!b^mFYH1%8g&}PE+NMRdy{Rgwkaa9QvrRQY2HJz)6`6H z9;J$!8p?T$p0J;N*Ye!J#ykH8M)iUCxVX5E!@pK|Rzc1t45Gxe-2E^GvsRWhY(8G+ zqQw!LH!;zIl^)J$8$X^IcCItbD!;xEnF(K*M&+X@JSfW~(%%?AjAD}I{FvT)!b;+< zT`3RVvHyDV#tr{F?pFSzX|tN{P8k1QHN6RI-9sVD@-lUEm%l0Eg`Uqb{CpIznVgoC zqUmmd=@Irb{U+;BnnF@S4JpEd=f8=bxA|}L4A?vsm9JMY?xEj%PSrz{(B9T6zCrD{ 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--git a/assets/slackreport.json b/assets/slackreport.json index 043d02f2..b6be7a75 100644 --- a/assets/slackreport.json +++ b/assets/slackreport.json @@ -3,7 +3,7 @@ { "fallback": "Plain-text summary of the attachment.", "color": "<% if (success) { %>good<% } else { %>danger<%} %>", - "author_name": "sanger-tol/readmapping v${version} - ${runName}", + "author_name": "nf-core/circrna v${version} - ${runName}", "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", "fields": [ diff --git a/conf/test_full.config b/conf/test_full.config index 7a280c2a..a3b229ad 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -10,8 +10,6 @@ ---------------------------------------------------------------------------------------- */ -cleanup = true - params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' diff --git a/docs/usage.md b/docs/usage.md index 6b8b01f5..850476f1 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -57,7 +57,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```bash -nextflow run nf-core/circrna --input samplesheet.csv --outdir --genome GRCh37 -profile docker +nextflow run nf-core/circrna --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -76,7 +76,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. > ⚠️ Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). -> The above pipeline run specified with a params file in yaml format: + +The above pipeline run specified with a params file in yaml format: ```bash nextflow run nf-core/circrna -profile docker -params-file params.yaml @@ -88,7 +89,6 @@ with `params.yaml` containing: input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' -input: 'data' <...> ``` diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy deleted file mode 100755 index 9b34804d..00000000 --- a/lib/NfcoreSchema.groovy +++ /dev/null @@ -1,530 +0,0 @@ -// -// This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template. -// - -import nextflow.Nextflow -import org.everit.json.schema.Schema -import org.everit.json.schema.loader.SchemaLoader -import org.everit.json.schema.ValidationException -import org.json.JSONObject -import org.json.JSONTokener -import org.json.JSONArray -import groovy.json.JsonSlurper -import groovy.json.JsonBuilder - -class NfcoreSchema { - - // - // Resolve Schema path relative to main workflow directory - // - public static String getSchemaPath(workflow, schema_filename='nextflow_schema.json') { - return "${workflow.projectDir}/${schema_filename}" - } - - // - // Function to loop over all parameters defined in schema and check - // whether the given parameters adhere to the specifications - // - /* groovylint-disable-next-line UnusedPrivateMethodParameter */ - public static void validateParameters(workflow, params, log, schema_filename='nextflow_schema.json') { - def has_error = false - //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// - // Check for nextflow core params and unexpected params - def json = new File(getSchemaPath(workflow, schema_filename=schema_filename)).text - def Map schemaParams = (Map) new JsonSlurper().parseText(json).get('definitions') - def nf_params = [ - // Options for base `nextflow` command - 'bg', - 'c', - 'C', - 'config', - 'd', - 'D', - 'dockerize', - 'h', - 'log', - 'q', - 'quiet', - 'syslog', - 'v', - - // Options for `nextflow run` command - 'ansi', - 'ansi-log', - 'bg', - 'bucket-dir', - 'c', - 'cache', - 'config', - 'dsl2', - 'dump-channels', - 'dump-hashes', - 'E', - 'entry', - 'latest', - 'lib', - 'main-script', - 'N', - 'name', - 'offline', - 'params-file', - 'pi', - 'plugins', - 'poll-interval', - 'pool-size', - 'profile', - 'ps', - 'qs', - 'queue-size', - 'r', - 'resume', - 'revision', - 'stdin', - 'stub', - 'stub-run', - 'test', - 'w', - 'with-apptainer', - 'with-charliecloud', - 'with-conda', - 'with-dag', - 'with-docker', - 'with-mpi', - 'with-notification', - 'with-podman', - 'with-report', - 'with-singularity', - 'with-timeline', - 'with-tower', - 'with-trace', - 'with-weblog', - 'without-docker', - 'without-podman', - 'work-dir' - ] - def unexpectedParams = [] - - // Collect expected parameters from the schema - def expectedParams = [] - def enums = [:] - for (group in schemaParams) { - for (p in group.value['properties']) { - expectedParams.push(p.key) - if (group.value['properties'][p.key].containsKey('enum')) { - enums[p.key] = group.value['properties'][p.key]['enum'] - } - } - } - - for (specifiedParam in params.keySet()) { - // nextflow params - if (nf_params.contains(specifiedParam)) { - log.error "ERROR: You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'" - has_error = true - } - // unexpected params - def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params' - def expectedParamsLowerCase = expectedParams.collect{ it.replace("-", "").toLowerCase() } - def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase() - def isCamelCaseBug = (specifiedParam.contains("-") && !expectedParams.contains(specifiedParam) && expectedParamsLowerCase.contains(specifiedParamLowerCase)) - if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !isCamelCaseBug) { - // Temporarily remove camelCase/camel-case params #1035 - def unexpectedParamsLowerCase = unexpectedParams.collect{ it.replace("-", "").toLowerCase()} - if (!unexpectedParamsLowerCase.contains(specifiedParamLowerCase)){ - unexpectedParams.push(specifiedParam) - } - } - } - - //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// - // Validate parameters against the schema - InputStream input_stream = new File(getSchemaPath(workflow, schema_filename=schema_filename)).newInputStream() - JSONObject raw_schema = new JSONObject(new JSONTokener(input_stream)) - - // Remove anything that's in params.schema_ignore_params - raw_schema = removeIgnoredParams(raw_schema, params) - - Schema schema = SchemaLoader.load(raw_schema) - - // Clean the parameters - def cleanedParams = cleanParameters(params) - - // Convert to JSONObject - def jsonParams = new JsonBuilder(cleanedParams) - JSONObject params_json = new JSONObject(jsonParams.toString()) - - // Validate - try { - schema.validate(params_json) - } catch (ValidationException e) { - println '' - log.error 'ERROR: Validation of pipeline parameters failed!' - JSONObject exceptionJSON = e.toJSON() - printExceptions(exceptionJSON, params_json, log, enums) - println '' - has_error = true - } - - // Check for unexpected parameters - if (unexpectedParams.size() > 0) { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - println '' - def warn_msg = 'Found unexpected parameters:' - for (unexpectedParam in unexpectedParams) { - warn_msg = warn_msg + "\n* --${unexpectedParam}: ${params[unexpectedParam].toString()}" - } - log.warn warn_msg - log.info "- ${colors.dim}Ignore this warning: params.schema_ignore_params = \"${unexpectedParams.join(',')}\" ${colors.reset}" - println '' - } - - if (has_error) { - Nextflow.error('Exiting!') - } - } - - // - // Beautify parameters for --help - // - public static String paramsHelp(workflow, params, command, schema_filename='nextflow_schema.json') { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - Integer num_hidden = 0 - String output = '' - output += 'Typical pipeline command:\n\n' - output += " ${colors.cyan}${command}${colors.reset}\n\n" - Map params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename)) - Integer max_chars = paramsMaxChars(params_map) + 1 - Integer desc_indent = max_chars + 14 - Integer dec_linewidth = 160 - desc_indent - for (group in params_map.keySet()) { - Integer num_params = 0 - String group_output = colors.underlined + colors.bold + group + colors.reset + '\n' - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (group_params.get(param).hidden && !params.show_hidden_params) { - num_hidden += 1 - continue; - } - def type = '[' + group_params.get(param).type + ']' - def description = group_params.get(param).description - def defaultValue = group_params.get(param).default != null ? " [default: " + group_params.get(param).default.toString() + "]" : '' - def description_default = description + colors.dim + defaultValue + colors.reset - // Wrap long description texts - // Loosely based on https://dzone.com/articles/groovy-plain-text-word-wrap - if (description_default.length() > dec_linewidth){ - List olines = [] - String oline = "" // " " * indent - description_default.split(" ").each() { wrd -> - if ((oline.size() + wrd.size()) <= dec_linewidth) { - oline += wrd + " " - } else { - olines += oline - oline = wrd + " " - } - } - olines += oline - description_default = olines.join("\n" + " " * desc_indent) - } - group_output += " --" + param.padRight(max_chars) + colors.dim + type.padRight(10) + colors.reset + description_default + '\n' - num_params += 1 - } - group_output += '\n' - if (num_params > 0){ - output += group_output - } - } - if (num_hidden > 0){ - output += colors.dim + "!! Hiding $num_hidden params, use --show_hidden_params to show them !!\n" + colors.reset - } - output += NfcoreTemplate.dashedLine(params.monochrome_logs) - return output - } - - // - // Groovy Map summarising parameters/workflow options used by the pipeline - // - public static LinkedHashMap paramsSummaryMap(workflow, params, schema_filename='nextflow_schema.json') { - // Get a selection of core Nextflow workflow options - def Map workflow_summary = [:] - if (workflow.revision) { - workflow_summary['revision'] = workflow.revision - } - workflow_summary['runName'] = workflow.runName - if (workflow.containerEngine) { - workflow_summary['containerEngine'] = workflow.containerEngine - } - if (workflow.container) { - workflow_summary['container'] = workflow.container - } - workflow_summary['launchDir'] = workflow.launchDir - workflow_summary['workDir'] = workflow.workDir - workflow_summary['projectDir'] = workflow.projectDir - workflow_summary['userName'] = workflow.userName - workflow_summary['profile'] = workflow.profile - workflow_summary['configFiles'] = workflow.configFiles.join(', ') - - // Get pipeline parameters defined in JSON Schema - def Map params_summary = [:] - def params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename)) - for (group in params_map.keySet()) { - def sub_params = new LinkedHashMap() - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (params.containsKey(param)) { - def params_value = params.get(param) - def schema_value = group_params.get(param).default - def param_type = group_params.get(param).type - if (schema_value != null) { - if (param_type == 'string') { - if (schema_value.contains('$projectDir') || schema_value.contains('${projectDir}')) { - def sub_string = schema_value.replace('\$projectDir', '') - sub_string = sub_string.replace('\${projectDir}', '') - if (params_value.contains(sub_string)) { - schema_value = params_value - } - } - if (schema_value.contains('$params.outdir') || schema_value.contains('${params.outdir}')) { - def sub_string = schema_value.replace('\$params.outdir', '') - sub_string = sub_string.replace('\${params.outdir}', '') - if ("${params.outdir}${sub_string}" == params_value) { - schema_value = params_value - } - } - } - } - - // We have a default in the schema, and this isn't it - if (schema_value != null && params_value != schema_value) { - sub_params.put(param, params_value) - } - // No default in the schema, and this isn't empty - else if (schema_value == null && params_value != "" && params_value != null && params_value != false) { - sub_params.put(param, params_value) - } - } - } - params_summary.put(group, sub_params) - } - return [ 'Core Nextflow options' : workflow_summary ] << params_summary - } - - // - // Beautify parameters for summary and return as string - // - public static String paramsSummaryLog(workflow, params) { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - String output = '' - def params_map = paramsSummaryMap(workflow, params) - def max_chars = paramsMaxChars(params_map) - for (group in params_map.keySet()) { - def group_params = params_map.get(group) // This gets the parameters of that particular group - if (group_params) { - output += colors.bold + group + colors.reset + '\n' - for (param in group_params.keySet()) { - output += " " + colors.blue + param.padRight(max_chars) + ": " + colors.green + group_params.get(param) + colors.reset + '\n' - } - output += '\n' - } - } - output += "!! Only displaying parameters that differ from the pipeline defaults !!\n" - output += NfcoreTemplate.dashedLine(params.monochrome_logs) - return output - } - - // - // Loop over nested exceptions and print the causingException - // - private static void printExceptions(ex_json, params_json, log, enums, limit=5) { - def causingExceptions = ex_json['causingExceptions'] - if (causingExceptions.length() == 0) { - def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/ - // Missing required param - if (m.matches()) { - log.error "* Missing required parameter: --${m[0][1]}" - } - // Other base-level error - else if (ex_json['pointerToViolation'] == '#') { - log.error "* ${ex_json['message']}" - } - // Error with specific param - else { - def param = ex_json['pointerToViolation'] - ~/^#\// - def param_val = params_json[param].toString() - if (enums.containsKey(param)) { - def error_msg = "* --${param}: '${param_val}' is not a valid choice (Available choices" - if (enums[param].size() > limit) { - log.error "${error_msg} (${limit} of ${enums[param].size()}): ${enums[param][0..limit-1].join(', ')}, ... )" - } else { - log.error "${error_msg}: ${enums[param].join(', ')})" - } - } else { - log.error "* --${param}: ${ex_json['message']} (${param_val})" - } - } - } - for (ex in causingExceptions) { - printExceptions(ex, params_json, log, enums) - } - } - - // - // Remove an element from a JSONArray - // - private static JSONArray removeElement(json_array, element) { - def list = [] - int len = json_array.length() - for (int i=0;i - if(raw_schema.keySet().contains('definitions')){ - raw_schema.definitions.each { definition -> - for (key in definition.keySet()){ - if (definition[key].get("properties").keySet().contains(ignore_param)){ - // Remove the param to ignore - definition[key].get("properties").remove(ignore_param) - // If the param was required, change this - if (definition[key].has("required")) { - def cleaned_required = removeElement(definition[key].required, ignore_param) - definition[key].put("required", cleaned_required) - } - } - } - } - } - if(raw_schema.keySet().contains('properties') && raw_schema.get('properties').keySet().contains(ignore_param)) { - raw_schema.get("properties").remove(ignore_param) - } - if(raw_schema.keySet().contains('required') && raw_schema.required.contains(ignore_param)) { - def cleaned_required = removeElement(raw_schema.required, ignore_param) - raw_schema.put("required", cleaned_required) - } - } - return raw_schema - } - - // - // Clean and check parameters relative to Nextflow native classes - // - private static Map cleanParameters(params) { - def new_params = params.getClass().newInstance(params) - for (p in params) { - // remove anything evaluating to false - if (!p['value']) { - new_params.remove(p.key) - } - // Cast MemoryUnit to String - if (p['value'].getClass() == nextflow.util.MemoryUnit) { - new_params.replace(p.key, p['value'].toString()) - } - // Cast Duration to String - if (p['value'].getClass() == nextflow.util.Duration) { - new_params.replace(p.key, p['value'].toString().replaceFirst(/d(?!\S)/, "day")) - } - // Cast LinkedHashMap to String - if (p['value'].getClass() == LinkedHashMap) { - new_params.replace(p.key, p['value'].toString()) - } - } - return new_params - } - - // - // This function tries to read a JSON params file - // - private static LinkedHashMap paramsLoad(String json_schema) { - def params_map = new LinkedHashMap() - try { - params_map = paramsRead(json_schema) - } catch (Exception e) { - println "Could not read parameters settings from JSON. $e" - params_map = new LinkedHashMap() - } - return params_map - } - - // - // Method to actually read in JSON file using Groovy. - // Group (as Key), values are all parameters - // - Parameter1 as Key, Description as Value - // - Parameter2 as Key, Description as Value - // .... - // Group - // - - private static LinkedHashMap paramsRead(String json_schema) throws Exception { - def json = new File(json_schema).text - def Map schema_definitions = (Map) new JsonSlurper().parseText(json).get('definitions') - def Map schema_properties = (Map) new JsonSlurper().parseText(json).get('properties') - /* Tree looks like this in nf-core schema - * definitions <- this is what the first get('definitions') gets us - group 1 - title - description - properties - parameter 1 - type - description - parameter 2 - type - description - group 2 - title - description - properties - parameter 1 - type - description - * properties <- parameters can also be ungrouped, outside of definitions - parameter 1 - type - description - */ - - // Grouped params - def params_map = new LinkedHashMap() - schema_definitions.each { key, val -> - def Map group = schema_definitions."$key".properties // Gets the property object of the group - def title = schema_definitions."$key".title - def sub_params = new LinkedHashMap() - group.each { innerkey, value -> - sub_params.put(innerkey, value) - } - params_map.put(title, sub_params) - } - - // Ungrouped params - def ungrouped_params = new LinkedHashMap() - schema_properties.each { innerkey, value -> - ungrouped_params.put(innerkey, value) - } - params_map.put("Other parameters", ungrouped_params) - - return params_map - } - - // - // Get maximum number of characters across all parameter names - // - private static Integer paramsMaxChars(params_map) { - Integer max_chars = 0 - for (group in params_map.keySet()) { - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (param.size() > max_chars) { - max_chars = param.size() - } - } - } - return max_chars - } -} diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 25a0a74a..408951ae 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -128,7 +128,7 @@ class NfcoreTemplate { def email_html = html_template.toString() // Render the sendmail template - def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] def sf = new File("$projectDir/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) diff --git a/lib/WorkflowCircrna.groovy b/lib/WorkflowCircrna.groovy index f990810a..e03279a4 100755 --- a/lib/WorkflowCircrna.groovy +++ b/lib/WorkflowCircrna.groovy @@ -11,6 +11,7 @@ class WorkflowCircrna { // Check and validate parameters // public static void initialise(params, log) { + genomeExistsError(params, log) @@ -46,15 +47,57 @@ class WorkflowCircrna { return yaml_file_text } - public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) { + // + // Generate methods description for MultiQC + // + + public static String toolCitationText(params) { + + // TODO Optionally add in-text citation tools to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def citation_text = [ + "Tools used in the workflow included:", + "FastQC (Andrews 2010),", + "MultiQC (Ewels et al. 2016)", + "." + ].join(' ').trim() + + return citation_text + } + + public static String toolBibliographyText(params) { + + // TODO Optionally add bibliographic entries to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "

  • Author (2023) Pub name, Journal, DOI
    • " : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def reference_text = [ + "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", + "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " + ].join(' ').trim() + + return reference_text + } + + public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) { // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file def meta = [:] meta.workflow = run_workflow.toMap() meta["manifest_map"] = run_workflow.manifest.toMap() + // Pipeline DOI meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + // Tool references + meta["tool_citations"] = "" + meta["tool_bibliography"] = "" + + // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! + //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") + //meta["tool_bibliography"] = toolBibliographyText(params) + + def methods_text = mqc_methods_yaml.text def engine = new SimpleTemplateEngine() diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 328c2764..69de09aa 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -20,40 +20,11 @@ class WorkflowMain { " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" } - // - // Generate help string - // - public static String help(workflow, params) { - def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" - def help_string = '' - help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs) - help_string += NfcoreSchema.paramsHelp(workflow, params, command) - help_string += '\n' + citation(workflow) + '\n' - help_string += NfcoreTemplate.dashedLine(params.monochrome_logs) - return help_string - } - - // - // Generate parameter summary log string - // - public static String paramsSummaryLog(workflow, params) { - def summary_log = '' - summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs) - summary_log += NfcoreSchema.paramsSummaryLog(workflow, params) - summary_log += '\n' + citation(workflow) + '\n' - summary_log += NfcoreTemplate.dashedLine(params.monochrome_logs) - return summary_log - } // // Validate parameters and print summary to screen // public static void initialise(workflow, params, log) { - // Print help to screen if required - if (params.help) { - log.info help(workflow, params) - System.exit(0) - } // Print workflow version and exit on --version if (params.version) { @@ -62,14 +33,6 @@ class WorkflowMain { System.exit(0) } - // Print parameter summary log to screen - log.info paramsSummaryLog(workflow, params) - - // Validate workflow parameters via the JSON schema - if (params.validate_params) { - NfcoreSchema.validateParameters(workflow, params, log) - } - // Check that a -profile or Nextflow config has been provided to run the pipeline NfcoreTemplate.checkConfigProvided(workflow, log) diff --git a/main.nf b/main.nf index 1c002ad4..2be2de64 100644 --- a/main.nf +++ b/main.nf @@ -25,6 +25,22 @@ params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta') ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ +include { validateParameters; paramsHelp } from 'plugin/nf-validation' + +// Print help message if needed +if (params.help) { + def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) + def citation = '\n' + WorkflowMain.citation(workflow) + '\n' + def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" + log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) + System.exit(0) +} + +// Validate input parameters +if (params.validate_params) { + validateParameters() +} + WorkflowMain.initialise(workflow, params, log) /* diff --git a/nextflow.config b/nextflow.config index 8ab54444..b39e2c9f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,12 +12,12 @@ params { // TODO nf-core: Specify your pipeline's command line flags // Input options input = null - - // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes' igenomes_ignore = false + + // MultiQC options multiqc_config = null multiqc_title = null @@ -27,7 +27,6 @@ params { // Boilerplate options outdir = null - tracedir = "${params.outdir}/pipeline_info" publish_dir_mode = 'copy' email = null email_on_fail = null @@ -36,19 +35,15 @@ params { hook_url = null help = false version = false - validate_params = true - show_hidden_params = false - schema_ignore_params = 'genomes' - // Config options + config_profile_name = null + config_profile_description = null custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" - config_profile_description = null config_profile_contact = null config_profile_url = null - config_profile_name = null - + // Max resource options // Defaults only, expecting to be overwritten @@ -56,6 +51,13 @@ params { max_cpus = 16 max_time = '240.h' + // Schema validation default options + validationFailUnrecognisedParams = false + validationLenientMode = false + validationSchemaIgnoreParams = 'genomes' + validationShowHiddenParams = false + validate_params = true + } // Load base.config by default for all pipelines @@ -75,13 +77,11 @@ try { // } catch (Exception e) { // System.err.println("WARNING: Could not load nf-core/config/circrna profiles: ${params.custom_config_base}/pipeline/circrna.config") // } - - profiles { debug { dumpHashes = true process.beforeScript = 'echo $HOSTNAME' - cleanup = false + cleanup = false } conda { conda.enabled = true @@ -104,7 +104,6 @@ profiles { } docker { docker.enabled = true - docker.registry = 'quay.io' docker.userEmulation = true conda.enabled = false singularity.enabled = false @@ -128,7 +127,6 @@ profiles { } podman { podman.enabled = true - podman.registry = 'quay.io' conda.enabled = false docker.enabled = false singularity.enabled = false @@ -172,6 +170,18 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } +// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled +// Set to your registry if you have a mirror of containers +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' + +// Nextflow plugins +plugins { + id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} // Load igenomes.config if required if (!params.igenomes_ignore) { @@ -179,8 +189,6 @@ if (!params.igenomes_ignore) { } else { params.genomes = [:] } - - // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -198,19 +206,19 @@ process.shell = ['/bin/bash', '-euo', 'pipefail'] def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true - file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html" } report { enabled = true - file = "${params.tracedir}/execution_report_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html" } trace { enabled = true - file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt" + file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt" } dag { enabled = true - file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html" } manifest { @@ -219,7 +227,7 @@ manifest { homePage = 'https://github.com/nf-core/circrna' description = """Quantification, miRNA target prediction and differential expression analysis of circular RNAs""" mainScript = 'main.nf' - nextflowVersion = '!>=22.10.1' + nextflowVersion = '!>=23.04.0' version = '1.0.0' doi = '' } diff --git a/nextflow_schema.json b/nextflow_schema.json index b225d480..972619c1 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -15,9 +15,9 @@ "input": { "type": "string", "format": "file-path", + "exists": true, "mimetype": "text/csv", "pattern": "^\\S+\\.csv$", - "schema": "assets/schema_input.json", "description": "Path to comma-separated file containing information about the samples in the experiment.", "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/circrna/usage#samplesheet-input).", "fa_icon": "fas fa-file-csv" @@ -57,6 +57,7 @@ "fasta": { "type": "string", "format": "file-path", + "exists": true, "mimetype": "text/plain", "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$", "description": "Path to FASTA genome file.", @@ -157,7 +158,7 @@ "description": "Maximum amount of time that can be requested for any single job.", "default": "240.h", "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$", + "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", "hidden": true, "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" } @@ -174,12 +175,14 @@ "type": "boolean", "description": "Display help text.", "fa_icon": "fas fa-question-circle", + "default": false, "hidden": true }, "version": { "type": "boolean", "description": "Display version and exit.", "fa_icon": "fas fa-question-circle", + "default": false, "hidden": true }, "publish_dir_mode": { @@ -203,6 +206,7 @@ "type": "boolean", "description": "Send plain-text email instead of HTML.", "fa_icon": "fas fa-remove-format", + "default": false, "hidden": true }, "max_multiqc_email_size": { @@ -217,6 +221,7 @@ "type": "boolean", "description": "Do not use coloured log outputs.", "fa_icon": "fas fa-palette", + "default": false, "hidden": true }, "hook_url": { @@ -228,6 +233,7 @@ }, "multiqc_config": { "type": "string", + "format": "file-path", "description": "Custom config file to supply to MultiQC.", "fa_icon": "fas fa-cog", "hidden": true @@ -243,13 +249,6 @@ "description": "Custom MultiQC yaml file containing HTML including a methods description.", "fa_icon": "fas fa-cog" }, - "tracedir": { - "type": "string", - "description": "Directory to keep pipeline Nextflow logs and reports.", - "default": "${params.outdir}/pipeline_info", - "fa_icon": "fas fa-cogs", - "hidden": true - }, "validate_params": { "type": "boolean", "description": "Boolean whether to validate parameters against the schema at runtime", @@ -257,12 +256,29 @@ "fa_icon": "fas fa-check-square", "hidden": true }, - "show_hidden_params": { + "validationShowHiddenParams": { "type": "boolean", "fa_icon": "far fa-eye-slash", "description": "Show all params when using `--help`", + "default": false, "hidden": true, "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." + }, + "validationFailUnrecognisedParams": { + "type": "boolean", + "fa_icon": "far fa-check-circle", + "description": "Validation of parameters fails when an unrecognised parameter is found.", + "default": false, + "hidden": true, + "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." + }, + "validationLenientMode": { + "type": "boolean", + "fa_icon": "far fa-check-circle", + "description": "Validation of parameters in lenient more.", + "default": false, + "hidden": true, + "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." } } } diff --git a/workflows/circrna.nf b/workflows/circrna.nf index 448b8fb1..1eaf2c91 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -1,21 +1,19 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - VALIDATE INPUTS + PRINT PARAMS SUMMARY ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params) +include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' -// Validate input parameters -WorkflowCircrna.initialise(params, log) +def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) +def citation = '\n' + WorkflowMain.citation(workflow) + '\n' +def summary_params = paramsSummaryMap(workflow) -// TODO nf-core: Add all file path parameters for the pipeline to the list below -// Check input path parameters to see if they exist -def checkPathParamList = [ params.input, params.multiqc_config, params.fasta ] -for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } } +// Print parameter summary log to screen +log.info logo + paramsSummaryLog(workflow) + citation -// Check mandatory parameters -if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' } +WorkflowCircrna.initialise(params, log) /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -69,9 +67,12 @@ workflow CIRCRNA { // SUBWORKFLOW: Read in samplesheet, validate and stage input files // INPUT_CHECK ( - ch_input + file(params.input) ) ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) + // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") + // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ + // ! There is currently no tooling to help you write a sample sheet schema // // MODULE: Run FastQC @@ -91,7 +92,7 @@ workflow CIRCRNA { workflow_summary = WorkflowCircrna.paramsSummaryMultiqc(workflow, summary_params) ch_workflow_summary = Channel.value(workflow_summary) - methods_description = WorkflowCircrna.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description) + methods_description = WorkflowCircrna.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) ch_methods_description = Channel.value(methods_description) ch_multiqc_files = Channel.empty() From 3605257f0b62da4052805955bb1c7cd8e609c94f Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 25 Sep 2023 15:16:33 +0000 Subject: [PATCH 044/491] Template update for nf-core/tools version 2.10 --- .devcontainer/devcontainer.json | 1 + .github/CONTRIBUTING.md | 4 +- .github/workflows/linting.yml | 2 +- .github/workflows/release-announcments.yml | 68 +++++++++ CITATIONS.md | 2 +- CODE_OF_CONDUCT.md | 133 ++++++++++++++---- README.md | 21 +-- assets/multiqc_config.yml | 6 +- conf/modules.config | 9 ++ docs/output.md | 5 +- docs/usage.md | 16 ++- lib/NfcoreTemplate.groovy | 16 +++ lib/WorkflowCircrna.groovy | 2 +- main.nf | 3 + modules.json | 6 +- .../custom/dumpsoftwareversions/main.nf | 2 +- modules/nf-core/fastqc/main.nf | 8 +- modules/nf-core/multiqc/main.nf | 2 +- nextflow.config | 7 +- nextflow_schema.json | 15 -- workflows/circrna.nf | 1 + 21 files changed, 253 insertions(+), 76 deletions(-) create mode 100644 .github/workflows/release-announcments.yml diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index ea27a584..4ecfbfe3 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -2,6 +2,7 @@ "name": "nfcore", "image": "nfcore/gitpod:latest", "remoteUser": "gitpod", + "runArgs": ["--privileged"], // Configure tool-specific properties. "customizations": { diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index c173003a..4da158df 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -9,7 +9,9 @@ Please use the pre-filled template to save time. However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;) -> If you need help using or modifying nf-core/circrna then the best place to ask is on the nf-core Slack [#circrna](https://nfcore.slack.com/channels/circrna) channel ([join our Slack here](https://nf-co.re/join/slack)). +:::info +If you need help using or modifying nf-core/circrna then the best place to ask is on the nf-core Slack [#circrna](https://nfcore.slack.com/channels/circrna) channel ([join our Slack here](https://nf-co.re/join/slack)). +::: ## Contribution workflow diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 888cb4bc..b8bdd214 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -78,7 +78,7 @@ jobs: - uses: actions/setup-python@v4 with: - python-version: "3.8" + python-version: "3.11" architecture: "x64" - name: Install dependencies diff --git a/.github/workflows/release-announcments.yml b/.github/workflows/release-announcments.yml new file mode 100644 index 00000000..6ad33927 --- /dev/null +++ b/.github/workflows/release-announcments.yml @@ -0,0 +1,68 @@ +name: release-announcements +# Automatic release toot and tweet anouncements +on: + release: + types: [published] + workflow_dispatch: + +jobs: + toot: + runs-on: ubuntu-latest + steps: + - uses: rzr/fediverse-action@master + with: + access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} + host: "mstdn.science" # custom host if not "mastodon.social" (default) + # GitHub event payload + # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release + message: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + + send-tweet: + runs-on: ubuntu-latest + + steps: + - uses: actions/setup-python@v4 + with: + python-version: "3.10" + - name: Install dependencies + run: pip install tweepy==4.14.0 + - name: Send tweet + shell: python + run: | + import os + import tweepy + + client = tweepy.Client( + access_token=os.getenv("TWITTER_ACCESS_TOKEN"), + access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"), + consumer_key=os.getenv("TWITTER_CONSUMER_KEY"), + consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"), + ) + tweet = os.getenv("TWEET") + client.create_tweet(text=tweet) + env: + TWEET: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }} + TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }} + TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }} + TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }} + + bsky-post: + runs-on: ubuntu-latest + steps: + - uses: zentered/bluesky-post-action@v0.0.2 + with: + post: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + env: + BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }} + BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }} + # diff --git a/CITATIONS.md b/CITATIONS.md index c3be1aad..fb3c1f6e 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,7 +12,7 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. + > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index f4fd052f..c089ec78 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -1,18 +1,20 @@ -# Code of Conduct at nf-core (v1.0) +# Code of Conduct at nf-core (v1.4) ## Our Pledge -In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core, pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of: +In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of: - Age +- Ability - Body size +- Caste - Familial status - Gender identity and expression - Geographical location - Level of experience - Nationality and national origins - Native language -- Physical and neurological ability +- Neurodiversity - Race or ethnicity - Religion - Sexual identity and orientation @@ -22,80 +24,133 @@ Please note that the list above is alphabetised and is therefore not ranked in a ## Preamble -> Note: This Code of Conduct (CoC) has been drafted by the nf-core Safety Officer and been edited after input from members of the nf-core team and others. "We", in this document, refers to the Safety Officer and members of the nf-core core team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will amended periodically to keep it up-to-date, and in case of any dispute, the most current version will apply. +:::note +This Code of Conduct (CoC) has been drafted by Renuka Kudva, Cris Tuñí, and Michael Heuer, with input from the nf-core Core Team and Susanna Marquez from the nf-core community. "We", in this document, refers to the Safety Officers and members of the nf-core Core Team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will be amended periodically to keep it up-to-date. In case of any dispute, the most current version will apply. +::: -An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). Our current safety officer is Renuka Kudva. +An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). + +Our Safety Officers are Saba Nafees, Cris Tuñí, and Michael Heuer. nf-core is a young and growing community that welcomes contributions from anyone with a shared vision for [Open Science Policies](https://www.fosteropenscience.eu/taxonomy/term/8). Open science policies encompass inclusive behaviours and we strive to build and maintain a safe and inclusive environment for all individuals. -We have therefore adopted this code of conduct (CoC), which we require all members of our community and attendees in nf-core events to adhere to in all our workspaces at all times. Workspaces include but are not limited to Slack, meetings on Zoom, Jitsi, YouTube live etc. +We have therefore adopted this CoC, which we require all members of our community and attendees of nf-core events to adhere to in all our workspaces at all times. Workspaces include, but are not limited to, Slack, meetings on Zoom, gather.town, YouTube live etc. -Our CoC will be strictly enforced and the nf-core team reserve the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities. +Our CoC will be strictly enforced and the nf-core team reserves the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities. -We ask all members of our community to help maintain a supportive and productive workspace and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC. +We ask all members of our community to help maintain supportive and productive workspaces and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC. -Questions, concerns or ideas on what we can include? Contact safety [at] nf-co [dot] re +Questions, concerns, or ideas on what we can include? Contact members of the Safety Team on Slack or email safety [at] nf-co [dot] re. ## Our Responsibilities -The safety officer is responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour. +Members of the Safety Team (the Safety Officers) are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour. -The safety officer in consultation with the nf-core core team have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. +The Safety Team, in consultation with the nf-core core team, have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this CoC, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. -Members of the core team or the safety officer who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and be subject to the same actions as others in violation of the CoC. +Members of the core team or the Safety Team who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and will be subject to the same actions as others in violation of the CoC. -## When are where does this Code of Conduct apply? +## When and where does this Code of Conduct apply? -Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events. This includes but is not limited to the following listed alphabetically and therefore in no order of preference: +Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events, such as hackathons, workshops, bytesize, and collaborative workspaces on gather.town. These guidelines include, but are not limited to, the following (listed alphabetically and therefore in no order of preference): - Communicating with an official project email address. - Communicating with community members within the nf-core Slack channel. - Participating in hackathons organised by nf-core (both online and in-person events). -- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence. -- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, Jitsi, YouTube live etc. +- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence, and on the nf-core gather.town workspace. +- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, gather.town, Jitsi, YouTube live etc. - Representing nf-core on social media. This includes both official and personal accounts. ## nf-core cares 😊 -nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include but are not limited to the following (listed in alphabetical order): +nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include, but are not limited to, the following (listed in alphabetical order): - Ask for consent before sharing another community member’s personal information (including photographs) on social media. - Be respectful of differing viewpoints and experiences. We are all here to learn from one another and a difference in opinion can present a good learning opportunity. -- Celebrate your accomplishments at events! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !) +- Celebrate your accomplishments! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !) - Demonstrate empathy towards other community members. (We don’t all have the same amount of time to dedicate to nf-core. If tasks are pending, don’t hesitate to gently remind members of your team. If you are leading a task, ask for help if you feel overwhelmed.) - Engage with and enquire after others. (This is especially important given the geographically remote nature of the nf-core community, so let’s do this the best we can) - Focus on what is best for the team and the community. (When in doubt, ask) -- Graciously accept constructive criticism, yet be unafraid to question, deliberate, and learn. +- Accept feedback, yet be unafraid to question, deliberate, and learn. - Introduce yourself to members of the community. (We’ve all been outsiders and we know that talking to strangers can be hard for some, but remember we’re interested in getting to know you and your visions for open science!) -- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communications to be kind.**) +- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communication to be kind.**) - Take breaks when you feel like you need them. -- Using welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack.) +- Use welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack) ## nf-core frowns on 😕 -The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this code of conduct. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces. +The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this CoC. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces: - Deliberate intimidation, stalking or following and sustained disruption of communication among participants of the community. This includes hijacking shared screens through actions such as using the annotate tool in conferencing software such as Zoom. - “Doxing” i.e. posting (or threatening to post) another person’s personal identifying information online. - Spamming or trolling of individuals on social media. -- Use of sexual or discriminatory imagery, comments, or jokes and unwelcome sexual attention. -- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion or work experience. +- Use of sexual or discriminatory imagery, comments, jokes, or unwelcome sexual attention. +- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion, or work experience. ### Online Trolling -The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the added issue of online trolling. This is unacceptable, reports of such behaviour will be taken very seriously, and perpetrators will be excluded from activities immediately. +The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the risk of online trolling. This is unacceptable — reports of such behaviour will be taken very seriously and perpetrators will be excluded from activities immediately. -All community members are required to ask members of the group they are working within for explicit consent prior to taking screenshots of individuals during video calls. +All community members are **required** to ask members of the group they are working with for explicit consent prior to taking screenshots of individuals during video calls. -## Procedures for Reporting CoC violations +## Procedures for reporting CoC violations If someone makes you feel uncomfortable through their behaviours or actions, report it as soon as possible. -You can reach out to members of the [nf-core core team](https://nf-co.re/about) and they will forward your concerns to the safety officer(s). +You can reach out to members of the Safety Team (Saba Nafees, Cris Tuñí, and Michael Heuer) on Slack. Alternatively, contact a member of the nf-core core team [nf-core core team](https://nf-co.re/about), and they will forward your concerns to the Safety Team. + +Issues directly concerning members of the Core Team or the Safety Team will be dealt with by other members of the core team and the safety manager — possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson and details will be shared in due course. + +All reports will be handled with the utmost discretion and confidentiality. + +You can also report any CoC violations to safety [at] nf-co [dot] re. In your email report, please do your best to include: + +- Your contact information. +- Identifying information (e.g. names, nicknames, pseudonyms) of the participant who has violated the Code of Conduct. +- The behaviour that was in violation and the circumstances surrounding the incident. +- The approximate time of the behaviour (if different than the time the report was made). +- Other people involved in the incident, if applicable. +- If you believe the incident is ongoing. +- If there is a publicly available record (e.g. mailing list record, a screenshot). +- Any additional information. + +After you file a report, one or more members of our Safety Team will contact you to follow up on your report. + +## Who will read and handle reports + +All reports will be read and handled by the members of the Safety Team at nf-core. + +If members of the Safety Team are deemed to have a conflict of interest with a report, they will be required to recuse themselves as per our Code of Conduct and will not have access to any follow-ups. + +To keep this first report confidential from any of the Safety Team members, please submit your first report by direct messaging on Slack/direct email to any of the nf-core members you are comfortable disclosing the information to, and be explicit about which member(s) you do not consent to sharing the information with. + +## Reviewing reports + +After receiving the report, members of the Safety Team will review the incident report to determine whether immediate action is required, for example, whether there is immediate threat to participants’ safety. + +The Safety Team, in consultation with members of the nf-core core team, will assess the information to determine whether the report constitutes a Code of Conduct violation, for them to decide on a course of action. + +In the case of insufficient information, one or more members of the Safety Team may contact the reporter, the reportee, or any other attendees to obtain more information. -Issues directly concerning members of the core team will be dealt with by other members of the core team and the safety manager, and possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson, and details will be shared in due course. +Once additional information is gathered, the Safety Team will collectively review and decide on the best course of action to take, if any. The Safety Team reserves the right to not act on a report. -All reports will be handled with utmost discretion and confidentially. +## Confidentiality + +All reports, and any additional information included, are only shared with the team of safety officers (and possibly members of the core team, in case the safety officer is in violation of the CoC). We will respect confidentiality requests for the purpose of protecting victims of abuse. + +We will not name harassment victims, beyond discussions between the safety officer and members of the nf-core team, without the explicit consent of the individuals involved. + +## Enforcement + +Actions taken by the nf-core’s Safety Team may include, but are not limited to: + +- Asking anyone to stop a behaviour. +- Asking anyone to leave the event and online spaces either temporarily, for the remainder of the event, or permanently. +- Removing access to the gather.town and Slack, either temporarily or permanently. +- Communicating to all participants to reinforce our expectations for conduct and remind what is unacceptable behaviour; this may be public for practical reasons. +- Communicating to all participants that an incident has taken place and how we will act or have acted — this may be for the purpose of letting event participants know we are aware of and dealing with the incident. +- Banning anyone from participating in nf-core-managed spaces, future events, and activities, either temporarily or permanently. +- No action. ## Attribution and Acknowledgements @@ -106,6 +161,22 @@ All reports will be handled with utmost discretion and confidentially. ## Changelog -### v1.0 - March 12th, 2021 +### v1.4 - February 8th, 2022 + +- Included a new member of the Safety Team. Corrected a typographical error in the text. + +### v1.3 - December 10th, 2021 + +- Added a statement that the CoC applies to nf-core gather.town workspaces. Corrected typographical errors in the text. + +### v1.2 - November 12th, 2021 + +- Removed information specific to reporting CoC violations at the Hackathon in October 2021. + +### v1.1 - October 14th, 2021 + +- Updated with names of new Safety Officers and specific information for the hackathon in October 2021. + +### v1.0 - March 15th, 2021 - Complete rewrite from original [Contributor Covenant](http://contributor-covenant.org/) CoC. diff --git a/README.md b/README.md index 12e662ff..57b75df6 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ # ![nf-core/circrna](docs/images/nf-core-circrna_logo_light.png#gh-light-mode-only) ![nf-core/circrna](docs/images/nf-core-circrna_logo_dark.png#gh-dark-mode-only) -[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/circrna/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![GitHub Actions CI Status](https://github.com/nf-core/circrna/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/circrna/actions?query=workflow%3A%22nf-core+CI%22) +[![GitHub Actions Linting Status](https://github.com/nf-core/circrna/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/circrna/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/circrna/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) @@ -29,10 +30,11 @@ ## Usage -> **Note** -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how -> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) -> with `-profile test` before running the workflow on actual data. +:::note +If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how +to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) +with `-profile test` before running the workflow on actual data. +::: - + diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 177ece08..9a1b5bda 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,9 +1,7 @@ report_comment: > - - This report has been generated by the nf-core/circrna + This report has been generated by the nf-core/circrna analysis pipeline. For information about how to interpret these results, please see the - documentation. - + documentation. report_section_order: "nf-core-circrna-methods-description": order: -1000 diff --git a/assets/slackreport.json b/assets/slackreport.json index b6be7a75..aa925620 100644 --- a/assets/slackreport.json +++ b/assets/slackreport.json @@ -3,7 +3,7 @@ { "fallback": "Plain-text summary of the attachment.", "color": "<% if (success) { %>good<% } else { %>danger<%} %>", - "author_name": "nf-core/circrna v${version} - ${runName}", + "author_name": "nf-core/circrna ${version} - ${runName}", "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", "fields": [ diff --git a/conf/modules.config b/conf/modules.config index 39e81386..d91c6aba 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -39,7 +39,7 @@ process { } withName: 'MULTIQC' { - ext.args = params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' + ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ path: { "${params.outdir}/multiqc" }, mode: params.publish_dir_mode, diff --git a/docs/usage.md b/docs/usage.md index 9be6ccc4..8960ea47 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -20,7 +20,7 @@ You will need to create a samplesheet with information about the samples you wou The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes: -```console +```csv title="samplesheet.csv" sample,fastq_1,fastq_2 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz @@ -33,7 +33,7 @@ The pipeline will auto-detect whether a sample is single- or paired-end using th A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice. -```console +```csv title="samplesheet.csv" sample,fastq_1,fastq_2 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 01b8653d..e248e4c3 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -4,6 +4,7 @@ import org.yaml.snakeyaml.Yaml import groovy.json.JsonOutput +import nextflow.extension.FilesEx class NfcoreTemplate { @@ -141,12 +142,14 @@ class NfcoreTemplate { try { if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail + def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") + sendmail_tf.withWriter { w -> w << sendmail_html } [ 'sendmail', '-t' ].execute() << sendmail_html log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" } catch (all) { // Catch failures and try with plaintext def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] - if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) { + if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) { mail_cmd += [ '-A', mqc_report ] } mail_cmd.execute() << email_html @@ -155,14 +158,16 @@ class NfcoreTemplate { } // Write summary e-mail HTML to a file - def output_d = new File("${params.outdir}/pipeline_info/") - if (!output_d.exists()) { - output_d.mkdirs() - } - def output_hf = new File(output_d, "pipeline_report.html") + def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - def output_tf = new File(output_d, "pipeline_report.txt") + FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html"); + output_hf.delete() + + // Write summary e-mail TXT to a file + def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } + FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt"); + output_tf.delete() } // @@ -227,15 +232,14 @@ class NfcoreTemplate { // Dump pipeline parameters in a json file // public static void dump_parameters(workflow, params) { - def output_d = new File("${params.outdir}/pipeline_info/") - if (!output_d.exists()) { - output_d.mkdirs() - } - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def output_pf = new File(output_d, "params_${timestamp}.json") + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") def jsonStr = JsonOutput.toJson(params) - output_pf.text = JsonOutput.prettyPrint(jsonStr) + temp_pf.text = JsonOutput.prettyPrint(jsonStr) + + FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json") + temp_pf.delete() } // diff --git a/modules.json b/modules.json index 21badbb0..0452434d 100644 --- a/modules.json +++ b/modules.json @@ -7,17 +7,17 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117", + "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "4ab13872435962dadc239979554d13709e20bf29", "installed_by": ["modules"] } } diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml new file mode 100644 index 00000000..f0c63f69 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -0,0 +1,7 @@ +name: custom_dumpsoftwareversions +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.17 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index ebc87273..7685b33c 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.14" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : + 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index c32657de..5f15a5fd 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,4 +1,4 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: @@ -16,7 +16,6 @@ input: type: file description: YML file containing software versions pattern: "*.yml" - output: - yml: type: file @@ -30,7 +29,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@drpatelh" - "@grst" +maintainers: + - "@drpatelh" + - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test new file mode 100644 index 00000000..eec1db10 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -0,0 +1,38 @@ +nextflow_process { + + name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" + script "../main.nf" + process "CUSTOM_DUMPSOFTWAREVERSIONS" + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "dumpsoftwareversions" + tag "custom/dumpsoftwareversions" + + test("Should run without failures") { + when { + process { + """ + def tool1_version = ''' + TOOL1: + tool1: 0.11.9 + '''.stripIndent() + + def tool2_version = ''' + TOOL2: + tool2: 1.9 + '''.stripIndent() + + input[0] = Channel.of(tool1_version, tool2_version).collectFile() + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap new file mode 100644 index 00000000..4274ed57 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -0,0 +1,27 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" + ], + "1": [ + "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" + ], + "2": [ + "versions.yml:md5,3843ac526e762117eedf8825b40683df" + ], + "mqc_yml": [ + "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" + ], + "versions": [ + "versions.yml:md5,3843ac526e762117eedf8825b40683df" + ], + "yml": [ + "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" + ] + } + ], + "timestamp": "2023-11-03T14:43:22.157011" + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml new file mode 100644 index 00000000..405aa24a --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml @@ -0,0 +1,2 @@ +custom/dumpsoftwareversions: + - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml new file mode 100644 index 00000000..1787b38a --- /dev/null +++ b/modules/nf-core/fastqc/environment.yml @@ -0,0 +1,7 @@ +name: fastqc +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 249f9064..9e19a74c 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -2,10 +2,10 @@ process FASTQC { tag "$meta.id" label 'process_medium' - conda "bioconda::fastqc=0.11.9" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : - 'biocontainers/fastqc:0.11.9--0' }" + 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : + 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" input: tuple val(meta), path(reads) @@ -37,7 +37,7 @@ process FASTQC { cat <<-END_VERSIONS > versions.yml "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) END_VERSIONS """ @@ -49,7 +49,7 @@ process FASTQC { cat <<-END_VERSIONS > versions.yml "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) END_VERSIONS """ } diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index 4da5bb5a..ee5507e0 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -50,3 +50,8 @@ authors: - "@grst" - "@ewels" - "@FelixKrueger" +maintainers: + - "@drpatelh" + - "@grst" + - "@ewels" + - "@FelixKrueger" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test new file mode 100644 index 00000000..b9e8f926 --- /dev/null +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -0,0 +1,109 @@ +nextflow_process { + + name "Test Process FASTQC" + script "../main.nf" + process "FASTQC" + tag "modules" + tag "modules_nfcore" + tag "fastqc" + + test("Single-Read") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id: 'test', single_end:true ], + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
    Mon 2 Oct 2023
    test.gz
    + // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + { assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" }, + { assert path(process.out.html.get(0).get(1)).getText().contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match("versions") }, + { assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" } + ) + } + } +// TODO +// // +// // Test with paired-end data +// // +// workflow test_fastqc_paired_end { +// input = [ +// [id: 'test', single_end: false], // meta map +// [ +// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), +// file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) +// ] +// ] + +// FASTQC ( input ) +// } + +// // +// // Test with interleaved data +// // +// workflow test_fastqc_interleaved { +// input = [ +// [id: 'test', single_end: false], // meta map +// file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) +// ] + +// FASTQC ( input ) +// } + +// // +// // Test with bam data +// // +// workflow test_fastqc_bam { +// input = [ +// [id: 'test', single_end: false], // meta map +// file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) +// ] + +// FASTQC ( input ) +// } + +// // +// // Test with multiple samples +// // +// workflow test_fastqc_multiple { +// input = [ +// [id: 'test', single_end: false], // meta map +// [ +// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), +// file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), +// file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true), +// file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) +// ] +// ] + +// FASTQC ( input ) +// } + +// // +// // Test with custom prefix +// // +// workflow test_fastqc_custom_prefix { +// input = [ +// [ id:'mysample', single_end:true ], // meta map +// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) +// ] + +// FASTQC ( input ) +// } +} diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap new file mode 100644 index 00000000..636a32ce --- /dev/null +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -0,0 +1,10 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "timestamp": "2023-10-09T23:40:54+0000" + } +} \ No newline at end of file diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml new file mode 100644 index 00000000..7834294b --- /dev/null +++ b/modules/nf-core/fastqc/tests/tags.yml @@ -0,0 +1,2 @@ +fastqc: + - modules/nf-core/fastqc/** diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml new file mode 100644 index 00000000..bc0bdb5b --- /dev/null +++ b/modules/nf-core/multiqc/environment.yml @@ -0,0 +1,7 @@ +name: multiqc +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.18 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 1fc387be..00cc48d2 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.14" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.18--pyhdfd78af_0' : + 'biocontainers/multiqc:1.18--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" @@ -25,12 +25,14 @@ process MULTIQC { def args = task.ext.args ?: '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' + def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' """ multiqc \\ --force \\ $args \\ $config \\ $extra_config \\ + $logo \\ . cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index f93b5ee5..f1aa660e 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,5 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json -name: MultiQC +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: multiqc description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: - QC @@ -13,7 +13,6 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] - input: - multiqc_files: type: file @@ -31,7 +30,6 @@ input: type: file description: Optional logo file for MultiQC pattern: "*.{png}" - output: - report: type: file @@ -54,3 +52,8 @@ authors: - "@bunop" - "@drpatelh" - "@jfy133" +maintainers: + - "@abhi18av" + - "@bunop" + - "@drpatelh" + - "@jfy133" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test new file mode 100644 index 00000000..c2dad217 --- /dev/null +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -0,0 +1,63 @@ +nextflow_process { + + name "Test Process MULTIQC" + script "../main.nf" + process "MULTIQC" + tag "modules" + tag "modules_nfcore" + tag "multiqc" + + test("MULTIQC: FASTQC") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = [] + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.report.get(0)).exists() }, + { assert path(process.out.data.get(0)).exists() }, + { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + ) + } + + } + + test("MULTIQC: FASTQC and a config file") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.report.get(0)).exists() }, + { assert path(process.out.data.get(0)).exists() }, + { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + ) + } + + } +} diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml new file mode 100644 index 00000000..bea6c0d3 --- /dev/null +++ b/modules/nf-core/multiqc/tests/tags.yml @@ -0,0 +1,2 @@ +multiqc: + - modules/nf-core/multiqc/** diff --git a/nextflow.config b/nextflow.config index 2dac3ee7..3893e1a3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -14,7 +14,7 @@ params { input = null // References genome = null - igenomes_base = 's3://ngi-igenomes/igenomes' + igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false @@ -82,6 +82,7 @@ profiles { dumpHashes = true process.beforeScript = 'echo $HOSTNAME' cleanup = false + nextflow.enable.configProcessNamesValidation = true } conda { conda.enabled = true @@ -104,13 +105,13 @@ profiles { } docker { docker.enabled = true - docker.userEmulation = true conda.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false + runOptions = '-u $(id -u):$(id -g)' } arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' @@ -181,7 +182,7 @@ singularity.registry = 'quay.io' // Nextflow plugins plugins { - id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet } // Load igenomes.config if required @@ -204,6 +205,9 @@ env { // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Disable process selector warnings by default. Use debug profile to enable warnings. +nextflow.enable.configProcessNamesValidation = false + def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true @@ -229,7 +233,7 @@ manifest { description = """Quantification, miRNA target prediction and differential expression analysis of circular RNAs""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.0.0' + version = 'dev' doi = '' } From 600c9afacf72c075480b786e261436d7178e3392 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 20 Dec 2023 15:56:43 +0000 Subject: [PATCH 080/491] Template update for nf-core/tools version 2.11.1 --- .../{release-announcments.yml => release-announcements.yml} | 0 nextflow.config | 4 ++-- 2 files changed, 2 insertions(+), 2 deletions(-) rename .github/workflows/{release-announcments.yml => release-announcements.yml} (100%) diff --git a/.github/workflows/release-announcments.yml b/.github/workflows/release-announcements.yml similarity index 100% rename from .github/workflows/release-announcments.yml rename to .github/workflows/release-announcements.yml diff --git a/nextflow.config b/nextflow.config index 3893e1a3..4b3b98de 100644 --- a/nextflow.config +++ b/nextflow.config @@ -111,10 +111,10 @@ profiles { shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false - runOptions = '-u $(id -u):$(id -g)' + docker.runOptions = '-u $(id -u):$(id -g)' } arm { - docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { singularity.enabled = true From 6894bb1e2506bcc651be8f1e0876a25b4e47919e Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 19 Dec 2022 12:04:47 +0000 Subject: [PATCH 081/491] Template update for nf-core/tools version 2.7.2 --- modules.json | 4 ++-- .../nf-core/custom/dumpsoftwareversions/main.nf | 2 +- modules/nf-core/fastqc/main.nf | 8 ++------ modules/nf-core/multiqc/main.nf | 2 +- nextflow.config | 4 ++++ nextflow_schema.json | 14 -------------- 6 files changed, 10 insertions(+), 24 deletions(-) diff --git a/modules.json b/modules.json index b6944888..ec1c9d84 100644 --- a/modules.json +++ b/modules.json @@ -47,7 +47,7 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "fastqc": { @@ -77,7 +77,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "samtools/flagstat": { diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index c9d014b1..d3a1cc25 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,7 +2,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.15" + conda "bioconda::multiqc=1.13" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 67209f79..7df41546 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -2,7 +2,7 @@ process FASTQC { tag "$meta.id" label 'process_medium' - conda "bioconda::fastqc=0.12.1" + conda "bioconda::fastqc=0.11.9" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" @@ -29,11 +29,7 @@ process FASTQC { printf "%s %s\\n" $rename_to | while read old_name new_name; do [ -f "\${new_name}" ] || ln -s \$old_name \$new_name done - - fastqc \\ - $args \\ - --threads $task.cpus \\ - $renamed_files + fastqc $args --threads $task.cpus $renamed_files cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 40a691eb..4c84d257 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,7 +1,7 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.17" + conda "bioconda::multiqc=1.13" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" diff --git a/nextflow.config b/nextflow.config index 4d0b2496..651c52df 100644 --- a/nextflow.config +++ b/nextflow.config @@ -80,6 +80,10 @@ params { hook_url = null help = false version = false + validate_params = true + show_hidden_params = false + schema_ignore_params = 'genomes' + // Config options config_profile_name = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 8f5e22b5..562d309d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -512,20 +512,6 @@ "description": "Show all params when using `--help`", "hidden": true, "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." - }, - "validationFailUnrecognisedParams": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters fails when an unrecognised parameter is found.", - "hidden": true, - "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." - }, - "validationLenientMode": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters in lenient more.", - "hidden": true, - "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." } } } From e61dc7fcd9d57192e57bfc2de5f6e0ec61f212ec Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 28 Apr 2023 14:19:44 +0000 Subject: [PATCH 082/491] Template update for nf-core/tools version 2.8 --- .github/workflows/linting.yml | 2 +- README.md | 48 +++++++++++++------ bin/check_samplesheet.py | 26 +++++++--- conf/igenomes.config | 8 ++++ docs/usage.md | 23 +++------ modules.json | 4 +- .../custom/dumpsoftwareversions/main.nf | 6 +-- modules/nf-core/multiqc/main.nf | 6 +-- nextflow.config | 2 + 9 files changed, 78 insertions(+), 47 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index b8bdd214..888cb4bc 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -78,7 +78,7 @@ jobs: - uses: actions/setup-python@v4 with: - python-version: "3.11" + python-version: "3.8" architecture: "x64" - name: Install dependencies diff --git a/README.md b/README.md index 8d0053fb..ebb5401e 100644 --- a/README.md +++ b/README.md @@ -44,34 +44,52 @@ On release, automated continuous integration tests run the pipeline on a full-si - Differential expression analysis [`DESeq2`](https://bioconductor.org/packages/release/bioc/html/DESeq2.html) - Circular - Linear ratio tests ['CircTest'](https://github.com/dieterich-lab/CircTest) -## Quick Start +## Usage -1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`) +> **Note** +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how +> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) +> with `-profile test` before running the workflow on actual data. -2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_. + ```bash nextflow run nf-core/circrna --input samplesheet.csv --outdir --genome GRCh37 -profile --tool 'ciriquant' --module 'circrna_discovery,mirna_prediction,differential_expression' --bsj_reads 2 ``` -## Documentation +```bash +nextflow run nf-core/circrna \ + -profile \ + --input samplesheet.csv \ + --outdir +``` + +> **Warning:** +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those +> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; +> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). -The nf-core/circrna pipeline comes with documentation about the pipeline [usage](https://nf-co.re/circrna/usage), [parameters](https://nf-co.re/circrna/parameters) and [output](https://nf-co.re/circrna/output). +For more details, please refer to the [usage documentation](https://nf-co.re/circrna/usage) and the [parameter documentation](https://nf-co.re/circrna/parameters). + +## Pipeline output + +To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/circrna/results) tab on the nf-core website pipeline page. +For more details about the output files and reports, please refer to the +[output documentation](https://nf-co.re/circrna/output). ```bash nextflow run nf-core/circrna \ diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index 0a5041b0..2baec583 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -34,12 +34,26 @@ def make_dir(path): raise exception -def print_error(error, context="Line", context_str=""): - error_str = f"ERROR: Please check samplesheet -> {error}" - if context != "" and context_str != "": - error_str = f"ERROR: Please check samplesheet -> {error}\n{context.strip()}: '{context_str.strip()}'" - print(error_str) - sys.exit(1) +def sniff_format(handle): + """ + Detect the tabular format. + + Args: + handle (text file): A handle to a `text file`_ object. The read position is + expected to be at the beginning (index 0). + + Returns: + csv.Dialect: The detected tabular format. + + .. _text file: + https://docs.python.org/3/glossary.html#term-text-file + + """ + peek = read_head(handle) + handle.seek(0) + sniffer = csv.Sniffer() + dialect = sniffer.sniff(peek) + return dialect def check_samplesheet(file_in, file_out): diff --git a/conf/igenomes.config b/conf/igenomes.config index f597c35a..ec1a5c26 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -37,6 +37,14 @@ params { mito_name = "chrM" species_id = "hsa" } + 'CHM13' { + fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/" + bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/" + gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf" + gff = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz" + mito_name = "chrM" + } 'GRCm38' { fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" fasta_fai = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa.fai" diff --git a/docs/usage.md b/docs/usage.md index 9a9286db..27523ba3 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -310,28 +310,17 @@ Specify the path to a specific config file (this is a core Nextflow command). Se Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. -For example, if the nf-core/rnaseq pipeline is failing after multiple re-submissions of the `STAR_ALIGN` process due to an exit code of `137` this would indicate that there is an out of memory issue: +To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website. -```console -[62/149eb0] NOTE: Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) -- Execution is retried (1) -Error executing process > 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)' +### Custom Containers -Caused by: - Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) +In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date. -Command executed: - STAR \ - --genomeDir star \ - --readFilesIn WT_REP1_trimmed.fq.gz \ - --runThreadN 2 \ - --outFileNamePrefix WT_REP1. \ - +To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. -Command exit status: - 137 +### Custom Tool Arguments -Command output: - (empty) +A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default. Command error: .command.sh: line 9: 30 Killed STAR --genomeDir star --readFilesIn WT_REP1_trimmed.fq.gz --runThreadN 2 --outFileNamePrefix WT_REP1. diff --git a/modules.json b/modules.json index ec1c9d84..2c7eaa94 100644 --- a/modules.json +++ b/modules.json @@ -47,7 +47,7 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543", "installed_by": ["modules"] }, "fastqc": { @@ -77,7 +77,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7", "installed_by": ["modules"] }, "samtools/flagstat": { diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index d3a1cc25..800a6099 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.13" + conda "bioconda::multiqc=1.14" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : - 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 4c84d257..4b604749 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.13" + conda "bioconda::multiqc=1.14" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : - 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/nextflow.config b/nextflow.config index 651c52df..03dbdb8e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -152,6 +152,7 @@ profiles { } docker { docker.enabled = true + docker.registry = 'quay.io' docker.userEmulation = true conda.enabled = false singularity.enabled = false @@ -175,6 +176,7 @@ profiles { } podman { podman.enabled = true + podman.registry = 'quay.io' conda.enabled = false docker.enabled = false singularity.enabled = false From 611e48f6fa79e0aaa31dc47109e2101c29846ecc Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 30 Jun 2023 16:12:56 +0000 Subject: [PATCH 083/491] Template update for nf-core/tools version 2.9 --- .github/workflows/ci.yml | 2 +- README.md | 6 +++--- assets/multiqc_config.yml | 8 +++----- docs/usage.md | 4 +--- lib/WorkflowCircrna.groovy | 2 +- nextflow.config | 13 ++++--------- nextflow_schema.json | 30 +++++++++++++++++++++++++++--- workflows/circrna.nf | 3 +++ 8 files changed, 43 insertions(+), 25 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2eb40246..e86fca57 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -24,7 +24,7 @@ jobs: strategy: matrix: NXF_VER: - - "22.10.1" + - "23.04.0" - "latest-everything" steps: diff --git a/README.md b/README.md index ebb5401e..cccd27a6 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ [![GitHub Actions CI Status](https://github.com/nf-core/circrna/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/circrna/actions?query=workflow%3A%22nf-core+CI%22) [![GitHub Actions Linting Status](https://github.com/nf-core/circrna/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/circrna/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/circrna/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-22aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -83,11 +83,11 @@ nextflow run nf-core/circrna \ > provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; > see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). -For more details, please refer to the [usage documentation](https://nf-co.re/circrna/usage) and the [parameter documentation](https://nf-co.re/circrna/parameters). +For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/circrna/usage) and the [parameter documentation](https://nf-co.re/circrna/parameters). ## Pipeline output -To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/circrna/results) tab on the nf-core website pipeline page. +To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/circrna/results) tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/circrna/output). diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index e6c9ce18..82a8c2de 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,9 +1,7 @@ report_comment: > - This report has been generated by the nf-core/circrna analysis pipeline. For information about how to - interpret these results, please see the documentation. - + This report has been generated by the nf-core/circrna + analysis pipeline. For information about how to interpret these results, please see the + documentation. report_section_order: "nf-core-circrna-methods-description": order: -1000 diff --git a/docs/usage.md b/docs/usage.md index 27523ba3..311b83fb 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -29,9 +29,7 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. -:::warning -Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). -::: +> ⚠️ Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). The above pipeline run specified with a params file in yaml format: diff --git a/lib/WorkflowCircrna.groovy b/lib/WorkflowCircrna.groovy index eae29c19..e03279a4 100755 --- a/lib/WorkflowCircrna.groovy +++ b/lib/WorkflowCircrna.groovy @@ -53,7 +53,7 @@ class WorkflowCircrna { public static String toolCitationText(params) { - // TODO nf-core: Optionally add in-text citation tools to this list. + // TODO Optionally add in-text citation tools to this list. // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", // Uncomment function in methodsDescriptionText to render in MultiQC report def citation_text = [ diff --git a/nextflow.config b/nextflow.config index 03dbdb8e..04d94707 100644 --- a/nextflow.config +++ b/nextflow.config @@ -71,7 +71,7 @@ params { multiqc_methods_description = null // Boilerplate options - outdir = './results' + outdir = null publish_dir_mode = 'copy' email = null email_on_fail = null @@ -80,10 +80,6 @@ params { hook_url = null help = false version = false - validate_params = true - show_hidden_params = false - schema_ignore_params = 'genomes' - // Config options config_profile_name = null @@ -93,7 +89,6 @@ params { config_profile_contact = null config_profile_url = null - // Max resource options max_memory = '300.GB' max_cpus = 50 @@ -105,7 +100,9 @@ params { validationSchemaIgnoreParams = 'genomes,igenomes_base' validationShowHiddenParams = false validate_params = true - + withName: INTEGRATE_SCVI { + cpus: 60 + } } // Load base.config by default for all pipelines @@ -152,7 +149,6 @@ profiles { } docker { docker.enabled = true - docker.registry = 'quay.io' docker.userEmulation = true conda.enabled = false singularity.enabled = false @@ -176,7 +172,6 @@ profiles { } podman { podman.enabled = true - podman.registry = 'quay.io' conda.enabled = false docker.enabled = false singularity.enabled = false diff --git a/nextflow_schema.json b/nextflow_schema.json index 562d309d..5d16b61a 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -14,10 +14,13 @@ "properties": { "input": { "type": "string", - "fa_icon": "fas fa-file-csv", + "format": "file-path", + "exists": true, "mimetype": "text/csv", - "description": "A 'samplehseet' CSV file containing the absolute paths to FASTQ files.", - "help_text": "An example of a valid CSV sample sheet is provided below, depicting paired-end control samples and single-end treatment samples. The headers `sample`, `fastq_1` and `fastq_2` must be included in the input CSV file.\n\n| sample \t| fastq_1 \t| fastq_2 \t|\n|-----------\t|--------------------------\t|--------------------------\t|\n| control_1 \t| /data/ctrl_1_R1.fastq.gz \t| /data/ctrl_1_R2.fastq.gz \t|\n| control_2 \t| /data/ctrl_2_R1.fastq.gz \t| /data/ctrl_2_R2.fastq.gz \t|\n| control_3 \t| /data/ctrl_3_R1.fastq.gz \t| /data/ctrl_3_R2.fastq.gz \t|\n| treated_1 \t| /data/trt_1_R1.fastq.gz \t| \t|\n| treated_2 \t| /data/trt_2_R1.fastq.gz \t| \t|\n| treated_3 \t| /data/trt_3_R1.fastq.gz \t| \t|" + "pattern": "^\\S+\\.csv$", + "description": "Path to comma-separated file containing information about the samples in the experiment.", + "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/circrna/usage#samplesheet-input).", + "fa_icon": "fas fa-file-csv" }, "outdir": { "type": "string", @@ -417,12 +420,14 @@ "type": "boolean", "description": "Display help text.", "fa_icon": "fas fa-question-circle", + "default": false, "hidden": true }, "version": { "type": "boolean", "description": "Display version and exit.", "fa_icon": "fas fa-question-circle", + "default": false, "hidden": true }, "publish_dir_mode": { @@ -453,6 +458,7 @@ "type": "boolean", "description": "Send plain-text email instead of HTML.", "fa_icon": "fas fa-remove-format", + "default": false, "hidden": true }, "multiqc_title": { @@ -472,6 +478,7 @@ "type": "boolean", "description": "Do not use coloured log outputs.", "fa_icon": "fas fa-palette", + "default": false, "hidden": true }, "hook_url": { @@ -510,8 +517,25 @@ "type": "boolean", "fa_icon": "far fa-eye-slash", "description": "Show all params when using `--help`", + "default": false, "hidden": true, "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." + }, + "validationFailUnrecognisedParams": { + "type": "boolean", + "fa_icon": "far fa-check-circle", + "description": "Validation of parameters fails when an unrecognised parameter is found.", + "default": false, + "hidden": true, + "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." + }, + "validationLenientMode": { + "type": "boolean", + "fa_icon": "far fa-check-circle", + "description": "Validation of parameters in lenient more.", + "default": false, + "hidden": true, + "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." } } } diff --git a/workflows/circrna.nf b/workflows/circrna.nf index e84a6561..74a3e420 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -131,6 +131,9 @@ workflow CIRCRNA { } .set { ch_fastq } ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) + // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") + // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ + // ! There is currently no tooling to help you write a sample sheet schema // MODULE: // Concatenate FastQ files from same sample if required From 4a567c341bf167ae76c8ec8059f6a6ea9b11e2be Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 25 Sep 2023 15:16:33 +0000 Subject: [PATCH 084/491] Template update for nf-core/tools version 2.10 --- .github/workflows/linting.yml | 2 +- CITATIONS.md | 2 +- README.md | 18 ++++++++++-------- assets/multiqc_config.yml | 6 ++++-- docs/usage.md | 4 +++- lib/WorkflowCircrna.groovy | 2 +- modules.json | 4 ++-- .../custom/dumpsoftwareversions/main.nf | 2 +- modules/nf-core/fastqc/main.nf | 10 +++++++--- modules/nf-core/multiqc/main.nf | 2 +- nextflow_schema.json | 7 ------- 11 files changed, 31 insertions(+), 28 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 888cb4bc..b8bdd214 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -78,7 +78,7 @@ jobs: - uses: actions/setup-python@v4 with: - python-version: "3.8" + python-version: "3.11" architecture: "x64" - name: Install dependencies diff --git a/CITATIONS.md b/CITATIONS.md index 2ee62d2b..7b0c25be 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -44,7 +44,7 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. + > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [find circ](https://doi.org/10.1038/nature11928) diff --git a/README.md b/README.md index cccd27a6..ac935b13 100644 --- a/README.md +++ b/README.md @@ -46,10 +46,11 @@ On release, automated continuous integration tests run the pipeline on a full-si ## Usage -> **Note** -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how -> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) -> with `-profile test` before running the workflow on actual data. +:::note +If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how +to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) +with `-profile test` before running the workflow on actual data. +::: - ```bash - nextflow run nf-core/circrna --input samplesheet.csv --outdir --genome GRCh37 -profile --tool 'ciriquant' --module 'circrna_discovery,mirna_prediction,differential_expression' --bsj_reads 2 - ``` +```bash +nextflow run nf-core/circrna --input samplesheet.csv --outdir --genome GRCh37 -profile --tool 'ciriquant' --module 'circrna_discovery,mirna_prediction,differential_expression' --bsj_reads 2 +``` ```bash nextflow run nf-core/circrna \ diff --git a/docs/usage.md b/docs/usage.md index 27523ba3..2f9684a0 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -323,12 +323,13 @@ To use a different container from the default container or conda environment spe A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default. Command error: - .command.sh: line 9: 30 Killed STAR --genomeDir star --readFilesIn WT_REP1_trimmed.fq.gz --runThreadN 2 --outFileNamePrefix WT_REP1. +.command.sh: line 9: 30 Killed STAR --genomeDir star --readFilesIn WT_REP1_trimmed.fq.gz --runThreadN 2 --outFileNamePrefix WT_REP1. Work dir: - /home/pipelinetest/work/9d/172ca5881234073e8d76f2a19c88fb +/home/pipelinetest/work/9d/172ca5881234073e8d76f2a19c88fb Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` -``` + +```` To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website. @@ -352,7 +353,7 @@ process { memory = 100.GB } } -``` +```` > **NB:** We specify the full process name i.e. `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN` in the config file because this takes priority over the short name (`STAR_ALIGN`) and allows existing configuration using the full process name to be correctly overridden. > From 57bb1395d0ca1bdb70ac5001e515c48e0d08cf1f Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 13 Jan 2024 11:38:03 +0100 Subject: [PATCH 088/491] Increase minimum nextflow version --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 7fb0bd97..b3699c50 100644 --- a/nextflow.config +++ b/nextflow.config @@ -280,7 +280,7 @@ manifest { homePage = 'https://github.com/nf-core/circrna' description = """Quantification, miRNA target prediction and differential expression analysis of circular RNAs""" mainScript = 'main.nf' - nextflowVersion = '!>=22.10.1' + nextflowVersion = '!>=23.04.0' version = 'dev' doi = '' } From ca64cd71c5b8b6a219e6a8a6fc3bfb1c04d12465 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 13 Jan 2024 11:42:56 +0100 Subject: [PATCH 089/491] Update nf-core modules --- modules.json | 83 +- .../bedtools/intersect/environment.yml | 3 +- modules/nf-core/bedtools/intersect/main.nf | 4 +- modules/nf-core/bedtools/sort/environment.yml | 3 +- modules/nf-core/bedtools/sort/main.nf | 4 +- modules/nf-core/bowtie/align/environment.yml | 7 + modules/nf-core/bowtie/align/main.nf | 4 +- modules/nf-core/bowtie/build/environment.yml | 7 + modules/nf-core/bowtie/build/main.nf | 2 +- modules/nf-core/bowtie2/align/environment.yml | 9 + modules/nf-core/bowtie2/align/main.nf | 17 +- .../bowtie2/align/tests/large_index.config | 5 + .../nf-core/bowtie2/align/tests/main.nf.test | 561 +++++++++++++ .../bowtie2/align/tests/main.nf.test.snap | 263 ++++++ .../nf-core/bowtie2/align/tests/sam.config | 5 + .../nf-core/bowtie2/align/tests/sam2.config | 5 + modules/nf-core/bowtie2/align/tests/tags.yml | 2 + modules/nf-core/bowtie2/build/environment.yml | 7 + modules/nf-core/bowtie2/build/main.nf | 6 +- .../nf-core/bowtie2/build/tests/main.nf.test | 31 + .../bowtie2/build/tests/main.nf.test.snap | 45 + modules/nf-core/bowtie2/build/tests/tags.yml | 2 + modules/nf-core/bwa/index/environment.yml | 7 + modules/nf-core/bwa/index/main.nf | 2 +- modules/nf-core/cat/cat/environment.yml | 1 + modules/nf-core/cat/cat/main.nf | 12 +- modules/nf-core/cat/cat/tests/main.nf.test | 26 + modules/nf-core/cat/fastq/environment.yml | 7 + modules/nf-core/cat/fastq/main.nf | 2 +- .../nf-core/cat/fastq/tests/main.nf.test.snap | 24 +- .../circexplorer2/annotate/environment.yml | 7 + .../nf-core/circexplorer2/annotate/main.nf | 2 +- .../circexplorer2/parse/environment.yml | 7 + modules/nf-core/circexplorer2/parse/main.nf | 2 +- .../dumpsoftwareversions/environment.yml | 2 +- .../custom/dumpsoftwareversions/main.nf | 4 +- .../dumpsoftwareversions/tests/main.nf.test | 7 +- .../tests/main.nf.test.snap | 50 +- modules/nf-core/fastqc/tests/main.nf.test | 271 ++++-- .../nf-core/fastqc/tests/main.nf.test.snap | 12 +- modules/nf-core/hisat2/align/environment.yml | 8 + modules/nf-core/hisat2/align/main.nf | 2 +- modules/nf-core/hisat2/build/environment.yml | 7 + modules/nf-core/hisat2/build/main.nf | 2 +- .../hisat2/extractsplicesites/environment.yml | 7 + .../nf-core/hisat2/extractsplicesites/main.nf | 2 +- modules/nf-core/miranda/environment.yml | 7 + modules/nf-core/miranda/main.nf | 2 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 6 +- modules/nf-core/multiqc/meta.yml | 1 - modules/nf-core/multiqc/tests/main.nf.test | 48 +- .../nf-core/multiqc/tests/main.nf.test.snap | 21 + .../nf-core/samtools/flagstat/environment.yml | 7 + modules/nf-core/samtools/flagstat/main.nf | 6 +- .../samtools/flagstat/tests/main.nf.test | 36 + .../samtools/flagstat/tests/main.nf.test.snap | 16 + .../nf-core/samtools/flagstat/tests/tags.yml | 2 + .../nf-core/samtools/idxstats/environment.yml | 7 + modules/nf-core/samtools/idxstats/main.nf | 6 +- .../samtools/idxstats/tests/main.nf.test | 36 + .../samtools/idxstats/tests/main.nf.test.snap | 16 + .../nf-core/samtools/idxstats/tests/tags.yml | 2 + .../nf-core/samtools/index/environment.yml | 7 + modules/nf-core/samtools/index/main.nf | 6 +- .../samtools/index/tests/csi.nextflow.config | 7 + .../nf-core/samtools/index/tests/main.nf.test | 87 ++ .../samtools/index/tests/main.nf.test.snap | 28 + modules/nf-core/samtools/index/tests/tags.yml | 2 + modules/nf-core/samtools/sort/environment.yml | 7 + modules/nf-core/samtools/sort/main.nf | 6 +- .../nf-core/samtools/sort/tests/main.nf.test | 5 +- .../samtools/sort/tests/main.nf.test.snap | 19 +- .../nf-core/samtools/stats/environment.yml | 7 + modules/nf-core/samtools/stats/main.nf | 6 +- .../nf-core/samtools/stats/tests/main.nf.test | 2 +- .../samtools/stats/tests/main.nf.test.snap | 20 +- modules/nf-core/samtools/view/environment.yml | 7 + modules/nf-core/samtools/view/main.nf | 19 +- .../nf-core/samtools/view/tests/bam.config | 3 + .../samtools/view/tests/bam_index.config | 3 + .../nf-core/samtools/view/tests/main.nf.test | 231 ++++++ .../samtools/view/tests/main.nf.test.snap | 140 ++++ modules/nf-core/samtools/view/tests/tags.yml | 2 + .../nf-core/segemehl/align/environment.yml | 7 + modules/nf-core/segemehl/align/main.nf | 2 +- .../nf-core/segemehl/index/environment.yml | 7 + modules/nf-core/segemehl/index/main.nf | 2 +- modules/nf-core/star/align/environment.yml | 9 + modules/nf-core/star/align/main.nf | 6 +- modules/nf-core/star/align/tests/main.nf.test | 339 ++++++++ .../star/align/tests/main.nf.test.snap | 769 ++++++++++++++++++ .../star/align/tests/nextflow.arriba.config | 14 + .../nf-core/star/align/tests/nextflow.config | 14 + .../align/tests/nextflow.starfusion.config | 14 + modules/nf-core/star/align/tests/tags.yml | 2 + .../star/genomegenerate/environment.yml | 11 + modules/nf-core/star/genomegenerate/main.nf | 89 +- .../star/genomegenerate/tests/main.nf.test | 117 +++ .../genomegenerate/tests/main.nf.test.snap | 22 + .../star/genomegenerate/tests/tags.yml | 2 + .../stringtie/stringtie/environment.yml | 7 + modules/nf-core/stringtie/stringtie/main.nf | 2 +- .../stringtie/stringtie/tests/main.nf.test | 108 +++ .../stringtie/tests/main.nf.test.snap | 186 +++++ .../stringtie/stringtie/tests/tags.yml | 2 + modules/nf-core/trimgalore/environment.yml | 7 + modules/nf-core/trimgalore/main.nf | 2 +- .../tests/main.nf.test | 14 +- .../tests/main.nf.test.snap | 302 ++----- .../bam_sort_stats_samtools/tests/tags.yml | 2 +- 111 files changed, 3940 insertions(+), 501 deletions(-) create mode 100644 modules/nf-core/bowtie/align/environment.yml create mode 100644 modules/nf-core/bowtie/build/environment.yml create mode 100644 modules/nf-core/bowtie2/align/environment.yml create mode 100644 modules/nf-core/bowtie2/align/tests/large_index.config create mode 100644 modules/nf-core/bowtie2/align/tests/main.nf.test create mode 100644 modules/nf-core/bowtie2/align/tests/main.nf.test.snap create mode 100644 modules/nf-core/bowtie2/align/tests/sam.config create mode 100644 modules/nf-core/bowtie2/align/tests/sam2.config create mode 100644 modules/nf-core/bowtie2/align/tests/tags.yml create mode 100644 modules/nf-core/bowtie2/build/environment.yml create mode 100644 modules/nf-core/bowtie2/build/tests/main.nf.test create mode 100644 modules/nf-core/bowtie2/build/tests/main.nf.test.snap create mode 100644 modules/nf-core/bowtie2/build/tests/tags.yml create mode 100644 modules/nf-core/bwa/index/environment.yml create mode 100644 modules/nf-core/cat/fastq/environment.yml create mode 100644 modules/nf-core/circexplorer2/annotate/environment.yml create mode 100644 modules/nf-core/circexplorer2/parse/environment.yml create mode 100644 modules/nf-core/hisat2/align/environment.yml create mode 100644 modules/nf-core/hisat2/build/environment.yml create mode 100644 modules/nf-core/hisat2/extractsplicesites/environment.yml create mode 100644 modules/nf-core/miranda/environment.yml create mode 100644 modules/nf-core/multiqc/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/flagstat/environment.yml create mode 100644 modules/nf-core/samtools/flagstat/tests/main.nf.test create mode 100644 modules/nf-core/samtools/flagstat/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/flagstat/tests/tags.yml create mode 100644 modules/nf-core/samtools/idxstats/environment.yml create mode 100644 modules/nf-core/samtools/idxstats/tests/main.nf.test create mode 100644 modules/nf-core/samtools/idxstats/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/idxstats/tests/tags.yml create mode 100644 modules/nf-core/samtools/index/environment.yml create mode 100644 modules/nf-core/samtools/index/tests/csi.nextflow.config create mode 100644 modules/nf-core/samtools/index/tests/main.nf.test create mode 100644 modules/nf-core/samtools/index/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/index/tests/tags.yml create mode 100644 modules/nf-core/samtools/sort/environment.yml create mode 100644 modules/nf-core/samtools/stats/environment.yml create mode 100644 modules/nf-core/samtools/view/environment.yml create mode 100644 modules/nf-core/samtools/view/tests/bam.config create mode 100644 modules/nf-core/samtools/view/tests/bam_index.config create mode 100644 modules/nf-core/samtools/view/tests/main.nf.test create mode 100644 modules/nf-core/samtools/view/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/view/tests/tags.yml create mode 100644 modules/nf-core/segemehl/align/environment.yml create mode 100644 modules/nf-core/segemehl/index/environment.yml create mode 100644 modules/nf-core/star/align/environment.yml create mode 100644 modules/nf-core/star/align/tests/main.nf.test create mode 100644 modules/nf-core/star/align/tests/main.nf.test.snap create mode 100644 modules/nf-core/star/align/tests/nextflow.arriba.config create mode 100644 modules/nf-core/star/align/tests/nextflow.config create mode 100644 modules/nf-core/star/align/tests/nextflow.starfusion.config create mode 100644 modules/nf-core/star/align/tests/tags.yml create mode 100644 modules/nf-core/star/genomegenerate/environment.yml create mode 100644 modules/nf-core/star/genomegenerate/tests/main.nf.test create mode 100644 modules/nf-core/star/genomegenerate/tests/main.nf.test.snap create mode 100644 modules/nf-core/star/genomegenerate/tests/tags.yml create mode 100644 modules/nf-core/stringtie/stringtie/environment.yml create mode 100644 modules/nf-core/stringtie/stringtie/tests/main.nf.test create mode 100644 modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap create mode 100644 modules/nf-core/stringtie/stringtie/tests/tags.yml create mode 100644 modules/nf-core/trimgalore/environment.yml diff --git a/modules.json b/modules.json index 2a84205f..57acc918 100644 --- a/modules.json +++ b/modules.json @@ -5,139 +5,164 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { + "bedtools/intersect": { + "branch": "master", + "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", + "installed_by": ["modules"] + }, + "bedtools/sort": { + "branch": "master", + "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", + "installed_by": ["modules"] + }, "bowtie/align": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde", "installed_by": ["modules"] }, "bowtie/build": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "bowtie2/align": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde", "installed_by": ["modules"] }, "bowtie2/build": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "1fea64f5132a813ec97c1c6d3a74e0aee7142b6d", "installed_by": ["modules"] }, "bwa/index": { "branch": "master", - "git_sha": "28a23ea6529caff44855c774f439a4074883027c", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": ["modules"] + }, + "cat/cat": { + "branch": "master", + "git_sha": "d593e8f6b7d1bbbb2acf43a4b9efeeac8d6720f2", "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", - "git_sha": "363a40e3af1f2dec0545379f4ede49c1fac089f1", + "git_sha": "e8940f18cfbbdcdcde38f4b3633df5ed4e48da10", "installed_by": ["modules"] }, "circexplorer2/annotate": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "circexplorer2/parse": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": ["modules"] + }, + "csvtk/split": { + "branch": "master", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e", + "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "617777a807a1770f73deb38c80004bac06807eef", + "installed_by": ["modules"] + }, + "gawk": { + "branch": "master", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "hisat2/align": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "hisat2/build": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "hisat2/extractsplicesites": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "miranda": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "4ab13872435962dadc239979554d13709e20bf29", + "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", "installed_by": ["modules"] }, "samtools/flagstat": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["bam_stats_samtools"] }, "samtools/idxstats": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["bam_sort_stats_samtools", "modules"] }, "samtools/sort": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["bam_sort_stats_samtools", "modules"] }, "samtools/stats": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["bam_stats_samtools"] }, "samtools/view": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["modules"] }, "segemehl/align": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "segemehl/index": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "star/align": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["modules"] }, "star/genomegenerate": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "d87a6e2156c2099c09280fa70776eaf0a824817a", "installed_by": ["modules"] }, "stringtie/stringtie": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "b0dcb44b018d9b2bcb35b1abb7bcd34061bc5a6d", "installed_by": ["modules"] }, "trimgalore": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] } } @@ -146,12 +171,12 @@ "nf-core": { "bam_sort_stats_samtools": { "branch": "master", - "git_sha": "7c8eeb2b37a6c6d3ffba0aef55ff60c8718c0ba6", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["subworkflows"] }, "bam_stats_samtools": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["bam_sort_stats_samtools"] } } diff --git a/modules/nf-core/bedtools/intersect/environment.yml b/modules/nf-core/bedtools/intersect/environment.yml index 55ce727a..2a343050 100644 --- a/modules/nf-core/bedtools/intersect/environment.yml +++ b/modules/nf-core/bedtools/intersect/environment.yml @@ -1,6 +1,7 @@ +name: bedtools_intersect channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::bedtools=2.30.0 + - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/intersect/main.nf b/modules/nf-core/bedtools/intersect/main.nf index 177fb5d5..d9e79e7f 100644 --- a/modules/nf-core/bedtools/intersect/main.nf +++ b/modules/nf-core/bedtools/intersect/main.nf @@ -4,8 +4,8 @@ process BEDTOOLS_INTERSECT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - 'biocontainers/bedtools:2.30.0--hc088bd4_0' }" + 'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_0' : + 'biocontainers/bedtools:2.31.1--hf5e1c6e_0' }" input: tuple val(meta), path(intervals1), path(intervals2) diff --git a/modules/nf-core/bedtools/sort/environment.yml b/modules/nf-core/bedtools/sort/environment.yml index ee820940..87b2e425 100644 --- a/modules/nf-core/bedtools/sort/environment.yml +++ b/modules/nf-core/bedtools/sort/environment.yml @@ -1,6 +1,7 @@ +name: bedtools_sort channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::bedtools=2.31.0 + - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/sort/main.nf b/modules/nf-core/bedtools/sort/main.nf index 5b748903..b833150a 100644 --- a/modules/nf-core/bedtools/sort/main.nf +++ b/modules/nf-core/bedtools/sort/main.nf @@ -4,8 +4,8 @@ process BEDTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bedtools:2.31.0--hf5e1c6e_2' : - 'biocontainers/bedtools:2.31.0--hf5e1c6e_2' }" + 'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_0' : + 'biocontainers/bedtools:2.31.1--hf5e1c6e_0' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/bowtie/align/environment.yml b/modules/nf-core/bowtie/align/environment.yml new file mode 100644 index 00000000..2617e6f0 --- /dev/null +++ b/modules/nf-core/bowtie/align/environment.yml @@ -0,0 +1,7 @@ +name: bowtie_align +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bowtie=1.3.0 diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index 082c0762..29e9cd53 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -2,7 +2,7 @@ process BOWTIE_ALIGN { tag "$meta.id" label 'process_high' - conda "bioconda::bowtie=1.3.0 bioconda::samtools=1.16.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:c84c7c55c45af231883d9ff4fe706ac44c479c36-0' : 'biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:c84c7c55c45af231883d9ff4fe706ac44c479c36-0' }" @@ -36,7 +36,7 @@ process BOWTIE_ALIGN { $unaligned \\ $args \\ $endedness \\ - 2> ${prefix}.out \\ + 2> >(tee ${prefix}.out >&2) \\ | samtools view $args2 -@ $task.cpus -bS -o ${prefix}.bam - if [ -f ${prefix}.unmapped.fastq ]; then diff --git a/modules/nf-core/bowtie/build/environment.yml b/modules/nf-core/bowtie/build/environment.yml new file mode 100644 index 00000000..0907b0f8 --- /dev/null +++ b/modules/nf-core/bowtie/build/environment.yml @@ -0,0 +1,7 @@ +name: bowtie_build +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bowtie=1.3.0 diff --git a/modules/nf-core/bowtie/build/main.nf b/modules/nf-core/bowtie/build/main.nf index 6de02e6e..05e22fe8 100644 --- a/modules/nf-core/bowtie/build/main.nf +++ b/modules/nf-core/bowtie/build/main.nf @@ -2,7 +2,7 @@ process BOWTIE_BUILD { tag "$fasta" label 'process_high' - conda "bioconda::bowtie=1.3.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1' : 'biocontainers/bowtie:1.3.0--py38hed8969a_1' }" diff --git a/modules/nf-core/bowtie2/align/environment.yml b/modules/nf-core/bowtie2/align/environment.yml new file mode 100644 index 00000000..d2796359 --- /dev/null +++ b/modules/nf-core/bowtie2/align/environment.yml @@ -0,0 +1,9 @@ +name: bowtie2_align +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bowtie2=2.5.2 + - bioconda::samtools=1.18 + - conda-forge::pigz=2.6 diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf index a77114d2..8c405ee3 100644 --- a/modules/nf-core/bowtie2/align/main.nf +++ b/modules/nf-core/bowtie2/align/main.nf @@ -2,10 +2,10 @@ process BOWTIE2_ALIGN { tag "$meta.id" label "process_high" - conda "bioconda::bowtie2=2.4.4 bioconda::samtools=1.16.1 conda-forge::pigz=2.6" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' : - 'biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:f70b31a2db15c023d641c32f433fb02cd04df5a6-0' : + 'biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:f70b31a2db15c023d641c32f433fb02cd04df5a6-0' }" input: tuple val(meta) , path(reads) @@ -52,7 +52,7 @@ process BOWTIE2_ALIGN { --threads $task.cpus \\ $unaligned \\ $args \\ - 2> ${prefix}.bowtie2.log \\ + 2> >(tee ${prefix}.bowtie2.log >&2) \\ | samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.${extension} - if [ -f ${prefix}.unmapped.fastq.1.gz ]; then @@ -76,12 +76,17 @@ process BOWTIE2_ALIGN { def prefix = task.ext.prefix ?: "${meta.id}" def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/ def extension = (args2 ==~ extension_pattern) ? (args2 =~ extension_pattern)[0][2].toLowerCase() : "bam" + def create_unmapped = "" + if (meta.single_end) { + create_unmapped = save_unaligned ? "touch ${prefix}.unmapped.fastq.gz" : "" + } else { + create_unmapped = save_unaligned ? "touch ${prefix}.unmapped_1.fastq.gz && touch ${prefix}.unmapped_2.fastq.gz" : "" + } """ touch ${prefix}.${extension} touch ${prefix}.bowtie2.log - touch ${prefix}.unmapped_1.fastq.gz - touch ${prefix}.unmapped_2.fastq.gz + ${create_unmapped} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bowtie2/align/tests/large_index.config b/modules/nf-core/bowtie2/align/tests/large_index.config new file mode 100644 index 00000000..fdc1c59d --- /dev/null +++ b/modules/nf-core/bowtie2/align/tests/large_index.config @@ -0,0 +1,5 @@ +process { + withName: BOWTIE2_BUILD { + ext.args = '--large-index' + } +} \ No newline at end of file diff --git a/modules/nf-core/bowtie2/align/tests/main.nf.test b/modules/nf-core/bowtie2/align/tests/main.nf.test new file mode 100644 index 00000000..a478d17b --- /dev/null +++ b/modules/nf-core/bowtie2/align/tests/main.nf.test @@ -0,0 +1,561 @@ +nextflow_process { + + name "Test Process BOWTIE2_ALIGN" + script "../main.nf" + process "BOWTIE2_ALIGN" + tag "modules" + tag "modules_nfcore" + tag "bowtie2" + tag "bowtie2/align" + + test("sarscov2 - fastq, index, false, false - bam") { + + setup { + run("BOWTIE2_BUILD") { + script "../../build/main.nf" + process { + """ + input[0] = [ + [ id:'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + input[1] = BOWTIE2_BUILD.out.index + input[2] = false //save_unaligned + input[3] = false //sort + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.aligned[0][1]).name, + process.out.log, + process.out.fastq, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - fastq, index, false, false - sam") { + + config "./sam.config" + setup { + run("BOWTIE2_BUILD") { + script "../../build/main.nf" + process { + """ + input[0] = [ + [ id:'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + input[1] = BOWTIE2_BUILD.out.index + input[2] = false //save_unaligned + input[3] = false //sort + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.aligned[0][1]).readLines()[0..4], + process.out.log, + process.out.fastq, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - fastq, index, false, false - sam2") { + + config "./sam2.config" + setup { + run("BOWTIE2_BUILD") { + script "../../build/main.nf" + process { + """ + input[0] = [ + [ id:'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + input[1] = BOWTIE2_BUILD.out.index + input[2] = false //save_unaligned + input[3] = false //sort + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.aligned[0][1]).readLines()[0..4], + process.out.log, + process.out.fastq, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - fastq, index, false, true - bam") { + + setup { + run("BOWTIE2_BUILD") { + script "../../build/main.nf" + process { + """ + input[0] = [ + [ id:'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + input[1] = BOWTIE2_BUILD.out.index + input[2] = false //save_unaligned + input[3] = true //sort + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.aligned[0][1]).name, + process.out.log, + process.out.fastq, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - [fastq1, fastq2], index, false, false - bam") { + + setup { + run("BOWTIE2_BUILD") { + script "../../build/main.nf" + process { + """ + input[0] = [ + [ id:'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + input[1] = BOWTIE2_BUILD.out.index + input[2] = false //save_unaligned + input[3] = false //sort + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.aligned[0][1]).name, + process.out.log, + process.out.fastq, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - [fastq1, fastq2], index, false, true - bam") { + + setup { + run("BOWTIE2_BUILD") { + script "../../build/main.nf" + process { + """ + input[0] = [ + [ id:'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + input[1] = BOWTIE2_BUILD.out.index + input[2] = false //save_unaligned + input[3] = true //sort + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.aligned[0][1]).name, + process.out.log, + process.out.fastq, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - fastq, large_index, false, false - bam") { + + config "./large_index.config" + setup { + run("BOWTIE2_BUILD") { + script "../../build/main.nf" + process { + """ + input[0] = [ + [ id:'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + input[1] = BOWTIE2_BUILD.out.index + input[2] = false //save_unaligned + input[3] = false //sort + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.aligned[0][1]).name, + process.out.log, + process.out.fastq, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - [fastq1, fastq2], large_index, false, false - bam") { + + config "./large_index.config" + setup { + run("BOWTIE2_BUILD") { + script "../../build/main.nf" + process { + """ + input[0] = [ + [ id:'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + input[1] = BOWTIE2_BUILD.out.index + input[2] = false //save_unaligned + input[3] = false //sort + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.aligned[0][1]).name, + process.out.log, + process.out.fastq, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - [fastq1, fastq2], index, true, false - bam") { + + setup { + run("BOWTIE2_BUILD") { + script "../../build/main.nf" + process { + """ + input[0] = [ + [ id:'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + input[1] = BOWTIE2_BUILD.out.index + input[2] = true //save_unaligned + input[3] = false //sort + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.aligned[0][1]).name, + process.out.log, + process.out.fastq, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - fastq, index, true, false - bam") { + + setup { + run("BOWTIE2_BUILD") { + script "../../build/main.nf" + process { + """ + input[0] = [ + [ id:'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + input[1] = BOWTIE2_BUILD.out.index + input[2] = true //save_unaligned + input[3] = false //sort + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.aligned[0][1]).name, + process.out.log, + process.out.fastq, + process.out.versions + ).match() } + + ) + } + + } + + test("sarscov2 - [fastq1, fastq2], index, false, false - stub") { + + options "-stub" + setup { + run("BOWTIE2_BUILD") { + script "../../build/main.nf" + process { + """ + input[0] = [ + [ id:'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + input[1] = BOWTIE2_BUILD.out.index + input[2] = false //save_unaligned + input[3] = false //sort + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.aligned[0][1]).name, + file(process.out.log[0][1]).name, + process.out.fastq, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - fastq, index, true, false - stub") { + + options "-stub" + setup { + run("BOWTIE2_BUILD") { + script "../../build/main.nf" + process { + """ + input[0] = [ + [ id:'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + input[1] = BOWTIE2_BUILD.out.index + input[2] = true //save_unaligned + input[3] = false //sort + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.aligned[0][1]).name, + file(process.out.log[0][1]).name, + file(process.out.fastq[0][1]).name, + process.out.versions + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/bowtie2/align/tests/main.nf.test.snap b/modules/nf-core/bowtie2/align/tests/main.nf.test.snap new file mode 100644 index 00000000..883dc7ec --- /dev/null +++ b/modules/nf-core/bowtie2/align/tests/main.nf.test.snap @@ -0,0 +1,263 @@ +{ + "sarscov2 - fastq, index, false, false - sam2": { + "content": [ + [ + "ERR5069949.2151832\t16\tMT192765.1\t17453\t42\t150M\t*\t0\t0\tACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGA\tAAAA\\n#nf-core-versions tbody:nth-child(even) {\\n background-color: #f2f2f2;\\n\\", + " }\\n\\n\\n \\n \\n \\n \\n \\n \\n \\n\\", + " \\n\\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n \\n \\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n\\n\\n \\n\\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\" + ], + [ + "CUSTOM_DUMPSOFTWAREVERSIONS:", + " python: 3.11.7", + " yaml: 5.4.1", + "TOOL1:", + " tool1: 0.11.9", + "TOOL2:", + " tool2: '1.9'", + "Workflow:" + ] ], - "timestamp": "2023-10-11T17:10:02.930699" + "timestamp": "2024-01-09T23:01:18.710682" } -} +} \ No newline at end of file diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index b9e8f926..ad9bc54f 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -3,23 +3,21 @@ nextflow_process { name "Test Process FASTQC" script "../main.nf" process "FASTQC" + tag "modules" tag "modules_nfcore" tag "fastqc" - test("Single-Read") { + test("sarscov2 single-end [fastq]") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = [ - [ id: 'test', single_end:true ], - [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ] + [ id: 'test', single_end:true ], + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] ] """ } @@ -28,82 +26,195 @@ nextflow_process { then { assertAll ( { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. // looks like this:
    Mon 2 Oct 2023
    test.gz
    // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - { assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" }, - { assert path(process.out.html.get(0).get(1)).getText().contains("") }, - { assert snapshot(process.out.versions).match("versions") }, - { assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" } + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 paired-end [fastq]") { + + when { + process { + """ + input[0] = [ + [id: 'test', single_end: false], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("") }, + { assert path(process.out.html[0][1][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 interleaved [fastq]") { + + when { + process { + """ + input[0] = [ + [id: 'test', single_end: false], // meta map + file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 paired-end [bam]") { + + when { + process { + """ + input[0] = [ + [id: 'test', single_end: false], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } ) } } -// TODO -// // -// // Test with paired-end data -// // -// workflow test_fastqc_paired_end { -// input = [ -// [id: 'test', single_end: false], // meta map -// [ -// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), -// file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) -// ] -// ] - -// FASTQC ( input ) -// } - -// // -// // Test with interleaved data -// // -// workflow test_fastqc_interleaved { -// input = [ -// [id: 'test', single_end: false], // meta map -// file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) -// ] - -// FASTQC ( input ) -// } - -// // -// // Test with bam data -// // -// workflow test_fastqc_bam { -// input = [ -// [id: 'test', single_end: false], // meta map -// file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) -// ] - -// FASTQC ( input ) -// } - -// // -// // Test with multiple samples -// // -// workflow test_fastqc_multiple { -// input = [ -// [id: 'test', single_end: false], // meta map -// [ -// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), -// file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), -// file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true), -// file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) -// ] -// ] - -// FASTQC ( input ) -// } - -// // -// // Test with custom prefix -// // -// workflow test_fastqc_custom_prefix { -// input = [ -// [ id:'mysample', single_end:true ], // meta map -// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) -// ] - -// FASTQC ( input ) -// } + + test("sarscov2 multiple [fastq]") { + + when { + process { + """ + input[0] = [ + [id: 'test', single_end: false], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, + { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, + { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("") }, + { assert path(process.out.html[0][1][1]).text.contains("") }, + { assert path(process.out.html[0][1][2]).text.contains("") }, + { assert path(process.out.html[0][1][3]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 custom_prefix") { + + when { + process { + """ + input[0] = [ + [ id:'mysample', single_end:true ], // meta map + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 single-end [fastq] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id: 'test', single_end:true ], + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.html.collect { file(it[1]).getName() } + + process.out.zip.collect { file(it[1]).getName() } + + process.out.versions ).match() } + ) + } + } + } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 636a32ce..5ef5afbd 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,10 +1,20 @@ { + "sarscov2 single-end [fastq] - stub": { + "content": [ + [ + "test.html", + "test.zip", + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "timestamp": "2023-12-29T02:48:05.126117287" + }, "versions": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], - "timestamp": "2023-10-09T23:40:54+0000" + "timestamp": "2023-12-29T02:46:49.507942667" } } \ No newline at end of file diff --git a/modules/nf-core/hisat2/align/environment.yml b/modules/nf-core/hisat2/align/environment.yml new file mode 100644 index 00000000..0c1415f9 --- /dev/null +++ b/modules/nf-core/hisat2/align/environment.yml @@ -0,0 +1,8 @@ +name: hisat2_align +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::hisat2=2.2.1 + - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf index db8e8bb6..2289a9fc 100644 --- a/modules/nf-core/hisat2/align/main.nf +++ b/modules/nf-core/hisat2/align/main.nf @@ -3,7 +3,7 @@ process HISAT2_ALIGN { label 'process_high' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda "bioconda::hisat2=2.2.1 bioconda::samtools=1.16.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2cdf6bf1e92acbeb9b2834b1c58754167173a410-0' : 'biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2cdf6bf1e92acbeb9b2834b1c58754167173a410-0' }" diff --git a/modules/nf-core/hisat2/build/environment.yml b/modules/nf-core/hisat2/build/environment.yml new file mode 100644 index 00000000..2e67cd3e --- /dev/null +++ b/modules/nf-core/hisat2/build/environment.yml @@ -0,0 +1,7 @@ +name: hisat2_build +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::hisat2=2.2.1 diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf index 90f8efcc..766e8731 100644 --- a/modules/nf-core/hisat2/build/main.nf +++ b/modules/nf-core/hisat2/build/main.nf @@ -4,7 +4,7 @@ process HISAT2_BUILD { label 'process_high_memory' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda "bioconda::hisat2=2.2.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' : 'biocontainers/hisat2:2.2.1--h1b792b2_3' }" diff --git a/modules/nf-core/hisat2/extractsplicesites/environment.yml b/modules/nf-core/hisat2/extractsplicesites/environment.yml new file mode 100644 index 00000000..4b03e5e4 --- /dev/null +++ b/modules/nf-core/hisat2/extractsplicesites/environment.yml @@ -0,0 +1,7 @@ +name: hisat2_extractsplicesites +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::hisat2=2.2.1 diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf index a6e59e20..b0c8513a 100644 --- a/modules/nf-core/hisat2/extractsplicesites/main.nf +++ b/modules/nf-core/hisat2/extractsplicesites/main.nf @@ -3,7 +3,7 @@ process HISAT2_EXTRACTSPLICESITES { label 'process_medium' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - conda "bioconda::hisat2=2.2.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' : 'biocontainers/hisat2:2.2.1--h1b792b2_3' }" diff --git a/modules/nf-core/miranda/environment.yml b/modules/nf-core/miranda/environment.yml new file mode 100644 index 00000000..a04ca7f8 --- /dev/null +++ b/modules/nf-core/miranda/environment.yml @@ -0,0 +1,7 @@ +name: miranda +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::miranda=3.3a diff --git a/modules/nf-core/miranda/main.nf b/modules/nf-core/miranda/main.nf index eb7f6e76..47a98253 100644 --- a/modules/nf-core/miranda/main.nf +++ b/modules/nf-core/miranda/main.nf @@ -2,7 +2,7 @@ process MIRANDA { tag "$meta.id" label 'process_medium' - conda "bioconda::miranda=3.3a" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/miranda:3.3a--h779adbc_3': 'biocontainers/miranda:3.3a--h779adbc_3' }" diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index bc0bdb5b..7625b752 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.18 + - bioconda::multiqc=1.19 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 00cc48d2..1b9f7c43 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.18--pyhdfd78af_0' : - 'biocontainers/multiqc:1.18--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : + 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" @@ -43,7 +43,7 @@ process MULTIQC { stub: """ - touch multiqc_data + mkdir multiqc_data touch multiqc_plots touch multiqc_report.html diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index f1aa660e..45a9bc35 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: multiqc description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index c2dad217..d0438eda 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -7,12 +7,9 @@ nextflow_process { tag "modules_nfcore" tag "multiqc" - test("MULTIQC: FASTQC") { + test("sarscov2 single-end [fastqc]") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) @@ -26,20 +23,17 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.report.get(0)).exists() }, - { assert path(process.out.data.get(0)).exists() }, - { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, + { assert process.out.data[0] ==~ ".*/multiqc_data" }, + { assert snapshot(process.out.versions).match("versions") } ) } } - test("MULTIQC: FASTQC and a config file") { + test("sarscov2 single-end [fastqc] [config]") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) @@ -53,9 +47,35 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.report.get(0)).exists() }, - { assert path(process.out.data.get(0)).exists() }, - { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, + { assert process.out.data[0] ==~ ".*/multiqc_data" }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 single-end [fastqc] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = [] + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.report.collect { file(it).getName() } + + process.out.data.collect { file(it).getName() } + + process.out.plots.collect { file(it).getName() } + + process.out.versions ).match() } ) } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap new file mode 100644 index 00000000..d37e7304 --- /dev/null +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -0,0 +1,21 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + ] + ], + "timestamp": "2024-01-09T23:02:49.911994" + }, + "sarscov2 single-end [fastqc] - stub": { + "content": [ + [ + "multiqc_report.html", + "multiqc_data", + "multiqc_plots", + "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + ] + ], + "timestamp": "2024-01-09T23:03:14.524346" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml new file mode 100644 index 00000000..5efae053 --- /dev/null +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -0,0 +1,7 @@ +name: samtools_flagstat +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.18 diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index b75707ec..f1893d7c 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_FLAGSTAT { tag "$meta.id" label 'process_single' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test b/modules/nf-core/samtools/flagstat/tests/main.nf.test new file mode 100644 index 00000000..c8dd8dc9 --- /dev/null +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test @@ -0,0 +1,36 @@ +nextflow_process { + + name "Test Process SAMTOOLS_FLAGSTAT" + script "../main.nf" + process "SAMTOOLS_FLAGSTAT" + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/flagstat" + + test("BAM") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.flagstat).match() }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } +} diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap new file mode 100644 index 00000000..880019f2 --- /dev/null +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap @@ -0,0 +1,16 @@ +{ + "BAM": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + ] + ] + ], + "timestamp": "2023-11-14T15:49:22.577133" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/flagstat/tests/tags.yml b/modules/nf-core/samtools/flagstat/tests/tags.yml new file mode 100644 index 00000000..2d2b7255 --- /dev/null +++ b/modules/nf-core/samtools/flagstat/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/flagstat: + - modules/nf-core/samtools/flagstat/** diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml new file mode 100644 index 00000000..2401db0f --- /dev/null +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -0,0 +1,7 @@ +name: samtools_idxstats +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.18 diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index 83c7c34b..00d916bb 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_IDXSTATS { tag "$meta.id" label 'process_single' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test b/modules/nf-core/samtools/idxstats/tests/main.nf.test new file mode 100644 index 00000000..f6c92150 --- /dev/null +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test @@ -0,0 +1,36 @@ +nextflow_process { + + name "Test Process SAMTOOLS_IDXSTATS" + script "../main.nf" + process "SAMTOOLS_IDXSTATS" + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/idxstats" + + test("BAM") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.idxstats).match() }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } +} diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap new file mode 100644 index 00000000..4c6c12bd --- /dev/null +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap @@ -0,0 +1,16 @@ +{ + "BAM": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + ] + ] + ], + "timestamp": "2023-11-14T15:52:19.875194" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/idxstats/tests/tags.yml b/modules/nf-core/samtools/idxstats/tests/tags.yml new file mode 100644 index 00000000..d3057c61 --- /dev/null +++ b/modules/nf-core/samtools/idxstats/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/idxstats: + - modules/nf-core/samtools/idxstats/** diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml new file mode 100644 index 00000000..296ed99e --- /dev/null +++ b/modules/nf-core/samtools/index/environment.yml @@ -0,0 +1,7 @@ +name: samtools_index +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.18 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 0b20aa4b..8ad18fdc 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_INDEX { tag "$meta.id" label 'process_low' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/index/tests/csi.nextflow.config b/modules/nf-core/samtools/index/tests/csi.nextflow.config new file mode 100644 index 00000000..0ed260ef --- /dev/null +++ b/modules/nf-core/samtools/index/tests/csi.nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: SAMTOOLS_INDEX { + ext.args = '-c' + } + +} diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test new file mode 100644 index 00000000..c76a9169 --- /dev/null +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -0,0 +1,87 @@ +nextflow_process { + + name "Test Process SAMTOOLS_INDEX" + script "../main.nf" + process "SAMTOOLS_INDEX" + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/index" + + test("sarscov2 [BAI]") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.bai).match("bai") }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } + + test("homo_sapiens [CRAI]") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.crai).match("crai") }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } + + test("homo_sapiens [CSI]") { + + config "./csi.nextflow.config" + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert path(process.out.csi.get(0).get(1)).exists() }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } +} diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap new file mode 100644 index 00000000..b3baee7f --- /dev/null +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -0,0 +1,28 @@ +{ + "crai": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ] + ], + "timestamp": "2023-11-15T15:17:37.30801" + }, + "bai": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ] + ], + "timestamp": "2023-11-15T15:17:30.869234" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/index/tests/tags.yml b/modules/nf-core/samtools/index/tests/tags.yml new file mode 100644 index 00000000..e0f58a7a --- /dev/null +++ b/modules/nf-core/samtools/index/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/index: + - modules/nf-core/samtools/index/** diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml new file mode 100644 index 00000000..cd50868c --- /dev/null +++ b/modules/nf-core/samtools/sort/environment.yml @@ -0,0 +1,7 @@ +name: samtools_sort +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.18 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 2b7753fd..4a666d42 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_SORT { tag "$meta.id" label 'process_medium' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index 1f72f3b9..abb80978 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -61,7 +61,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + file(process.out.bam[0][1]).name, + process.out.versions + ).match() } ) } diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index a43566da..ff722259 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -8,14 +8,14 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,a29570e7607d217c2fa4d75829e09cd7" + "test.sorted.bam:md5,ea6a0fef94eb534e901f107a05a33a06" ] ], "1": [ ], "2": [ - "versions.yml:md5,46f7a36082fa1f68285fe30d689244e8" + "versions.yml:md5,33b6a403dc19a0d28e4219ccab0a1d80" ], "bam": [ [ @@ -23,17 +23,26 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,a29570e7607d217c2fa4d75829e09cd7" + "test.sorted.bam:md5,ea6a0fef94eb534e901f107a05a33a06" ] ], "csi": [ ], "versions": [ - "versions.yml:md5,46f7a36082fa1f68285fe30d689244e8" + "versions.yml:md5,33b6a403dc19a0d28e4219ccab0a1d80" ] } ], - "timestamp": "2023-10-17T17:21:46.5427968" + "timestamp": "2023-12-04T11:11:22.005628301" + }, + "test_samtools_sort_stub": { + "content": [ + "test.sorted.bam", + [ + "versions.yml:md5,33b6a403dc19a0d28e4219ccab0a1d80" + ] + ], + "timestamp": "2023-12-04T17:47:22.314445935" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml new file mode 100644 index 00000000..b89ce647 --- /dev/null +++ b/modules/nf-core/samtools/stats/environment.yml @@ -0,0 +1,7 @@ +name: samtools_stats +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.18 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 4a2607de..7539140a 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_STATS { tag "$meta.id" label 'process_single' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test b/modules/nf-core/samtools/stats/tests/main.nf.test index e037132c..20c3efe1 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test +++ b/modules/nf-core/samtools/stats/tests/main.nf.test @@ -4,7 +4,7 @@ nextflow_process { script "../main.nf" process "SAMTOOLS_STATS" tag "modules" - tag "modules/nf-core" + tag "modules_nfcore" tag "samtools" tag "samtools/stats" diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap index 516b2b01..025c83a5 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -8,11 +8,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,6e768486d5df0257351c5419a79f9c9b" + "test.stats:md5,045a48208b1c6f5b8af4347fe31f4def" ] ], "1": [ - "versions.yml:md5,08035f3409d934d47a416150884bb0df" + "versions.yml:md5,650a365c6635001436008350ae83337c" ], "stats": [ [ @@ -20,15 +20,15 @@ "id": "test", "single_end": false }, - "test.stats:md5,6e768486d5df0257351c5419a79f9c9b" + "test.stats:md5,045a48208b1c6f5b8af4347fe31f4def" ] ], "versions": [ - "versions.yml:md5,08035f3409d934d47a416150884bb0df" + "versions.yml:md5,650a365c6635001436008350ae83337c" ] } ], - "timestamp": "2023-10-18T12:12:42.998746" + "timestamp": "2023-12-04T11:07:28.26821485" }, "SAMTOOLS CRAM Should run without failures": { "content": [ @@ -39,11 +39,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,7c9ee5747793cceb9d6f4d733345641a" + "test.stats:md5,dfbfa130d4a6925ddd1931dcd8354a43" ] ], "1": [ - "versions.yml:md5,08035f3409d934d47a416150884bb0df" + "versions.yml:md5,650a365c6635001436008350ae83337c" ], "stats": [ [ @@ -51,14 +51,14 @@ "id": "test", "single_end": false }, - "test.stats:md5,7c9ee5747793cceb9d6f4d733345641a" + "test.stats:md5,dfbfa130d4a6925ddd1931dcd8354a43" ] ], "versions": [ - "versions.yml:md5,08035f3409d934d47a416150884bb0df" + "versions.yml:md5,650a365c6635001436008350ae83337c" ] } ], - "timestamp": "2023-10-18T12:13:30.747222" + "timestamp": "2023-12-04T11:07:50.356233402" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml new file mode 100644 index 00000000..99aa69d0 --- /dev/null +++ b/modules/nf-core/samtools/view/environment.yml @@ -0,0 +1,7 @@ +name: samtools_view +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.18 diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index cb91facf..0b5a2912 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_VIEW { tag "$meta.id" label 'process_low' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(input), path(index) @@ -53,10 +53,19 @@ process SAMTOOLS_VIEW { """ stub: + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + def file_type = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt bam") ? "bam" : + args.contains("--output-fmt cram") ? "cram" : + input.getExtension() + if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + + def index = args.contains("--write-index") ? "touch ${prefix}.csi" : "" + """ - touch ${prefix}.bam - touch ${prefix}.cram + touch ${prefix}.${file_type} + ${index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/view/tests/bam.config b/modules/nf-core/samtools/view/tests/bam.config new file mode 100644 index 00000000..c10d1081 --- /dev/null +++ b/modules/nf-core/samtools/view/tests/bam.config @@ -0,0 +1,3 @@ +process { + ext.args = "--output-fmt bam" +} \ No newline at end of file diff --git a/modules/nf-core/samtools/view/tests/bam_index.config b/modules/nf-core/samtools/view/tests/bam_index.config new file mode 100644 index 00000000..771ae033 --- /dev/null +++ b/modules/nf-core/samtools/view/tests/bam_index.config @@ -0,0 +1,3 @@ +process { + ext.args = "--output-fmt bam --write-index" +} \ No newline at end of file diff --git a/modules/nf-core/samtools/view/tests/main.nf.test b/modules/nf-core/samtools/view/tests/main.nf.test new file mode 100644 index 00000000..89ed3555 --- /dev/null +++ b/modules/nf-core/samtools/view/tests/main.nf.test @@ -0,0 +1,231 @@ +nextflow_process { + + name "Test Process SAMTOOLS_VIEW" + script "../main.nf" + process "SAMTOOLS_VIEW" + + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/view" + + test("sarscov2 - [bam, []], [], []") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), + [] + ] + input[1] = [[],[]] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.bam[0][1]).name, + process.out.cram, + process.out.sam, + process.out.bai, + process.out.crai, + process.out.csi, + process.out.versions + ).match() } + ) + } + + } + + test("homo_sapiens - [cram, crai], fasta, []") { + + when { + process { + """ + input[0] = [ + [ id: 'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + ] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.cram[0][1]).name, + process.out.bam, + process.out.sam, + process.out.bai, + process.out.crai, + process.out.csi, + process.out.versions + ).match() } + ) + } + + } + + test("homo_sapiens - [cram, []], fasta, [] - bam output") { + + config "./bam.config" + + when { + process { + """ + input[0] = [ + [ id: 'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + ] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.bam[0][1]).name, + process.out.cram, + process.out.sam, + process.out.bai, + process.out.crai, + process.out.csi, + process.out.versions + ).match() } + ) + } + + } + + test("homo_sapiens - [cram, []], fasta, [] - bam & index output") { + + config "./bam_index.config" + + when { + process { + """ + input[0] = [ + [ id: 'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + ] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.bam[0][1]).name, + process.out.cram, + process.out.sam, + file(process.out.csi[0][1]).name, + process.out.crai, + process.out.bai, + process.out.versions + ).match() } + ) + } + + } + + test("homo_sapiens - [cram, []], fasta, qname - bam & index output") { + + config "./bam_index.config" + + when { + process { + """ + input[0] = [ + [ id: 'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome' ], + file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + ] + input[2] = Channel.of("testN:2817", "testN:2814").collectFile(name: "readnames.list", newLine: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.bam[0][1]).name, + process.out.cram, + process.out.sam, + file(process.out.csi[0][1]).name, + process.out.crai, + process.out.bai, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - [bam, []], [], [] - stub") { + + options "-stub" + config "./bam_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), + [] + ] + input[1] = [[],[]] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.bam[0][1]).name, + process.out.cram, + process.out.sam, + file(process.out.csi[0][1]).name, + process.out.crai, + process.out.bai, + process.out.versions + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap new file mode 100644 index 00000000..83427491 --- /dev/null +++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap @@ -0,0 +1,140 @@ +{ + "homo_sapiens - [cram, []], fasta, [] - bam output": { + "content": [ + "test.bam", + [ + + ], + [ + + ], + [ + + ], + [ + + ], + [ + + ], + [ + "versions.yml:md5,06b9049228b111e7bed5c52fe8a98d9b" + ] + ], + "timestamp": "2023-12-04T17:41:17.563069206" + }, + "sarscov2 - [bam, []], [], []": { + "content": [ + "test.bam", + [ + + ], + [ + + ], + [ + + ], + [ + + ], + [ + + ], + [ + "versions.yml:md5,06b9049228b111e7bed5c52fe8a98d9b" + ] + ], + "timestamp": "2023-12-04T17:41:03.206994564" + }, + "homo_sapiens - [cram, []], fasta, qname - bam & index output": { + "content": [ + "test.bam", + [ + + ], + [ + + ], + "test.bam.csi", + [ + + ], + [ + + ], + [ + "versions.yml:md5,06b9049228b111e7bed5c52fe8a98d9b" + ] + ], + "timestamp": "2023-12-04T17:44:39.165289759" + }, + "homo_sapiens - [cram, []], fasta, [] - bam & index output": { + "content": [ + "test.bam", + [ + + ], + [ + + ], + "test.bam.csi", + [ + + ], + [ + + ], + [ + "versions.yml:md5,06b9049228b111e7bed5c52fe8a98d9b" + ] + ], + "timestamp": "2023-12-04T17:44:32.25731224" + }, + "sarscov2 - [bam, []], [], [] - stub": { + "content": [ + "test.bam", + [ + + ], + [ + + ], + "test.csi", + [ + + ], + [ + + ], + [ + "versions.yml:md5,06b9049228b111e7bed5c52fe8a98d9b" + ] + ], + "timestamp": "2023-12-04T17:44:45.81037195" + }, + "homo_sapiens - [cram, crai], fasta, []": { + "content": [ + "test.cram", + [ + + ], + [ + + ], + [ + + ], + [ + + ], + [ + + ], + [ + "versions.yml:md5,06b9049228b111e7bed5c52fe8a98d9b" + ] + ], + "timestamp": "2023-12-04T17:41:10.730011823" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/view/tests/tags.yml b/modules/nf-core/samtools/view/tests/tags.yml new file mode 100644 index 00000000..4fdf1dd1 --- /dev/null +++ b/modules/nf-core/samtools/view/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/view: + - "modules/nf-core/samtools/view/**" diff --git a/modules/nf-core/segemehl/align/environment.yml b/modules/nf-core/segemehl/align/environment.yml new file mode 100644 index 00000000..e7dbc662 --- /dev/null +++ b/modules/nf-core/segemehl/align/environment.yml @@ -0,0 +1,7 @@ +name: segemehl_align +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::segemehl=0.3.4 diff --git a/modules/nf-core/segemehl/align/main.nf b/modules/nf-core/segemehl/align/main.nf index 768cd384..77f88820 100644 --- a/modules/nf-core/segemehl/align/main.nf +++ b/modules/nf-core/segemehl/align/main.nf @@ -2,7 +2,7 @@ process SEGEMEHL_ALIGN { tag "$meta.id" label 'process_high' - conda "bioconda::segemehl=0.3.4" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/segemehl:0.3.4--hc2ea5fd_5': 'biocontainers/segemehl:0.3.4--hc2ea5fd_5' }" diff --git a/modules/nf-core/segemehl/index/environment.yml b/modules/nf-core/segemehl/index/environment.yml new file mode 100644 index 00000000..c0641330 --- /dev/null +++ b/modules/nf-core/segemehl/index/environment.yml @@ -0,0 +1,7 @@ +name: segemehl_index +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::segemehl=0.3.4 diff --git a/modules/nf-core/segemehl/index/main.nf b/modules/nf-core/segemehl/index/main.nf index 4a9146fe..ea912c6e 100644 --- a/modules/nf-core/segemehl/index/main.nf +++ b/modules/nf-core/segemehl/index/main.nf @@ -2,7 +2,7 @@ process SEGEMEHL_INDEX { tag "$fasta" label 'process_high' - conda "bioconda::segemehl=0.3.4" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/segemehl:0.3.4--hc2ea5fd_5': 'biocontainers/segemehl:0.3.4--hc2ea5fd_5' }" diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml new file mode 100644 index 00000000..36fcd022 --- /dev/null +++ b/modules/nf-core/star/align/environment.yml @@ -0,0 +1,9 @@ +name: star_align +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::star=2.7.10a + - bioconda::samtools=1.18 + - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index d0e20384..8e9c48b1 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -2,10 +2,10 @@ process STAR_ALIGN { tag "$meta.id" label 'process_high' - conda "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' : - 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' : + 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' }" input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/star/align/tests/main.nf.test b/modules/nf-core/star/align/tests/main.nf.test new file mode 100644 index 00000000..4c878474 --- /dev/null +++ b/modules/nf-core/star/align/tests/main.nf.test @@ -0,0 +1,339 @@ +nextflow_process { + + name "Test Process STAR_ALIGN" + script "../main.nf" + process "STAR_ALIGN" + tag "modules" + tag "modules_nfcore" + tag "star" + tag "star/align" + + test("homo_sapiens - single_end") { + config "./nextflow.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true) ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - single_end - log_final") }, + { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - single_end - log_out") }, + { assert snapshot(process.out.bam).match("homo_sapiens - single_end - bam") }, + { assert snapshot(process.out.bam_sorted).match("homo_sapiens - single_end - bam_sorted") }, + { assert snapshot(process.out.bam_transcript).match("homo_sapiens - single_end - bam_transcript") }, + { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - single_end - bam_unsorted") }, + { assert snapshot(process.out.bedgraph).match("homo_sapiens - single_end - bedgraph") }, + { assert snapshot(process.out.fastq).match("homo_sapiens - single_end - fastq") }, + { assert snapshot(process.out.junction).match("homo_sapiens - single_end - junction") }, + { assert snapshot(process.out.log_progress).match("homo_sapiens - single_end - log_progress") }, + { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - single_end - read_per_gene_tab") }, + { assert snapshot(process.out.sam).match("homo_sapiens - single_end - sam") }, + { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - single_end - spl_junc_tab") }, + { assert snapshot(process.out.tab).match("homo_sapiens - single_end - tab") }, + { assert snapshot(process.out.wig).match("homo_sapiens - single_end - wig") }, + { assert snapshot(process.out.versions).match("homo_sapiens - single_end - versions") } + ) + } + } + + test("homo_sapiens - paired_end") { + config "./nextflow.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - log_final") }, + { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - log_out") }, + { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - bam") }, + { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - bam_sorted") }, + { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - bam_transcript") }, + { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - bam_unsorted") }, + { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - bedgraph") }, + { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - fastq") }, + { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - junction") }, + { assert snapshot(process.out.log_progress).match("homo_sapiens - paired_end - log_progress") }, + { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - read_per_gene_tab") }, + { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - sam") }, + { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - spl_junc_tab") }, + { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - tab") }, + { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - wig") }, + { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - versions") } + ) + } + } + + test("homo_sapiens - paired_end - arriba") { + config "./nextflow.arriba.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - arriba - log_final") }, + { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - arriba - log_out") }, + { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - arriba - log_progress") }, + { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - arriba - bam") }, + { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - arriba - bam_sorted") }, + { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - arriba - bam_transcript") }, + { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - arriba - bam_unsorted") }, + { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - arriba - bedgraph") }, + { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - arriba - fastq") }, + { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - arriba - junction") }, + { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - arriba - read_per_gene_tab") }, + { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - arriba - sam") }, + { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - arriba - spl_junc_tab") }, + { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - arriba - tab") }, + { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - arriba - wig") }, + { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - arriba - versions") } + ) + } + } + + test("homo_sapiens - paired_end - starfusion") { + config "./nextflow.starfusion.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_final") }, + { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_out") }, + { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_progress") }, + { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - starfusion - bam") }, + { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - starfusion - bam_sorted") }, + { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - starfusion - bam_transcript") }, + { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - starfusion - bam_unsorted") }, + { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - starfusion - bedgraph") }, + { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - starfusion - fastq") }, + { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - starfusion - junction") }, + { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - starfusion - read_per_gene_tab") }, + { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - starfusion - sam") }, + { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - starfusion - spl_junc_tab") }, + { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - starfusion - tab") }, + { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - starfusion - wig") }, + { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - starfusion - versions") } + ) + } + } + + test("homo_sapiens - paired_end - multiple") { + config "./nextflow.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - multiple - log_final") }, + { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - multiple - log_out") }, + { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - multiple - log_progress") }, + { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - multiple - bam") }, + { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - multiple - bam_sorted") }, + { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - multiple - bam_transcript") }, + { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - multiple - bam_unsorted") }, + { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - multiple - bedgraph") }, + { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - multiple - fastq") }, + { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - multiple - junction") }, + { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - multiple - read_per_gene_tab") }, + { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - multiple - sam") }, + { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - multiple - spl_junc_tab") }, + { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - multiple - tab") }, + { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - multiple - wig") }, + { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - multiple - versions") } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/star/align/tests/main.nf.test.snap b/modules/nf-core/star/align/tests/main.nf.test.snap new file mode 100644 index 00000000..08edb914 --- /dev/null +++ b/modules/nf-core/star/align/tests/main.nf.test.snap @@ -0,0 +1,769 @@ +{ + "homo_sapiens - paired_end - multiple - bam_sorted": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.sortedByCoord.out.bam:md5,ab07c21d63ab0a6c07d171d213c81d5a" + ] + ] + ], + "timestamp": "2023-12-04T18:01:19.968225733" + }, + "homo_sapiens - 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single_end - spl_junc_tab": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.SJ.out.tab:md5,75a516ab950fb958f40b29996474949c" + ] + ] + ], + "timestamp": "2023-12-04T17:53:26.50932751" + }, + "homo_sapiens - paired_end - starfusion - spl_junc_tab": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.SJ.out.tab:md5,19c3faa1bfa9a0cc5e4c45f17065b53a" + ] + ] + ], + "timestamp": "2023-12-04T17:59:58.731699486" + }, + "homo_sapiens - single_end - log_out": { + "content": [ + "test.Log.out" + ], + "timestamp": "2023-11-23T13:22:55.126286" + }, + "homo_sapiens - paired_end - log_final": { + "content": [ + "test.Log.final.out" + ], + "timestamp": "2023-11-23T13:23:33.253884" + }, + "homo_sapiens - single_end - log_final": { + "content": [ + "test.Log.final.out" + ], + "timestamp": "2023-11-23T13:22:55.11799" + }, + "homo_sapiens - paired_end - bam_transcript": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:23:33.287684" + }, + "homo_sapiens - paired_end - starfusion - log_progress": { + "content": [ + "test.Log.progress.out" + ], + "timestamp": "2023-11-23T13:27:55.971484" + }, + "homo_sapiens - paired_end - multiple - bam_transcript": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:29:01.264176" + }, + "homo_sapiens - paired_end - multiple - read_per_gene_tab": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:29:01.596406" + }, + "homo_sapiens - single_end - read_per_gene_tab": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:22:55.205936" + }, + "homo_sapiens - paired_end - junction": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:23:33.340653" + }, + "homo_sapiens - paired_end - spl_junc_tab": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.SJ.out.tab:md5,844af19ab0fc8cd9a3f75228445aca0d" + ] + ] + ], + "timestamp": "2023-12-04T17:54:12.185730856" + }, + "homo_sapiens - paired_end - starfusion - sam": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:27:56.300637" + }, + "homo_sapiens - paired_end - arriba - bam": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.out.bam:md5,c1b1747f5873f2d17762725636e891d5" + ] + ] + ], + "timestamp": "2023-12-04T17:56:12.190560178" + }, + "homo_sapiens - single_end - log_progress": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.Log.progress.out:md5,b2bd061d6cbaaf3d6d3b1fed547f69b8" + ] + ] + ], + "timestamp": "2023-12-04T17:53:26.450352138" + }, + "homo_sapiens - paired_end - starfusion - wig": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:27:56.422018" + }, + "homo_sapiens - paired_end - wig": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:23:33.429457" + }, + "homo_sapiens - paired_end - starfusion - log_out": { + "content": [ + "test.Log.out" + ], + "timestamp": "2023-11-23T13:27:55.93945" + } +} \ No newline at end of file diff --git a/modules/nf-core/star/align/tests/nextflow.arriba.config b/modules/nf-core/star/align/tests/nextflow.arriba.config new file mode 100644 index 00000000..2324b9e5 --- /dev/null +++ b/modules/nf-core/star/align/tests/nextflow.arriba.config @@ -0,0 +1,14 @@ +process { + + withName: STAR_GENOMEGENERATE { + ext.args = '--genomeSAindexNbases 9' + } + + withName: STAR_ALIGN { + ext.args = '--readFilesCommand zcat --outSAMtype BAM Unsorted --outSAMunmapped Within --outBAMcompression 0 --outFilterMultimapNmax 50 --peOverlapNbasesMin 10 --alignSplicedMateMapLminOverLmate 0.5 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentMin 10 --chimOutType WithinBAM HardClip --chimJunctionOverhangMin 10 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --chimSegmentReadGapMax 3 --chimMultimapNmax 50' + } + +} + +// Fix chown issue for the output star folder +docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/modules/nf-core/star/align/tests/nextflow.config b/modules/nf-core/star/align/tests/nextflow.config new file mode 100644 index 00000000..c4ac5808 --- /dev/null +++ b/modules/nf-core/star/align/tests/nextflow.config @@ -0,0 +1,14 @@ +process { + + withName: STAR_GENOMEGENERATE { + ext.args = '--genomeSAindexNbases 9' + } + + withName: STAR_ALIGN { + ext.args = '--readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigType bedGraph --outWigStrand Unstranded' + } + +} + +// Fix chown issue for the output star folder +docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/modules/nf-core/star/align/tests/nextflow.starfusion.config b/modules/nf-core/star/align/tests/nextflow.starfusion.config new file mode 100644 index 00000000..467b6497 --- /dev/null +++ b/modules/nf-core/star/align/tests/nextflow.starfusion.config @@ -0,0 +1,14 @@ +process { + + withName: STAR_GENOMEGENERATE { + ext.args = '--genomeSAindexNbases 9' + } + + withName: STAR_ALIGN { + ext.args = '--readFilesCommand zcat --outSAMtype BAM Unsorted --outReadsUnmapped None --twopassMode Basic --outSAMstrandField intronMotif --outSAMunmapped Within --chimSegmentMin 12 --chimJunctionOverhangMin 8 --chimOutJunctionFormat 1 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --chimMultimapScoreRange 3 --chimScoreJunctionNonGTAG -4 --chimMultimapNmax 20 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --alignInsertionFlush Right --alignSplicedMateMapLminOverLmate 0 --alignSplicedMateMapLmin 30' + } + +} + +// Fix chown issue for the output star folder +docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/modules/nf-core/star/align/tests/tags.yml b/modules/nf-core/star/align/tests/tags.yml new file mode 100644 index 00000000..8beace16 --- /dev/null +++ b/modules/nf-core/star/align/tests/tags.yml @@ -0,0 +1,2 @@ +star/align: + - modules/nf-core/star/align/** diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml new file mode 100644 index 00000000..93e4476a --- /dev/null +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -0,0 +1,11 @@ +name: star_genomegenerate + +channels: + - conda-forge + - bioconda + - defaults + +dependencies: + - bioconda::samtools=1.18 + - bioconda::star=2.7.10a + - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index 43424042..b8855715 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -2,10 +2,10 @@ process STAR_GENOMEGENERATE { tag "$fasta" label 'process_high' - conda "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' : - 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' : + 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' }" input: tuple val(meta), path(fasta) @@ -19,9 +19,10 @@ process STAR_GENOMEGENERATE { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def args_list = args.tokenize() - def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : '' + def args = task.ext.args ?: '' + def args_list = args.tokenize() + def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : '' + def include_gtf = gtf ? "--sjdbGTFfile $gtf" : '' if (args_list.contains('--genomeSAindexNbases')) { """ mkdir star @@ -29,7 +30,7 @@ process STAR_GENOMEGENERATE { --runMode genomeGenerate \\ --genomeDir star/ \\ --genomeFastaFiles $fasta \\ - --sjdbGTFfile $gtf \\ + $include_gtf \\ --runThreadN $task.cpus \\ $memory \\ $args @@ -51,7 +52,7 @@ process STAR_GENOMEGENERATE { --runMode genomeGenerate \\ --genomeDir star/ \\ --genomeFastaFiles $fasta \\ - --sjdbGTFfile $gtf \\ + $include_gtf \\ --runThreadN $task.cpus \\ --genomeSAindexNbases \$NUM_BASES \\ $memory \\ @@ -67,30 +68,52 @@ process STAR_GENOMEGENERATE { } stub: - """ - mkdir star - touch star/Genome - touch star/Log.out - touch star/SA - touch star/SAindex - touch star/chrLength.txt - touch star/chrName.txt - touch star/chrNameLength.txt - touch star/chrStart.txt - touch star/exonGeTrInfo.tab - touch star/exonInfo.tab - touch star/geneInfo.tab - touch star/genomeParameters.txt - touch star/sjdbInfo.txt - touch star/sjdbList.fromGTF.out.tab - touch star/sjdbList.out.tab - touch star/transcriptInfo.tab + if (gtf) { + """ + mkdir star + touch star/Genome + touch star/Log.out + touch star/SA + touch star/SAindex + touch star/chrLength.txt + touch star/chrName.txt + touch star/chrNameLength.txt + touch star/chrStart.txt + touch star/exonGeTrInfo.tab + touch star/exonInfo.tab + touch star/geneInfo.tab + touch star/genomeParameters.txt + touch star/sjdbInfo.txt + touch star/sjdbList.fromGTF.out.tab + touch star/sjdbList.out.tab + touch star/transcriptInfo.tab - cat <<-END_VERSIONS > versions.yml - "${task.process}": - star: \$(STAR --version | sed -e "s/STAR_//g") - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//') - END_VERSIONS - """ + cat <<-END_VERSIONS > versions.yml + "${task.process}": + star: \$(STAR --version | sed -e "s/STAR_//g") + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//') + END_VERSIONS + """ + } else { + """ + mkdir star + touch star/Genome + touch star/Log.out + touch star/SA + touch star/SAindex + touch star/chrLength.txt + touch star/chrName.txt + touch star/chrNameLength.txt + touch star/chrStart.txt + touch star/genomeParameters.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + star: \$(STAR --version | sed -e "s/STAR_//g") + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//') + END_VERSIONS + """ + } } diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test b/modules/nf-core/star/genomegenerate/tests/main.nf.test new file mode 100644 index 00000000..af0c9421 --- /dev/null +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test @@ -0,0 +1,117 @@ +nextflow_process { + + name "Test Process STAR_GENOMEGENERATE" + script "../main.nf" + process "STAR_GENOMEGENERATE" + tag "modules" + tag "modules_nfcore" + tag "star" + tag "star/genomegenerate" + + test("homo_sapiens") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_with_gtf") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + + test("homo_sapiens-stub") { + + options '-stub' + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_with_gtf") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + + test("homo_sapiens-without_gtf") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ [], [] ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_without_gtf") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + + test("homo_sapiens-without_gtf-stub") { + + options '-stub' + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ [], [] ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_without_gtf") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap new file mode 100644 index 00000000..9de08c74 --- /dev/null +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap @@ -0,0 +1,22 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + ] + ], + "timestamp": "2023-12-19T11:05:51.741109" + }, + "index_with_gtf": { + "content": [ + "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]" + ], + "timestamp": "2023-12-19T11:38:14.551548" + }, + "index_without_gtf": { + "content": [ + "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]" + ], + "timestamp": "2023-12-19T11:38:22.382905" + } +} \ No newline at end of file diff --git a/modules/nf-core/star/genomegenerate/tests/tags.yml b/modules/nf-core/star/genomegenerate/tests/tags.yml new file mode 100644 index 00000000..79f619bf --- /dev/null +++ b/modules/nf-core/star/genomegenerate/tests/tags.yml @@ -0,0 +1,2 @@ +star/genomegenerate: + - modules/nf-core/star/genomegenerate/** diff --git a/modules/nf-core/stringtie/stringtie/environment.yml b/modules/nf-core/stringtie/stringtie/environment.yml new file mode 100644 index 00000000..7a0eccdb --- /dev/null +++ b/modules/nf-core/stringtie/stringtie/environment.yml @@ -0,0 +1,7 @@ +name: stringtie_stringtie +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::stringtie=2.2.1 diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf index d0f8b563..6e25ba27 100644 --- a/modules/nf-core/stringtie/stringtie/main.nf +++ b/modules/nf-core/stringtie/stringtie/main.nf @@ -2,7 +2,7 @@ process STRINGTIE_STRINGTIE { tag "$meta.id" label 'process_medium' - conda "bioconda::stringtie=2.2.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : 'biocontainers/stringtie:2.2.1--hecb563c_2' }" diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test b/modules/nf-core/stringtie/stringtie/tests/main.nf.test new file mode 100644 index 00000000..68786b74 --- /dev/null +++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test @@ -0,0 +1,108 @@ +nextflow_process { + + name "Test Process STRINGTIE_STRINGTIE" + script "../main.nf" + process "STRINGTIE_STRINGTIE" + tag "modules" + tag "modules_nfcore" + tag "stringtie" + tag "stringtie/stringtie" + + test("sarscov2 [bam] - forward strandedness") { + + when { + process { + """ + input[0] = [ + [ id:'test', strandedness:'forward' ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.transcript_gtf).match("fs_transcript_gtf") }, + { assert snapshot(process.out.abundance).match("fs_abundance") }, + { assert snapshot(process.out.versions).match("fs_versions") } + ) + } + } + + test("sarscov2 [bam] - forward strandedness + reference annotation") { + + when { + process { + """ + input[0] = [ + [ id:'test', strandedness:'forward' ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] + ] + input[1] = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.transcript_gtf).match("fs_gtf_transcript_gtf") }, + { assert snapshot(process.out.abundance).match("fs_gtf_abundance") }, + { assert snapshot(process.out.ballgown).match("fs_gtf_ballgown") }, + { assert snapshot(process.out.versions).match("fs_gtf_versions") } + ) + } + } + + test("sarscov2 [bam] - reverse strandedness") { + + when { + process { + """ + input[0] = [ + [ id:'test', strandedness:'reverse' ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.transcript_gtf).match("rs_transcript_gtf") }, + { assert snapshot(process.out.abundance).match("rs_abundance") }, + { assert snapshot(process.out.versions).match("rs_versions") } + ) + } + } + + test("sarscov2 [bam] - reverse strandedness + reference annotation") { + + when { + process { + """ + input[0] = [ + [ id:'test', strandedness:'reverse' ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] + ] + input[1] = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.transcript_gtf).match("rs_gtf_transcript_gtf") }, + { assert snapshot(process.out.abundance).match("rs_gtf_abundance") }, + { assert snapshot(process.out.ballgown).match("rs_gtf_ballgown") }, + { assert snapshot(process.out.versions).match("rs_gtf_versions") } + ) + } + } +} diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap new file mode 100644 index 00000000..bf751636 --- /dev/null +++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap @@ -0,0 +1,186 @@ +{ + "fs_abundance": { + "content": [ + [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.gene.abundance.txt:md5,d6f5c8cadb8458f1df0427cf790246e3" + ] + ] + ], + "timestamp": "2023-11-23T13:55:41.032044613" + }, + "fs_transcript_gtf": { + "content": [ + [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.transcripts.gtf:md5,569137af5be452413086b50653a97203" + ] + ] + ], + "timestamp": "2023-11-23T13:55:41.017978904" + }, + "rs_abundance": { + "content": [ + [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.gene.abundance.txt:md5,d6f5c8cadb8458f1df0427cf790246e3" + ] + ] + ], + "timestamp": "2023-11-23T13:56:13.601112933" + }, + "fs_gtf_versions": { + "content": [ + [ + "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + ] + ], + "timestamp": "2023-11-23T13:56:00.523797974" + }, + "fs_gtf_transcript_gtf": { + "content": [ + [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.transcripts.gtf:md5,f56cf8aba2c4a5673bc7963ba5f12d04" + ] + ] + ], + "timestamp": "2023-11-23T13:56:00.475164879" + }, + "rs_versions": { + "content": [ + [ + "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + ] + ], + "timestamp": "2023-11-23T13:56:13.623892691" + }, + "rs_gtf_transcript_gtf": { + "content": [ + [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.transcripts.gtf:md5,bb346053a8c156b803b055133376c7fa" + ] + ] + ], + "timestamp": "2023-11-23T13:56:22.693599559" + }, + "fs_gtf_abundance": { + "content": [ + [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.gene.abundance.txt:md5,7d8bce7f2a922e367cedccae7267c22e" + ] + ] + ], + "timestamp": "2023-11-23T13:56:00.482135418" + }, + "rs_gtf_ballgown": { + "content": [ + [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + [ + "e2t.ctab:md5,e981c0038295ae54b63cedb1083f1540", + "e_data.ctab:md5,879b6696029d19c4737b562e9d149218", + "i2t.ctab:md5,8a117c8aa4334b4c2d4711932b006fb4", + "i_data.ctab:md5,be3abe09740603213f83d50dcf81427f", + "t_data.ctab:md5,3b66c065da73ae0dd41cc332eff6a818" + ] + ] + ] + ], + "timestamp": "2023-11-23T13:56:22.715698347" + }, + "rs_transcript_gtf": { + "content": [ + [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.transcripts.gtf:md5,31c34aec2bf36bb0ea3c16c2afeeeb1f" + ] + ] + ], + "timestamp": "2023-11-23T13:56:13.590054035" + }, + "rs_gtf_versions": { + "content": [ + [ + "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + ] + ], + "timestamp": "2023-11-23T13:56:22.725513476" + }, + "fs_gtf_ballgown": { + "content": [ + [ + [ + { + "id": "test", + "strandedness": "forward" + }, + [ + "e2t.ctab:md5,e981c0038295ae54b63cedb1083f1540", + "e_data.ctab:md5,6b4cf69bc03f3f69890f972a0e8b7471", + "i2t.ctab:md5,8a117c8aa4334b4c2d4711932b006fb4", + "i_data.ctab:md5,be3abe09740603213f83d50dcf81427f", + "t_data.ctab:md5,3b66c065da73ae0dd41cc332eff6a818" + ] + ] + ] + ], + "timestamp": "2023-11-23T13:56:00.494299817" + }, + "fs_versions": { + "content": [ + [ + "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + ] + ], + "timestamp": "2023-11-23T13:55:41.049417582" + }, + "rs_gtf_abundance": { + "content": [ + [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.gene.abundance.txt:md5,7385b870b955dae2c2ab78a70cf05cce" + ] + ] + ], + "timestamp": "2023-11-23T13:56:22.701059059" + } +} diff --git a/modules/nf-core/stringtie/stringtie/tests/tags.yml b/modules/nf-core/stringtie/stringtie/tests/tags.yml new file mode 100644 index 00000000..da9b051c --- /dev/null +++ b/modules/nf-core/stringtie/stringtie/tests/tags.yml @@ -0,0 +1,2 @@ +stringtie/stringtie: + - modules/nf-core/stringtie/stringtie/** diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml new file mode 100644 index 00000000..6cd0f51b --- /dev/null +++ b/modules/nf-core/trimgalore/environment.yml @@ -0,0 +1,7 @@ +name: trimgalore +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::trim-galore=0.6.7 diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index dcb77ae7..24ead871 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -2,7 +2,7 @@ process TRIMGALORE { tag "$meta.id" label 'process_high' - conda "bioconda::trim-galore=0.6.7" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0' : 'biocontainers/trim-galore:0.6.7--hdfd78af_0' }" diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test index a8a13f2a..59b749d8 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test @@ -5,7 +5,9 @@ nextflow_workflow { workflow "BAM_SORT_STATS_SAMTOOLS" tag "subworkflows" tag "subworkflows_nfcore" + tag "subworkflows/bam_sort_stats_samtools" tag "bam_sort_stats_samtools" + tag "subworkflows/bam_stats_samtools" tag "bam_stats_samtools" tag "samtools" tag "samtools/index" @@ -35,7 +37,11 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out).match()} + { assert workflow.out.bam.get(0).get(1) ==~ ".*.bam"}, + { assert workflow.out.bai.get(0).get(1) ==~ ".*.bai"}, + { assert snapshot(workflow.out.stats).match("test_bam_sort_stats_samtools_single_end_stats") }, + { assert snapshot(workflow.out.flagstat).match("test_bam_sort_stats_samtools_single_end_flagstats") }, + { assert snapshot(workflow.out.idxstats).match("test_bam_sort_stats_samtools_single_end_idxstats") } ) } } @@ -61,7 +67,11 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out).match()} + { assert workflow.out.bam.get(0).get(1) ==~ ".*.bam"}, + { assert workflow.out.bai.get(0).get(1) ==~ ".*.bai"}, + { assert snapshot(workflow.out.stats).match("test_bam_sort_stats_samtools_paired_end_stats") }, + { assert snapshot(workflow.out.flagstat).match("test_bam_sort_stats_samtools_paired_end_flagstats") }, + { assert snapshot(workflow.out.idxstats).match("test_bam_sort_stats_samtools_paired_end_idxstats") } ) } } diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap index 50ffde60..77afbf17 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap @@ -1,236 +1,86 @@ { - "test_bam_sort_stats_samtools_single_end": { + "test_bam_sort_stats_samtools_paired_end_flagstats": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,2cf8fe8dbba3da7eb4fb251c79f428dc" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam.bai:md5,002488588110dcee464e65f68c4726e8" - ] - ], - "2": [ - - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.stats:md5,796f45f791f06291b76329528fae0a54" - ] - ], - "4": [ - [ - { - "id": "test", - "single_end": false - }, - "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53" - ] - ], - "5": [ - [ - { - "id": "test", - "single_end": false - }, - "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20" - ] - ], - "6": [ - "versions.yml:md5,176f12ceae81f76341e481988c799c15", - "versions.yml:md5,7beadfaf6b22ea0ae6e655b41447803f", - "versions.yml:md5,bfcdd8e2d5151a14dac15a9332d73d52", - "versions.yml:md5,dd8f44a9bfef10555ef1c8cc0267ff9c", - "versions.yml:md5,f2eb7aba102adae159006c9a443c301b" - ], - "bai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam.bai:md5,002488588110dcee464e65f68c4726e8" - ] - ], - "bam": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,2cf8fe8dbba3da7eb4fb251c79f428dc" - ] - ], - "csi": [ - - ], - "flagstat": [ - [ - { - "id": "test", - "single_end": false - }, - "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53" - ] - ], - "idxstats": [ - [ - { - "id": "test", - "single_end": false - }, - "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20" - ] - ], - "stats": [ - [ - { - "id": "test", - "single_end": false - }, - "test.stats:md5,796f45f791f06291b76329528fae0a54" - ] - ], - "versions": [ - "versions.yml:md5,176f12ceae81f76341e481988c799c15", - "versions.yml:md5,7beadfaf6b22ea0ae6e655b41447803f", - "versions.yml:md5,bfcdd8e2d5151a14dac15a9332d73d52", - "versions.yml:md5,dd8f44a9bfef10555ef1c8cc0267ff9c", - "versions.yml:md5,f2eb7aba102adae159006c9a443c301b" + [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" ] - } + ] ], - "timestamp": "2023-10-18T09:34:31.989804787" + "timestamp": "2023-10-22T20:25:03.687121177" }, - "test_bam_sort_stats_samtools_paired_end": { + "test_bam_sort_stats_samtools_paired_end_idxstats": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,81adec7882577c0ad17962599acf7745" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam.bai:md5,9e6427a796975290b1110c9d542ac79d" - ] - ], - "2": [ - - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.stats:md5,f3f0e5aad236aae678ac5361b529a664" - ] - ], - "4": [ - [ - { - "id": "test", - "single_end": false - }, - "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" - ] - ], - "5": [ - [ - { - "id": "test", - "single_end": false - }, - "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" - ] - ], - "6": [ - "versions.yml:md5,176f12ceae81f76341e481988c799c15", - "versions.yml:md5,7beadfaf6b22ea0ae6e655b41447803f", - "versions.yml:md5,bfcdd8e2d5151a14dac15a9332d73d52", - "versions.yml:md5,dd8f44a9bfef10555ef1c8cc0267ff9c", - "versions.yml:md5,f2eb7aba102adae159006c9a443c301b" - ], - "bai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam.bai:md5,9e6427a796975290b1110c9d542ac79d" - ] - ], - "bam": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,81adec7882577c0ad17962599acf7745" - ] - ], - "csi": [ - - ], - "flagstat": [ - [ - { - "id": "test", - "single_end": false - }, - "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" - ] - ], - "idxstats": [ - [ - { - "id": "test", - "single_end": false - }, - "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" - ] - ], - "stats": [ - [ - { - "id": "test", - "single_end": false - }, - "test.stats:md5,f3f0e5aad236aae678ac5361b529a664" - ] - ], - "versions": [ - "versions.yml:md5,176f12ceae81f76341e481988c799c15", - "versions.yml:md5,7beadfaf6b22ea0ae6e655b41447803f", - "versions.yml:md5,bfcdd8e2d5151a14dac15a9332d73d52", - "versions.yml:md5,dd8f44a9bfef10555ef1c8cc0267ff9c", - "versions.yml:md5,f2eb7aba102adae159006c9a443c301b" + [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" ] - } + ] ], - "timestamp": "2023-10-18T09:34:57.682759147" + "timestamp": "2023-10-22T20:25:03.709648916" + }, + "test_bam_sort_stats_samtools_single_end_stats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,f281507081517414eb1a04b2d9c855b2" + ] + ] + ], + "timestamp": "2023-12-04T11:06:50.951881479" + }, + "test_bam_sort_stats_samtools_paired_end_stats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,e32e7e49dce1fbe327a89e0fb7bc01b1" + ] + ] + ], + "timestamp": "2023-12-04T11:06:59.253905951" + }, + "test_bam_sort_stats_samtools_single_end_idxstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20" + ] + ] + ], + "timestamp": "2023-10-22T20:25:58.451364604" + }, + "test_bam_sort_stats_samtools_single_end_flagstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53" + ] + ] + ], + "timestamp": "2023-10-22T20:25:58.416859285" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/tags.yml b/subworkflows/nf-core/bam_sort_stats_samtools/tests/tags.yml index a8274109..30b69d6a 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/tags.yml +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/tags.yml @@ -1,2 +1,2 @@ -bam_sort_stats_samtools: +subworkflows/bam_sort_stats_samtools: - subworkflows/nf-core/bam_sort_stats_samtools/** From 38ef8e13bbf751d419a467c73a3ea27c5f32887f Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 13 Jan 2024 11:45:45 +0100 Subject: [PATCH 090/491] Remove config artifact --- nextflow.config | 3 --- 1 file changed, 3 deletions(-) diff --git a/nextflow.config b/nextflow.config index b3699c50..0b995eda 100644 --- a/nextflow.config +++ b/nextflow.config @@ -100,9 +100,6 @@ params { validationSchemaIgnoreParams = 'genomes,igenomes_base' validationShowHiddenParams = false validate_params = true - withName: INTEGRATE_SCVI { - cpus: 60 - } } // Load base.config by default for all pipelines From 1b96c1ba1427e2a4480e6a083c44fd300fab5eb3 Mon Sep 17 00:00:00 2001 From: nictru Date: Sun, 22 Oct 2023 14:37:05 +0200 Subject: [PATCH 091/491] Prevent meta alteration --- subworkflows/local/circrna_discovery.nf | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 09428987..d75f6ed0 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -80,7 +80,7 @@ workflow CIRCRNA_DISCOVERY { // SEGEMEHL WORKFLOW: // SEGEMEHL_ALIGN( reads, fasta, segemehl_index ) - segemehl_filter = SEGEMEHL_ALIGN.out.results.map{ meta, results -> meta.tool = "segemehl"; return [ meta, results ] } + segemehl_filter = SEGEMEHL_ALIGN.out.results.map{ meta, results -> [ meta + [tool: "segemehl"], results ] } SEGEMEHL_FILTER( segemehl_filter, bsj_reads ) ch_versions = ch_versions.mix(SEGEMEHL_ALIGN.out.versions) @@ -110,7 +110,7 @@ workflow CIRCRNA_DISCOVERY { CIRCEXPLORER2_REF( gtf ) CIRCEXPLORER2_PAR( STAR_2ND_PASS.out.junction ) CIRCEXPLORER2_ANN( CIRCEXPLORER2_PAR.out.junction, fasta, CIRCEXPLORER2_REF.out.txt ) - circexplorer2_filter = CIRCEXPLORER2_ANN.out.txt.map{ meta, txt -> meta.tool = "circexplorer2"; return [ meta, txt ] } + circexplorer2_filter = CIRCEXPLORER2_ANN.out.txt.map{ meta, txt -> [ meta + [tool: "circexplorer2"], txt ] } CIRCEXPLORER2_FLT( circexplorer2_filter, bsj_reads ) ch_versions = ch_versions.mix(CIRCEXPLORER2_REF.out.versions) @@ -123,7 +123,7 @@ workflow CIRCRNA_DISCOVERY { // circrna_finder_stage = STAR_2ND_PASS.out.sam.join( STAR_2ND_PASS.out.junction).join(STAR_2ND_PASS.out.tab) - circrna_finder_filter = circrna_finder_stage.map{ meta, sam, junction, tab -> meta.tool = "circrna_finder"; return [ meta, sam, junction, tab ] } + circrna_finder_filter = circrna_finder_stage.map{ meta, sam, junction, tab -> [ meta + [tool: "circrna_finder"], sam, junction, tab ] } CIRCRNA_FINDER_FILTER( circrna_finder_filter, fasta, bsj_reads ) ch_versions = ch_versions.mix(CIRCRNA_FINDER_FILTER.out.versions) @@ -137,7 +137,7 @@ workflow CIRCRNA_DISCOVERY { SAMTOOLS_VIEW( FIND_CIRC_ALIGN.out.aligned.join( SAMTOOLS_INDEX.out.bai ), fasta_tuple, [] ) FIND_CIRC_ANCHORS( SAMTOOLS_VIEW.out.bam ) FIND_CIRC( FIND_CIRC_ANCHORS.out.anchors, bowtie2_index.collect(), fasta ) - find_circ_filter = FIND_CIRC.out.bed.map{ meta, bed -> meta.tool = "find_circ"; return [ meta, bed ] } + find_circ_filter = FIND_CIRC.out.bed.map{ meta, bed -> [ meta + [tool: "find_circ"], bed ] } FIND_CIRC_FILTER( find_circ_filter, bsj_reads ) ch_versions = ch_versions.mix(FIND_CIRC_ALIGN.out.versions) @@ -155,7 +155,7 @@ workflow CIRCRNA_DISCOVERY { // do not want to upset the collect declr for all indices just for this. CIRIQUANT_YML( gtf, fasta, bwa_index.map{ meta, index -> return index }, hisat2_index.map{ meta, index -> return index } ) CIRIQUANT( reads, CIRIQUANT_YML.out.yml.collect() ) - CIRIQUANT_FILTER( CIRIQUANT.out.gtf.map{ meta, gtf -> meta.tool = "ciriquant"; return [ meta, gtf ] }, bsj_reads ) + CIRIQUANT_FILTER( CIRIQUANT.out.gtf.map{ meta, gtf -> [ meta + [tool: "ciriquant"], gtf ] }, bsj_reads ) ch_versions = ch_versions.mix(CIRIQUANT.out.versions) ch_versions = ch_versions.mix(CIRIQUANT_FILTER.out.versions) @@ -191,7 +191,7 @@ workflow CIRCRNA_DISCOVERY { dcc = dcc_stage.map{ it -> [ it[0], it[1], it[2] ?: [], it[3] ?: [] ] } DCC( dcc, fasta, gtf ) - DCC_FILTER( DCC.out.txt.map{ meta, txt -> meta.tool = "dcc"; return [ meta, txt ] }, bsj_reads ) + DCC_FILTER( DCC.out.txt.map{ meta, txt -> [ meta + [tool: "dcc"], txt ] }, bsj_reads ) ch_versions = ch_versions.mix(DCC_MATE1_1ST_PASS.out.versions) ch_versions = ch_versions.mix(DCC_MATE1_SJDB.out.versions) @@ -210,7 +210,7 @@ workflow CIRCRNA_DISCOVERY { MAPSPLICE_ALIGN( reads, bowtie_index.collect(), chromosomes, gtf ) MAPSPLICE_PARSE( MAPSPLICE_ALIGN.out.raw_fusions ) MAPSPLICE_ANNOTATE( MAPSPLICE_PARSE.out.junction, fasta, MAPSPLICE_REFERENCE.out.txt ) - mapsplice_filter = MAPSPLICE_ANNOTATE.out.txt.map{ meta, txt -> meta.tool = "mapsplice"; return [ meta, txt ] } + mapsplice_filter = MAPSPLICE_ANNOTATE.out.txt.map{ meta, txt -> [ meta + [tool: "mapsplice"], txt ] } MAPSPLICE_FILTER( mapsplice_filter, bsj_reads ) ch_versions = ch_versions.mix(MAPSPLICE_REFERENCE.out.versions) @@ -258,7 +258,7 @@ workflow CIRCRNA_DISCOVERY { if( tools_selected.size() > 1){ - MERGE_TOOLS( ch_matrix.map{ meta, bed -> var = [:]; var.id = meta.id; return [ var, bed ] }.groupTuple(), tool_filter, duplicates_fun ) + MERGE_TOOLS( ch_matrix.map{ meta, bed -> [ [id: meta.id], bed ] }.groupTuple(), tool_filter, duplicates_fun ) COUNTS_COMBINED( MERGE_TOOLS.out.merged.map{ meta, bed -> return [ bed ] }.collect() ) @@ -269,7 +269,7 @@ workflow CIRCRNA_DISCOVERY { }else{ - COUNTS_SINGLE( ch_matrix.map{ meta, bed -> var = [:]; var.tool = meta.tool; return [ var, bed ] }.groupTuple() ) + COUNTS_SINGLE( ch_matrix.map{ meta, bed -> [ [tool: meta.tool], bed ] }.groupTuple() ) dea_matrix = COUNTS_SINGLE.out.dea_matrix clr_matrix = COUNTS_SINGLE.out.clr_matrix From 690ab3c88f74608e062337a98b3c2f86580c522f Mon Sep 17 00:00:00 2001 From: nictru Date: Tue, 24 Oct 2023 15:32:37 +0200 Subject: [PATCH 092/491] Fix problems which prevent proper caching --- bin/circRNA_counts_matrix.py | 2 ++ modules/local/count_matrix/combined/main.nf | 4 +-- .../local/count_matrix/merge_tools/main.nf | 2 +- modules/local/fasta/main.nf | 9 +++--- subworkflows/local/circrna_discovery.nf | 20 ++++--------- subworkflows/local/differential_expression.nf | 10 ++----- subworkflows/local/prepare_genome.nf | 30 ++++++++----------- 7 files changed, 28 insertions(+), 49 deletions(-) diff --git a/bin/circRNA_counts_matrix.py b/bin/circRNA_counts_matrix.py index 07999b23..3f6e24f6 100755 --- a/bin/circRNA_counts_matrix.py +++ b/bin/circRNA_counts_matrix.py @@ -1,3 +1,5 @@ +#!/usr/bin/env python + import sys, glob from collections import defaultdict diff --git a/modules/local/count_matrix/combined/main.nf b/modules/local/count_matrix/combined/main.nf index e277ffff..353da918 100644 --- a/modules/local/count_matrix/combined/main.nf +++ b/modules/local/count_matrix/combined/main.nf @@ -20,12 +20,12 @@ process COUNTS_COMBINED { script: def args = task.ext.args ?: '' """ - python ${workflow.projectDir}/bin/circRNA_counts_matrix.py > matrix.txt + circRNA_counts_matrix.py > matrix.txt ## handle non-canon chromosomes here (https://stackoverflow.com/questions/71479919/joining-columns-based-on-number-of-fields) n_samps=\$(ls *.bed | wc -l) canon=\$(awk -v a="\$n_samps" 'BEGIN {print a + 4}') awk -v n="\$canon" '{ for (i = 2; i <= NF - n + 1; ++i) { \$1 = \$1"-"\$i; \$i=""; } } 1' matrix.txt | awk -v OFS="\t" '\$1=\$1' > circRNA_matrix.txt - Rscript ${workflow.projectDir}/bin/reformat_count_matrix.R + reformat_count_matrix.R cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/count_matrix/merge_tools/main.nf b/modules/local/count_matrix/merge_tools/main.nf index cc6818dd..106df47b 100644 --- a/modules/local/count_matrix/merge_tools/main.nf +++ b/modules/local/count_matrix/merge_tools/main.nf @@ -31,7 +31,7 @@ process MERGE_TOOLS { ## Use intersection of "n" (params.tool_filter) circRNAs called by tools ## remove duplicate IDs, keep highest count. - Rscript ${workflow.projectDir}/bin/consolidate_algorithms_intersection.R samples.csv $tool_filter $duplicates_fun + consolidate_algorithms_intersection.R samples.csv $tool_filter $duplicates_fun mv combined_counts.bed ${prefix}.bed cat <<-END_VERSIONS > versions.yml diff --git a/modules/local/fasta/main.nf b/modules/local/fasta/main.nf index e33edeed..904cecc3 100644 --- a/modules/local/fasta/main.nf +++ b/modules/local/fasta/main.nf @@ -8,8 +8,8 @@ process FASTA { 'quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_2' }" input: - tuple val(meta), path(bed) - path fasta + tuple val(meta), path(bed, name: "bed.input") + path fasta, name: "fasta.input" output: tuple val(meta), path("${prefix}.fa"), emit: analysis_fasta @@ -24,15 +24,14 @@ process FASTA { prefix = task.ext.prefix ?: "${meta.id}" """ ## FASTA sequences (bedtools does not like the extra annotation info - split will not work properly) - cut -d\$'\t' -f1-12 ${prefix}.bed > bed12.tmp + cut -d\$'\t' -f1-12 bed.input > bed12.tmp bedtools getfasta -fi $fasta -bed bed12.tmp -s -split -name > circ_seq.tmp ## clean fasta header grep -A 1 '>' circ_seq.tmp | cut -d: -f1,2,3 > ${prefix}.fa && rm circ_seq.tmp ## add backsplice sequence for miRanda Targetscan, publish canonical FASTA to results. - rm $fasta - bash ${workflow.projectDir}/bin/backsplice_gen.sh ${prefix}.fa + backsplice_gen.sh ${prefix}.fa cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index d75f6ed0..2949f9c0 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -60,20 +60,10 @@ workflow CIRCRNA_DISCOVERY { main: ch_versions = Channel.empty() - ch_fasta = Channel.fromPath(fasta) - ch_gtf = Channel.fromPath(gtf) - - ch_fasta.map{ it -> - meta = [:] - meta.id = it.simpleName - return [ meta, [it] ] - }.set{ fasta_tuple } - - gtf_tuple = ch_gtf.map{ it -> - meta = [:] - meta.id = it.simpleName - return [ meta, [it] ] - }.collect() + ch_fasta = Channel.value(fasta) + ch_gtf = Channel.value(gtf) + fasta_tuple = Channel.value([[id: "fasta"], fasta]) + gtf_tuple = Channel.value([[id: "gtf"], gtf]) // @@ -207,7 +197,7 @@ workflow CIRCRNA_DISCOVERY { // MAPSPLICE_REFERENCE( gtf ) - MAPSPLICE_ALIGN( reads, bowtie_index.collect(), chromosomes, gtf ) + MAPSPLICE_ALIGN( reads, bowtie_index.collect(), chromosomes, ch_gtf ) MAPSPLICE_PARSE( MAPSPLICE_ALIGN.out.raw_fusions ) MAPSPLICE_ANNOTATE( MAPSPLICE_PARSE.out.junction, fasta, MAPSPLICE_REFERENCE.out.txt ) mapsplice_filter = MAPSPLICE_ANNOTATE.out.txt.map{ meta, txt -> [ meta + [tool: "mapsplice"], txt ] } diff --git a/subworkflows/local/differential_expression.nf b/subworkflows/local/differential_expression.nf index aa92527a..2964c3fb 100644 --- a/subworkflows/local/differential_expression.nf +++ b/subworkflows/local/differential_expression.nf @@ -29,16 +29,10 @@ workflow DIFFERENTIAL_EXPRESSION { ch_fasta = Channel.fromPath(fasta) ch_gtf = Channel.fromPath(gtf) - ch_fasta.map{ it -> - meta = [:] - meta.id = it.simpleName - return [ meta, [it] ] + ch_fasta.map{ it -> [ [id: it.simpleName], [it] ] }.set{ fasta_tuple } - ch_gtf.map{ it -> - meta = [:] - meta.id = it.simpleName - return [ meta, [it] ] + ch_gtf.map{ it -> [ [id: it.simpleName], [it] ] }.set{ gtf_tuple } // diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 496002ff..84d932db 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -18,33 +18,27 @@ workflow PREPARE_GENOME { ch_fasta = Channel.fromPath(fasta) ch_gtf = Channel.fromPath(gtf) + fasta_tuple = Channel.value([[id: "fasta"], fasta]) + gtf_tuple = Channel.value([[id: "gtf"], gtf]) // MapSplice & find_circ requires reference genome to be split per chromosome: if( ( params.tool.contains('mapsplice') || params.tool.contains('find_circ') ) && params.module.contains('circrna_discovery') ){ - file("${params.outdir}/references/chromosomes").mkdirs() - ch_fasta.splitFasta( record: [id:true] ) + directory = file("${params.outdir}/references/chromosomes") + + if ( !directory.exists() ) { + directory.mkdirs() + ch_fasta.splitFasta( record: [id:true] ) .map{ record -> record.id.toString() } .set{ ID } - ch_fasta.splitFasta( file: true ) - .merge( ID ).map{ file, id -> file.copyTo("${params.outdir}/references/chromosomes/${id}.fa") } + ch_fasta.splitFasta( file: true ) + .merge( ID ).map{ file, id -> file.copyTo(directory + "/${id}.fa") } + } - stage_chromosomes = Channel.value("${workflow.launchDir}/${params.outdir}/references/chromosomes") + stage_chromosomes = Channel.value(directory) } - ch_fasta.map{ it -> - meta = [:] - meta.id = it.simpleName - return [ meta, [it] ] - }.set{ fasta_tuple } - - ch_gtf.map{ it -> - meta = [:] - meta.id = it.simpleName - return [ meta, [it] ] - }.set{ gtf_tuple } - - BOWTIE_BUILD(fasta) + BOWTIE_BUILD(ch_fasta) BOWTIE2_BUILD(fasta_tuple) From 7036c933dfb5d79becd564d907c1e1e9f0368e55 Mon Sep 17 00:00:00 2001 From: nictru Date: Sun, 19 Nov 2023 08:19:38 +0100 Subject: [PATCH 093/491] Escape tab characters --- modules/local/annotation/full_annotation/main.nf | 2 +- modules/local/annotation/parent_gene/main.nf | 4 ++-- modules/local/circexplorer2/filter/main.nf | 4 ++-- modules/local/circexplorer2/reference/main.nf | 2 +- modules/local/circrna_finder/filter/main.nf | 4 ++-- modules/local/ciriquant/filter/main.nf | 6 +++--- modules/local/count_matrix/combined/main.nf | 2 +- modules/local/count_matrix/single/main.nf | 2 +- modules/local/dcc/dcc/main.nf | 4 ++-- modules/local/dcc/filter/main.nf | 4 ++-- modules/local/fasta/main.nf | 2 +- modules/local/find_circ/filter/main.nf | 4 ++-- modules/local/mirna_targets/main.nf | 8 ++++---- modules/local/segemehl/filter/main.nf | 6 +++--- modules/local/stringtie/prepde/main.nf | 2 +- modules/local/targetscan/predict/main.nf | 2 +- 16 files changed, 29 insertions(+), 29 deletions(-) diff --git a/modules/local/annotation/full_annotation/main.nf b/modules/local/annotation/full_annotation/main.nf index a8954311..789c884f 100644 --- a/modules/local/annotation/full_annotation/main.nf +++ b/modules/local/annotation/full_annotation/main.nf @@ -33,7 +33,7 @@ process ANNOTATION { annotate_outputs.sh $exon_boundary &> ${prefix}.log mv master_bed12.bed ${prefix}.bed.tmp - awk -v FS="\t" '{print \$11}' ${prefix}.bed.tmp > mature_len.tmp + awk -v FS="\\t" '{print \$11}' ${prefix}.bed.tmp > mature_len.tmp awk -v FS="," '{for(i=t=0;i mature_length paste ${prefix}.bed.tmp mature_length > ${prefix}.bed diff --git a/modules/local/annotation/parent_gene/main.nf b/modules/local/annotation/parent_gene/main.nf index ed035527..9566f015 100644 --- a/modules/local/annotation/parent_gene/main.nf +++ b/modules/local/annotation/parent_gene/main.nf @@ -35,14 +35,14 @@ process PARENT_GENE { start=\$(echo \$line | cut -d- -f1 | cut -d: -f2) stop=\$(echo \$line | cut -d- -f2 | cut -d: -f1) sign=\$(echo \$line | cut -d: -f3) - echo -e "\$chr\t\$start\t\$stop\t\$name\t0\t\$sign" >> \${name}.bed + echo -e "\$chr\\t\$start\\t\$stop\\t\$name\\t0\\t\$sign" >> \${name}.bed done < IDs.txt cat *.bed > merged.txt && rm IDs.txt && rm *.bed && mv merged.txt circs.bed # Re-use annotation script to identify the host gene. annotate_outputs.sh $exon_boundary &> annotation.log - awk -v OFS="\t" '{print \$4, \$14}' master_bed12.bed > circrna_host-gene.txt + awk -v OFS="\\t" '{print \$4, \$14}' master_bed12.bed > circrna_host-gene.txt cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/circexplorer2/filter/main.nf b/modules/local/circexplorer2/filter/main.nf index e0973753..3b6cc9bf 100644 --- a/modules/local/circexplorer2/filter/main.nf +++ b/modules/local/circexplorer2/filter/main.nf @@ -24,9 +24,9 @@ process CIRCEXPLORER2_FILTER { prefix = task.ext.prefix ?: "${meta.id}" def VERSION = '1.3.4' """ - awk '{if(\$13 >= ${bsj_reads}) print \$0}' ${prefix}.txt | awk -v OFS="\t" '{print \$1,\$2,\$3,\$6,\$13}' > ${prefix}_${meta.tool}.bed + awk '{if(\$13 >= ${bsj_reads}) print \$0}' ${prefix}.txt | awk -v OFS="\\t" '{print \$1,\$2,\$3,\$6,\$13}' > ${prefix}_${meta.tool}.bed - awk -v OFS="\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_${meta.tool}.bed > ${prefix}_${meta.tool}_circs.bed + awk -v OFS="\\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_${meta.tool}.bed > ${prefix}_${meta.tool}_circs.bed cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/circexplorer2/reference/main.nf b/modules/local/circexplorer2/reference/main.nf index 6bb46f78..07571e4a 100644 --- a/modules/local/circexplorer2/reference/main.nf +++ b/modules/local/circexplorer2/reference/main.nf @@ -27,7 +27,7 @@ process CIRCEXPLORER2_REFERENCE { $gtf \ ${prefix}.genepred - awk -v OFS="\t" '{print \$12, \$1, \$2, \$3, \$4, \$5, \$6, \$7, \$8, \$9, \$10}' ${prefix}.genepred > ${prefix}.txt + awk -v OFS="\\t" '{print \$12, \$1, \$2, \$3, \$4, \$5, \$6, \$7, \$8, \$9, \$10}' ${prefix}.genepred > ${prefix}.txt cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/circrna_finder/filter/main.nf b/modules/local/circrna_finder/filter/main.nf index 0cda828e..1182442f 100644 --- a/modules/local/circrna_finder/filter/main.nf +++ b/modules/local/circrna_finder/filter/main.nf @@ -29,9 +29,9 @@ process CIRCRNA_FINDER_FILTER { mkdir -p star_dir && mv *.tab *.junction *.sam star_dir postProcessStarAlignment.pl --starDir star_dir/ --outDir ./ - awk '{if(\$5 >= ${bsj_reads}) print \$0}' ${prefix}.filteredJunctions.bed | awk -v OFS="\t" -F"\t" '{print \$1,\$2,\$3,\$6,\$5}' > ${prefix}_circrna_finder.bed + awk '{if(\$5 >= ${bsj_reads}) print \$0}' ${prefix}.filteredJunctions.bed | awk -v OFS="\\t" -F"\\t" '{print \$1,\$2,\$3,\$6,\$5}' > ${prefix}_circrna_finder.bed - awk -v OFS="\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_circrna_finder.bed > ${prefix}_circrna_finder_circs.bed + awk -v OFS="\\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_circrna_finder.bed > ${prefix}_circrna_finder_circs.bed cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/ciriquant/filter/main.nf b/modules/local/ciriquant/filter/main.nf index 518555a3..c36e4638 100644 --- a/modules/local/ciriquant/filter/main.nf +++ b/modules/local/ciriquant/filter/main.nf @@ -24,16 +24,16 @@ process CIRIQUANT_FILTER { def VERSION = '1.3.4' """ grep -v "#" ${prefix}.gtf | awk '{print \$14}' | cut -d '.' -f1 > counts - grep -v "#" ${prefix}.gtf | awk -v OFS="\t" '{print \$1,\$4,\$5,\$7}' > ${prefix}.tmp + grep -v "#" ${prefix}.gtf | awk -v OFS="\\t" '{print \$1,\$4,\$5,\$7}' > ${prefix}.tmp paste ${prefix}.tmp counts > ${prefix}_unfilt.bed awk '{if(\$5 >= ${bsj_reads}) print \$0}' ${prefix}_unfilt.bed > ${prefix}_filt.bed grep -v '^\$' ${prefix}_filt.bed > ${prefix}_ciriquant - awk -v OFS="\t" '{\$2-=1;print}' ${prefix}_ciriquant > ${prefix}_ciriquant.bed + awk -v OFS="\\t" '{\$2-=1;print}' ${prefix}_ciriquant > ${prefix}_ciriquant.bed rm ${prefix}.gtf - awk -v OFS="\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_ciriquant.bed > ${prefix}_ciriquant_circs.bed + awk -v OFS="\\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_ciriquant.bed > ${prefix}_ciriquant_circs.bed cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/count_matrix/combined/main.nf b/modules/local/count_matrix/combined/main.nf index 353da918..4c299853 100644 --- a/modules/local/count_matrix/combined/main.nf +++ b/modules/local/count_matrix/combined/main.nf @@ -24,7 +24,7 @@ process COUNTS_COMBINED { ## handle non-canon chromosomes here (https://stackoverflow.com/questions/71479919/joining-columns-based-on-number-of-fields) n_samps=\$(ls *.bed | wc -l) canon=\$(awk -v a="\$n_samps" 'BEGIN {print a + 4}') - awk -v n="\$canon" '{ for (i = 2; i <= NF - n + 1; ++i) { \$1 = \$1"-"\$i; \$i=""; } } 1' matrix.txt | awk -v OFS="\t" '\$1=\$1' > circRNA_matrix.txt + awk -v n="\$canon" '{ for (i = 2; i <= NF - n + 1; ++i) { \$1 = \$1"-"\$i; \$i=""; } } 1' matrix.txt | awk -v OFS="\\t" '\$1=\$1' > circRNA_matrix.txt reformat_count_matrix.R cat <<-END_VERSIONS > versions.yml diff --git a/modules/local/count_matrix/single/main.nf b/modules/local/count_matrix/single/main.nf index 59f628c8..856ffa7e 100644 --- a/modules/local/count_matrix/single/main.nf +++ b/modules/local/count_matrix/single/main.nf @@ -33,7 +33,7 @@ process COUNTS_SINGLE { ## handle non-canon chromosomes here (https://stackoverflow.com/questions/71479919/joining-columns-based-on-number-of-fields) n_samps=\$(ls *.bed | wc -l) canon=\$(awk -v a="\$n_samps" 'BEGIN {print a + 4}') - awk -v n="\$canon" '{ for (i = 2; i <= NF - n + 1; ++i) { \$1 = \$1"-"\$i; \$i=""; } } 1' matrix.txt | awk -v OFS="\t" '\$1=\$1' > circRNA_matrix.txt + awk -v n="\$canon" '{ for (i = 2; i <= NF - n + 1; ++i) { \$1 = \$1"-"\$i; \$i=""; } } 1' matrix.txt | awk -v OFS="\\t" '\$1=\$1' > circRNA_matrix.txt Rscript ${workflow.projectDir}/bin/reformat_count_matrix.R cat <<-END_VERSIONS > versions.yml diff --git a/modules/local/dcc/dcc/main.nf b/modules/local/dcc/dcc/main.nf index b8db483f..77dc2c55 100644 --- a/modules/local/dcc/dcc/main.nf +++ b/modules/local/dcc/dcc/main.nf @@ -31,7 +31,7 @@ process DCC { DCC @samplesheet -D -an $gtf -Pi -ss -F -M -Nr 1 1 -fg -A $fasta -N -T ${task.cpus} awk '{print \$6}' CircCoordinates >> strand - paste CircRNACount strand | tail -n +2 | awk -v OFS="\t" '{print \$1,\$2,\$3,\$5,\$4}' >> ${prefix}.txt + paste CircRNACount strand | tail -n +2 | awk -v OFS="\\t" '{print \$1,\$2,\$3,\$5,\$4}' >> ${prefix}.txt cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -49,7 +49,7 @@ process DCC { DCC @samplesheet -mt1 @mate1file -mt2 @mate2file -D -an $gtf -Pi -ss -F -M -Nr 1 1 -fg -A $fasta -N -T ${task.cpus} awk '{print \$6}' CircCoordinates >> strand - paste CircRNACount strand | tail -n +2 | awk -v OFS="\t" '{print \$1,\$2,\$3,\$5,\$4}' >> ${prefix}.txt + paste CircRNACount strand | tail -n +2 | awk -v OFS="\\t" '{print \$1,\$2,\$3,\$5,\$4}' >> ${prefix}.txt cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/dcc/filter/main.nf b/modules/local/dcc/filter/main.nf index 4c7d235e..78d3e571 100644 --- a/modules/local/dcc/filter/main.nf +++ b/modules/local/dcc/filter/main.nf @@ -24,8 +24,8 @@ process DCC_FILTER { def VERSION = '1.3.4' """ awk '{if(\$5 >= ${bsj_reads}) print \$0}' ${prefix}.txt > ${prefix}_dcc.filtered - awk -v OFS="\t" '{\$2-=1;print}' ${prefix}_dcc.filtered > ${prefix}_dcc.bed - awk -v OFS="\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_dcc.bed > ${prefix}_dcc_circs.bed + awk -v OFS="\\t" '{\$2-=1;print}' ${prefix}_dcc.filtered > ${prefix}_dcc.bed + awk -v OFS="\\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_dcc.bed > ${prefix}_dcc_circs.bed cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/fasta/main.nf b/modules/local/fasta/main.nf index 904cecc3..aff89fde 100644 --- a/modules/local/fasta/main.nf +++ b/modules/local/fasta/main.nf @@ -24,7 +24,7 @@ process FASTA { prefix = task.ext.prefix ?: "${meta.id}" """ ## FASTA sequences (bedtools does not like the extra annotation info - split will not work properly) - cut -d\$'\t' -f1-12 bed.input > bed12.tmp + cut -d\$'\\t' -f1-12 bed.input > bed12.tmp bedtools getfasta -fi $fasta -bed bed12.tmp -s -split -name > circ_seq.tmp ## clean fasta header diff --git a/modules/local/find_circ/filter/main.nf b/modules/local/find_circ/filter/main.nf index a12c15ba..c8e4f3a7 100644 --- a/modules/local/find_circ/filter/main.nf +++ b/modules/local/find_circ/filter/main.nf @@ -30,9 +30,9 @@ process FIND_CIRC_FILTER { maxlength.py 100000 \ > ${prefix}.txt - tail -n +2 ${prefix}.txt | awk -v OFS="\t" '{print \$1,\$2,\$3,\$6,\$5}' > ${prefix}_find_circ.bed + tail -n +2 ${prefix}.txt | awk -v OFS="\\t" '{print \$1,\$2,\$3,\$6,\$5}' > ${prefix}_find_circ.bed - awk -v OFS="\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_find_circ.bed > ${prefix}_find_circ_circs.bed + awk -v OFS="\\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_find_circ.bed > ${prefix}_find_circ_circs.bed cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/mirna_targets/main.nf b/modules/local/mirna_targets/main.nf index 0891e6e4..fdfee556 100644 --- a/modules/local/mirna_targets/main.nf +++ b/modules/local/mirna_targets/main.nf @@ -22,8 +22,8 @@ process MIRNA_TARGETS { prefix = task.ext.prefix ?: "${meta.id}" """ ## reformat and sort miRanda, TargetScan outputs, convert to BED for overlaps. - tail -n +2 $targetscan | sort -k1,1 -k4n | awk -v OFS="\t" '{print \$1, \$2, \$4, \$5, \$9}' | awk -v OFS="\t" '{print \$2, \$3, \$4, \$1, "0", \$5}' > targetscan.bed - tail -n +2 $miranda | sort -k2,2 -k7n | awk -v OFS="\t" '{print \$2, \$1, \$3, \$4, \$7, \$8}' | awk -v OFS="\t" '{print \$2, \$5, \$6, \$1, \$3, \$4}' | sed 's/^[^-]*-//g' > miranda.bed + tail -n +2 $targetscan | sort -k1,1 -k4n | awk -v OFS="\\t" '{print \$1, \$2, \$4, \$5, \$9}' | awk -v OFS="\t" '{print \$2, \$3, \$4, \$1, "0", \$5}' > targetscan.bed + tail -n +2 $miranda | sort -k2,2 -k7n | awk -v OFS="\\t" '{print \$2, \$1, \$3, \$4, \$7, \$8}' | awk -v OFS="\t" '{print \$2, \$5, \$6, \$1, \$3, \$4}' | sed 's/^[^-]*-//g' > miranda.bed ## intersect, consolidate miRanda, TargetScan information about miRs. ## -wa to output miRanda hits - targetscan makes it difficult to resolve duplicate miRNAs at MRE sites. @@ -32,8 +32,8 @@ process MIRNA_TARGETS { ## remove duplicate miRNA entries at MRE sites. ## strategy: sory by circs, sort by start position, sort by site type - the goal is to take the best site type (i.e rank site type found at MRE site). - paste ${prefix}.mirnas.tmp mirna_type | sort -k3,3 -k2n -k7r | awk -v OFS="\t" '{print \$4,\$1,\$2,\$3,\$5,\$6,\$7}' | awk -F "\t" '{if (!seen[\$1,\$2,\$3,\$4,\$5,\$6]++)print}' | sort -k1,1 -k3n > ${prefix}.mirna_targets.tmp - echo -e "circRNA\tmiRNA\tStart\tEnd\tScore\tEnergy_KcalMol\tSite_type" | cat - ${prefix}.mirna_targets.tmp > ${prefix}.mirna_targets.txt + paste ${prefix}.mirnas.tmp mirna_type | sort -k3,3 -k2n -k7r | awk -v OFS="\\t" '{print \$4,\$1,\$2,\$3,\$5,\$6,\$7}' | awk -F "\\t" '{if (!seen[\$1,\$2,\$3,\$4,\$5,\$6]++)print}' | sort -k1,1 -k3n > ${prefix}.mirna_targets.tmp + echo -e "circRNA\\tmiRNA\\tStart\\tEnd\\tScore\\tEnergy_KcalMol\\tSite_type" | cat - ${prefix}.mirna_targets.tmp > ${prefix}.mirna_targets.txt cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/segemehl/filter/main.nf b/modules/local/segemehl/filter/main.nf index a3c1c7a8..a1cf9929 100644 --- a/modules/local/segemehl/filter/main.nf +++ b/modules/local/segemehl/filter/main.nf @@ -24,11 +24,11 @@ process SEGEMEHL_FILTER { prefix = task.ext.prefix ?: "${meta.id}" def VERSION = '1.3.4' """ - grep ';C;' ${prefix}.sngl.bed | awk -v OFS="\t" '{print \$1,\$2,\$3,\$6}' | sort | uniq -c | awk -v OFS="\t" '{print \$2,\$3,\$4,\$5,\$1}' > ${prefix}_collapsed.bed + grep ';C;' ${prefix}.sngl.bed | awk -v OFS="\\t" '{print \$1,\$2,\$3,\$6}' | sort | uniq -c | awk -v OFS="\\t" '{print \$2,\$3,\$4,\$5,\$1}' > ${prefix}_collapsed.bed - awk -v OFS="\t" -v BSJ=${bsj_reads} '{if(\$5>=BSJ) print \$0}' ${prefix}_collapsed.bed > ${prefix}_segemehl.bed + awk -v OFS="\\t" -v BSJ=${bsj_reads} '{if(\$5>=BSJ) print \$0}' ${prefix}_collapsed.bed > ${prefix}_segemehl.bed - awk -v OFS="\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_segemehl.bed > ${prefix}_segemehl_circs.bed + awk -v OFS="\\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_segemehl.bed > ${prefix}_segemehl_circs.bed cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/stringtie/prepde/main.nf b/modules/local/stringtie/prepde/main.nf index 92f4680c..eb72483b 100644 --- a/modules/local/stringtie/prepde/main.nf +++ b/modules/local/stringtie/prepde/main.nf @@ -19,7 +19,7 @@ process STRINGTIE_PREPDE { script: """ - for file in \$(ls *.gtf); do sample_id=\${file%".transcripts.gtf"}; touch samples.txt; printf "\$sample_id\t\$file\\n" >> samples.txt ; done + for file in \$(ls *.gtf); do sample_id=\${file%".transcripts.gtf"}; touch samples.txt; printf "\$sample_id\\t\$file\\n" >> samples.txt ; done prepDE.py -i samples.txt diff --git a/modules/local/targetscan/predict/main.nf b/modules/local/targetscan/predict/main.nf index 62599ab8..e8e5567f 100644 --- a/modules/local/targetscan/predict/main.nf +++ b/modules/local/targetscan/predict/main.nf @@ -25,7 +25,7 @@ process TARGETSCAN { ##format for targetscan cat $fasta | grep ">" | sed 's/>//g' > id cat $fasta | grep -v ">" > seq - paste id seq | awk -v OFS="\t" '{print \$1, "0000", \$2}' > ${prefix}_ts.txt + paste id seq | awk -v OFS="\\t" '{print \$1, "0000", \$2}' > ${prefix}_ts.txt # run targetscan targetscan_70.pl mature.txt ${prefix}_ts.txt ${prefix}.txt From 099b99784a11eb6809232abf9793d5a78b5344fd Mon Sep 17 00:00:00 2001 From: nictru Date: Fri, 10 Nov 2023 08:26:15 +0100 Subject: [PATCH 094/491] Fix problems with illegal R column names --- bin/reformat_count_matrix.R | 2 +- modules/local/count_matrix/combined/main.nf | 2 -- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/bin/reformat_count_matrix.R b/bin/reformat_count_matrix.R index 8afabe6f..3c635b29 100755 --- a/bin/reformat_count_matrix.R +++ b/bin/reformat_count_matrix.R @@ -4,7 +4,7 @@ ## License: MIT library(dplyr) -mat <- read.table("circRNA_matrix.txt", sep="\t", header=T, stringsAsFactors=F) +mat <- read.table("circRNA_matrix.txt", sep="\t", header=T, stringsAsFactors=F, check.names=F) mat$ID <- with(mat, paste0(Chr, sep=":", Start, sep="-", Stop, sep=":", Strand)) mat <- mat[,-c(1:4)] mat1 <- mat %>% select(ID, everything()) diff --git a/modules/local/count_matrix/combined/main.nf b/modules/local/count_matrix/combined/main.nf index 4c299853..0c4719ab 100644 --- a/modules/local/count_matrix/combined/main.nf +++ b/modules/local/count_matrix/combined/main.nf @@ -31,9 +31,7 @@ process COUNTS_COMBINED { "${task.process}": awk: \$(awk --version | head -n 1 | cut -d' ' -f3 | sed 's/,//g') r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//') - argparser: \$(Rscript -e "library(arparser); cat(as.character(packageVersion('argparser')))") dplyr: \$(Rscript -e "library(dplyr); cat(as.character(packageVersion('dplyr')))") - python: \$(python --version | sed -e 's/Python //g') END_VERSIONS """ } From bcfb46ebc1ba876f61302b4dada3bef3d3cf5a47 Mon Sep 17 00:00:00 2001 From: nictru Date: Tue, 31 Oct 2023 14:49:53 +0100 Subject: [PATCH 095/491] Recycle general STAR run for DCC --- subworkflows/local/circrna_discovery.nf | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 2949f9c0..8501cffb 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -154,10 +154,6 @@ workflow CIRCRNA_DISCOVERY { // DCC WORKFLOW // - DCC_1ST_PASS( reads, star_index, gtf_tuple, star_ignore_sjdbgtf, seq_platform, seq_center ) - DCC_SJDB( DCC_1ST_PASS.out.tab.map{ meta, tab -> return tab }.collect().map{[[id: "dcc_sjdb"], it]}, bsj_reads ) - DCC_2ND_PASS( reads, star_index, DCC_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) - mate1 = reads.filter{ meta, reads -> !meta.single_end }.map{ meta, reads -> return [ [id: meta.id, single_end: true], reads[0] ] } DCC_MATE1_1ST_PASS( mate1, star_index, gtf_tuple, star_ignore_sjdbgtf, seq_platform, seq_center ) DCC_MATE1_SJDB( DCC_MATE1_1ST_PASS.out.tab.map{ meta, tab -> return tab }.collect().map{[[id: "mate1_sjdb"], it]}, bsj_reads ) @@ -168,7 +164,7 @@ workflow CIRCRNA_DISCOVERY { DCC_MATE2_SJDB( DCC_MATE2_1ST_PASS.out.tab.map{ meta, tab -> return tab }.collect().map{[[id: "mate2_sjdb"], it]}, bsj_reads ) DCC_MATE2_2ND_PASS( mate2, star_index, DCC_MATE2_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) - dcc_stage = DCC_2ND_PASS.out.junction.map{ meta, junction -> return [ meta.id, meta, junction]} + dcc_stage = STAR_2ND_PASS.out.junction.map{ meta, junction -> return [ meta.id, meta, junction]} .join( DCC_MATE1_2ND_PASS.out.junction.map{ meta, junction -> return [ meta.id, junction] }, remainder: true From eecedfd202450fcfc31b02983c15bfa51326890e Mon Sep 17 00:00:00 2001 From: nictru Date: Tue, 5 Dec 2023 09:57:46 +0100 Subject: [PATCH 096/491] Remove unnecessary input naming --- modules/local/fasta/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/local/fasta/main.nf b/modules/local/fasta/main.nf index aff89fde..086fd61a 100644 --- a/modules/local/fasta/main.nf +++ b/modules/local/fasta/main.nf @@ -8,8 +8,8 @@ process FASTA { 'quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_2' }" input: - tuple val(meta), path(bed, name: "bed.input") - path fasta, name: "fasta.input" + tuple val(meta), path(bed) + path fasta output: tuple val(meta), path("${prefix}.fa"), emit: analysis_fasta @@ -24,7 +24,7 @@ process FASTA { prefix = task.ext.prefix ?: "${meta.id}" """ ## FASTA sequences (bedtools does not like the extra annotation info - split will not work properly) - cut -d\$'\\t' -f1-12 bed.input > bed12.tmp + cut -d\$'\\t' -f1-12 $bed > bed12.tmp bedtools getfasta -fi $fasta -bed bed12.tmp -s -split -name > circ_seq.tmp ## clean fasta header From f38dd944bb577a4cbb2702941f424182e5bb6c66 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 13 Jan 2024 17:45:22 +0100 Subject: [PATCH 097/491] Unify test config --- .github/workflows/ci.yml | 2 +- conf/test.config | 20 ++++++++++---------- conf/test_cache.config | 34 ---------------------------------- nextflow.config | 5 +++-- 4 files changed, 14 insertions(+), 47 deletions(-) delete mode 100644 conf/test_cache.config diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 82c8f42a..79f1ee44 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -67,4 +67,4 @@ jobs: - name: Run pipeline with test data run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets + nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets diff --git a/conf/test.config b/conf/test.config index f8694df1..c0444832 100644 --- a/conf/test.config +++ b/conf/test.config @@ -19,16 +19,16 @@ params { max_memory = 6.GB max_time = 6.h - // Input data for test data - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/circrna/samples.csv' - fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/circrna/reference/chrI.fa' - gtf = 'https://raw.githubusercontent.com/nf-core/test-datasets/circrna/reference/chrI.gtf' - mature = 'https://raw.githubusercontent.com/nf-core/test-datasets/circrna/reference/mature.fa' - species = 'cel' - tool = 'circexplorer2' - phenotype = 'https://raw.githubusercontent.com/nf-core/test-datasets/circrna/phenotype.csv' + // Test input data + input = "${params.test_data_base}/samples.csv" + fasta = "${params.test_data_base}/reference/chrI.fa" + gtf = "${params.test_data_base}/reference/chrI.gtf" + mature = "${params.test_data_base}/reference/mature.fa" + tool = "circexplorer2" + phenotype = "${params.test_data_base}/phenotype.csv" skip_trimming = false - module = 'circrna_discovery,mirna_prediction,differential_expression' - outdir = 'results/' + module = "circrna_discovery,mirna_prediction,differential_expression" + outdir = "results/" bsj_reads = 2 + species = "cel" } diff --git a/conf/test_cache.config b/conf/test_cache.config deleted file mode 100644 index c0444832..00000000 --- a/conf/test_cache.config +++ /dev/null @@ -1,34 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running minimal tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines input files and everything required to run a fast and simple pipeline test. - - Use as follows: - nextflow run nf-core/circrna -profile test, --outdir - ----------------------------------------------------------------------------------------- -*/ - -params { - config_profile_name = 'Test profile' - config_profile_description = 'Minimal test dataset to check pipeline function' - - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 6.h - - // Test input data - input = "${params.test_data_base}/samples.csv" - fasta = "${params.test_data_base}/reference/chrI.fa" - gtf = "${params.test_data_base}/reference/chrI.gtf" - mature = "${params.test_data_base}/reference/mature.fa" - tool = "circexplorer2" - phenotype = "${params.test_data_base}/phenotype.csv" - skip_trimming = false - module = "circrna_discovery,mirna_prediction,differential_expression" - outdir = "results/" - bsj_reads = 2 - species = "cel" -} diff --git a/nextflow.config b/nextflow.config index 0b995eda..26d79e5c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -94,10 +94,12 @@ params { max_cpus = 50 max_time = '240.h' + test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/circrna' + // Schema validation default options validationFailUnrecognisedParams = false validationLenientMode = false - validationSchemaIgnoreParams = 'genomes,igenomes_base' + validationSchemaIgnoreParams = 'genomes,igenomes_base,test_data_base' validationShowHiddenParams = false validate_params = true } @@ -211,7 +213,6 @@ profiles { executor.memory = 8.GB } test { includeConfig 'conf/test.config' } - test_cache { includeConfig 'conf/test_cache.config' } test_igenomes { includeConfig 'conf/test_igenomes.config' } full { includeConfig 'conf/full.config' } test_full { includeConfig 'conf/test_full.config' } From 2f08d15ed151c18c6e4ae14b11201e84849d608f Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Wed, 24 Jan 2024 16:13:53 +0100 Subject: [PATCH 098/491] add missing defaults to documentation --- README.md | 8 +++----- docs/usage.md | 20 ++++++++------------ nextflow_schema.json | 27 ++++++++++++++++++--------- 3 files changed, 29 insertions(+), 26 deletions(-) diff --git a/README.md b/README.md index f59c42c0..fefe74a4 100644 --- a/README.md +++ b/README.md @@ -76,11 +76,9 @@ nextflow run nf-core/circrna \ --outdir ``` -:::warning -Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those -provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; -see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). -::: +> [!WARNING] +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; +> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/circrna/usage) and the [parameter documentation](https://nf-co.re/circrna/parameters). diff --git a/docs/usage.md b/docs/usage.md index 2f9684a0..b7b18c5c 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -29,9 +29,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. -:::warning -Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). -::: +> [!WARNING] +> Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). The above pipeline run specified with a params file in yaml format: @@ -70,9 +69,8 @@ This version number will be logged in reports when you run the pipeline, so that To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. -:::tip -If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. -::: +> [!TIP] +> If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. # Input specifications @@ -250,9 +248,8 @@ To view the outputs of the module, please see the output [documentation](https:/ ## Core Nextflow arguments -:::note -These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen). -::: +> [!NOTE] +> These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen). ### `-profile` @@ -260,9 +257,8 @@ Use this parameter to choose a configuration profile. Profiles can give configur Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below. -:::info -We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. -::: +> [!INFO] +> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). diff --git a/nextflow_schema.json b/nextflow_schema.json index 70ac90d7..8dc62486 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -163,7 +163,8 @@ "type": "boolean", "fa_icon": "fas fa-save", "description": "Where possible, save unaligned reads from either STAR, HISAT2 or Salmon to the results directory.", - "help_text": "This may either be in the form of FastQ or BAM files depending on the options available for that particular tool." + "help_text": "This may either be in the form of FastQ or BAM files depending on the options available for that particular tool.", + "default": false } } }, @@ -279,44 +280,52 @@ "type": "boolean", "description": "Skip the adapter trimming step.", "help_text": "Use this if your input FastQ files have already been trimmed outside of the workflow or if you're very confident that there is no adapter contamination in your data.", - "fa_icon": "fas fa-fast-forward" + "fa_icon": "fas fa-fast-forward", + "default": false }, "save_trimmed": { "type": "boolean", "description": "Save the trimmed FastQ files in the results directory.", "help_text": "By default, trimmed FastQ files will not be saved to the results directory. Specify this flag (or set to true in your config file) to copy these files to the results directory when complete.", - "fa_icon": "fas fa-save" + "fa_icon": "fas fa-save", + "default": false }, "skip_fastqc": { "type": "boolean", "description": "Skip FastQC quality control of the sequencing reads.", - "fa_icon": "fas fa-terminal" + "fa_icon": "fas fa-terminal", + "default": false }, "clip_r1": { "type": "integer", "description": "Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads).", - "fa_icon": "fas fa-cut" + "fa_icon": "fas fa-cut", + "default": null }, "clip_r2": { "type": "integer", "description": "Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only).", - "fa_icon": "fas fa-cut" + "fa_icon": "fas fa-cut", + "default": null }, "three_prime_clip_r1": { "type": "integer", "description": "Instructs Trim Galore to remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.", - "fa_icon": "fas fa-cut" + "fa_icon": "fas fa-cut", + "default": null }, "three_prime_clip_r2": { "type": "integer", "description": "Instructs Trim Galore to remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed.", - "fa_icon": "fas fa-cut" + "fa_icon": "fas fa-cut", + "default": null }, "trim_nextseq": { "type": "integer", "description": "Instructs Trim Galore to apply the --nextseq=X option, to trim based on quality after removing poly-G tails.", "help_text": "This enables the option Cutadapt `--nextseq-trim=3'CUTOFF` option via Trim Galore, which will set a quality cutoff (that is normally given with -q instead), but qualities of G bases are ignored. This trimming is in common for the NextSeq- and NovaSeq-platforms, where basecalls without any signal are called as high-quality G bases.", - "fa_icon": "fas fa-cut" + "fa_icon": "fas fa-cut", + "default": null }, "min_trimmed_reads": { "type": "integer", From 87b10267276bcc754121257b6d1a093c73b392a7 Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Thu, 25 Jan 2024 17:04:35 +0100 Subject: [PATCH 099/491] fix wrong default params (null for int) and prettier --- .devcontainer/devcontainer.json | 8 ++++---- nextflow_schema.json | 15 +++++---------- 2 files changed, 9 insertions(+), 14 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 4ecfbfe3..4a9bc5c7 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -18,11 +18,11 @@ "python.linting.flake8Path": "/opt/conda/bin/flake8", "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", - "python.linting.pylintPath": "/opt/conda/bin/pylint" + "python.linting.pylintPath": "/opt/conda/bin/pylint", }, // Add the IDs of extensions you want installed when the container is created. - "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] - } - } + "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"], + }, + }, } diff --git a/nextflow_schema.json b/nextflow_schema.json index 8dc62486..71fb9ef2 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -299,33 +299,28 @@ "clip_r1": { "type": "integer", "description": "Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads).", - "fa_icon": "fas fa-cut", - "default": null + "fa_icon": "fas fa-cut" }, "clip_r2": { "type": "integer", "description": "Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only).", - "fa_icon": "fas fa-cut", - "default": null + "fa_icon": "fas fa-cut" }, "three_prime_clip_r1": { "type": "integer", "description": "Instructs Trim Galore to remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.", - "fa_icon": "fas fa-cut", - "default": null + "fa_icon": "fas fa-cut" }, "three_prime_clip_r2": { "type": "integer", "description": "Instructs Trim Galore to remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed.", - "fa_icon": "fas fa-cut", - "default": null + "fa_icon": "fas fa-cut" }, "trim_nextseq": { "type": "integer", "description": "Instructs Trim Galore to apply the --nextseq=X option, to trim based on quality after removing poly-G tails.", "help_text": "This enables the option Cutadapt `--nextseq-trim=3'CUTOFF` option via Trim Galore, which will set a quality cutoff (that is normally given with -q instead), but qualities of G bases are ignored. This trimming is in common for the NextSeq- and NovaSeq-platforms, where basecalls without any signal are called as high-quality G bases.", - "fa_icon": "fas fa-cut", - "default": null + "fa_icon": "fas fa-cut" }, "min_trimmed_reads": { "type": "integer", From cf629aea1e6c02092bd6460e6a92a98d7fffc204 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sun, 28 Jan 2024 21:45:27 +0100 Subject: [PATCH 100/491] Fix problems with backsplice_gen.sh script in fasta extraction --- modules/local/fasta/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/fasta/main.nf b/modules/local/fasta/main.nf index 086fd61a..63381c1b 100644 --- a/modules/local/fasta/main.nf +++ b/modules/local/fasta/main.nf @@ -9,7 +9,7 @@ process FASTA { input: tuple val(meta), path(bed) - path fasta + path(fasta, stageAs: 'fasta.input') // TODO: Remove input renaming, currently necessary to prevent problems with the backsplice_gen.sh script output: tuple val(meta), path("${prefix}.fa"), emit: analysis_fasta From b0214b71f454682dd6eaed739bbfd93162aec279 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 29 Jan 2024 14:49:58 +0000 Subject: [PATCH 101/491] Template update for nf-core/tools version 2.12 --- .editorconfig | 8 + .github/workflows/awsfulltest.yml | 2 +- .github/workflows/awstest.yml | 2 +- .github/workflows/branch.yml | 2 +- .github/workflows/clean-up.yml | 2 +- .github/workflows/download_pipeline.yml | 67 +++++ .github/workflows/fix-linting.yml | 72 +++-- .github/workflows/linting.yml | 61 +--- .github/workflows/linting_comment.yml | 2 +- .github/workflows/release-announcements.yml | 4 +- .gitpod.yml | 1 + .pre-commit-config.yaml | 7 +- README.md | 8 +- assets/email_template.html | 2 +- assets/email_template.txt | 2 +- assets/nf-core-circrna_logo_light.png | Bin 64214 -> 67279 bytes docs/images/nf-core-circrna_logo_dark.png | Bin 64294 -> 25192 bytes docs/images/nf-core-circrna_logo_light.png | Bin 64214 -> 21840 bytes lib/WorkflowMain.groovy | 16 +- lib/nfcore_external_java_deps.jar | Bin 2291171 -> 0 bytes main.nf | 2 +- modules.json | 6 +- .../dumpsoftwareversions/environment.yml | 2 +- .../custom/dumpsoftwareversions/main.nf | 4 +- .../dumpsoftwareversions/tests/main.nf.test | 7 +- .../tests/main.nf.test.snap | 50 ++-- modules/nf-core/fastqc/tests/main.nf.test | 265 ++++++++++++------ .../nf-core/fastqc/tests/main.nf.test.snap | 12 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 6 +- modules/nf-core/multiqc/meta.yml | 1 - modules/nf-core/multiqc/tests/main.nf.test | 48 +++- .../nf-core/multiqc/tests/main.nf.test.snap | 21 ++ nextflow.config | 3 +- pyproject.toml | 17 +- workflows/circrna.nf | 7 + 36 files changed, 490 insertions(+), 221 deletions(-) create mode 100644 .github/workflows/download_pipeline.yml delete mode 100644 lib/nfcore_external_java_deps.jar create mode 100644 modules/nf-core/multiqc/tests/main.nf.test.snap diff --git a/.editorconfig b/.editorconfig index b6b31907..9b990088 100644 --- a/.editorconfig +++ b/.editorconfig @@ -22,3 +22,11 @@ indent_size = unset [/assets/email*] indent_size = unset + +# ignore Readme +[README.md] +indent_style = unset + +# ignore python +[*.{py}] +indent_style = unset diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 552540b6..7b6bd16d 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -31,7 +31,7 @@ jobs: } profiles: test_full - - uses: actions/upload-artifact@v3 + - uses: actions/upload-artifact@v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 75cde376..9590dcae 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@v3 + - uses: actions/upload-artifact@v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 343d881e..a9339b73 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -19,7 +19,7 @@ jobs: # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets - name: Post PR comment if: failure() - uses: mshick/add-pr-comment@v1 + uses: mshick/add-pr-comment@v2 with: message: | ## This PR is against the `master` branch :x: diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index 694e90ec..e37cfda5 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@v7 + - uses: actions/stale@v9 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml new file mode 100644 index 00000000..8611458a --- /dev/null +++ b/.github/workflows/download_pipeline.yml @@ -0,0 +1,67 @@ +name: Test successful pipeline download with 'nf-core download' + +# Run the workflow when: +# - dispatched manually +# - when a PR is opened or reopened to master branch +# - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. +on: + workflow_dispatch: + pull_request: + types: + - opened + branches: + - master + pull_request_target: + branches: + - master + +env: + NXF_ANSI_LOG: false + +jobs: + download: + runs-on: ubuntu-latest + steps: + - name: Install Nextflow + uses: nf-core/setup-nextflow@v1 + + - uses: actions/setup-python@v5 + with: + python-version: "3.11" + architecture: "x64" + - uses: eWaterCycle/setup-singularity@v7 + with: + singularity-version: 3.8.3 + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install git+https://github.com/nf-core/tools.git@dev + + - name: Get the repository name and current branch set as environment variable + run: | + echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} + echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} + echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV} + + - name: Download the pipeline + env: + NXF_SINGULARITY_CACHEDIR: ./ + run: | + nf-core download ${{ env.REPO_LOWERCASE }} \ + --revision ${{ env.REPO_BRANCH }} \ + --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ + --compress "none" \ + --container-system 'singularity' \ + --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ + --container-cache-utilisation 'amend' \ + --download-configuration + + - name: Inspect download + run: tree ./${{ env.REPOTITLE_LOWERCASE }} + + - name: Run the downloaded pipeline + env: + NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_HOME_MOUNT: true + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 7e6550db..505d843c 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -4,7 +4,7 @@ on: types: [created] jobs: - deploy: + fix-linting: # Only run if comment is on a PR with the main repo, and if it contains the magic keywords if: > contains(github.event.comment.html_url, '/pull/') && @@ -13,10 +13,17 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@v4 + - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 with: token: ${{ secrets.nf_core_bot_auth_token }} + # indication that the linting is being fixed + - name: React on comment + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: eyes + # Action runs on the issue comment, so we don't get the PR by default # Use the gh cli to check out the PR - name: Checkout Pull Request @@ -24,32 +31,59 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - - uses: actions/setup-node@v4 + # Install and run pre-commit + - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + with: + python-version: 3.11 - - name: Install Prettier - run: npm install -g prettier @prettier/plugin-php + - name: Install pre-commit + run: pip install pre-commit - # Check that we actually need to fix something - - name: Run 'prettier --check' - id: prettier_status - run: | - if prettier --check ${GITHUB_WORKSPACE}; then - echo "result=pass" >> $GITHUB_OUTPUT - else - echo "result=fail" >> $GITHUB_OUTPUT - fi + - name: Run pre-commit + id: pre-commit + run: pre-commit run --all-files + continue-on-error: true - - name: Run 'prettier --write' - if: steps.prettier_status.outputs.result == 'fail' - run: prettier --write ${GITHUB_WORKSPACE} + # indication that the linting has finished + - name: react if linting finished succesfully + if: steps.pre-commit.outcome == 'success' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: "+1" - name: Commit & push changes - if: steps.prettier_status.outputs.result == 'fail' + id: commit-and-push + if: steps.pre-commit.outcome == 'failure' run: | git config user.email "core@nf-co.re" git config user.name "nf-core-bot" git config push.default upstream git add . git status - git commit -m "[automated] Fix linting with Prettier" + git commit -m "[automated] Fix code linting" git push + + - name: react if linting errors were fixed + id: react-if-fixed + if: steps.commit-and-push.outcome == 'success' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: hooray + + - name: react if linting errors were not fixed + if: steps.commit-and-push.outcome == 'failure' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: confused + + - name: react if linting errors were not fixed + if: steps.commit-and-push.outcome == 'failure' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + issue-number: ${{ github.event.issue.number }} + body: | + @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually. + See [CI log](https://github.com/nf-core/circrna/actions/runs/${{ github.run_id }}) for more details. diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 905c58e4..81cd098e 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -11,61 +11,22 @@ on: types: [published] jobs: - EditorConfig: + pre-commit: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - uses: actions/setup-node@v4 - - - name: Install editorconfig-checker - run: npm install -g editorconfig-checker - - - name: Run ECLint check - run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile') - - Prettier: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - - uses: actions/setup-node@v4 - - - name: Install Prettier - run: npm install -g prettier - - - name: Run Prettier --check - run: prettier --check ${GITHUB_WORKSPACE} - - PythonBlack: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - - name: Check code lints with Black - uses: psf/black@stable - - # If the above check failed, post a comment on the PR explaining the failure - - name: Post PR comment - if: failure() - uses: mshick/add-pr-comment@v1 + - name: Set up Python 3.11 + uses: actions/setup-python@v5 with: - message: | - ## Python linting (`black`) is failing - - To keep the code consistent with lots of contributors, we run automated code consistency checks. - To fix this CI test, please run: - - * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black` - * Fix formatting errors in your pipeline: `black .` - - Once you push these changes the test should pass, and you can hide this comment :+1: + python-version: 3.11 + cache: "pip" - We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help! + - name: Install pre-commit + run: pip install pre-commit - Thanks again for your contribution! - repo-token: ${{ secrets.GITHUB_TOKEN }} - allow-repeats: false + - name: Run pre-commit + run: pre-commit run --all-files nf-core: runs-on: ubuntu-latest @@ -76,7 +37,7 @@ jobs: - name: Install Nextflow uses: nf-core/setup-nextflow@v1 - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: python-version: "3.11" architecture: "x64" @@ -99,7 +60,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 0bbcd30f..147bcd10 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@v2 + uses: dawidd6/action-download-artifact@v3 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 6ad33927..21ac3f06 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -24,7 +24,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: python-version: "3.10" - name: Install dependencies @@ -56,7 +56,7 @@ jobs: bsky-post: runs-on: ubuntu-latest steps: - - uses: zentered/bluesky-post-action@v0.0.2 + - uses: zentered/bluesky-post-action@v0.1.0 with: post: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! diff --git a/.gitpod.yml b/.gitpod.yml index acf72695..363d5b1d 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -7,6 +7,7 @@ tasks: - name: unset JAVA_TOOL_OPTIONS command: | unset JAVA_TOOL_OPTIONS + vscode: extensions: # based on nf-core.nf-core-extensionpack - codezombiech.gitignore # Language support for .gitignore files diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0c31cdb9..af57081f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,5 +1,10 @@ repos: - repo: https://github.com/pre-commit/mirrors-prettier - rev: "v2.7.1" + rev: "v3.1.0" hooks: - id: prettier + - repo: https://github.com/editorconfig-checker/editorconfig-checker.python + rev: "2.7.3" + hooks: + - id: editorconfig-checker + alias: ec diff --git a/README.md b/README.md index ba556c75..496a65ac 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,9 @@ -# ![nf-core/circrna](docs/images/nf-core-circrna_logo_light.png#gh-light-mode-only) ![nf-core/circrna](docs/images/nf-core-circrna_logo_dark.png#gh-dark-mode-only) - +

    + + + nf-core/circrna + +

    [![GitHub Actions CI Status](https://github.com/nf-core/circrna/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/circrna/actions?query=workflow%3A%22nf-core+CI%22) [![GitHub Actions Linting Status](https://github.com/nf-core/circrna/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/circrna/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/circrna/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) diff --git a/assets/email_template.html b/assets/email_template.html index 03b6ba6e..ddd62126 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -12,7 +12,7 @@ -

    nf-core/circrna v${version}

    +

    nf-core/circrna ${version}

    Run Name: $runName

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b/modules.json index 0452434d..67813eca 100644 --- a/modules.json +++ b/modules.json @@ -7,17 +7,17 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e", + "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53", + "git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "4ab13872435962dadc239979554d13709e20bf29", + "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", "installed_by": ["modules"] } } diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml index f0c63f69..9b3272bc 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.17 + - bioconda::multiqc=1.19 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index 7685b33c..f2187611 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -4,8 +4,8 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : - 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : + 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test index eec1db10..b1e1630b 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -31,7 +31,12 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.versions, + file(process.out.mqc_yml[0]).readLines()[0..10], + file(process.out.yml[0]).readLines()[0..7] + ).match() + } ) } } diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap index 4274ed57..5f59a936 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -1,27 +1,33 @@ { "Should run without failures": { "content": [ - { - "0": [ - "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" - ], - "1": [ - "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" - ], - "2": [ - "versions.yml:md5,3843ac526e762117eedf8825b40683df" - ], - "mqc_yml": [ - "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" - ], - "versions": [ - "versions.yml:md5,3843ac526e762117eedf8825b40683df" - ], - "yml": [ - "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" - ] - } + [ + "versions.yml:md5,76d454d92244589d32455833f7c1ba6d" + ], + [ + "data: \"\\n

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Please remove the comma from the end of the profile string.\nHint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`." + } + if (args[0]) { + log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${args[0]}` has been detected.\n Hint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`." + } + } } diff --git a/lib/nfcore_external_java_deps.jar b/lib/nfcore_external_java_deps.jar deleted file mode 100644 index 805c8bb5e4fd43a12a5891eea5a68788309629b0..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 2291171 zcma%i1CS<7mu}m(-Ea4_?dhK8v~AnAZQHhO+qP}n-E-&Lf8*Yb{bM(7MpZ;s){{|L znGpxiIY(9k6buar3JMCSNkdW|=)W{*ATS^)VMTsgF=-L{?{Od?P#{?eNT`1hApZ%I z{U0Zz{YCuW$x{5%Vj{u{igZ#U4^op8k`lCZbMO+hRMV3)4e|_&%)3YSbmCGpVp4NX zni_mKLGakt&P12{r^KCD0GPa9sIuy`fu+agt?8O-hY9i{WloGe}y@kSsDEY_Fud9 z-?2ab4J)MQXe4E3Xl-U<>PRMQZ)0m@@90KnV5#Te5Tz`pvZ0Lj4F<9%Flh(`Qb;Tn zMV!iFmH{S^fF*j#MCKRUd`7m>9||*;WE32I_6pg4-Q1C#ke$$aVmP-TtfJ+j+N9;Q z>bxN=bCVQkg$Jzty71(+~A9}ZfANuYIVnTdW!??Sj)Ti-Qpk8XgPDab8pk2QD&dwUl=iFhd1c$C2uMVagr zWc@z9s$#g__{3?VGb#)^fSNp^lZh zU>MI!D?+L)nyth{@@L0+B&_M8iR08L)G6#PZQLFmvz-9DlZkwRWigRIyI4xYr7>tRJ-N6MlBB`nJQ!!8D)mI2lB3PP;dC{<{Td>^ 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    Process Name \\", + " \\ Software Version
    CUSTOM_DUMPSOFTWAREVERSIONSpython3.11.7
    yaml5.4.1
    TOOL1tool10.11.9
    TOOL2tool21.9
    WorkflowNextflow
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    \\n \\n \\n \\n \\n \\n \\n \\n\\", + " \\n\\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n \\n \\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n\\n\\n \\n\\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\" + ], + [ + "CUSTOM_DUMPSOFTWAREVERSIONS:", + " python: 3.11.7", + " yaml: 5.4.1", + "TOOL1:", + " tool1: 0.11.9", + "TOOL2:", + " tool2: '1.9'", + "Workflow:" + ] ], - "timestamp": "2023-11-03T14:43:22.157011" + "timestamp": "2024-01-09T23:01:18.710682" } -} +} \ No newline at end of file diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index b9e8f926..1f21c664 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -3,24 +3,20 @@ nextflow_process { name "Test Process FASTQC" script "../main.nf" process "FASTQC" + tag "modules" tag "modules_nfcore" tag "fastqc" - test("Single-Read") { + test("sarscov2 single-end [fastq]") { when { - params { - outdir = "$outputDir" - } process { """ - input[0] = [ + input[0] = Channel.of([ [ id: 'test', single_end:true ], - [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ] - ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + ]) """ } } @@ -28,82 +24,189 @@ nextflow_process { then { assertAll ( { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. // looks like this:
    Mon 2 Oct 2023
    test.gz
    // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - { assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" }, - { assert path(process.out.html.get(0).get(1)).getText().contains("    ") }, - { assert snapshot(process.out.versions).match("versions") }, - { assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" } + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 paired-end [fastq]") { + + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("") }, + { assert path(process.out.html[0][1][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 interleaved [fastq]") { + + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } ) } } -// TODO -// // -// // Test with paired-end data -// // -// workflow test_fastqc_paired_end { -// input = [ -// [id: 'test', single_end: false], // meta map -// [ -// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), -// file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) -// ] -// ] - -// FASTQC ( input ) -// } - -// // -// // Test with interleaved data -// // -// workflow test_fastqc_interleaved { -// input = [ -// [id: 'test', single_end: false], // meta map -// file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) -// ] - -// FASTQC ( input ) -// } - -// // -// // Test with bam data -// // -// workflow test_fastqc_bam { -// input = [ -// [id: 'test', single_end: false], // meta map -// file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) -// ] - -// FASTQC ( input ) -// } - -// // -// // Test with multiple samples -// // -// workflow test_fastqc_multiple { -// input = [ -// [id: 'test', single_end: false], // meta map -// [ -// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), -// file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), -// file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true), -// file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) -// ] -// ] - -// FASTQC ( input ) -// } - -// // -// // Test with custom prefix -// // -// workflow test_fastqc_custom_prefix { -// input = [ -// [ id:'mysample', single_end:true ], // meta map -// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) -// ] - -// FASTQC ( input ) -// } + + test("sarscov2 paired-end [bam]") { + + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 multiple [fastq]") { + + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, + { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, + { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("") }, + { assert path(process.out.html[0][1][1]).text.contains("") }, + { assert path(process.out.html[0][1][2]).text.contains("") }, + { assert path(process.out.html[0][1][3]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 custom_prefix") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'mysample', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 single-end [fastq] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id: 'test', single_end:true ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.html.collect { file(it[1]).getName() } + + process.out.zip.collect { file(it[1]).getName() } + + process.out.versions ).match() } + ) + } + } + } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 636a32ce..5d624bb8 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,10 +1,20 @@ { + "sarscov2 single-end [fastq] - stub": { + "content": [ + [ + "test.html", + "test.zip", + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "timestamp": "2024-01-17T18:40:57.254299" + }, "versions": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], - "timestamp": "2023-10-09T23:40:54+0000" + "timestamp": "2024-01-17T18:36:50.033627" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index bc0bdb5b..7625b752 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.18 + - bioconda::multiqc=1.19 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 00cc48d2..1b9f7c43 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.18--pyhdfd78af_0' : - 'biocontainers/multiqc:1.18--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : + 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" @@ -43,7 +43,7 @@ process MULTIQC { stub: """ - touch multiqc_data + mkdir multiqc_data touch multiqc_plots touch multiqc_report.html diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index f1aa660e..45a9bc35 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: multiqc description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index c2dad217..d0438eda 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -7,12 +7,9 @@ nextflow_process { tag "modules_nfcore" tag "multiqc" - test("MULTIQC: FASTQC") { + test("sarscov2 single-end [fastqc]") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) @@ -26,20 +23,17 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.report.get(0)).exists() }, - { assert path(process.out.data.get(0)).exists() }, - { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, + { assert process.out.data[0] ==~ ".*/multiqc_data" }, + { assert snapshot(process.out.versions).match("versions") } ) } } - test("MULTIQC: FASTQC and a config file") { + test("sarscov2 single-end [fastqc] [config]") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) @@ -53,9 +47,35 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.report.get(0)).exists() }, - { assert path(process.out.data.get(0)).exists() }, - { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, + { assert process.out.data[0] ==~ ".*/multiqc_data" }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 single-end [fastqc] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = [] + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.report.collect { file(it).getName() } + + process.out.data.collect { file(it).getName() } + + process.out.plots.collect { file(it).getName() } + + process.out.versions ).match() } ) } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap new file mode 100644 index 00000000..d37e7304 --- /dev/null +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -0,0 +1,21 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + ] + ], + "timestamp": "2024-01-09T23:02:49.911994" + }, + "sarscov2 single-end [fastqc] - stub": { + "content": [ + [ + "multiqc_report.html", + "multiqc_data", + "multiqc_plots", + "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + ] + ], + "timestamp": "2024-01-09T23:03:14.524346" + } +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 4b3b98de..4d098309 100644 --- a/nextflow.config +++ b/nextflow.config @@ -71,7 +71,7 @@ try { } // Load nf-core/circrna custom profiles from different institutions. -// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs! +// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs! // try { // includeConfig "${params.custom_config_base}/pipeline/circrna.config" // } catch (Exception e) { @@ -91,6 +91,7 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false + channels = ['conda-forge', 'bioconda', 'defaults'] apptainer.enabled = false } mamba { diff --git a/pyproject.toml b/pyproject.toml index 0d62beb6..7d08e1c8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,10 +1,13 @@ -# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black. +# Config file for Python. Mostly used to configure linting of bin/*.py with Ruff. # Should be kept the same as nf-core/tools to avoid fighting with template synchronisation. -[tool.black] +[tool.ruff] line-length = 120 -target_version = ["py37", "py38", "py39", "py310"] +target-version = "py38" +select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"] +cache-dir = "~/.cache/ruff" -[tool.isort] -profile = "black" -known_first_party = ["nf_core"] -multi_line_output = 3 +[tool.ruff.isort] +known-first-party = ["nf_core"] + +[tool.ruff.per-file-ignores] +"__init__.py" = ["E402", "F401"] diff --git a/workflows/circrna.nf b/workflows/circrna.nf index 5ae33065..10ecc0ac 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -127,6 +127,13 @@ workflow.onComplete { } } +workflow.onError { + if (workflow.errorReport.contains("Process requirement exceeds available memory")) { + println("🛑 Default resources exceed availability 🛑 ") + println("💡 See here on how to configure pipeline: https://nf-co.re/docs/usage/configuration#tuning-workflow-resources 💡") + } +} + /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ THE END From c8dbd82dd33c7ddc032d4657821dce8a801e886e Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Thu, 1 Feb 2024 10:59:10 +0100 Subject: [PATCH 102/491] prettier --- .github/workflows/download_pipeline.yml | 2 +- README.md | 1 + docs/output.md | 1 - 3 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 8611458a..8a330045 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -64,4 +64,4 @@ jobs: env: NXF_SINGULARITY_CACHEDIR: ./ NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results diff --git a/README.md b/README.md index 9b16eaf1..e13dcc3d 100644 --- a/README.md +++ b/README.md @@ -74,6 +74,7 @@ CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz Each row represents a fastq file (single-end) or a pair of fastq files (paired end). --> + Now, you can run the pipeline using: ```bash diff --git a/docs/output.md b/docs/output.md index eb711ae2..a92ce05e 100644 --- a/docs/output.md +++ b/docs/output.md @@ -162,7 +162,6 @@ The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They m - `SAMtoolsIndex`: Directory containing `SAMtools` index file. - `STARIndex`: Directory containing `STAR` indices. - `SegemehlIndex`: Directory containing `Segemehl` index file. - - `pipeline_info/` - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. From 1cf63900ac6c569a964829dcae73448e48d15b90 Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Thu, 1 Feb 2024 14:24:03 +0100 Subject: [PATCH 103/491] add change to trigger test --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index c915d9c1..dd0f6ed0 100644 --- a/main.nf +++ b/main.nf @@ -9,7 +9,7 @@ ---------------------------------------------------------------------------------------- */ -nextflow.enable.dsl = 2 +nextflow.enable.dsl = 2 /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From 7033540dc560a99926b3d3fe0431a2d0066c41c4 Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Thu, 1 Feb 2024 15:12:13 +0100 Subject: [PATCH 104/491] linting: fix results wiht params schema --- main.nf | 2 +- nextflow.config | 2 +- nextflow_schema.json | 6 +++--- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/main.nf b/main.nf index dd0f6ed0..c915d9c1 100644 --- a/main.nf +++ b/main.nf @@ -9,7 +9,7 @@ ---------------------------------------------------------------------------------------- */ -nextflow.enable.dsl = 2 +nextflow.enable.dsl = 2 /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/nextflow.config b/nextflow.config index d2c4da73..8ed4fd36 100644 --- a/nextflow.config +++ b/nextflow.config @@ -71,7 +71,7 @@ params { multiqc_methods_description = null // Boilerplate options - outdir = null + outdir = './results' publish_dir_mode = 'copy' email = null email_on_fail = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 71fb9ef2..654a7f80 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -252,7 +252,7 @@ }, "segemehl": { "type": "string", - "default": "None", + "default": null, "fa_icon": "fab fa-stripe-s", "description": "Path to Segemehl Index **file**." }, @@ -388,7 +388,7 @@ "max_cpus": { "type": "integer", "description": "Maximum number of CPUs that can be requested for any single job.", - "default": 16, + "default": 50, "fa_icon": "fas fa-microchip", "hidden": true, "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`" @@ -396,7 +396,7 @@ "max_memory": { "type": "string", "description": "Maximum amount of memory that can be requested for any single job.", - "default": "128.GB", + "default": "300.GB", "fa_icon": "fas fa-memory", "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", "hidden": true, From e092a8bed8db19bf00140d5710706b1f70e26caa Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Thu, 1 Feb 2024 15:14:18 +0100 Subject: [PATCH 105/491] linting: fix logo files --- assets/nf-core-circrna_logo_light.png | Bin 64214 -> 67266 bytes docs/images/nf-core-circrna_logo_dark.png | Bin 25192 -> 25216 bytes docs/images/nf-core-circrna_logo_light.png | Bin 21840 -> 21837 bytes 3 files changed, 0 insertions(+), 0 deletions(-) diff --git a/assets/nf-core-circrna_logo_light.png b/assets/nf-core-circrna_logo_light.png index d3cd49c1fffb4c615ab9d6e96f131be71830d2b2..cb307a2b40d6de041c576c4653e1fc77e66d7459 100644 GIT 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zM^IMa)pIQi&Tj6Y{Y^y}A2S|WpD0NhbUbR{H38$Y=^zolm<K?)C z&_i915lIp^borBVnxG1pe{R0eh`tDBen}xejY6YJ310lZgTecRx5fy@c?WS>FqL>^ z=gLJlstxW0amG%MIl(ox7Q^EdtAmdPCo~G|Ik@DTQJ0UkC$x9Gz)U}OFD_6C-{+$w!E(!>-8NpT^3mSoq#(AutZ7O7EAOb ztJ7j6PXuEg3=k~y;>6e+Xc=dm4#{-6gC z0eg!_iw90il01Yc`;E#x?Sb$~A#wL*6L88(^d4Ads?U6^g;DDZ7DvYVGrG{(PpQ>mKkow|W08~kTW~vyW1FKo*v-2L zh7|fkN4X1Qf?YxrWhZiVVwz&?X5sNTELloFro0aceS+Wf2a!WFrIVc7}-<)f~X-qivYJ;))Z;* zMC^(7{z)j`#d)7BYjm%Mxi1vVZtnqo`Lu?7SUsQtF)>4&>Jv7(#W=~N^Y`4lj0}jB zO0lxvju?{A|8}{AwLLz_+H9}E$_=vOB*19;E|ZQaJE}PW3N@&uslss*BV(&)S`1hz z9$pA_zzW@VC>U@NC7lDRP_3t+1KD0ssMRxSIxonD*cM9XT(bR~zhs+maD(?A?jO5N VTHWu^B&-79gF@OOo}2n6{STf|Sf>C0 From 3cbf35951bc98f002f38ecaa1e0e683bea67a9d5 Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Thu, 1 Feb 2024 15:31:55 +0100 Subject: [PATCH 106/491] fix error with args --- lib/WorkflowMain.groovy | 2 +- main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index a2ed646d..03790911 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -24,7 +24,7 @@ class WorkflowMain { // // Validate parameters and print summary to screen // - public static void initialise(workflow, params, log) { + public static void initialise(workflow, params, log, args) { // Print workflow version and exit on --version if (params.version) { diff --git a/main.nf b/main.nf index c915d9c1..61a893e9 100644 --- a/main.nf +++ b/main.nf @@ -48,7 +48,7 @@ if (params.validate_params) { validateParameters() } -WorkflowMain.initialise(workflow, params, log) +WorkflowMain.initialise(workflow, params, log, args) /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From 563e4e93f496e5283ea94cb760703e4735b5fe15 Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Thu, 1 Feb 2024 15:34:38 +0100 Subject: [PATCH 107/491] fix required yaml package --- .../dumpsoftwareversions/templates/dumpsoftwareversions.py | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py index b10e0a5c..da033408 100755 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -4,6 +4,7 @@ """Provide functions to merge multiple versions.yml files.""" +import yaml import platform from textwrap import dedent From e806c705ba9673977b69f10f88d562fab620d7a0 Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Thu, 1 Feb 2024 16:18:51 +0100 Subject: [PATCH 108/491] set outdir to null as default --- nextflow.config | 2 +- nextflow_schema.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index 8ed4fd36..84fd7b9c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -11,7 +11,7 @@ params { // Input options input = null - outdir = './results' + outdir = null phenotype = null // workflow options diff --git a/nextflow_schema.json b/nextflow_schema.json index 654a7f80..98c9bc80 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -27,7 +27,7 @@ "format": "directory-path", "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", "fa_icon": "fas fa-folder-open", - "default": "./results" + "default": null }, "phenotype": { "type": "string", From d6ef74a7ae3a38ff359f8e7c369330dcdef73969 Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Thu, 1 Feb 2024 16:27:41 +0100 Subject: [PATCH 109/491] fix whitespace for pre-commit --- .gitignore | 2 +- bin/check_samplesheet.py | 8 ++++---- docs/usage.md | 8 ++++---- nextflow.config | 2 +- subworkflows/local/circrna_discovery.nf | 4 ++-- 5 files changed, 12 insertions(+), 12 deletions(-) diff --git a/.gitignore b/.gitignore index fe288886..8800274c 100644 --- a/.gitignore +++ b/.gitignore @@ -8,4 +8,4 @@ testing* *.pyc test_outdir/ nf-* -!modules/* \ No newline at end of file +!modules/* diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index 2baec583..95346faf 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -1,11 +1,11 @@ #!/usr/bin/env python3 """ - Borrowed from nf-core/rnaseq, the original from template 2.6 kept breaking at: - "[CRITICAL] The given sample sheet does not appear to contain a header." - Even though the input samplesheet looked to be perfectly fine using vim :set list. + Borrowed from nf-core/rnaseq, the original from template 2.6 kept breaking at: + "[CRITICAL] The given sample sheet does not appear to contain a header." + Even though the input samplesheet looked to be perfectly fine using vim :set list. - Strandedness commented out should you wish to include this in future releases. + Strandedness commented out should you wish to include this in future releases. """ diff --git a/docs/usage.md b/docs/usage.md index 5e105b0c..28e1fd7e 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -135,18 +135,18 @@ When running the differential expression analysis module via the `--module diffe ```R colnames(phenotype) - [1] 'Sample_ID' 'condition' + [1] 'Sample_ID' 'condition' print(dds$design) - [1] ' ~ condition' + [1] ' ~ condition' ``` ```R colnames(phenotype) - [1] 'Sample_ID' 'condition' 'replicates' 'location' + [1] 'Sample_ID' 'condition' 'replicates' 'location' print(dds$design) - [1] ' ~ location + replicates + condition' + [1] ' ~ location + replicates + condition' ``` It is recommended to construct your input CSV file in conjunction with your phenotype file as the first column denoting sample names **must match** the first column of the `phenotype.csv` file. diff --git a/nextflow.config b/nextflow.config index 84fd7b9c..04b028f1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -88,7 +88,7 @@ params { custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null - + // Max resource options max_memory = '300.GB' diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 8501cffb..70aaf854 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -165,11 +165,11 @@ workflow CIRCRNA_DISCOVERY { DCC_MATE2_2ND_PASS( mate2, star_index, DCC_MATE2_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) dcc_stage = STAR_2ND_PASS.out.junction.map{ meta, junction -> return [ meta.id, meta, junction]} - .join( + .join( DCC_MATE1_2ND_PASS.out.junction.map{ meta, junction -> return [ meta.id, junction] }, remainder: true ) - .join( + .join( DCC_MATE2_2ND_PASS.out.junction.map{ meta, junction -> return [ meta.id, junction] }, remainder: true ) From e9d50a1423afc5ee27270aa91ad394a50e21ef80 Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Thu, 1 Feb 2024 17:14:34 +0100 Subject: [PATCH 110/491] prettier --- .devcontainer/devcontainer.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 4a9bc5c7..4ecfbfe3 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -18,11 +18,11 @@ "python.linting.flake8Path": "/opt/conda/bin/flake8", "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", - "python.linting.pylintPath": "/opt/conda/bin/pylint", + "python.linting.pylintPath": "/opt/conda/bin/pylint" }, // Add the IDs of extensions you want installed when the container is created. - "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"], - }, - }, + "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] + } + } } From 9fc9fd1f9f67267e1e29a3af6c807365c893d8a4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Thu, 1 Feb 2024 16:15:57 +0000 Subject: [PATCH 111/491] pull logo changes manually from TEMPLATE --- assets/nf-core-circrna_logo_light.png | Bin 67266 -> 67279 bytes docs/images/nf-core-circrna_logo_dark.png | Bin 25216 -> 25192 bytes docs/images/nf-core-circrna_logo_light.png | Bin 21837 -> 21840 bytes 3 files changed, 0 insertions(+), 0 deletions(-) diff --git a/assets/nf-core-circrna_logo_light.png b/assets/nf-core-circrna_logo_light.png index cb307a2b40d6de041c576c4653e1fc77e66d7459..85a200b325d8ef5ec381b5863b8300262d646720 100644 GIT binary patch delta 34092 zcmeFZcT`ka^Df+&7;yw=3=9HdIDkkLP%`K^qKBv=Nuq%?NY3$KKpX|s)8y1BNy(Bk zhzhoZ7EqduNDGpoktFG>!_2(*{`vjZy6e9GTxKyd(B1pgu6pXJ+Eulw4cS5q*^>L4 zFUEXnrFgRL^Y61U_VRa4cYCw`^3yK(M}5Z@eAlm+s*vRSTYkMMfB(Z7bkog)k1w40 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From dbcbf1a301b15a5de745318c615a8e36f26dfbd3 Mon Sep 17 00:00:00 2001 From: Marieke Vromman <74721287+MariekeVromman@users.noreply.github.com> Date: Fri, 2 Feb 2024 09:31:11 +0100 Subject: [PATCH 112/491] fix typo in docs/output.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index a92ce05e..9e218636 100644 --- a/docs/output.md +++ b/docs/output.md @@ -133,7 +133,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d `nf-core/circrna` outputs quality control plots of normalised _log2_ expression data from `DESeq2` to assess heterogeneity in the experiment samples. These plots can be useful to assess sample-sample similarity and to identify potential batch effects within the experiment. Plots are generated for both circRNAs and RNA-Seq data when the differential expression analysis module has been selected by the user (see `--module` [documentation](https://nf-co.re/circrna/dev/parameters#pipeline-options)). :::note -The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. +The FastQC plots displayed in the MultiQC report show _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. ::: ### MultiQC From e0a01236bd7b092c4a641e9845ac0f97fd80839e Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Fri, 2 Feb 2024 09:33:45 +0100 Subject: [PATCH 113/491] remove redundant output declaration --- nextflow.config | 1 - 1 file changed, 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 04b028f1..458e66e5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -71,7 +71,6 @@ params { multiqc_methods_description = null // Boilerplate options - outdir = './results' publish_dir_mode = 'copy' email = null email_on_fail = null From 313ba3a9c918d8c2b695688529e825622749fa70 Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Wed, 14 Feb 2024 08:58:37 +0100 Subject: [PATCH 114/491] make /tmp dir in work dir (sort) to avoid error on cluster --- modules/local/star/sjdb/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/star/sjdb/main.nf b/modules/local/star/sjdb/main.nf index b2e0ebc0..557a2f3f 100644 --- a/modules/local/star/sjdb/main.nf +++ b/modules/local/star/sjdb/main.nf @@ -21,7 +21,7 @@ process SJDB { script: def VERSION = '1.3.4' """ - cat *.tab | awk -v BSJ=${bsj_reads} '(\$7 >= BSJ && \$6==0)' | cut -f1-6 | sort | uniq > dataset.SJ.out.tab + cat *.tab | awk -v BSJ=${bsj_reads} '(\$7 >= BSJ && \$6==0)' | cut -f1-6 | sort -T ./tmp/ | uniq > dataset.SJ.out.tab cat <<-END_VERSIONS > versions.yml "${task.process}": From b7f37683d957d5fb88b13288cefd854508952c84 Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Wed, 14 Feb 2024 09:16:20 +0100 Subject: [PATCH 115/491] add tmp dir --- modules/local/star/sjdb/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/local/star/sjdb/main.nf b/modules/local/star/sjdb/main.nf index 557a2f3f..8550647d 100644 --- a/modules/local/star/sjdb/main.nf +++ b/modules/local/star/sjdb/main.nf @@ -21,6 +21,7 @@ process SJDB { script: def VERSION = '1.3.4' """ + mkdir tmp cat *.tab | awk -v BSJ=${bsj_reads} '(\$7 >= BSJ && \$6==0)' | cut -f1-6 | sort -T ./tmp/ | uniq > dataset.SJ.out.tab cat <<-END_VERSIONS > versions.yml From 0660b3e4c5d88f850261aacd6452c56ca714c4be Mon Sep 17 00:00:00 2001 From: Marieke Vromman <74721287+MariekeVromman@users.noreply.github.com> Date: Wed, 14 Feb 2024 09:46:26 +0100 Subject: [PATCH 116/491] Update modules/local/star/sjdb/main.nf MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- modules/local/star/sjdb/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/star/sjdb/main.nf b/modules/local/star/sjdb/main.nf index 8550647d..c2a52a9e 100644 --- a/modules/local/star/sjdb/main.nf +++ b/modules/local/star/sjdb/main.nf @@ -23,7 +23,7 @@ process SJDB { """ mkdir tmp cat *.tab | awk -v BSJ=${bsj_reads} '(\$7 >= BSJ && \$6==0)' | cut -f1-6 | sort -T ./tmp/ | uniq > dataset.SJ.out.tab - +rm -rf tmp cat <<-END_VERSIONS > versions.yml "${task.process}": mawk: $VERSION From cb5f8ff8e57c57d389220e39bc56b5e2d9faf1af Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Wed, 14 Feb 2024 10:13:09 +0100 Subject: [PATCH 117/491] fix indentation --- modules/local/star/sjdb/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/star/sjdb/main.nf b/modules/local/star/sjdb/main.nf index c2a52a9e..835f4e21 100644 --- a/modules/local/star/sjdb/main.nf +++ b/modules/local/star/sjdb/main.nf @@ -23,7 +23,7 @@ process SJDB { """ mkdir tmp cat *.tab | awk -v BSJ=${bsj_reads} '(\$7 >= BSJ && \$6==0)' | cut -f1-6 | sort -T ./tmp/ | uniq > dataset.SJ.out.tab -rm -rf tmp + rm -rf tmp cat <<-END_VERSIONS > versions.yml "${task.process}": mawk: $VERSION From d8c6073a9446871b0362ae34f51bab1a91fe3b6c Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Wed, 14 Feb 2024 16:47:01 +0100 Subject: [PATCH 118/491] clean up fasta (not working correctly yet) --- conf/modules.config | 7 +++++++ modules/nf-core/gawk/main.nf | 2 +- subworkflows/local/prepare_genome.nf | 10 ++++++++++ 3 files changed, 18 insertions(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 52b47439..d0b2e405 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -68,6 +68,13 @@ if (!params.skip_trimming) { } // PREPARE GENOME + withName: CLEAN_FASTA { + ext.args2 = '\'/>/{ gsub(\$2, "",\$2);gsub(" ", "") };{print}\'' + ext.prefix = 'clean' + ext.suffix = 'fa' + + } + withName: BOWTIE_BUILD { ext.when = { params.fasta && !params.bowtie && params.tool.split(',').contains('mapsplice') && params.module.split(',').contains('circrna_discovery') } publishDir = [ diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf index 854bae00..a8f2f741 100644 --- a/modules/nf-core/gawk/main.nf +++ b/modules/nf-core/gawk/main.nf @@ -12,7 +12,7 @@ process GAWK { path(program_file) output: - tuple val(meta), path("${prefix}.${suffix}"), emit: output + path("${prefix}.${suffix}"), emit: output path "versions.yml" , emit: versions when: diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 84d932db..fb94ab3c 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -6,6 +6,7 @@ include { HISAT2_EXTRACTSPLICESITES } from '../../modules/nf-core/hisat2/extract include { HISAT2_BUILD } from '../../modules/nf-core/hisat2/build/main' include { STAR_GENOMEGENERATE } from '../../modules/nf-core/star/genomegenerate/main' include { SEGEMEHL_INDEX } from '../../modules/nf-core/segemehl/index/main' +include { GAWK as CLEAN_FASTA } from '../../modules/nf-core/gawk/main' workflow PREPARE_GENOME { @@ -21,6 +22,15 @@ workflow PREPARE_GENOME { fasta_tuple = Channel.value([[id: "fasta"], fasta]) gtf_tuple = Channel.value([[id: "gtf"], gtf]) + // MapSplice cannot deal with extra field in the fasta headers + // this removes all additional fields in the headers of the input fasta file + if( params.tool.contains('mapsplice') && params.module.contains('circrna_discovery') ) { + + CLEAN_FASTA(fasta_tuple, []) + ch_fasta = CLEAN_FASTA.out.output + + } + // MapSplice & find_circ requires reference genome to be split per chromosome: if( ( params.tool.contains('mapsplice') || params.tool.contains('find_circ') ) && params.module.contains('circrna_discovery') ){ directory = file("${params.outdir}/references/chromosomes") From 02a5eff888d8e078940456a8fe1bf3dada2a9557 Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Mon, 19 Feb 2024 11:11:31 +0100 Subject: [PATCH 119/491] fix value channel for star index --- subworkflows/local/circrna_discovery.nf | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 70aaf854..80ba9a19 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -85,10 +85,10 @@ workflow CIRCRNA_DISCOVERY { seq_center = params.seq_center ?: '' seq_platform = '' - STAR_1ST_PASS( reads, star_index, gtf_tuple, star_ignore_sjdbgtf, seq_platform, seq_center) + STAR_1ST_PASS( reads, star_index.first(), gtf_tuple, star_ignore_sjdbgtf, seq_platform, seq_center) sjdb = STAR_1ST_PASS.out.tab.map{ meta, tab -> return tab }.collect().map{[[id: "star_sjdb"], it]} STAR_SJDB( sjdb, bsj_reads ) - STAR_2ND_PASS( reads, star_index, STAR_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) + STAR_2ND_PASS( reads, star_index.first(), STAR_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) ch_versions = ch_versions.mix(STAR_1ST_PASS.out.versions) ch_versions = ch_versions.mix(STAR_2ND_PASS.out.versions) @@ -155,14 +155,14 @@ workflow CIRCRNA_DISCOVERY { // mate1 = reads.filter{ meta, reads -> !meta.single_end }.map{ meta, reads -> return [ [id: meta.id, single_end: true], reads[0] ] } - DCC_MATE1_1ST_PASS( mate1, star_index, gtf_tuple, star_ignore_sjdbgtf, seq_platform, seq_center ) + DCC_MATE1_1ST_PASS( mate1, star_index.first(), gtf_tuple, star_ignore_sjdbgtf, seq_platform, seq_center ) DCC_MATE1_SJDB( DCC_MATE1_1ST_PASS.out.tab.map{ meta, tab -> return tab }.collect().map{[[id: "mate1_sjdb"], it]}, bsj_reads ) - DCC_MATE1_2ND_PASS( mate1, star_index, DCC_MATE1_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) + DCC_MATE1_2ND_PASS( mate1, star_index.first(), DCC_MATE1_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) mate2 = reads.filter{ meta, reads -> !meta.single_end }.map{ meta, reads -> return [ [id: meta.id, single_end: true], reads[1] ] } - DCC_MATE2_1ST_PASS( mate2, star_index, gtf_tuple, star_ignore_sjdbgtf, seq_platform, seq_center ) + DCC_MATE2_1ST_PASS( mate2, star_index.first(), gtf_tuple, star_ignore_sjdbgtf, seq_platform, seq_center ) DCC_MATE2_SJDB( DCC_MATE2_1ST_PASS.out.tab.map{ meta, tab -> return tab }.collect().map{[[id: "mate2_sjdb"], it]}, bsj_reads ) - DCC_MATE2_2ND_PASS( mate2, star_index, DCC_MATE2_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) + DCC_MATE2_2ND_PASS( mate2, star_index.first(), DCC_MATE2_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) dcc_stage = STAR_2ND_PASS.out.junction.map{ meta, junction -> return [ meta.id, meta, junction]} .join( From 994176388040fa777ccfab60b5c52a82b6fec0dc Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Tue, 20 Feb 2024 14:55:33 +0100 Subject: [PATCH 120/491] resolve gawk bug, prefix/sufix issue and publish dir --- conf/modules.config | 9 ++++++--- modules/nf-core/gawk/main.nf | 4 ++-- subworkflows/local/prepare_genome.nf | 11 ++++++++--- 3 files changed, 16 insertions(+), 8 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index d0b2e405..ec8ec07e 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -70,9 +70,12 @@ if (!params.skip_trimming) { // PREPARE GENOME withName: CLEAN_FASTA { ext.args2 = '\'/>/{ gsub(\$2, "",\$2);gsub(" ", "") };{print}\'' - ext.prefix = 'clean' - ext.suffix = 'fa' - + publishDir = [ + path: { "${params.outdir}/references/clean_fasta" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + enabled: params.save_reference + ] } withName: BOWTIE_BUILD { diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf index a8f2f741..f856a1f8 100644 --- a/modules/nf-core/gawk/main.nf +++ b/modules/nf-core/gawk/main.nf @@ -12,7 +12,7 @@ process GAWK { path(program_file) output: - path("${prefix}.${suffix}"), emit: output + tuple val(meta), path("${prefix}.${suffix}"), emit: output path "versions.yml" , emit: versions when: @@ -22,7 +22,7 @@ process GAWK { def args = task.ext.args ?: '' // args is used for the main arguments of the tool def args2 = task.ext.args2 ?: '' // args2 is used to specify a program when no program file has been given prefix = task.ext.prefix ?: "${meta.id}" - suffix = task.ext.suffix ?: "${input.getExtension}" + suffix = task.ext.suffix ?: "${input.getExtension()}" program = program_file ? "-f ${program_file}" : "${args2}" diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index fb94ab3c..d35b6b5b 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -17,7 +17,6 @@ workflow PREPARE_GENOME { main: ch_versions = Channel.empty() - ch_fasta = Channel.fromPath(fasta) ch_gtf = Channel.fromPath(gtf) fasta_tuple = Channel.value([[id: "fasta"], fasta]) gtf_tuple = Channel.value([[id: "gtf"], gtf]) @@ -26,8 +25,14 @@ workflow PREPARE_GENOME { // this removes all additional fields in the headers of the input fasta file if( params.tool.contains('mapsplice') && params.module.contains('circrna_discovery') ) { - CLEAN_FASTA(fasta_tuple, []) - ch_fasta = CLEAN_FASTA.out.output + CLEAN_FASTA(Channel.value([[id: "${fasta.baseName}" + "_clean" ], fasta]), []) + + ch_fasta = CLEAN_FASTA.out.output.map{ it.last() } + } + + else { + + ch_fasta = Channel.fromPath(fasta) } From 9107e83f98cafcbc7ff3a2ac0ca93ac4fd4f0307 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 20 Feb 2024 15:28:12 +0000 Subject: [PATCH 121/491] Template update for nf-core/tools version 2.13 --- .editorconfig | 9 +- .github/workflows/awsfulltest.yml | 4 +- .github/workflows/awstest.yml | 4 +- .github/workflows/branch.yml | 2 +- .github/workflows/ci.yml | 7 +- .github/workflows/clean-up.yml | 2 +- .github/workflows/download_pipeline.yml | 17 +- .github/workflows/linting.yml | 12 +- .github/workflows/linting_comment.yml | 4 +- .github/workflows/release-announcements.yml | 11 +- README.md | 5 +- assets/multiqc_config.yml | 2 + assets/schema_input.json | 21 +- bin/check_samplesheet.py | 259 ----------- conf/modules.config | 8 - lib/NfcoreTemplate.groovy | 356 -------------- lib/Utils.groovy | 47 -- lib/WorkflowCircrna.groovy | 122 ----- lib/WorkflowMain.groovy | 77 --- main.nf | 100 ++-- modules.json | 28 +- modules/local/samplesheet_check.nf | 31 -- .../dumpsoftwareversions/environment.yml | 7 - .../custom/dumpsoftwareversions/main.nf | 24 - .../custom/dumpsoftwareversions/meta.yml | 37 -- .../templates/dumpsoftwareversions.py | 102 ---- .../dumpsoftwareversions/tests/main.nf.test | 43 -- .../tests/main.nf.test.snap | 33 -- .../dumpsoftwareversions/tests/tags.yml | 2 - modules/nf-core/fastqc/tests/main.nf.test | 14 +- .../nf-core/fastqc/tests/main.nf.test.snap | 76 ++- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- modules/nf-core/multiqc/tests/main.nf.test | 13 +- .../nf-core/multiqc/tests/main.nf.test.snap | 32 +- nextflow.config | 5 +- nextflow_schema.json | 1 + pyproject.toml | 8 +- subworkflows/local/input_check.nf | 44 -- .../utils_nfcore_circrna_pipeline/main.nf | 247 ++++++++++ .../nf-core/utils_nextflow_pipeline/main.nf | 126 +++++ .../nf-core/utils_nextflow_pipeline/meta.yml | 38 ++ .../tests/main.function.nf.test | 54 +++ .../tests/main.function.nf.test.snap | 12 + .../tests/main.workflow.nf.test | 123 +++++ .../tests/nextflow.config | 9 + .../utils_nextflow_pipeline/tests/tags.yml | 2 + .../nf-core/utils_nfcore_pipeline/main.nf | 440 ++++++++++++++++++ .../nf-core/utils_nfcore_pipeline/meta.yml | 24 + .../tests/main.function.nf.test | 134 ++++++ .../tests/main.function.nf.test.snap | 138 ++++++ .../tests/main.workflow.nf.test | 29 ++ .../tests/main.workflow.nf.test.snap | 15 + .../tests/nextflow.config | 9 + .../utils_nfcore_pipeline/tests/tags.yml | 2 + .../nf-core/utils_nfvalidation_plugin/main.nf | 62 +++ .../utils_nfvalidation_plugin/meta.yml | 44 ++ .../tests/main.nf.test | 200 ++++++++ .../tests/nextflow_schema.json | 96 ++++ .../utils_nfvalidation_plugin/tests/tags.yml | 2 + workflows/circrna.nf | 133 ++---- 61 files changed, 2108 insertions(+), 1406 deletions(-) delete mode 100755 bin/check_samplesheet.py delete mode 100755 lib/NfcoreTemplate.groovy delete mode 100644 lib/Utils.groovy delete mode 100755 lib/WorkflowCircrna.groovy delete mode 100755 lib/WorkflowMain.groovy delete mode 100644 modules/local/samplesheet_check.nf delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/environment.yml delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/main.nf delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/meta.yml delete mode 100755 modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml delete mode 100644 subworkflows/local/input_check.nf create mode 100644 subworkflows/local/utils_nfcore_circrna_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/meta.yml create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/meta.yml create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/main.nf create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml diff --git a/.editorconfig b/.editorconfig index 9b990088..dd9ffa53 100644 --- a/.editorconfig +++ b/.editorconfig @@ -18,7 +18,12 @@ end_of_line = unset insert_final_newline = unset trim_trailing_whitespace = unset indent_style = unset -indent_size = unset +[/subworkflows/nf-core/**] +charset = unset +end_of_line = unset +insert_final_newline = unset +trim_trailing_whitespace = unset +indent_style = unset [/assets/email*] indent_size = unset @@ -28,5 +33,5 @@ indent_size = unset indent_style = unset # ignore python -[*.{py}] +[*.{py,md}] indent_style = unset diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 7b6bd16d..94521ebc 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v2 + uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -31,7 +31,7 @@ jobs: } profiles: test_full - - uses: actions/upload-artifact@v4 + - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 9590dcae..5307e9aa 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v2 + uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@v4 + - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index a9339b73..777845e7 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -19,7 +19,7 @@ jobs: # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets - name: Post PR comment if: failure() - uses: mshick/add-pr-comment@v2 + uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 with: message: | ## This PR is against the `master` branch :x: diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f0ac13e2..4e5754df 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -28,13 +28,16 @@ jobs: - "latest-everything" steps: - name: Check out pipeline code - uses: actions/checkout@v4 + uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 with: version: "${{ matrix.NXF_VER }}" + - name: Disk space cleanup + uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + - name: Run pipeline with test data # TODO nf-core: You can customise CI pipeline run tests as required # For example: adding multiple test runs with different parameters diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index e37cfda5..0b6b1f27 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@v9 + - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 8611458a..f823210d 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -6,6 +6,11 @@ name: Test successful pipeline download with 'nf-core download' # - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. on: workflow_dispatch: + inputs: + testbranch: + description: "The specific branch you wish to utilize for the test execution of nf-core download." + required: true + default: "dev" pull_request: types: - opened @@ -23,13 +28,13 @@ jobs: runs-on: ubuntu-latest steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 - - uses: actions/setup-python@v5 + - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: python-version: "3.11" architecture: "x64" - - uses: eWaterCycle/setup-singularity@v7 + - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 with: singularity-version: 3.8.3 @@ -42,13 +47,13 @@ jobs: run: | echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} - echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV} + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} - name: Download the pipeline env: NXF_SINGULARITY_CACHEDIR: ./ run: | - nf-core download ${{ env.REPO_LOWERCASE }} \ + nf-core download ${{ env.REPO_LOWERCASE }} \ --revision ${{ env.REPO_BRANCH }} \ --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ --compress "none" \ @@ -64,4 +69,4 @@ jobs: env: NXF_SINGULARITY_CACHEDIR: ./ NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 81cd098e..748b4311 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,10 +14,10 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Set up Python 3.11 - uses: actions/setup-python@v5 + uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: python-version: 3.11 cache: "pip" @@ -32,12 +32,12 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@v4 + uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 - - uses: actions/setup-python@v5 + - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: python-version: "3.11" architecture: "x64" @@ -60,7 +60,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 147bcd10..b706875f 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@v3 + uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3 with: workflow: linting.yml workflow_conclusion: completed @@ -21,7 +21,7 @@ jobs: run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@v2 + uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 21ac3f06..c3674af2 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -9,6 +9,11 @@ jobs: toot: runs-on: ubuntu-latest steps: + - name: get topics and convert to hashtags + id: get_topics + run: | + curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' > $GITHUB_OUTPUT + - uses: rzr/fediverse-action@master with: access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} @@ -20,11 +25,13 @@ jobs: Please see the changelog: ${{ github.event.release.html_url }} + ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics + send-tweet: runs-on: ubuntu-latest steps: - - uses: actions/setup-python@v5 + - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: python-version: "3.10" - name: Install dependencies @@ -56,7 +63,7 @@ jobs: bsky-post: runs-on: ubuntu-latest steps: - - uses: zentered/bluesky-post-action@v0.1.0 + - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0 with: post: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! diff --git a/README.md b/README.md index 496a65ac..18919fd1 100644 --- a/README.md +++ b/README.md @@ -4,8 +4,9 @@ nf-core/circrna -[![GitHub Actions CI Status](https://github.com/nf-core/circrna/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/circrna/actions?query=workflow%3A%22nf-core+CI%22) -[![GitHub Actions Linting Status](https://github.com/nf-core/circrna/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/circrna/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/circrna/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) + +[![GitHub Actions CI Status](https://github.com/nf-core/circrna/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/circrna/actions/workflows/ci.yml) +[![GitHub Actions Linting Status](https://github.com/nf-core/circrna/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/circrna/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/circrna/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 9a1b5bda..570f6c0d 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -11,3 +11,5 @@ report_section_order: order: -1002 export_plots: true + +disable_version_detection: true diff --git a/assets/schema_input.json b/assets/schema_input.json index 41716366..fe551cb8 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -10,25 +10,22 @@ "sample": { "type": "string", "pattern": "^\\S+$", - "errorMessage": "Sample name must be provided and cannot contain spaces" + "errorMessage": "Sample name must be provided and cannot contain spaces", + "meta": ["id"] }, "fastq_1": { "type": "string", + "format": "file-path", + "exists": true, "pattern": "^\\S+\\.f(ast)?q\\.gz$", "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" }, "fastq_2": { - "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", - "anyOf": [ - { - "type": "string", - "pattern": "^\\S+\\.f(ast)?q\\.gz$" - }, - { - "type": "string", - "maxLength": 0 - } - ] + "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.f(ast)?q\\.gz$", + "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" } }, "required": ["sample", "fastq_1"] diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py deleted file mode 100755 index 4a758fe0..00000000 --- a/bin/check_samplesheet.py +++ /dev/null @@ -1,259 +0,0 @@ -#!/usr/bin/env python - - -"""Provide a command line tool to validate and transform tabular samplesheets.""" - - -import argparse -import csv -import logging -import sys -from collections import Counter -from pathlib import Path - -logger = logging.getLogger() - - -class RowChecker: - """ - Define a service that can validate and transform each given row. - - Attributes: - modified (list): A list of dicts, where each dict corresponds to a previously - validated and transformed row. The order of rows is maintained. - - """ - - VALID_FORMATS = ( - ".fq.gz", - ".fastq.gz", - ) - - def __init__( - self, - sample_col="sample", - first_col="fastq_1", - second_col="fastq_2", - single_col="single_end", - **kwargs, - ): - """ - Initialize the row checker with the expected column names. - - Args: - sample_col (str): The name of the column that contains the sample name - (default "sample"). - first_col (str): The name of the column that contains the first (or only) - FASTQ file path (default "fastq_1"). - second_col (str): The name of the column that contains the second (if any) - FASTQ file path (default "fastq_2"). - single_col (str): The name of the new column that will be inserted and - records whether the sample contains single- or paired-end sequencing - reads (default "single_end"). - - """ - super().__init__(**kwargs) - self._sample_col = sample_col - self._first_col = first_col - self._second_col = second_col - self._single_col = single_col - self._seen = set() - self.modified = [] - - def validate_and_transform(self, row): - """ - Perform all validations on the given row and insert the read pairing status. - - Args: - row (dict): A mapping from column headers (keys) to elements of that row - (values). - - """ - self._validate_sample(row) - self._validate_first(row) - self._validate_second(row) - self._validate_pair(row) - self._seen.add((row[self._sample_col], row[self._first_col])) - self.modified.append(row) - - def _validate_sample(self, row): - """Assert that the sample name exists and convert spaces to underscores.""" - if len(row[self._sample_col]) <= 0: - raise AssertionError("Sample input is required.") - # Sanitize samples slightly. - row[self._sample_col] = row[self._sample_col].replace(" ", "_") - - def _validate_first(self, row): - """Assert that the first FASTQ entry is non-empty and has the right format.""" - if len(row[self._first_col]) <= 0: - raise AssertionError("At least the first FASTQ file is required.") - self._validate_fastq_format(row[self._first_col]) - - def _validate_second(self, row): - """Assert that the second FASTQ entry has the right format if it exists.""" - if len(row[self._second_col]) > 0: - self._validate_fastq_format(row[self._second_col]) - - def _validate_pair(self, row): - """Assert that read pairs have the same file extension. Report pair status.""" - if row[self._first_col] and row[self._second_col]: - row[self._single_col] = False - first_col_suffix = Path(row[self._first_col]).suffixes[-2:] - second_col_suffix = Path(row[self._second_col]).suffixes[-2:] - if first_col_suffix != second_col_suffix: - raise AssertionError("FASTQ pairs must have the same file extensions.") - else: - row[self._single_col] = True - - def _validate_fastq_format(self, filename): - """Assert that a given filename has one of the expected FASTQ extensions.""" - if not any(filename.endswith(extension) for extension in self.VALID_FORMATS): - raise AssertionError( - f"The FASTQ file has an unrecognized extension: {filename}\n" - f"It should be one of: {', '.join(self.VALID_FORMATS)}" - ) - - def validate_unique_samples(self): - """ - Assert that the combination of sample name and FASTQ filename is unique. - - In addition to the validation, also rename all samples to have a suffix of _T{n}, where n is the - number of times the same sample exist, but with different FASTQ files, e.g., multiple runs per experiment. - - """ - if len(self._seen) != len(self.modified): - raise AssertionError("The pair of sample name and FASTQ must be unique.") - seen = Counter() - for row in self.modified: - sample = row[self._sample_col] - seen[sample] += 1 - row[self._sample_col] = f"{sample}_T{seen[sample]}" - - -def read_head(handle, num_lines=10): - """Read the specified number of lines from the current position in the file.""" - lines = [] - for idx, line in enumerate(handle): - if idx == num_lines: - break - lines.append(line) - return "".join(lines) - - -def sniff_format(handle): - """ - Detect the tabular format. - - Args: - handle (text file): A handle to a `text file`_ object. The read position is - expected to be at the beginning (index 0). - - Returns: - csv.Dialect: The detected tabular format. - - .. _text file: - https://docs.python.org/3/glossary.html#term-text-file - - """ - peek = read_head(handle) - handle.seek(0) - sniffer = csv.Sniffer() - dialect = sniffer.sniff(peek) - return dialect - - -def check_samplesheet(file_in, file_out): - """ - Check that the tabular samplesheet has the structure expected by nf-core pipelines. - - Validate the general shape of the table, expected columns, and each row. Also add - an additional column which records whether one or two FASTQ reads were found. - - Args: - file_in (pathlib.Path): The given tabular samplesheet. The format can be either - CSV, TSV, or any other format automatically recognized by ``csv.Sniffer``. - file_out (pathlib.Path): Where the validated and transformed samplesheet should - be created; always in CSV format. - - Example: - This function checks that the samplesheet follows the following structure, - see also the `viral recon samplesheet`_:: - - sample,fastq_1,fastq_2 - SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz - SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz - SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz, - - .. _viral recon samplesheet: - https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv - - """ - required_columns = {"sample", "fastq_1", "fastq_2"} - # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. - with file_in.open(newline="") as in_handle: - reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle)) - # Validate the existence of the expected header columns. - if not required_columns.issubset(reader.fieldnames): - req_cols = ", ".join(required_columns) - logger.critical(f"The sample sheet **must** contain these column headers: {req_cols}.") - sys.exit(1) - # Validate each row. - checker = RowChecker() - for i, row in enumerate(reader): - try: - checker.validate_and_transform(row) - except AssertionError as error: - logger.critical(f"{str(error)} On line {i + 2}.") - sys.exit(1) - checker.validate_unique_samples() - header = list(reader.fieldnames) - header.insert(1, "single_end") - # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. - with file_out.open(mode="w", newline="") as out_handle: - writer = csv.DictWriter(out_handle, header, delimiter=",") - writer.writeheader() - for row in checker.modified: - writer.writerow(row) - - -def parse_args(argv=None): - """Define and immediately parse command line arguments.""" - parser = argparse.ArgumentParser( - description="Validate and transform a tabular samplesheet.", - epilog="Example: python check_samplesheet.py samplesheet.csv samplesheet.valid.csv", - ) - parser.add_argument( - "file_in", - metavar="FILE_IN", - type=Path, - help="Tabular input samplesheet in CSV or TSV format.", - ) - parser.add_argument( - "file_out", - metavar="FILE_OUT", - type=Path, - help="Transformed output samplesheet in CSV format.", - ) - parser.add_argument( - "-l", - "--log-level", - help="The desired log level (default WARNING).", - choices=("CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"), - default="WARNING", - ) - return parser.parse_args(argv) - - -def main(argv=None): - """Coordinate argument parsing and program execution.""" - args = parse_args(argv) - logging.basicConfig(level=args.log_level, format="[%(levelname)s] %(message)s") - if not args.file_in.is_file(): - logger.error(f"The given input file {args.file_in} was not found!") - sys.exit(2) - args.file_out.parent.mkdir(parents=True, exist_ok=True) - check_samplesheet(args.file_in, args.file_out) - - -if __name__ == "__main__": - sys.exit(main()) diff --git a/conf/modules.config b/conf/modules.config index d91c6aba..e3ea8fa6 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -18,14 +18,6 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - withName: SAMPLESHEET_CHECK { - publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - withName: FASTQC { ext.args = '--quiet' } diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy deleted file mode 100755 index e248e4c3..00000000 --- a/lib/NfcoreTemplate.groovy +++ /dev/null @@ -1,356 +0,0 @@ -// -// This file holds several functions used within the nf-core pipeline template. -// - -import org.yaml.snakeyaml.Yaml -import groovy.json.JsonOutput -import nextflow.extension.FilesEx - -class NfcoreTemplate { - - // - // Check AWS Batch related parameters have been specified correctly - // - public static void awsBatch(workflow, params) { - if (workflow.profile.contains('awsbatch')) { - // Check params.awsqueue and params.awsregion have been set if running on AWSBatch - assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!" - // Check outdir paths to be S3 buckets if running on AWSBatch - assert params.outdir.startsWith('s3:') : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!" - } - } - - // - // Warn if a -profile or Nextflow config has not been provided to run the pipeline - // - public static void checkConfigProvided(workflow, log) { - if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + - "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + - " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + - " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + - " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + - "Please refer to the quick start section and usage docs for the pipeline.\n " - } - } - - // - // Generate version string - // - public static String version(workflow) { - String version_string = "" - - if (workflow.manifest.version) { - def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' - version_string += "${prefix_v}${workflow.manifest.version}" - } - - if (workflow.commitId) { - def git_shortsha = workflow.commitId.substring(0, 7) - version_string += "-g${git_shortsha}" - } - - return version_string - } - - // - // Construct and send completion email - // - public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) { - - // Set up the e-mail variables - def subject = "[$workflow.manifest.name] Successful: $workflow.runName" - if (!workflow.success) { - subject = "[$workflow.manifest.name] FAILED: $workflow.runName" - } - - def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['Date Started'] = workflow.start - misc_fields['Date Completed'] = workflow.complete - misc_fields['Pipeline script file path'] = workflow.scriptFile - misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository - if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId - if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build - misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp - - def email_fields = [:] - email_fields['version'] = NfcoreTemplate.version(workflow) - email_fields['runName'] = workflow.runName - email_fields['success'] = workflow.success - email_fields['dateComplete'] = workflow.complete - email_fields['duration'] = workflow.duration - email_fields['exitStatus'] = workflow.exitStatus - email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - email_fields['errorReport'] = (workflow.errorReport ?: 'None') - email_fields['commandLine'] = workflow.commandLine - email_fields['projectDir'] = workflow.projectDir - email_fields['summary'] = summary << misc_fields - - // On success try attach the multiqc report - def mqc_report = null - try { - if (workflow.success) { - mqc_report = multiqc_report.getVal() - if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { - if (mqc_report.size() > 1) { - log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" - } - mqc_report = mqc_report[0] - } - } - } catch (all) { - if (multiqc_report) { - log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" - } - } - - // Check if we are only sending emails on failure - def email_address = params.email - if (!params.email && params.email_on_fail && !workflow.success) { - email_address = params.email_on_fail - } - - // Render the TXT template - def engine = new groovy.text.GStringTemplateEngine() - def tf = new File("$projectDir/assets/email_template.txt") - def txt_template = engine.createTemplate(tf).make(email_fields) - def email_txt = txt_template.toString() - - // Render the HTML template - def hf = new File("$projectDir/assets/email_template.html") - def html_template = engine.createTemplate(hf).make(email_fields) - def email_html = html_template.toString() - - // Render the sendmail template - def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] - def sf = new File("$projectDir/assets/sendmail_template.txt") - def sendmail_template = engine.createTemplate(sf).make(smail_fields) - def sendmail_html = sendmail_template.toString() - - // Send the HTML e-mail - Map colors = logColours(params.monochrome_logs) - if (email_address) { - try { - if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } - // Try to send HTML e-mail using sendmail - def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") - sendmail_tf.withWriter { w -> w << sendmail_html } - [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" - } catch (all) { - // Catch failures and try with plaintext - def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] - if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) { - mail_cmd += [ '-A', mqc_report ] - } - mail_cmd.execute() << email_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" - } - } - - // Write summary e-mail HTML to a file - def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") - output_hf.withWriter { w -> w << email_html } - FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html"); - output_hf.delete() - - // Write summary e-mail TXT to a file - def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") - output_tf.withWriter { w -> w << email_txt } - FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt"); - output_tf.delete() - } - - // - // Construct and send a notification to a web server as JSON - // e.g. Microsoft Teams and Slack - // - public static void IM_notification(workflow, params, summary_params, projectDir, log) { - def hook_url = params.hook_url - - def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) misc_fields['repository'] = workflow.repository - if (workflow.commitId) misc_fields['commitid'] = workflow.commitId - if (workflow.revision) misc_fields['revision'] = workflow.revision - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp - - def msg_fields = [:] - msg_fields['version'] = NfcoreTemplate.version(workflow) - msg_fields['runName'] = workflow.runName - msg_fields['success'] = workflow.success - msg_fields['dateComplete'] = workflow.complete - msg_fields['duration'] = workflow.duration - msg_fields['exitStatus'] = workflow.exitStatus - msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - msg_fields['errorReport'] = (workflow.errorReport ?: 'None') - msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") - msg_fields['projectDir'] = workflow.projectDir - msg_fields['summary'] = summary << misc_fields - - // Render the JSON template - def engine = new groovy.text.GStringTemplateEngine() - // Different JSON depending on the service provider - // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format - def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" - def hf = new File("$projectDir/assets/${json_path}") - def json_template = engine.createTemplate(hf).make(msg_fields) - def json_message = json_template.toString() - - // POST - def post = new URL(hook_url).openConnection(); - post.setRequestMethod("POST") - post.setDoOutput(true) - post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")); - def postRC = post.getResponseCode(); - if (! postRC.equals(200)) { - log.warn(post.getErrorStream().getText()); - } - } - - // - // Dump pipeline parameters in a json file - // - public static void dump_parameters(workflow, params) { - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = JsonOutput.toJson(params) - temp_pf.text = JsonOutput.prettyPrint(jsonStr) - - FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json") - temp_pf.delete() - } - - // - // Print pipeline summary on completion - // - public static void summary(workflow, params, log) { - Map colors = logColours(params.monochrome_logs) - if (workflow.success) { - if (workflow.stats.ignoredCount == 0) { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" - } - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" - } - } - - // - // ANSII Colours used for terminal logging - // - public static Map logColours(Boolean monochrome_logs) { - Map colorcodes = [:] - - // Reset / Meta - colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" - colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" - colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" - colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" - colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" - colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" - colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" - - // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" - - // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" - - // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" - - // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" - - // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" - - return colorcodes - } - - // - // Does what is says on the tin - // - public static String dashedLine(monochrome_logs) { - Map colors = logColours(monochrome_logs) - return "-${colors.dim}----------------------------------------------------${colors.reset}-" - } - - // - // nf-core logo - // - public static String logo(workflow, monochrome_logs) { - Map colors = logColours(monochrome_logs) - String workflow_version = NfcoreTemplate.version(workflow) - String.format( - """\n - ${dashedLine(monochrome_logs)} - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} - ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} - ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} - ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} ${workflow_version}${colors.reset} - ${dashedLine(monochrome_logs)} - """.stripIndent() - ) - } -} diff --git a/lib/Utils.groovy b/lib/Utils.groovy deleted file mode 100644 index 8d030f4e..00000000 --- a/lib/Utils.groovy +++ /dev/null @@ -1,47 +0,0 @@ -// -// This file holds several Groovy functions that could be useful for any Nextflow pipeline -// - -import org.yaml.snakeyaml.Yaml - -class Utils { - - // - // When running with -profile conda, warn if channels have not been set-up appropriately - // - public static void checkCondaChannels(log) { - Yaml parser = new Yaml() - def channels = [] - try { - def config = parser.load("conda config --show channels".execute().text) - channels = config.channels - } catch(NullPointerException | IOException e) { - log.warn "Could not verify conda channel configuration." - return - } - - // Check that all channels are present - // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] - def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean - - // Check that they are in the right order - def channel_priority_violation = false - def n = required_channels_in_order.size() - for (int i = 0; i < n - 1; i++) { - channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) - } - - if (channels_missing | channel_priority_violation) { - log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " There is a problem with your Conda configuration!\n\n" + - " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/\n" + - " The observed channel order is \n" + - " ${channels}\n" + - " but the following channel order is required:\n" + - " ${required_channels_in_order}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - } - } -} diff --git a/lib/WorkflowCircrna.groovy b/lib/WorkflowCircrna.groovy deleted file mode 100755 index eae29c19..00000000 --- a/lib/WorkflowCircrna.groovy +++ /dev/null @@ -1,122 +0,0 @@ -// -// This file holds several functions specific to the workflow/circrna.nf in the nf-core/circrna pipeline -// - -import nextflow.Nextflow -import groovy.text.SimpleTemplateEngine - -class WorkflowCircrna { - - // - // Check and validate parameters - // - public static void initialise(params, log) { - - genomeExistsError(params, log) - - - if (!params.fasta) { - Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." - } - } - - // - // Get workflow summary for MultiQC - // - public static String paramsSummaryMultiqc(workflow, summary) { - String summary_section = '' - for (group in summary.keySet()) { - def group_params = summary.get(group) // This gets the parameters of that particular group - if (group_params) { - summary_section += "

    $group

    \n" - summary_section += "
    \n" - for (param in group_params.keySet()) { - summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" - } - summary_section += "
    \n" - } - } - - String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" - return yaml_file_text - } - - // - // Generate methods description for MultiQC - // - - public static String toolCitationText(params) { - - // TODO nf-core: Optionally add in-text citation tools to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report - def citation_text = [ - "Tools used in the workflow included:", - "FastQC (Andrews 2010),", - "MultiQC (Ewels et al. 2016)", - "." - ].join(' ').trim() - - return citation_text - } - - public static String toolBibliographyText(params) { - - // TODO Optionally add bibliographic entries to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report - def reference_text = [ - "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", - "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " - ].join(' ').trim() - - return reference_text - } - - public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) { - // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file - def meta = [:] - meta.workflow = run_workflow.toMap() - meta["manifest_map"] = run_workflow.manifest.toMap() - - // Pipeline DOI - meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" - meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " - - // Tool references - meta["tool_citations"] = "" - meta["tool_bibliography"] = "" - - // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! - //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") - //meta["tool_bibliography"] = toolBibliographyText(params) - - - def methods_text = mqc_methods_yaml.text - - def engine = new SimpleTemplateEngine() - def description_html = engine.createTemplate(methods_text).make(meta) - - return description_html - } - - // - // Exit pipeline if incorrect --genome key provided - // - private static void genomeExistsError(params, log) { - if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { - def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + - " Currently, the available genome keys are:\n" + - " ${params.genomes.keySet().join(", ")}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - Nextflow.error(error_string) - } - } -} diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy deleted file mode 100755 index 79426ea9..00000000 --- a/lib/WorkflowMain.groovy +++ /dev/null @@ -1,77 +0,0 @@ -// -// This file holds several functions specific to the main.nf workflow in the nf-core/circrna pipeline -// - -import nextflow.Nextflow - -class WorkflowMain { - - // - // Citation string for pipeline - // - public static String citation(workflow) { - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - // TODO nf-core: Add Zenodo DOI for pipeline after first release - //"* The pipeline\n" + - //" https://doi.org/10.5281/zenodo.XXXXXXX\n\n" + - "* The nf-core framework\n" + - " https://doi.org/10.1038/s41587-020-0439-x\n\n" + - "* Software dependencies\n" + - " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" - } - - - // - // Validate parameters and print summary to screen - // - public static void initialise(workflow, params, log, args) { - - // Print workflow version and exit on --version - if (params.version) { - String workflow_version = NfcoreTemplate.version(workflow) - log.info "${workflow.manifest.name} ${workflow_version}" - System.exit(0) - } - - // Check that a -profile or Nextflow config has been provided to run the pipeline - NfcoreTemplate.checkConfigProvided(workflow, log) - // Check that the profile doesn't contain spaces and doesn't end with a trailing comma - checkProfile(workflow.profile, args, log) - - // Check that conda channels are set-up correctly - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - Utils.checkCondaChannels(log) - } - - // Check AWS batch settings - NfcoreTemplate.awsBatch(workflow, params) - - // Check input has been provided - if (!params.input) { - Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'") - } - } - // - // Get attribute from genome config file e.g. fasta - // - public static Object getGenomeAttribute(params, attribute) { - if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { - if (params.genomes[ params.genome ].containsKey(attribute)) { - return params.genomes[ params.genome ][ attribute ] - } - } - return null - } - - // - // Exit pipeline if --profile contains spaces - // - private static void checkProfile(profile, args, log) { - if (profile.endsWith(',')) { - Nextflow.error "Profile cannot end with a trailing comma. Please remove the comma from the end of the profile string.\nHint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`." - } - if (args[0]) { - log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${args[0]}` has been detected.\n Hint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`." - } - } -} diff --git a/main.nf b/main.nf index 32aabbc7..810b3959 100644 --- a/main.nf +++ b/main.nf @@ -13,66 +13,96 @@ nextflow.enable.dsl = 2 /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - GENOME PARAMETER VALUES + IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// TODO nf-core: Remove this line if you don't need a FASTA file -// This is an example of how to use getGenomeAttribute() to fetch parameters -// from igenomes.config using `--genome` -params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta') +include { CIRCRNA } from './workflows/circrna' +include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_circrna_pipeline' +include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_circrna_pipeline' + +include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_circrna_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - VALIDATE & PRINT PARAMETER SUMMARY + GENOME PARAMETER VALUES ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { validateParameters; paramsHelp } from 'plugin/nf-validation' - -// Print help message if needed -if (params.help) { - def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) - def citation = '\n' + WorkflowMain.citation(workflow) + '\n' - def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" - log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) - System.exit(0) -} - -// Validate input parameters -if (params.validate_params) { - validateParameters() -} - -WorkflowMain.initialise(workflow, params, log, args) +// TODO nf-core: Remove this line if you don't need a FASTA file +// This is an example of how to use getGenomeAttribute() to fetch parameters +// from igenomes.config using `--genome` +params.fasta = getGenomeAttribute('fasta') /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - NAMED WORKFLOW FOR PIPELINE + NAMED WORKFLOWS FOR PIPELINE ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { CIRCRNA } from './workflows/circrna' - // -// WORKFLOW: Run main nf-core/circrna analysis pipeline +// WORKFLOW: Run main analysis pipeline depending on type of input // workflow NFCORE_CIRCRNA { - CIRCRNA () -} + take: + samplesheet // channel: samplesheet read in from --input + + main: + + // + // WORKFLOW: Run pipeline + // + CIRCRNA ( + samplesheet + ) + + emit: + multiqc_report = CIRCRNA.out.multiqc_report // channel: /path/to/multiqc_report.html + +} /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - RUN ALL WORKFLOWS + RUN MAIN WORKFLOW ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// -// WORKFLOW: Execute a single named workflow for the pipeline -// See: https://github.com/nf-core/rnaseq/issues/619 -// workflow { - NFCORE_CIRCRNA () + + main: + + // + // SUBWORKFLOW: Run initialisation tasks + // + PIPELINE_INITIALISATION ( + params.version, + params.help, + params.validate_params, + params.monochrome_logs, + args, + params.outdir, + params.input + ) + + // + // WORKFLOW: Run main workflow + // + NFCORE_CIRCRNA ( + PIPELINE_INITIALISATION.out.samplesheet + ) + + // + // SUBWORKFLOW: Run completion tasks + // + PIPELINE_COMPLETION ( + params.email, + params.email_on_fail, + params.plaintext_email, + params.outdir, + params.monochrome_logs, + params.hook_url, + NFCORE_CIRCRNA.out.multiqc_report + ) } /* diff --git a/modules.json b/modules.json index 67813eca..8cca7fba 100644 --- a/modules.json +++ b/modules.json @@ -5,22 +5,36 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { - "custom/dumpsoftwareversions": { - "branch": "master", - "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", - "installed_by": ["modules"] - }, "fastqc": { "branch": "master", - "git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9", + "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", + "git_sha": "ccacf6f5de6df3bc6d73b665c1fd2933d8bbc290", "installed_by": ["modules"] } } + }, + "subworkflows": { + "nf-core": { + "utils_nextflow_pipeline": { + "branch": "master", + "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "installed_by": ["subworkflows"] + }, + "utils_nfcore_pipeline": { + "branch": "master", + "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8", + "installed_by": ["subworkflows"] + }, + "utils_nfvalidation_plugin": { + "branch": "master", + "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "installed_by": ["subworkflows"] + } + } } } } diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf deleted file mode 100644 index e102f46d..00000000 --- a/modules/local/samplesheet_check.nf +++ /dev/null @@ -1,31 +0,0 @@ -process SAMPLESHEET_CHECK { - tag "$samplesheet" - label 'process_single' - - conda "conda-forge::python=3.8.3" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'biocontainers/python:3.8.3' }" - - input: - path samplesheet - - output: - path '*.csv' , emit: csv - path "versions.yml", emit: versions - - when: - task.ext.when == null || task.ext.when - - script: // This script is bundled with the pipeline, in nf-core/circrna/bin/ - """ - check_samplesheet.py \\ - $samplesheet \\ - samplesheet.valid.csv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - python: \$(python --version | sed 's/Python //g') - END_VERSIONS - """ -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml deleted file mode 100644 index 9b3272bc..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: custom_dumpsoftwareversions -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::multiqc=1.19 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf deleted file mode 100644 index f2187611..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ /dev/null @@ -1,24 +0,0 @@ -process CUSTOM_DUMPSOFTWAREVERSIONS { - label 'process_single' - - // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : - 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" - - input: - path versions - - output: - path "software_versions.yml" , emit: yml - path "software_versions_mqc.yml", emit: mqc_yml - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - template 'dumpsoftwareversions.py' -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml deleted file mode 100644 index 5f15a5fd..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ /dev/null @@ -1,37 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json -name: custom_dumpsoftwareversions -description: Custom module used to dump software versions within the nf-core pipeline template -keywords: - - custom - - dump - - version -tools: - - custom: - description: Custom module used to dump software versions within the nf-core pipeline template - homepage: https://github.com/nf-core/tools - documentation: https://github.com/nf-core/tools - licence: ["MIT"] -input: - - versions: - type: file - description: YML file containing software versions - pattern: "*.yml" -output: - - yml: - type: file - description: Standard YML file containing software versions - pattern: "software_versions.yml" - - mqc_yml: - type: file - description: MultiQC custom content YML file containing software versions - pattern: "software_versions_mqc.yml" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@drpatelh" - - "@grst" -maintainers: - - "@drpatelh" - - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py deleted file mode 100755 index e55b8d43..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ /dev/null @@ -1,102 +0,0 @@ -#!/usr/bin/env python - - -"""Provide functions to merge multiple versions.yml files.""" - - -import platform -from textwrap import dedent - -import yaml - - -def _make_versions_html(versions): - """Generate a tabular HTML output of all versions for MultiQC.""" - html = [ - dedent( - """\\ - -
    Process Name \\", + " \\ Software Version
    CUSTOM_DUMPSOFTWAREVERSIONSpython3.11.7
    yaml5.4.1
    TOOL1tool10.11.9
    TOOL2tool21.9
    WorkflowNextflow
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    - - - - - - - - """ - ) - ] - for process, tmp_versions in sorted(versions.items()): - html.append("") - for i, (tool, version) in enumerate(sorted(tmp_versions.items())): - html.append( - dedent( - f"""\\ - - - - - - """ - ) - ) - html.append("") - html.append("
    Process Name Software Version
    {process if (i == 0) else ''}{tool}{version}
    ") - return "\\n".join(html) - - -def main(): - """Load all version files and generate merged output.""" - versions_this_module = {} - versions_this_module["${task.process}"] = { - "python": platform.python_version(), - "yaml": yaml.__version__, - } - - with open("$versions") as f: - versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module - - # aggregate versions by the module name (derived from fully-qualified process name) - versions_by_module = {} - for process, process_versions in versions_by_process.items(): - module = process.split(":")[-1] - try: - if versions_by_module[module] != process_versions: - raise AssertionError( - "We assume that software versions are the same between all modules. " - "If you see this error-message it means you discovered an edge-case " - "and should open an issue in nf-core/tools. " - ) - except KeyError: - versions_by_module[module] = process_versions - - versions_by_module["Workflow"] = { - "Nextflow": "$workflow.nextflow.version", - "$workflow.manifest.name": "$workflow.manifest.version", - } - - versions_mqc = { - "id": "software_versions", - "section_name": "${workflow.manifest.name} Software Versions", - "section_href": "https://github.com/${workflow.manifest.name}", - "plot_type": "html", - "description": "are collected at run time from the software output.", - "data": _make_versions_html(versions_by_module), - } - - with open("software_versions.yml", "w") as f: - yaml.dump(versions_by_module, f, default_flow_style=False) - with open("software_versions_mqc.yml", "w") as f: - yaml.dump(versions_mqc, f, default_flow_style=False) - - with open("versions.yml", "w") as f: - yaml.dump(versions_this_module, f, default_flow_style=False) - - -if __name__ == "__main__": - main() diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test deleted file mode 100644 index b1e1630b..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test +++ /dev/null @@ -1,43 +0,0 @@ -nextflow_process { - - name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" - script "../main.nf" - process "CUSTOM_DUMPSOFTWAREVERSIONS" - tag "modules" - tag "modules_nfcore" - tag "custom" - tag "dumpsoftwareversions" - tag "custom/dumpsoftwareversions" - - test("Should run without failures") { - when { - process { - """ - def tool1_version = ''' - TOOL1: - tool1: 0.11.9 - '''.stripIndent() - - def tool2_version = ''' - TOOL2: - tool2: 1.9 - '''.stripIndent() - - input[0] = Channel.of(tool1_version, tool2_version).collectFile() - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.versions, - file(process.out.mqc_yml[0]).readLines()[0..10], - file(process.out.yml[0]).readLines()[0..7] - ).match() - } - ) - } - } -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap deleted file mode 100644 index 5f59a936..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap +++ /dev/null @@ -1,33 +0,0 @@ -{ - "Should run without failures": { - "content": [ - [ - "versions.yml:md5,76d454d92244589d32455833f7c1ba6d" - ], - [ - "data: \"\\n\\n \\n \\n \\n \\n \\n \\n \\n\\", - " \\n\\n\\n \\n \\n\\", - " \\ \\n\\n\\n\\n \\n \\", - " \\ \\n \\n\\n\\n\\n\\", - " \\n\\n \\n \\n\\", - " \\ \\n\\n\\n\\n\\n\\n \\n\\", - " \\ \\n \\n\\n\\n\\n\\", - " \\n\\n \\n \\n\\" - ], - [ - "CUSTOM_DUMPSOFTWAREVERSIONS:", - " python: 3.11.7", - " yaml: 5.4.1", - "TOOL1:", - " tool1: 0.11.9", - "TOOL2:", - " tool2: '1.9'", - "Workflow:" - ] - ], - "timestamp": "2024-01-09T23:01:18.710682" - } -} \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml deleted file mode 100644 index 405aa24a..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -custom/dumpsoftwareversions: - - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 1f21c664..70edae4d 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -33,7 +33,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_single") } ) } } @@ -63,7 +63,7 @@ nextflow_process { { assert path(process.out.html[0][1][0]).text.contains("") }, { assert path(process.out.html[0][1][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_paired") } ) } } @@ -89,7 +89,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } ) } } @@ -115,7 +115,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_bam") } ) } } @@ -153,7 +153,7 @@ nextflow_process { { assert path(process.out.html[0][1][2]).text.contains("") }, { assert path(process.out.html[0][1][3]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } ) } } @@ -179,7 +179,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } ) } } @@ -204,7 +204,7 @@ nextflow_process { { assert process.success }, { assert snapshot(process.out.html.collect { file(it[1]).getName() } + process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match() } + process.out.versions ).match("fastqc_stub") } ) } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 5d624bb8..86f7c311 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,5 +1,17 @@ { - "sarscov2 single-end [fastq] - stub": { + "fastqc_versions_interleaved": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:40:07.293713" + }, + "fastqc_stub": { "content": [ [ "test.html", @@ -7,14 +19,70 @@ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], - "timestamp": "2024-01-17T18:40:57.254299" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:31:01.425198" + }, + "fastqc_versions_multiple": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:40:55.797907" + }, + "fastqc_versions_bam": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:40:26.795862" + }, + "fastqc_versions_single": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:39:27.043675" + }, + "fastqc_versions_paired": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:39:47.584191" }, - "versions": { + "fastqc_versions_custom_prefix": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], - "timestamp": "2024-01-17T18:36:50.033627" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:41:14.576531" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 7625b752..2212096a 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.19 + - bioconda::multiqc=1.20 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 1b9f7c43..354f4430 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : - 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_0' : + 'biocontainers/multiqc:1.20--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index d0438eda..f1c4242e 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -3,6 +3,7 @@ nextflow_process { name "Test Process MULTIQC" script "../main.nf" process "MULTIQC" + tag "modules" tag "modules_nfcore" tag "multiqc" @@ -12,7 +13,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = [] input[2] = [] input[3] = [] @@ -25,7 +26,7 @@ nextflow_process { { assert process.success }, { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("multiqc_versions_single") } ) } @@ -36,7 +37,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] @@ -49,7 +50,7 @@ nextflow_process { { assert process.success }, { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("multiqc_versions_config") } ) } } @@ -61,7 +62,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = [] input[2] = [] input[3] = [] @@ -75,7 +76,7 @@ nextflow_process { { assert snapshot(process.out.report.collect { file(it).getName() } + process.out.data.collect { file(it).getName() } + process.out.plots.collect { file(it).getName() } + - process.out.versions ).match() } + process.out.versions ).match("multiqc_stub") } ) } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index d37e7304..c204b488 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -1,21 +1,41 @@ { - "versions": { + "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" ] ], - "timestamp": "2024-01-09T23:02:49.911994" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T09:28:51.744211298" }, - "sarscov2 single-end [fastqc] - stub": { + "multiqc_stub": { "content": [ [ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" ] ], - "timestamp": "2024-01-09T23:03:14.524346" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T09:29:28.847433492" + }, + "multiqc_versions_config": { + "content": [ + [ + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T09:29:13.223621555" } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 4d098309..564acf64 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,9 +16,7 @@ params { genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false - - - // MultiQC options + fasta = null// MultiQC options multiqc_config = null multiqc_title = null multiqc_logo = null @@ -43,7 +41,6 @@ params { custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null - // Max resource options // Defaults only, expecting to be overwritten diff --git a/nextflow_schema.json b/nextflow_schema.json index 075e8b33..01ffcd21 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -16,6 +16,7 @@ "type": "string", "format": "file-path", "exists": true, + "schema": "assets/schema_input.json", "mimetype": "text/csv", "pattern": "^\\S+\\.csv$", "description": "Path to comma-separated file containing information about the samples in the experiment.", diff --git a/pyproject.toml b/pyproject.toml index 7d08e1c8..56110621 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,11 +3,13 @@ [tool.ruff] line-length = 120 target-version = "py38" -select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"] cache-dir = "~/.cache/ruff" -[tool.ruff.isort] +[tool.ruff.lint] +select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"] + +[tool.ruff.lint.isort] known-first-party = ["nf_core"] -[tool.ruff.per-file-ignores] +[tool.ruff.lint.per-file-ignores] "__init__.py" = ["E402", "F401"] diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf deleted file mode 100644 index 0aecf87f..00000000 --- a/subworkflows/local/input_check.nf +++ /dev/null @@ -1,44 +0,0 @@ -// -// Check input samplesheet and get read channels -// - -include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check' - -workflow INPUT_CHECK { - take: - samplesheet // file: /path/to/samplesheet.csv - - main: - SAMPLESHEET_CHECK ( samplesheet ) - .csv - .splitCsv ( header:true, sep:',' ) - .map { create_fastq_channel(it) } - .set { reads } - - emit: - reads // channel: [ val(meta), [ reads ] ] - versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ] -} - -// Function to get list of [ meta, [ fastq_1, fastq_2 ] ] -def create_fastq_channel(LinkedHashMap row) { - // create meta map - def meta = [:] - meta.id = row.sample - meta.single_end = row.single_end.toBoolean() - - // add path(s) of the fastq file(s) to the meta map - def fastq_meta = [] - if (!file(row.fastq_1).exists()) { - exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}" - } - if (meta.single_end) { - fastq_meta = [ meta, [ file(row.fastq_1) ] ] - } else { - if (!file(row.fastq_2).exists()) { - exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}" - } - fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ] - } - return fastq_meta -} diff --git a/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf b/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf new file mode 100644 index 00000000..dc90ad90 --- /dev/null +++ b/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf @@ -0,0 +1,247 @@ +// +// Subworkflow with functionality specific to the nf-core/pipeline pipeline +// + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' +include { paramsSummaryMap } from 'plugin/nf-validation' +include { fromSamplesheet } from 'plugin/nf-validation' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' +include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' +include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' +include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' +include { imNotification } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' +include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' + +/* +======================================================================================== + SUBWORKFLOW TO INITIALISE PIPELINE +======================================================================================== +*/ + +workflow PIPELINE_INITIALISATION { + + take: + version // boolean: Display version and exit + help // boolean: Display help text + validate_params // boolean: Boolean whether to validate parameters against the schema at runtime + monochrome_logs // boolean: Do not use coloured log outputs + nextflow_cli_args // array: List of positional nextflow CLI args + outdir // string: The output directory where the results will be saved + input // string: Path to input samplesheet + + main: + + ch_versions = Channel.empty() + + // + // Print version and exit if required and dump pipeline parameters to JSON file + // + UTILS_NEXTFLOW_PIPELINE ( + version, + true, + outdir, + workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 + ) + + // + // Validate parameters and generate parameter summary to stdout + // + pre_help_text = nfCoreLogo(monochrome_logs) + post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs) + def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " + UTILS_NFVALIDATION_PLUGIN ( + help, + workflow_command, + pre_help_text, + post_help_text, + validate_params, + "nextflow_schema.json" + ) + + // + // Check config provided to the pipeline + // + UTILS_NFCORE_PIPELINE ( + nextflow_cli_args + ) + // + // Custom validation for pipeline parameters + // + validateInputParameters() + + // + // Create channel from input file provided through params.input + // + Channel + .fromSamplesheet("input") + .map { + meta, fastq_1, fastq_2 -> + if (!fastq_2) { + return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] + } else { + return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] + } + } + .groupTuple() + .map { + validateInputSamplesheet(it) + } + .map { + meta, fastqs -> + return [ meta, fastqs.flatten() ] + } + .set { ch_samplesheet } + + emit: + samplesheet = ch_samplesheet + versions = ch_versions +} + +/* +======================================================================================== + SUBWORKFLOW FOR PIPELINE COMPLETION +======================================================================================== +*/ + +workflow PIPELINE_COMPLETION { + + take: + email // string: email address + email_on_fail // string: email address sent on pipeline failure + plaintext_email // boolean: Send plain-text email instead of HTML + outdir // path: Path to output directory where results will be published + monochrome_logs // boolean: Disable ANSI colour codes in log output + hook_url // string: hook URL for notifications + multiqc_report // string: Path to MultiQC report + + main: + + summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + + // + // Completion email and summary + // + workflow.onComplete { + if (email || email_on_fail) { + completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) + } + + completionSummary(monochrome_logs) + + if (hook_url) { + imNotification(summary_params, hook_url) + } + } +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ +// +// Check and validate pipeline parameters +// +def validateInputParameters() { + genomeExistsError() +}// +// Validate channels from input samplesheet +// +def validateInputSamplesheet(input) { + def (metas, fastqs) = input[1..2] + + // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end + def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 + if (!endedness_ok) { + error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") + } + + return [ metas[0], fastqs ] +} +// +// Get attribute from genome config file e.g. fasta +// +def getGenomeAttribute(attribute) { + if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { + if (params.genomes[ params.genome ].containsKey(attribute)) { + return params.genomes[ params.genome ][ attribute ] + } + } + return null +} + +// +// Exit pipeline if incorrect --genome key provided +// +def genomeExistsError() { + if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { + def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + + " Currently, the available genome keys are:\n" + + " ${params.genomes.keySet().join(", ")}\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + error(error_string) + } +}// +// Generate methods description for MultiQC +// +def toolCitationText() { + // TODO nf-core: Optionally add in-text citation tools to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def citation_text = [ + "Tools used in the workflow included:", + "FastQC (Andrews 2010),", + "MultiQC (Ewels et al. 2016)", + "." + ].join(' ').trim() + + return citation_text +} + +def toolBibliographyText() { + // TODO nf-core: Optionally add bibliographic entries to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def reference_text = [ + "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", + "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " + ].join(' ').trim() + + return reference_text +} + +def methodsDescriptionText(mqc_methods_yaml) { + // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file + def meta = [:] + meta.workflow = workflow.toMap() + meta["manifest_map"] = workflow.manifest.toMap() + + // Pipeline DOI + meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" + meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + + // Tool references + meta["tool_citations"] = "" + meta["tool_bibliography"] = "" + + // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! + // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") + // meta["tool_bibliography"] = toolBibliographyText() + + + def methods_text = mqc_methods_yaml.text + + def engine = new groovy.text.SimpleTemplateEngine() + def description_html = engine.createTemplate(methods_text).make(meta) + + return description_html.toString() +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf new file mode 100644 index 00000000..ac31f28f --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -0,0 +1,126 @@ +// +// Subworkflow with functionality that may be useful for any Nextflow pipeline +// + +import org.yaml.snakeyaml.Yaml +import groovy.json.JsonOutput +import nextflow.extension.FilesEx + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow UTILS_NEXTFLOW_PIPELINE { + + take: + print_version // boolean: print version + dump_parameters // boolean: dump parameters + outdir // path: base directory used to publish pipeline results + check_conda_channels // boolean: check conda channels + + main: + + // + // Print workflow version and exit on --version + // + if (print_version) { + log.info "${workflow.manifest.name} ${getWorkflowVersion()}" + System.exit(0) + } + + // + // Dump pipeline parameters to a JSON file + // + if (dump_parameters && outdir) { + dumpParametersToJSON(outdir) + } + + // + // When running with Conda, warn if channels have not been set-up appropriately + // + if (check_conda_channels) { + checkCondaChannels() + } + + emit: + dummy_emit = true +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ + +// +// Generate version string +// +def getWorkflowVersion() { + String version_string = "" + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string +} + +// +// Dump pipeline parameters to a JSON file +// +def dumpParametersToJSON(outdir) { + def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = JsonOutput.toJson(params) + temp_pf.text = JsonOutput.prettyPrint(jsonStr) + + FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + temp_pf.delete() +} + +// +// When running with -profile conda, warn if channels have not been set-up appropriately +// +def checkCondaChannels() { + Yaml parser = new Yaml() + def channels = [] + try { + def config = parser.load("conda config --show channels".execute().text) + channels = config.channels + } catch(NullPointerException | IOException e) { + log.warn "Could not verify conda channel configuration." + return + } + + // Check that all channels are present + // This channel list is ordered by required channel priority. + def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean + + // Check that they are in the right order + def channel_priority_violation = false + def n = required_channels_in_order.size() + for (int i = 0; i < n - 1; i++) { + channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) + } + + if (channels_missing | channel_priority_violation) { + log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " There is a problem with your Conda configuration!\n\n" + + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + + " Please refer to https://bioconda.github.io/\n" + + " The observed channel order is \n" + + " ${channels}\n" + + " but the following channel order is required:\n" + + " ${required_channels_in_order}\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml new file mode 100644 index 00000000..e5c3a0a8 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml @@ -0,0 +1,38 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NEXTFLOW_PIPELINE" +description: Subworkflow with functionality that may be useful for any Nextflow pipeline +keywords: + - utility + - pipeline + - initialise + - version +components: [] +input: + - print_version: + type: boolean + description: | + Print the version of the pipeline and exit + - dump_parameters: + type: boolean + description: | + Dump the parameters of the pipeline to a JSON file + - output_directory: + type: directory + description: Path to output dir to write JSON file to. + pattern: "results/" + - check_conda_channel: + type: boolean + description: | + Check if the conda channel priority is correct. +output: + - dummy_emit: + type: boolean + description: | + Dummy emit to make nf-core subworkflows lint happy +authors: + - "@adamrtalbot" + - "@drpatelh" +maintainers: + - "@adamrtalbot" + - "@drpatelh" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test new file mode 100644 index 00000000..8ed4310c --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test @@ -0,0 +1,54 @@ + +nextflow_function { + + name "Test Functions" + script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf" + config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" + tag 'subworkflows' + tag 'utils_nextflow_pipeline' + tag 'subworkflows/utils_nextflow_pipeline' + + test("Test Function getWorkflowVersion") { + + function "getWorkflowVersion" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function dumpParametersToJSON") { + + function "dumpParametersToJSON" + + when { + function { + """ + // define inputs of the function here. Example: + input[0] = "$outputDir" + """.stripIndent() + } + } + + then { + assertAll( + { assert function.success } + ) + } + } + + test("Test Function checkCondaChannels") { + + function "checkCondaChannels" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap new file mode 100644 index 00000000..db2030f8 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap @@ -0,0 +1,12 @@ +{ + "Test Function getWorkflowVersion": { + "content": [ + "v9.9.9" + ], + "timestamp": "2024-01-19T11:32:36.031083" + }, + "Test Function checkCondaChannels": { + "content": null, + "timestamp": "2024-01-19T11:32:50.456" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test new file mode 100644 index 00000000..f7c54bc6 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -0,0 +1,123 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NEXTFLOW_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" + workflow "UTILS_NEXTFLOW_PIPELINE" + tag 'subworkflows' + tag 'utils_nextflow_pipeline' + tag 'subworkflows/utils_nextflow_pipeline' + + test("Should run no inputs") { + + when { + params { + outdir = "tests/results" + } + workflow { + """ + print_version = false + dump_parameters = false + outdir = null + check_conda_channels = false + + input[0] = print_version + input[1] = dump_parameters + input[2] = outdir + input[3] = check_conda_channels + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should print version") { + + when { + params { + outdir = "tests/results" + } + workflow { + """ + print_version = true + dump_parameters = false + outdir = null + check_conda_channels = false + + input[0] = print_version + input[1] = dump_parameters + input[2] = outdir + input[3] = check_conda_channels + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } + ) + } + } + + test("Should dump params") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + print_version = false + dump_parameters = true + outdir = params.outdir + check_conda_channels = false + + input[0] = false + input[1] = true + input[2] = params.outdir + input[3] = false + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should not create params JSON if no output directory") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + print_version = false + dump_parameters = true + outdir = params.outdir + check_conda_channels = false + + input[0] = false + input[1] = true + input[2] = null + input[3] = false + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config new file mode 100644 index 00000000..53574ffe --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -0,0 +1,9 @@ +manifest { + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" + nextflowVersion = '!>=23.04.0' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml new file mode 100644 index 00000000..f8476112 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nextflow_pipeline: + - subworkflows/nf-core/utils_nextflow_pipeline/** diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf new file mode 100644 index 00000000..a8b55d6f --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -0,0 +1,440 @@ +// +// Subworkflow with utility functions specific to the nf-core pipeline template +// + +import org.yaml.snakeyaml.Yaml +import nextflow.extension.FilesEx + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow UTILS_NFCORE_PIPELINE { + + take: + nextflow_cli_args + + main: + valid_config = checkConfigProvided() + checkProfileProvided(nextflow_cli_args) + + emit: + valid_config +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ + +// +// Warn if a -profile or Nextflow config has not been provided to run the pipeline +// +def checkConfigProvided() { + valid_config = true + if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { + log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + + "Please refer to the quick start section and usage docs for the pipeline.\n " + valid_config = false + } + return valid_config +} + +// +// Exit pipeline if --profile contains spaces +// +def checkProfileProvided(nextflow_cli_args) { + if (workflow.profile.endsWith(',')) { + error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + } + if (nextflow_cli_args[0]) { + log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + } +} + +// +// Citation string for pipeline +// +def workflowCitation() { + return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + + "* The pipeline\n" + + " ${workflow.manifest.doi}\n\n" + + "* The nf-core framework\n" + + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + + "* Software dependencies\n" + + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" +} + +// +// Generate workflow version string +// +def getWorkflowVersion() { + String version_string = "" + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string +} + +// +// Get software versions for pipeline +// +def processVersionsFromYAML(yaml_file) { + Yaml yaml = new Yaml() + versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + return yaml.dumpAsMap(versions).trim() +} + +// +// Get workflow version for pipeline +// +def workflowVersionToYAML() { + return """ + Workflow: + $workflow.manifest.name: ${getWorkflowVersion()} + Nextflow: $workflow.nextflow.version + """.stripIndent().trim() +} + +// +// Get channel of software versions used in pipeline in YAML format +// +def softwareVersionsToYAML(ch_versions) { + return ch_versions + .unique() + .map { processVersionsFromYAML(it) } + .unique() + .mix(Channel.of(workflowVersionToYAML())) +} + +// +// Get workflow summary for MultiQC +// +def paramsSummaryMultiqc(summary_params) { + def summary_section = '' + for (group in summary_params.keySet()) { + def group_params = summary_params.get(group) // This gets the parameters of that particular group + if (group_params) { + summary_section += "

    $group

    \n" + summary_section += "
    \n" + for (param in group_params.keySet()) { + summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" + } + summary_section += "
    \n" + } + } + + String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" + + return yaml_file_text +} + +// +// nf-core logo +// +def nfCoreLogo(monochrome_logs=true) { + Map colors = logColours(monochrome_logs) + String.format( + """\n + ${dashedLine(monochrome_logs)} + ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} + ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} + ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} + ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} + ${colors.green}`._,._,\'${colors.reset} + ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset} + ${dashedLine(monochrome_logs)} + """.stripIndent() + ) +} + +// +// Return dashed line +// +def dashedLine(monochrome_logs=true) { + Map colors = logColours(monochrome_logs) + return "-${colors.dim}----------------------------------------------------${colors.reset}-" +} + +// +// ANSII colours used for terminal logging +// +def logColours(monochrome_logs=true) { + Map colorcodes = [:] + + // Reset / Meta + colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" + colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" + colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" + colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" + colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" + colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" + colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" + + // Regular Colors + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + + // Bold + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + + // Underline + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + + // High Intensity + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + + // Bold High Intensity + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + + return colorcodes +} + +// +// Attach the multiqc report to email +// +def attachMultiqcReport(multiqc_report) { + def mqc_report = null + try { + if (workflow.success) { + mqc_report = multiqc_report.getVal() + if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { + if (mqc_report.size() > 1) { + log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" + } + mqc_report = mqc_report[0] + } + } + } catch (all) { + if (multiqc_report) { + log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" + } + } + return mqc_report +} + +// +// Construct and send completion email +// +def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { + + // Set up the e-mail variables + def subject = "[$workflow.manifest.name] Successful: $workflow.runName" + if (!workflow.success) { + subject = "[$workflow.manifest.name] FAILED: $workflow.runName" + } + + def summary = [:] + for (group in summary_params.keySet()) { + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['Date Started'] = workflow.start + misc_fields['Date Completed'] = workflow.complete + misc_fields['Pipeline script file path'] = workflow.scriptFile + misc_fields['Pipeline script hash ID'] = workflow.scriptId + if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository + if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId + if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build + misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp + + def email_fields = [:] + email_fields['version'] = getWorkflowVersion() + email_fields['runName'] = workflow.runName + email_fields['success'] = workflow.success + email_fields['dateComplete'] = workflow.complete + email_fields['duration'] = workflow.duration + email_fields['exitStatus'] = workflow.exitStatus + email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + email_fields['errorReport'] = (workflow.errorReport ?: 'None') + email_fields['commandLine'] = workflow.commandLine + email_fields['projectDir'] = workflow.projectDir + email_fields['summary'] = summary << misc_fields + + // On success try attach the multiqc report + def mqc_report = attachMultiqcReport(multiqc_report) + + // Check if we are only sending emails on failure + def email_address = email + if (!email && email_on_fail && !workflow.success) { + email_address = email_on_fail + } + + // Render the TXT template + def engine = new groovy.text.GStringTemplateEngine() + def tf = new File("${workflow.projectDir}/assets/email_template.txt") + def txt_template = engine.createTemplate(tf).make(email_fields) + def email_txt = txt_template.toString() + + // Render the HTML template + def hf = new File("${workflow.projectDir}/assets/email_template.html") + def html_template = engine.createTemplate(hf).make(email_fields) + def email_html = html_template.toString() + + // Render the sendmail template + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit + def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] + def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") + def sendmail_template = engine.createTemplate(sf).make(smail_fields) + def sendmail_html = sendmail_template.toString() + + // Send the HTML e-mail + Map colors = logColours(monochrome_logs) + if (email_address) { + try { + if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } + // Try to send HTML e-mail using sendmail + def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") + sendmail_tf.withWriter { w -> w << sendmail_html } + [ 'sendmail', '-t' ].execute() << sendmail_html + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" + } catch (all) { + // Catch failures and try with plaintext + def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] + mail_cmd.execute() << email_html + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" + } + } + + // Write summary e-mail HTML to a file + def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") + output_hf.withWriter { w -> w << email_html } + FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + output_hf.delete() + + // Write summary e-mail TXT to a file + def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") + output_tf.withWriter { w -> w << email_txt } + FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + output_tf.delete() +} + +// +// Print pipeline summary on completion +// +def completionSummary(monochrome_logs=true) { + Map colors = logColours(monochrome_logs) + if (workflow.success) { + if (workflow.stats.ignoredCount == 0) { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" + } else { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + } + } else { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" + } +} + +// +// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack +// +def imNotification(summary_params, hook_url) { + def summary = [:] + for (group in summary_params.keySet()) { + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) misc_fields['repository'] = workflow.repository + if (workflow.commitId) misc_fields['commitid'] = workflow.commitId + if (workflow.revision) misc_fields['revision'] = workflow.revision + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + + def msg_fields = [:] + msg_fields['version'] = getWorkflowVersion() + msg_fields['runName'] = workflow.runName + msg_fields['success'] = workflow.success + msg_fields['dateComplete'] = workflow.complete + msg_fields['duration'] = workflow.duration + msg_fields['exitStatus'] = workflow.exitStatus + msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + msg_fields['errorReport'] = (workflow.errorReport ?: 'None') + msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") + msg_fields['projectDir'] = workflow.projectDir + msg_fields['summary'] = summary << misc_fields + + // Render the JSON template + def engine = new groovy.text.GStringTemplateEngine() + // Different JSON depending on the service provider + // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format + def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" + def hf = new File("${workflow.projectDir}/assets/${json_path}") + def json_template = engine.createTemplate(hf).make(msg_fields) + def json_message = json_template.toString() + + // POST + def post = new URL(hook_url).openConnection(); + post.setRequestMethod("POST") + post.setDoOutput(true) + post.setRequestProperty("Content-Type", "application/json") + post.getOutputStream().write(json_message.getBytes("UTF-8")); + def postRC = post.getResponseCode(); + if (! postRC.equals(200)) { + log.warn(post.getErrorStream().getText()); + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml new file mode 100644 index 00000000..d08d2434 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml @@ -0,0 +1,24 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NFCORE_PIPELINE" +description: Subworkflow with utility functions specific to the nf-core pipeline template +keywords: + - utility + - pipeline + - initialise + - version +components: [] +input: + - nextflow_cli_args: + type: list + description: | + Nextflow CLI positional arguments +output: + - success: + type: boolean + description: | + Dummy output to indicate success +authors: + - "@adamrtalbot" +maintainers: + - "@adamrtalbot" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test new file mode 100644 index 00000000..1dc317f8 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test @@ -0,0 +1,134 @@ + +nextflow_function { + + name "Test Functions" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Test Function checkConfigProvided") { + + function "checkConfigProvided" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function checkProfileProvided") { + + function "checkProfileProvided" + + when { + function { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function workflowCitation") { + + function "workflowCitation" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function nfCoreLogo") { + + function "nfCoreLogo" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function dashedLine") { + + function "dashedLine" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function without logColours") { + + function "logColours" + + when { + function { + """ + input[0] = true + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function with logColours") { + function "logColours" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap new file mode 100644 index 00000000..10f948e6 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -0,0 +1,138 @@ +{ + "Test Function checkProfileProvided": { + "content": null, + "timestamp": "2024-02-09T15:43:55.145717" + }, + "Test Function checkConfigProvided": { + "content": [ + true + ], + "timestamp": "2024-01-19T11:34:13.548431224" + }, + "Test Function nfCoreLogo": { + "content": [ + "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" + ], + "timestamp": "2024-01-19T11:34:38.840454873" + }, + "Test Function workflowCitation": { + "content": [ + "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" + ], + "timestamp": "2024-01-19T11:34:22.24352016" + }, + "Test Function without logColours": { + "content": [ + { + "reset": "", + "bold": "", + "dim": "", + "underlined": "", + "blink": "", + "reverse": "", + "hidden": "", + "black": "", + "red": "", + "green": "", + "yellow": "", + "blue": "", + "purple": "", + "cyan": "", + "white": "", + "bblack": "", + "bred": "", + "bgreen": "", + "byellow": "", + "bblue": "", + "bpurple": "", + "bcyan": "", + "bwhite": "", + "ublack": "", + "ured": "", + "ugreen": "", + "uyellow": "", + "ublue": "", + "upurple": "", + "ucyan": "", + "uwhite": "", + "iblack": "", + "ired": "", + "igreen": "", + "iyellow": "", + "iblue": "", + "ipurple": "", + "icyan": "", + "iwhite": "", + "biblack": "", + "bired": "", + "bigreen": "", + "biyellow": "", + "biblue": "", + "bipurple": "", + "bicyan": "", + "biwhite": "" + } + ], + "timestamp": "2024-01-19T11:35:04.418416984" + }, + "Test Function dashedLine": { + "content": [ + "-\u001b[2m----------------------------------------------------\u001b[0m-" + ], + "timestamp": "2024-01-19T11:34:55.420000755" + }, + "Test Function with logColours": { + "content": [ + { + "reset": "\u001b[0m", + "bold": "\u001b[1m", + "dim": "\u001b[2m", + "underlined": "\u001b[4m", + "blink": "\u001b[5m", + "reverse": "\u001b[7m", + "hidden": "\u001b[8m", + "black": "\u001b[0;30m", + "red": "\u001b[0;31m", + "green": "\u001b[0;32m", + "yellow": "\u001b[0;33m", + "blue": "\u001b[0;34m", + "purple": "\u001b[0;35m", + "cyan": "\u001b[0;36m", + "white": "\u001b[0;37m", + "bblack": "\u001b[1;30m", + "bred": "\u001b[1;31m", + "bgreen": "\u001b[1;32m", + "byellow": "\u001b[1;33m", + "bblue": "\u001b[1;34m", + "bpurple": "\u001b[1;35m", + "bcyan": "\u001b[1;36m", + "bwhite": "\u001b[1;37m", + "ublack": "\u001b[4;30m", + "ured": "\u001b[4;31m", + "ugreen": "\u001b[4;32m", + "uyellow": "\u001b[4;33m", + "ublue": "\u001b[4;34m", + "upurple": "\u001b[4;35m", + "ucyan": "\u001b[4;36m", + "uwhite": "\u001b[4;37m", + "iblack": "\u001b[0;90m", + "ired": "\u001b[0;91m", + "igreen": "\u001b[0;92m", + "iyellow": "\u001b[0;93m", + "iblue": "\u001b[0;94m", + "ipurple": "\u001b[0;95m", + "icyan": "\u001b[0;96m", + "iwhite": "\u001b[0;97m", + "biblack": "\u001b[1;90m", + "bired": "\u001b[1;91m", + "bigreen": "\u001b[1;92m", + "biyellow": "\u001b[1;93m", + "biblue": "\u001b[1;94m", + "bipurple": "\u001b[1;95m", + "bicyan": "\u001b[1;96m", + "biwhite": "\u001b[1;97m" + } + ], + "timestamp": "2024-01-19T11:35:13.436366565" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test new file mode 100644 index 00000000..8940d32d --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test @@ -0,0 +1,29 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NFCORE_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + workflow "UTILS_NFCORE_PIPELINE" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Should run without failures") { + + when { + workflow { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap new file mode 100644 index 00000000..d07ce54c --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap @@ -0,0 +1,15 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + true + ], + "valid_config": [ + true + ] + } + ], + "timestamp": "2024-01-19T11:35:22.538940073" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config new file mode 100644 index 00000000..d0a926bf --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config @@ -0,0 +1,9 @@ +manifest { + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" + nextflowVersion = '!>=23.04.0' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml new file mode 100644 index 00000000..ac8523c9 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nfcore_pipeline: + - subworkflows/nf-core/utils_nfcore_pipeline/** diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf new file mode 100644 index 00000000..2585b65d --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf @@ -0,0 +1,62 @@ +// +// Subworkflow that uses the nf-validation plugin to render help text and parameter summary +// + +/* +======================================================================================== + IMPORT NF-VALIDATION PLUGIN +======================================================================================== +*/ + +include { paramsHelp } from 'plugin/nf-validation' +include { paramsSummaryLog } from 'plugin/nf-validation' +include { validateParameters } from 'plugin/nf-validation' + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow UTILS_NFVALIDATION_PLUGIN { + + take: + print_help // boolean: print help + workflow_command // string: default commmand used to run pipeline + pre_help_text // string: string to be printed before help text and summary log + post_help_text // string: string to be printed after help text and summary log + validate_params // boolean: validate parameters + schema_filename // path: JSON schema file, null to use default value + + main: + + log.debug "Using schema file: ${schema_filename}" + + // Default values for strings + pre_help_text = pre_help_text ?: '' + post_help_text = post_help_text ?: '' + workflow_command = workflow_command ?: '' + + // + // Print help message if needed + // + if (print_help) { + log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text + System.exit(0) + } + + // + // Print parameter summary to stdout + // + log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text + + // + // Validate parameters relative to the parameter JSON schema + // + if (validate_params){ + validateParameters(parameters_schema: schema_filename) + } + + emit: + dummy_emit = true +} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml new file mode 100644 index 00000000..3d4a6b04 --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml @@ -0,0 +1,44 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NFVALIDATION_PLUGIN" +description: Use nf-validation to initiate and validate a pipeline +keywords: + - utility + - pipeline + - initialise + - validation +components: [] +input: + - print_help: + type: boolean + description: | + Print help message and exit + - workflow_command: + type: string + description: | + The command to run the workflow e.g. "nextflow run main.nf" + - pre_help_text: + type: string + description: | + Text to print before the help message + - post_help_text: + type: string + description: | + Text to print after the help message + - validate_params: + type: boolean + description: | + Validate the parameters and error if invalid. + - schema_filename: + type: string + description: | + The filename of the schema to validate against. +output: + - dummy_emit: + type: boolean + description: | + Dummy emit to make nf-core subworkflows lint happy +authors: + - "@adamrtalbot" +maintainers: + - "@adamrtalbot" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test new file mode 100644 index 00000000..517ee54e --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test @@ -0,0 +1,200 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NFVALIDATION_PLUGIN" + script "../main.nf" + workflow "UTILS_NFVALIDATION_PLUGIN" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "plugin/nf-validation" + tag "'plugin/nf-validation'" + tag "utils_nfvalidation_plugin" + tag "subworkflows/utils_nfvalidation_plugin" + + test("Should run nothing") { + + when { + + params { + monochrome_logs = true + test_data = '' + } + + workflow { + """ + help = false + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should run help") { + + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } } + ) + } + } + + test("Should run help with command") { + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = "nextflow run noorg/doesntexist" + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } } + ) + } + } + + test("Should run help with extra text") { + + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = "nextflow run noorg/doesntexist" + pre_help_text = "pre-help-text" + post_help_text = "post-help-text" + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('pre-help-text') } }, + { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } }, + { assert workflow.stdout.any { it.contains('post-help-text') } } + ) + } + } + + test("Should validate params") { + + when { + + params { + monochrome_logs = true + test_data = '' + outdir = 1 + } + workflow { + """ + help = false + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = true + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } } + ) + } + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json new file mode 100644 index 00000000..7626c1c9 --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json @@ -0,0 +1,96 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", + "title": ". pipeline parameters", + "description": "", + "type": "object", + "definitions": { + "input_output_options": { + "title": "Input/output options", + "type": "object", + "fa_icon": "fas fa-terminal", + "description": "Define where the pipeline should find input data and save output data.", + "required": ["outdir"], + "properties": { + "validate_params": { + "type": "boolean", + "description": "Validate parameters?", + "default": true, + "hidden": true + }, + "outdir": { + "type": "string", + "format": "directory-path", + "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", + "fa_icon": "fas fa-folder-open" + }, + "test_data_base": { + "type": "string", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules", + "description": "Base for test data directory", + "hidden": true + }, + "test_data": { + "type": "string", + "description": "Fake test data param", + "hidden": true + } + } + }, + "generic_options": { + "title": "Generic options", + "type": "object", + "fa_icon": "fas fa-file-import", + "description": "Less common options for the pipeline, typically set in a config file.", + "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", + "properties": { + "help": { + "type": "boolean", + "description": "Display help text.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "version": { + "type": "boolean", + "description": "Display version and exit.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "logo": { + "type": "boolean", + "default": true, + "description": "Display nf-core logo in console output.", + "fa_icon": "fas fa-image", + "hidden": true + }, + "singularity_pull_docker_container": { + "type": "boolean", + "description": "Pull Singularity container from Docker?", + "hidden": true + }, + "publish_dir_mode": { + "type": "string", + "default": "copy", + "description": "Method used to save pipeline results to output directory.", + "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", + "fa_icon": "fas fa-copy", + "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], + "hidden": true + }, + "monochrome_logs": { + "type": "boolean", + "description": "Use monochrome_logs", + "hidden": true + } + } + } + }, + "allOf": [ + { + "$ref": "#/definitions/input_output_options" + }, + { + "$ref": "#/definitions/generic_options" + } + ] +} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml new file mode 100644 index 00000000..60b1cfff --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nfvalidation_plugin: + - subworkflows/nf-core/utils_nfvalidation_plugin/** diff --git a/workflows/circrna.nf b/workflows/circrna.nf index 10ecc0ac..5e577f9b 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -1,54 +1,15 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - PRINT PARAMS SUMMARY + IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' - -def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) -def citation = '\n' + WorkflowMain.citation(workflow) + '\n' -def summary_params = paramsSummaryMap(workflow) - -// Print parameter summary log to screen -log.info logo + paramsSummaryLog(workflow) + citation - -WorkflowCircrna.initialise(params, log) - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CONFIG FILES -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) -ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty() -ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty() -ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT LOCAL MODULES/SUBWORKFLOWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// -// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules -// -include { INPUT_CHECK } from '../subworkflows/local/input_check' - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT NF-CORE MODULES/SUBWORKFLOWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// -// MODULE: Installed directly from nf-core/modules -// -include { FASTQC } from '../modules/nf-core/fastqc/main' -include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' +include { FASTQC } from '../modules/nf-core/fastqc/main' +include { MULTIQC } from '../modules/nf-core/multiqc/main' +include { paramsSummaryMap } from 'plugin/nf-validation' +include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_circrna_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -56,50 +17,45 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoft ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// Info required for completion email and summary -def multiqc_report = [] - workflow CIRCRNA { - ch_versions = Channel.empty() + take: + ch_samplesheet // channel: samplesheet read in from --input - // - // SUBWORKFLOW: Read in samplesheet, validate and stage input files - // - INPUT_CHECK ( - file(params.input) - ) - ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) - // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") - // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ - // ! There is currently no tooling to help you write a sample sheet schema + main: + + ch_versions = Channel.empty() + ch_multiqc_files = Channel.empty() // // MODULE: Run FastQC // FASTQC ( - INPUT_CHECK.out.reads + ch_samplesheet ) + ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) ch_versions = ch_versions.mix(FASTQC.out.versions.first()) - CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique().collectFile(name: 'collated_versions.yml') - ) + // + // Collate and save software versions + // + softwareVersionsToYAML(ch_versions) + .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true) + .set { ch_collated_versions } // // MODULE: MultiQC // - workflow_summary = WorkflowCircrna.paramsSummaryMultiqc(workflow, summary_params) - ch_workflow_summary = Channel.value(workflow_summary) - - methods_description = WorkflowCircrna.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) - ch_methods_description = Channel.value(methods_description) - - ch_multiqc_files = Channel.empty() - ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) + ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) + ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() + ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() + summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) + ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) + ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) + ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) + ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false)) MULTIQC ( ch_multiqc_files.collect(), @@ -107,31 +63,10 @@ workflow CIRCRNA { ch_multiqc_custom_config.toList(), ch_multiqc_logo.toList() ) - multiqc_report = MULTIQC.out.report.toList() -} - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - COMPLETION EMAIL AND SUMMARY -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -workflow.onComplete { - if (params.email || params.email_on_fail) { - NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report) - } - NfcoreTemplate.dump_parameters(workflow, params) - NfcoreTemplate.summary(workflow, params, log) - if (params.hook_url) { - NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log) - } -} -workflow.onError { - if (workflow.errorReport.contains("Process requirement exceeds available memory")) { - println("🛑 Default resources exceed availability 🛑 ") - println("💡 See here on how to configure pipeline: https://nf-co.re/docs/usage/configuration#tuning-workflow-resources 💡") - } + emit: + multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + versions = ch_versions // channel: [ path(versions.yml) ] } /* From 195e3da0a4a4cee0c816a408a7a590aa3e21d010 Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Thu, 22 Feb 2024 11:52:02 +0100 Subject: [PATCH 122/491] try to fix disapearing folder --- subworkflows/local/prepare_genome.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index d35b6b5b..672fb794 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -25,7 +25,7 @@ workflow PREPARE_GENOME { // this removes all additional fields in the headers of the input fasta file if( params.tool.contains('mapsplice') && params.module.contains('circrna_discovery') ) { - CLEAN_FASTA(Channel.value([[id: "${fasta.baseName}" + "_clean" ], fasta]), []) + CLEAN_FASTA(Channel.value([[id: "${fasta_tuple.map{ it.last() }.baseName}" + "_clean" ], fasta]), []) ch_fasta = CLEAN_FASTA.out.output.map{ it.last() } } From b30d0b380e348056603a1b168961ac7dc5839596 Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Thu, 22 Feb 2024 11:59:22 +0100 Subject: [PATCH 123/491] try to fix naming --- subworkflows/local/prepare_genome.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 672fb794..0dc71884 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -25,7 +25,7 @@ workflow PREPARE_GENOME { // this removes all additional fields in the headers of the input fasta file if( params.tool.contains('mapsplice') && params.module.contains('circrna_discovery') ) { - CLEAN_FASTA(Channel.value([[id: "${fasta_tuple.map{ it.last() }.baseName}" + "_clean" ], fasta]), []) + CLEAN_FASTA(Channel.value([[id: fasta_tuple.map{ it.last() }.baseName + "_clean" ], fasta]), []) ch_fasta = CLEAN_FASTA.out.output.map{ it.last() } } From e4bf00fc0fea2e7c2e211734403aae09685371a6 Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Thu, 22 Feb 2024 12:04:24 +0100 Subject: [PATCH 124/491] try to fix basename --- subworkflows/local/prepare_genome.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 0dc71884..6360fcb2 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -25,7 +25,7 @@ workflow PREPARE_GENOME { // this removes all additional fields in the headers of the input fasta file if( params.tool.contains('mapsplice') && params.module.contains('circrna_discovery') ) { - CLEAN_FASTA(Channel.value([[id: fasta_tuple.map{ it.last() }.baseName + "_clean" ], fasta]), []) + CLEAN_FASTA(Channel.value([[id: fasta_tuple.map{ it.last() }.getBaseName() + "_clean" ], fasta]), []) ch_fasta = CLEAN_FASTA.out.output.map{ it.last() } } From a541cc44f75842b2b29485d518f0b57a37355b65 Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Thu, 22 Feb 2024 12:09:07 +0100 Subject: [PATCH 125/491] change order --- subworkflows/local/prepare_genome.nf | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 6360fcb2..2e46b826 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -17,15 +17,11 @@ workflow PREPARE_GENOME { main: ch_versions = Channel.empty() - ch_gtf = Channel.fromPath(gtf) - fasta_tuple = Channel.value([[id: "fasta"], fasta]) - gtf_tuple = Channel.value([[id: "gtf"], gtf]) - // MapSplice cannot deal with extra field in the fasta headers // this removes all additional fields in the headers of the input fasta file if( params.tool.contains('mapsplice') && params.module.contains('circrna_discovery') ) { - CLEAN_FASTA(Channel.value([[id: fasta_tuple.map{ it.last() }.getBaseName() + "_clean" ], fasta]), []) + CLEAN_FASTA(Channel.value([[id: "${fasta.baseName}" + "_clean" ], fasta]), []) ch_fasta = CLEAN_FASTA.out.output.map{ it.last() } } @@ -36,6 +32,11 @@ workflow PREPARE_GENOME { } + + ch_gtf = Channel.fromPath(gtf) + fasta_tuple = Channel.value([[id: "fasta"], fasta]) + gtf_tuple = Channel.value([[id: "gtf"], gtf]) + // MapSplice & find_circ requires reference genome to be split per chromosome: if( ( params.tool.contains('mapsplice') || params.tool.contains('find_circ') ) && params.module.contains('circrna_discovery') ){ directory = file("${params.outdir}/references/chromosomes") From 38df3d1466e5920a3762164c807f2cafbd7dd171 Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Thu, 22 Feb 2024 16:20:29 +0100 Subject: [PATCH 126/491] update naming new fasta file --- subworkflows/local/prepare_genome.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 2e46b826..96045cfc 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -21,7 +21,7 @@ workflow PREPARE_GENOME { // this removes all additional fields in the headers of the input fasta file if( params.tool.contains('mapsplice') && params.module.contains('circrna_discovery') ) { - CLEAN_FASTA(Channel.value([[id: "${fasta.baseName}" + "_clean" ], fasta]), []) + CLEAN_FASTA(Channel.value([[id: "${fasta.baseName}" + ".clean_headers" ], fasta]), []) ch_fasta = CLEAN_FASTA.out.output.map{ it.last() } } From 12ad8f44be9e57d5ea619c0c1af7a8f01053d277 Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Fri, 23 Feb 2024 09:07:32 +0100 Subject: [PATCH 127/491] update gawk module --- modules.json | 2 +- modules/nf-core/gawk/environment.yml | 1 + modules/nf-core/gawk/meta.yml | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/modules.json b/modules.json index e1a5c225..6413c338 100644 --- a/modules.json +++ b/modules.json @@ -77,7 +77,7 @@ }, "gawk": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "dc3527855e7358c6d8400828754c0caa5f11698f", "installed_by": ["modules"] }, "hisat2/align": { diff --git a/modules/nf-core/gawk/environment.yml b/modules/nf-core/gawk/environment.yml index 710fbfd1..34513c7f 100644 --- a/modules/nf-core/gawk/environment.yml +++ b/modules/nf-core/gawk/environment.yml @@ -1,3 +1,4 @@ +name: gawk channels: - conda-forge - bioconda diff --git a/modules/nf-core/gawk/meta.yml b/modules/nf-core/gawk/meta.yml index 1bc978e1..2b6033b0 100644 --- a/modules/nf-core/gawk/meta.yml +++ b/modules/nf-core/gawk/meta.yml @@ -15,7 +15,7 @@ tools: homepage: "https://www.gnu.org/software/gawk/" documentation: "https://www.gnu.org/software/gawk/manual/" tool_dev_url: "https://www.gnu.org/prep/ftp.html" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map From 0a31971808db0df25dc22562296c1bde6af18d0b Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 20 Feb 2024 15:28:12 +0000 Subject: [PATCH 128/491] Template update for nf-core/tools version 2.13 --- .editorconfig | 9 +- .github/workflows/awsfulltest.yml | 4 +- .github/workflows/awstest.yml | 4 +- .github/workflows/branch.yml | 2 +- .github/workflows/ci.yml | 13 +- .github/workflows/clean-up.yml | 2 +- .github/workflows/download_pipeline.yml | 15 +- .github/workflows/linting.yml | 12 +- .github/workflows/linting_comment.yml | 4 +- .github/workflows/release-announcements.yml | 11 +- README.md | 5 +- assets/multiqc_config.yml | 2 + assets/schema_input.json | 21 +- bin/check_samplesheet.py | 166 ------- lib/NfcoreTemplate.groovy | 356 -------------- lib/Utils.groovy | 47 -- lib/WorkflowCircrna.groovy | 122 ----- lib/WorkflowMain.groovy | 81 ---- main.nf | 98 ++-- modules.json | 21 +- modules/local/samplesheet_check.nf | 31 -- .../dumpsoftwareversions/environment.yml | 7 - .../custom/dumpsoftwareversions/main.nf | 24 - .../custom/dumpsoftwareversions/meta.yml | 37 -- .../templates/dumpsoftwareversions.py | 101 ---- .../dumpsoftwareversions/tests/main.nf.test | 43 -- .../tests/main.nf.test.snap | 33 -- .../dumpsoftwareversions/tests/tags.yml | 2 - modules/nf-core/fastqc/tests/main.nf.test | 14 +- .../nf-core/fastqc/tests/main.nf.test.snap | 76 ++- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- modules/nf-core/multiqc/tests/main.nf.test | 13 +- .../nf-core/multiqc/tests/main.nf.test.snap | 32 +- nextflow.config | 1 - nextflow_schema.json | 1 + pyproject.toml | 8 +- subworkflows/local/input_check.nf | 77 --- .../utils_nfcore_circrna_pipeline/main.nf | 247 ++++++++++ .../nf-core/utils_nextflow_pipeline/main.nf | 126 +++++ .../nf-core/utils_nextflow_pipeline/meta.yml | 38 ++ .../tests/main.function.nf.test | 54 +++ .../tests/main.function.nf.test.snap | 12 + .../tests/main.workflow.nf.test | 123 +++++ .../tests/nextflow.config | 9 + .../utils_nextflow_pipeline/tests/tags.yml | 2 + .../nf-core/utils_nfcore_pipeline/main.nf | 440 ++++++++++++++++++ .../nf-core/utils_nfcore_pipeline/meta.yml | 24 + .../tests/main.function.nf.test | 134 ++++++ .../tests/main.function.nf.test.snap | 138 ++++++ .../tests/main.workflow.nf.test | 29 ++ .../tests/main.workflow.nf.test.snap | 15 + .../tests/nextflow.config | 9 + .../utils_nfcore_pipeline/tests/tags.yml | 2 + .../nf-core/utils_nfvalidation_plugin/main.nf | 62 +++ .../utils_nfvalidation_plugin/meta.yml | 44 ++ .../tests/main.nf.test | 200 ++++++++ .../tests/nextflow_schema.json | 96 ++++ .../utils_nfvalidation_plugin/tests/tags.yml | 2 + workflows/circrna.nf | 41 +- 60 files changed, 2084 insertions(+), 1264 deletions(-) delete mode 100755 bin/check_samplesheet.py delete mode 100755 lib/NfcoreTemplate.groovy delete mode 100644 lib/Utils.groovy delete mode 100755 lib/WorkflowCircrna.groovy delete mode 100755 lib/WorkflowMain.groovy delete mode 100644 modules/local/samplesheet_check.nf delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/environment.yml delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/main.nf delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/meta.yml delete mode 100755 modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml delete mode 100644 subworkflows/local/input_check.nf create mode 100644 subworkflows/local/utils_nfcore_circrna_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/meta.yml create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/meta.yml create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/main.nf create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml diff --git a/.editorconfig b/.editorconfig index 9b990088..dd9ffa53 100644 --- a/.editorconfig +++ b/.editorconfig @@ -18,7 +18,12 @@ end_of_line = unset insert_final_newline = unset trim_trailing_whitespace = unset indent_style = unset -indent_size = unset +[/subworkflows/nf-core/**] +charset = unset +end_of_line = unset +insert_final_newline = unset +trim_trailing_whitespace = unset +indent_style = unset [/assets/email*] indent_size = unset @@ -28,5 +33,5 @@ indent_size = unset indent_style = unset # ignore python -[*.{py}] +[*.{py,md}] indent_style = unset diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 7b6bd16d..94521ebc 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v2 + uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -31,7 +31,7 @@ jobs: } profiles: test_full - - uses: actions/upload-artifact@v4 + - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 9590dcae..5307e9aa 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v2 + uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@v4 + - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index a9339b73..777845e7 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -19,7 +19,7 @@ jobs: # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets - name: Post PR comment if: failure() - uses: mshick/add-pr-comment@v2 + uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 with: message: | ## This PR is against the `master` branch :x: diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 79f1ee44..790f3b8d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -29,15 +29,20 @@ jobs: steps: - name: Check out pipeline code - uses: actions/checkout@v4 + uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 with: version: "${{ matrix.NXF_VER }}" - - name: Hash Github Workspace - id: hash_workspace + - name: Disk space cleanup + uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + + - name: Run pipeline with test data + # TODO nf-core: You can customise CI pipeline run tests as required + # For example: adding multiple test runs with different parameters + # Remember that you can parallelise this by using strategy.matrix run: | echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index e37cfda5..0b6b1f27 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@v9 + - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 8a330045..f823210d 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -6,6 +6,11 @@ name: Test successful pipeline download with 'nf-core download' # - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. on: workflow_dispatch: + inputs: + testbranch: + description: "The specific branch you wish to utilize for the test execution of nf-core download." + required: true + default: "dev" pull_request: types: - opened @@ -23,13 +28,13 @@ jobs: runs-on: ubuntu-latest steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 - - uses: actions/setup-python@v5 + - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: python-version: "3.11" architecture: "x64" - - uses: eWaterCycle/setup-singularity@v7 + - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 with: singularity-version: 3.8.3 @@ -42,13 +47,13 @@ jobs: run: | echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} - echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV} + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} - name: Download the pipeline env: NXF_SINGULARITY_CACHEDIR: ./ run: | - nf-core download ${{ env.REPO_LOWERCASE }} \ + nf-core download ${{ env.REPO_LOWERCASE }} \ --revision ${{ env.REPO_BRANCH }} \ --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ --compress "none" \ diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 81cd098e..748b4311 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,10 +14,10 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Set up Python 3.11 - uses: actions/setup-python@v5 + uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: python-version: 3.11 cache: "pip" @@ -32,12 +32,12 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@v4 + uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 - - uses: actions/setup-python@v5 + - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: python-version: "3.11" architecture: "x64" @@ -60,7 +60,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 147bcd10..b706875f 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@v3 + uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3 with: workflow: linting.yml workflow_conclusion: completed @@ -21,7 +21,7 @@ jobs: run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@v2 + uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 21ac3f06..c3674af2 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -9,6 +9,11 @@ jobs: toot: runs-on: ubuntu-latest steps: + - name: get topics and convert to hashtags + id: get_topics + run: | + curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' > $GITHUB_OUTPUT + - uses: rzr/fediverse-action@master with: access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} @@ -20,11 +25,13 @@ jobs: Please see the changelog: ${{ github.event.release.html_url }} + ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics + send-tweet: runs-on: ubuntu-latest steps: - - uses: actions/setup-python@v5 + - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: python-version: "3.10" - name: Install dependencies @@ -56,7 +63,7 @@ jobs: bsky-post: runs-on: ubuntu-latest steps: - - uses: zentered/bluesky-post-action@v0.1.0 + - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0 with: post: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! diff --git a/README.md b/README.md index e13dcc3d..83a0804b 100644 --- a/README.md +++ b/README.md @@ -4,8 +4,9 @@ nf-core/circrna -[![GitHub Actions CI Status](https://github.com/nf-core/circrna/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/circrna/actions?query=workflow%3A%22nf-core+CI%22) -[![GitHub Actions Linting Status](https://github.com/nf-core/circrna/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/circrna/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/circrna/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) + +[![GitHub Actions CI Status](https://github.com/nf-core/circrna/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/circrna/actions/workflows/ci.yml) +[![GitHub Actions Linting Status](https://github.com/nf-core/circrna/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/circrna/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/circrna/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![GitHub Actions CI Status](https://github.com/nf-core/circrna/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/circrna/actions?query=workflow%3A%22nf-core+CI%22) [![GitHub Actions Linting Status](https://github.com/nf-core/circrna/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/circrna/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/circrna/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 9a1b5bda..570f6c0d 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -11,3 +11,5 @@ report_section_order: order: -1002 export_plots: true + +disable_version_detection: true diff --git a/assets/schema_input.json b/assets/schema_input.json index 41716366..fe551cb8 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -10,25 +10,22 @@ "sample": { "type": "string", "pattern": "^\\S+$", - "errorMessage": "Sample name must be provided and cannot contain spaces" + "errorMessage": "Sample name must be provided and cannot contain spaces", + "meta": ["id"] }, "fastq_1": { "type": "string", + "format": "file-path", + "exists": true, "pattern": "^\\S+\\.f(ast)?q\\.gz$", "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" }, "fastq_2": { - "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", - "anyOf": [ - { - "type": "string", - "pattern": "^\\S+\\.f(ast)?q\\.gz$" - }, - { - "type": "string", - "maxLength": 0 - } - ] + "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.f(ast)?q\\.gz$", + "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" } }, "required": ["sample", "fastq_1"] diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py deleted file mode 100755 index 95346faf..00000000 --- a/bin/check_samplesheet.py +++ /dev/null @@ -1,166 +0,0 @@ -#!/usr/bin/env python3 - -""" - Borrowed from nf-core/rnaseq, the original from template 2.6 kept breaking at: - "[CRITICAL] The given sample sheet does not appear to contain a header." - Even though the input samplesheet looked to be perfectly fine using vim :set list. - - Strandedness commented out should you wish to include this in future releases. -""" - - -import os -import sys -import errno -import argparse - - -def parse_args(args=None): - Description = "Reformat nf-core/rnaseq samplesheet file and check its contents." - Epilog = "Example usage: python check_samplesheet.py " - - parser = argparse.ArgumentParser(description=Description, epilog=Epilog) - parser.add_argument("FILE_IN", help="Input samplesheet file.") - parser.add_argument("FILE_OUT", help="Output file.") - return parser.parse_args(args) - - -def make_dir(path): - if len(path) > 0: - try: - os.makedirs(path) - except OSError as exception: - if exception.errno != errno.EEXIST: - raise exception - - -def sniff_format(handle): - """ - Detect the tabular format. - - Args: - handle (text file): A handle to a `text file`_ object. The read position is - expected to be at the beginning (index 0). - - Returns: - csv.Dialect: The detected tabular format. - - .. _text file: - https://docs.python.org/3/glossary.html#term-text-file - - """ - peek = read_head(handle) - handle.seek(0) - sniffer = csv.Sniffer() - dialect = sniffer.sniff(peek) - return dialect - - -def check_samplesheet(file_in, file_out): - """ - This function checks that the samplesheet follows the following structure: - sample,fastq_1,fastq_2,strandedness - SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz,forward - SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz,forward - SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz,,forward - For an example see: - https://github.com/nf-core/test-datasets/blob/rnaseq/samplesheet/v3.1/samplesheet_test.csv - """ - - sample_mapping_dict = {} - with open(file_in, "r", encoding="utf-8-sig") as fin: - ## Check header - MIN_COLS = 2 ## edit by BDigby as not using strandedness yet. - HEADER = ["sample", "fastq_1", "fastq_2"] - header = [x.strip('"') for x in fin.readline().strip().split(",")] - if header[: len(HEADER)] != HEADER: - print(f"ERROR: Please check samplesheet header -> {','.join(header)} != {','.join(HEADER)}") - sys.exit(1) - - ## Check sample entries - for line in fin: - if line.strip(): - lspl = [x.strip().strip('"') for x in line.strip().split(",")] - - ## Check valid number of columns per row - if len(lspl) < len(HEADER): - print_error( - f"Invalid number of columns (minimum = {len(HEADER)})!", - "Line", - line, - ) - - num_cols = len([x for x in lspl if x]) - if num_cols < MIN_COLS: - print_error( - f"Invalid number of populated columns (minimum = {MIN_COLS})!", - "Line", - line, - ) - - ## Check sample name entries - sample, fastq_1, fastq_2 = lspl[: len(HEADER)] - if sample.find(" ") != -1: - print(f"WARNING: Spaces have been replaced by underscores for sample: {sample}") - sample = sample.replace(" ", "_") - if not sample: - print_error("Sample entry has not been specified!", "Line", line) - - ## Check FastQ file extension - for fastq in [fastq_1, fastq_2]: - if fastq: - if fastq.find(" ") != -1: - print_error("FastQ file contains spaces!", "Line", line) - if not fastq.endswith(".fastq.gz") and not fastq.endswith(".fq.gz"): - print_error( - "FastQ file does not have extension '.fastq.gz' or '.fq.gz'!", - "Line", - line, - ) - - ## Auto-detect paired-end/single-end - sample_info = [] ## [single_end, fastq_1, fastq_2, strandedness] - if sample and fastq_1 and fastq_2: ## Paired-end short reads - sample_info = ["0", fastq_1, fastq_2] - elif sample and fastq_1 and not fastq_2: ## Single-end short reads - sample_info = ["1", fastq_1, fastq_2] - else: - print_error("Invalid combination of columns provided!", "Line", line) - - ## Create sample mapping dictionary = {sample: [[ single_end, fastq_1, fastq_2, strandedness ]]} - if sample not in sample_mapping_dict: - sample_mapping_dict[sample] = [sample_info] - else: - if sample_info in sample_mapping_dict[sample]: - print_error("Samplesheet contains duplicate rows!", "Line", line) - else: - sample_mapping_dict[sample].append(sample_info) - - ## Write validated samplesheet with appropriate columns - if len(sample_mapping_dict) > 0: - out_dir = os.path.dirname(file_out) - make_dir(out_dir) - with open(file_out, "w") as fout: - fout.write(",".join(["sample", "single_end", "fastq_1", "fastq_2"]) + "\n") - for sample in sorted(sample_mapping_dict.keys()): - ## Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end - if not all(x[0] == sample_mapping_dict[sample][0][0] for x in sample_mapping_dict[sample]): - print_error( - f"Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end!", - "Sample", - sample, - ) - - for idx, val in enumerate(sample_mapping_dict[sample]): - fout.write(",".join([f"{sample}_T{idx+1}"] + val) + "\n") - else: - print_error(f"No entries to process!", "Samplesheet: {file_in}") - - -def main(args=None): - args = parse_args(args) - check_samplesheet(args.FILE_IN, args.FILE_OUT) - - -if __name__ == "__main__": - sys.exit(main()) diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy deleted file mode 100755 index e248e4c3..00000000 --- a/lib/NfcoreTemplate.groovy +++ /dev/null @@ -1,356 +0,0 @@ -// -// This file holds several functions used within the nf-core pipeline template. -// - -import org.yaml.snakeyaml.Yaml -import groovy.json.JsonOutput -import nextflow.extension.FilesEx - -class NfcoreTemplate { - - // - // Check AWS Batch related parameters have been specified correctly - // - public static void awsBatch(workflow, params) { - if (workflow.profile.contains('awsbatch')) { - // Check params.awsqueue and params.awsregion have been set if running on AWSBatch - assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!" - // Check outdir paths to be S3 buckets if running on AWSBatch - assert params.outdir.startsWith('s3:') : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!" - } - } - - // - // Warn if a -profile or Nextflow config has not been provided to run the pipeline - // - public static void checkConfigProvided(workflow, log) { - if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + - "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + - " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + - " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + - " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + - "Please refer to the quick start section and usage docs for the pipeline.\n " - } - } - - // - // Generate version string - // - public static String version(workflow) { - String version_string = "" - - if (workflow.manifest.version) { - def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' - version_string += "${prefix_v}${workflow.manifest.version}" - } - - if (workflow.commitId) { - def git_shortsha = workflow.commitId.substring(0, 7) - version_string += "-g${git_shortsha}" - } - - return version_string - } - - // - // Construct and send completion email - // - public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) { - - // Set up the e-mail variables - def subject = "[$workflow.manifest.name] Successful: $workflow.runName" - if (!workflow.success) { - subject = "[$workflow.manifest.name] FAILED: $workflow.runName" - } - - def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['Date Started'] = workflow.start - misc_fields['Date Completed'] = workflow.complete - misc_fields['Pipeline script file path'] = workflow.scriptFile - misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository - if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId - if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build - misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp - - def email_fields = [:] - email_fields['version'] = NfcoreTemplate.version(workflow) - email_fields['runName'] = workflow.runName - email_fields['success'] = workflow.success - email_fields['dateComplete'] = workflow.complete - email_fields['duration'] = workflow.duration - email_fields['exitStatus'] = workflow.exitStatus - email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - email_fields['errorReport'] = (workflow.errorReport ?: 'None') - email_fields['commandLine'] = workflow.commandLine - email_fields['projectDir'] = workflow.projectDir - email_fields['summary'] = summary << misc_fields - - // On success try attach the multiqc report - def mqc_report = null - try { - if (workflow.success) { - mqc_report = multiqc_report.getVal() - if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { - if (mqc_report.size() > 1) { - log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" - } - mqc_report = mqc_report[0] - } - } - } catch (all) { - if (multiqc_report) { - log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" - } - } - - // Check if we are only sending emails on failure - def email_address = params.email - if (!params.email && params.email_on_fail && !workflow.success) { - email_address = params.email_on_fail - } - - // Render the TXT template - def engine = new groovy.text.GStringTemplateEngine() - def tf = new File("$projectDir/assets/email_template.txt") - def txt_template = engine.createTemplate(tf).make(email_fields) - def email_txt = txt_template.toString() - - // Render the HTML template - def hf = new File("$projectDir/assets/email_template.html") - def html_template = engine.createTemplate(hf).make(email_fields) - def email_html = html_template.toString() - - // Render the sendmail template - def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] - def sf = new File("$projectDir/assets/sendmail_template.txt") - def sendmail_template = engine.createTemplate(sf).make(smail_fields) - def sendmail_html = sendmail_template.toString() - - // Send the HTML e-mail - Map colors = logColours(params.monochrome_logs) - if (email_address) { - try { - if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } - // Try to send HTML e-mail using sendmail - def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") - sendmail_tf.withWriter { w -> w << sendmail_html } - [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" - } catch (all) { - // Catch failures and try with plaintext - def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] - if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) { - mail_cmd += [ '-A', mqc_report ] - } - mail_cmd.execute() << email_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" - } - } - - // Write summary e-mail HTML to a file - def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") - output_hf.withWriter { w -> w << email_html } - FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html"); - output_hf.delete() - - // Write summary e-mail TXT to a file - def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") - output_tf.withWriter { w -> w << email_txt } - FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt"); - output_tf.delete() - } - - // - // Construct and send a notification to a web server as JSON - // e.g. Microsoft Teams and Slack - // - public static void IM_notification(workflow, params, summary_params, projectDir, log) { - def hook_url = params.hook_url - - def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) misc_fields['repository'] = workflow.repository - if (workflow.commitId) misc_fields['commitid'] = workflow.commitId - if (workflow.revision) misc_fields['revision'] = workflow.revision - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp - - def msg_fields = [:] - msg_fields['version'] = NfcoreTemplate.version(workflow) - msg_fields['runName'] = workflow.runName - msg_fields['success'] = workflow.success - msg_fields['dateComplete'] = workflow.complete - msg_fields['duration'] = workflow.duration - msg_fields['exitStatus'] = workflow.exitStatus - msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - msg_fields['errorReport'] = (workflow.errorReport ?: 'None') - msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") - msg_fields['projectDir'] = workflow.projectDir - msg_fields['summary'] = summary << misc_fields - - // Render the JSON template - def engine = new groovy.text.GStringTemplateEngine() - // Different JSON depending on the service provider - // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format - def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" - def hf = new File("$projectDir/assets/${json_path}") - def json_template = engine.createTemplate(hf).make(msg_fields) - def json_message = json_template.toString() - - // POST - def post = new URL(hook_url).openConnection(); - post.setRequestMethod("POST") - post.setDoOutput(true) - post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")); - def postRC = post.getResponseCode(); - if (! postRC.equals(200)) { - log.warn(post.getErrorStream().getText()); - } - } - - // - // Dump pipeline parameters in a json file - // - public static void dump_parameters(workflow, params) { - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = JsonOutput.toJson(params) - temp_pf.text = JsonOutput.prettyPrint(jsonStr) - - FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json") - temp_pf.delete() - } - - // - // Print pipeline summary on completion - // - public static void summary(workflow, params, log) { - Map colors = logColours(params.monochrome_logs) - if (workflow.success) { - if (workflow.stats.ignoredCount == 0) { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" - } - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" - } - } - - // - // ANSII Colours used for terminal logging - // - public static Map logColours(Boolean monochrome_logs) { - Map colorcodes = [:] - - // Reset / Meta - colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" - colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" - colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" - colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" - colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" - colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" - colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" - - // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" - - // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" - - // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" - - // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" - - // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" - - return colorcodes - } - - // - // Does what is says on the tin - // - public static String dashedLine(monochrome_logs) { - Map colors = logColours(monochrome_logs) - return "-${colors.dim}----------------------------------------------------${colors.reset}-" - } - - // - // nf-core logo - // - public static String logo(workflow, monochrome_logs) { - Map colors = logColours(monochrome_logs) - String workflow_version = NfcoreTemplate.version(workflow) - String.format( - """\n - ${dashedLine(monochrome_logs)} - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} - ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} - ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} - ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} ${workflow_version}${colors.reset} - ${dashedLine(monochrome_logs)} - """.stripIndent() - ) - } -} diff --git a/lib/Utils.groovy b/lib/Utils.groovy deleted file mode 100644 index 8d030f4e..00000000 --- a/lib/Utils.groovy +++ /dev/null @@ -1,47 +0,0 @@ -// -// This file holds several Groovy functions that could be useful for any Nextflow pipeline -// - -import org.yaml.snakeyaml.Yaml - -class Utils { - - // - // When running with -profile conda, warn if channels have not been set-up appropriately - // - public static void checkCondaChannels(log) { - Yaml parser = new Yaml() - def channels = [] - try { - def config = parser.load("conda config --show channels".execute().text) - channels = config.channels - } catch(NullPointerException | IOException e) { - log.warn "Could not verify conda channel configuration." - return - } - - // Check that all channels are present - // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] - def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean - - // Check that they are in the right order - def channel_priority_violation = false - def n = required_channels_in_order.size() - for (int i = 0; i < n - 1; i++) { - channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) - } - - if (channels_missing | channel_priority_violation) { - log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " There is a problem with your Conda configuration!\n\n" + - " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/\n" + - " The observed channel order is \n" + - " ${channels}\n" + - " but the following channel order is required:\n" + - " ${required_channels_in_order}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - } - } -} diff --git a/lib/WorkflowCircrna.groovy b/lib/WorkflowCircrna.groovy deleted file mode 100755 index eae29c19..00000000 --- a/lib/WorkflowCircrna.groovy +++ /dev/null @@ -1,122 +0,0 @@ -// -// This file holds several functions specific to the workflow/circrna.nf in the nf-core/circrna pipeline -// - -import nextflow.Nextflow -import groovy.text.SimpleTemplateEngine - -class WorkflowCircrna { - - // - // Check and validate parameters - // - public static void initialise(params, log) { - - genomeExistsError(params, log) - - - if (!params.fasta) { - Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." - } - } - - // - // Get workflow summary for MultiQC - // - public static String paramsSummaryMultiqc(workflow, summary) { - String summary_section = '' - for (group in summary.keySet()) { - def group_params = summary.get(group) // This gets the parameters of that particular group - if (group_params) { - summary_section += "

    $group

    \n" - summary_section += "
    \n" - for (param in group_params.keySet()) { - summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" - } - summary_section += "
    \n" - } - } - - String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" - return yaml_file_text - } - - // - // Generate methods description for MultiQC - // - - public static String toolCitationText(params) { - - // TODO nf-core: Optionally add in-text citation tools to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report - def citation_text = [ - "Tools used in the workflow included:", - "FastQC (Andrews 2010),", - "MultiQC (Ewels et al. 2016)", - "." - ].join(' ').trim() - - return citation_text - } - - public static String toolBibliographyText(params) { - - // TODO Optionally add bibliographic entries to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report - def reference_text = [ - "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", - "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " - ].join(' ').trim() - - return reference_text - } - - public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) { - // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file - def meta = [:] - meta.workflow = run_workflow.toMap() - meta["manifest_map"] = run_workflow.manifest.toMap() - - // Pipeline DOI - meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" - meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " - - // Tool references - meta["tool_citations"] = "" - meta["tool_bibliography"] = "" - - // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! - //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") - //meta["tool_bibliography"] = toolBibliographyText(params) - - - def methods_text = mqc_methods_yaml.text - - def engine = new SimpleTemplateEngine() - def description_html = engine.createTemplate(methods_text).make(meta) - - return description_html - } - - // - // Exit pipeline if incorrect --genome key provided - // - private static void genomeExistsError(params, log) { - if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { - def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + - " Currently, the available genome keys are:\n" + - " ${params.genomes.keySet().join(", ")}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - Nextflow.error(error_string) - } - } -} diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy deleted file mode 100755 index 03790911..00000000 --- a/lib/WorkflowMain.groovy +++ /dev/null @@ -1,81 +0,0 @@ -// -// This file holds several functions specific to the main.nf workflow in the nf-core/circrna pipeline -// - -import nextflow.Nextflow - -class WorkflowMain { - - // - // Citation string for pipeline - // - public static String citation(workflow) { - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - // TODO nf-core: Add Zenodo DOI for pipeline after first release - //"* The pipeline\n" + - //" https://doi.org/10.5281/zenodo.XXXXXXX\n\n" + - "* The nf-core framework\n" + - " https://doi.org/10.1038/s41587-020-0439-x\n\n" + - "* Software dependencies\n" + - " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" - } - - - // - // Validate parameters and print summary to screen - // - public static void initialise(workflow, params, log, args) { - - // Print workflow version and exit on --version - if (params.version) { - String workflow_version = NfcoreTemplate.version(workflow) - log.info "${workflow.manifest.name} ${workflow_version}" - System.exit(0) - } - - // Check that a -profile or Nextflow config has been provided to run the pipeline - NfcoreTemplate.checkConfigProvided(workflow, log) - // Check that the profile doesn't contain spaces and doesn't end with a trailing comma - checkProfile(workflow.profile, args, log) - - // Check that conda channels are set-up correctly - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - Utils.checkCondaChannels(log) - } - - // Check AWS batch settings - NfcoreTemplate.awsBatch(workflow, params) - - // Check input has been provided - if (!params.input) { - Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'") - } - - if (!params.species) { - Nextflow.error("Please provide a species to the pipeline e.g. '--species hsa'") - } - } - // - // Get attribute from genome config file e.g. fasta - // - public static Object getGenomeAttribute(params, attribute) { - if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { - if (params.genomes[ params.genome ].containsKey(attribute)) { - return params.genomes[ params.genome ][ attribute ] - } - } - return null - } - - // - // Exit pipeline if --profile contains spaces - // - private static void checkProfile(profile, args, log) { - if (profile.endsWith(',')) { - Nextflow.error "Profile cannot end with a trailing comma. Please remove the comma from the end of the profile string.\nHint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`." - } - if (args[0]) { - log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${args[0]}` has been detected.\n Hint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`." - } - } -} diff --git a/main.nf b/main.nf index 61a893e9..66917a46 100644 --- a/main.nf +++ b/main.nf @@ -11,6 +11,18 @@ nextflow.enable.dsl = 2 +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +include { CIRCRNA } from './workflows/circrna' +include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_circrna_pipeline' +include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_circrna_pipeline' + +include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_circrna_pipeline' + /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GENOME PARAMETER VALUES @@ -28,55 +40,73 @@ params.species = WorkflowMain.getGenomeAttribute(params, 'species_id') /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - VALIDATE & PRINT PARAMETER SUMMARY + NAMED WORKFLOWS FOR PIPELINE ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { validateParameters; paramsHelp } from 'plugin/nf-validation' +// +// WORKFLOW: Run main analysis pipeline depending on type of input +// +workflow NFCORE_CIRCRNA { -// Print help message if needed -if (params.help) { - def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) - def citation = '\n' + WorkflowMain.citation(workflow) + '\n' - def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" - log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) - System.exit(0) -} + take: + samplesheet // channel: samplesheet read in from --input -// Validate input parameters -if (params.validate_params) { - validateParameters() -} + main: -WorkflowMain.initialise(workflow, params, log, args) + // + // WORKFLOW: Run pipeline + // + CIRCRNA ( + samplesheet + ) -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - NAMED WORKFLOW FOR PIPELINE -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ + emit: + multiqc_report = CIRCRNA.out.multiqc_report // channel: /path/to/multiqc_report.html -include { CIRCRNA } from './workflows/circrna' - -// -// WORKFLOW: Run main nf-core/circrna analysis pipeline -// -workflow NFCORE_CIRCRNA { - CIRCRNA () } - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - RUN ALL WORKFLOWS + RUN MAIN WORKFLOW ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// -// WORKFLOW: Execute a single named workflow for the pipeline -// See: https://github.com/nf-core/rnaseq/issues/619 -// workflow { - NFCORE_CIRCRNA () + + main: + + // + // SUBWORKFLOW: Run initialisation tasks + // + PIPELINE_INITIALISATION ( + params.version, + params.help, + params.validate_params, + params.monochrome_logs, + args, + params.outdir, + params.input + ) + + // + // WORKFLOW: Run main workflow + // + NFCORE_CIRCRNA ( + PIPELINE_INITIALISATION.out.samplesheet + ) + + // + // SUBWORKFLOW: Run completion tasks + // + PIPELINE_COMPLETION ( + params.email, + params.email_on_fail, + params.plaintext_email, + params.outdir, + params.monochrome_logs, + params.hook_url, + NFCORE_CIRCRNA.out.multiqc_report + ) } /* diff --git a/modules.json b/modules.json index e1a5c225..59be5c70 100644 --- a/modules.json +++ b/modules.json @@ -102,7 +102,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", + "git_sha": "ccacf6f5de6df3bc6d73b665c1fd2933d8bbc290", "installed_by": ["modules"] }, "samtools/flagstat": { @@ -180,6 +180,25 @@ "installed_by": ["bam_sort_stats_samtools"] } } + }, + "subworkflows": { + "nf-core": { + "utils_nextflow_pipeline": { + "branch": "master", + "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "installed_by": ["subworkflows"] + }, + "utils_nfcore_pipeline": { + "branch": "master", + "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8", + "installed_by": ["subworkflows"] + }, + "utils_nfvalidation_plugin": { + "branch": "master", + "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "installed_by": ["subworkflows"] + } + } } } } diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf deleted file mode 100644 index e102f46d..00000000 --- a/modules/local/samplesheet_check.nf +++ /dev/null @@ -1,31 +0,0 @@ -process SAMPLESHEET_CHECK { - tag "$samplesheet" - label 'process_single' - - conda "conda-forge::python=3.8.3" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'biocontainers/python:3.8.3' }" - - input: - path samplesheet - - output: - path '*.csv' , emit: csv - path "versions.yml", emit: versions - - when: - task.ext.when == null || task.ext.when - - script: // This script is bundled with the pipeline, in nf-core/circrna/bin/ - """ - check_samplesheet.py \\ - $samplesheet \\ - samplesheet.valid.csv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - python: \$(python --version | sed 's/Python //g') - END_VERSIONS - """ -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml deleted file mode 100644 index 9b3272bc..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: custom_dumpsoftwareversions -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::multiqc=1.19 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf deleted file mode 100644 index f2187611..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ /dev/null @@ -1,24 +0,0 @@ -process CUSTOM_DUMPSOFTWAREVERSIONS { - label 'process_single' - - // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : - 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" - - input: - path versions - - output: - path "software_versions.yml" , emit: yml - path "software_versions_mqc.yml", emit: mqc_yml - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - template 'dumpsoftwareversions.py' -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml deleted file mode 100644 index 5f15a5fd..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ /dev/null @@ -1,37 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json -name: custom_dumpsoftwareversions -description: Custom module used to dump software versions within the nf-core pipeline template -keywords: - - custom - - dump - - version -tools: - - custom: - description: Custom module used to dump software versions within the nf-core pipeline template - homepage: https://github.com/nf-core/tools - documentation: https://github.com/nf-core/tools - licence: ["MIT"] -input: - - versions: - type: file - description: YML file containing software versions - pattern: "*.yml" -output: - - yml: - type: file - description: Standard YML file containing software versions - pattern: "software_versions.yml" - - mqc_yml: - type: file - description: MultiQC custom content YML file containing software versions - pattern: "software_versions_mqc.yml" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@drpatelh" - - "@grst" -maintainers: - - "@drpatelh" - - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py deleted file mode 100755 index da033408..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ /dev/null @@ -1,101 +0,0 @@ -#!/usr/bin/env python - - -"""Provide functions to merge multiple versions.yml files.""" - - -import yaml -import platform -from textwrap import dedent - - -def _make_versions_html(versions): - """Generate a tabular HTML output of all versions for MultiQC.""" - html = [ - dedent( - """\\ - -
    Process Name \\", - " \\ Software Version
    CUSTOM_DUMPSOFTWAREVERSIONSpython3.11.7
    yaml5.4.1
    TOOL1tool10.11.9
    TOOL2tool21.9
    WorkflowNextflow
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    - - - - - - - - """ - ) - ] - for process, tmp_versions in sorted(versions.items()): - html.append("") - for i, (tool, version) in enumerate(sorted(tmp_versions.items())): - html.append( - dedent( - f"""\\ - - - - - - """ - ) - ) - html.append("") - html.append("
    Process Name Software Version
    {process if (i == 0) else ''}{tool}{version}
    ") - return "\\n".join(html) - - -def main(): - """Load all version files and generate merged output.""" - versions_this_module = {} - versions_this_module["${task.process}"] = { - "python": platform.python_version(), - "yaml": yaml.__version__, - } - - with open("$versions") as f: - versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module - - # aggregate versions by the module name (derived from fully-qualified process name) - versions_by_module = {} - for process, process_versions in versions_by_process.items(): - module = process.split(":")[-1] - try: - if versions_by_module[module] != process_versions: - raise AssertionError( - "We assume that software versions are the same between all modules. " - "If you see this error-message it means you discovered an edge-case " - "and should open an issue in nf-core/tools. " - ) - except KeyError: - versions_by_module[module] = process_versions - - versions_by_module["Workflow"] = { - "Nextflow": "$workflow.nextflow.version", - "$workflow.manifest.name": "$workflow.manifest.version", - } - - versions_mqc = { - "id": "software_versions", - "section_name": "${workflow.manifest.name} Software Versions", - "section_href": "https://github.com/${workflow.manifest.name}", - "plot_type": "html", - "description": "are collected at run time from the software output.", - "data": _make_versions_html(versions_by_module), - } - - with open("software_versions.yml", "w") as f: - yaml.dump(versions_by_module, f, default_flow_style=False) - with open("software_versions_mqc.yml", "w") as f: - yaml.dump(versions_mqc, f, default_flow_style=False) - - with open("versions.yml", "w") as f: - yaml.dump(versions_this_module, f, default_flow_style=False) - - -if __name__ == "__main__": - main() diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test deleted file mode 100644 index b1e1630b..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test +++ /dev/null @@ -1,43 +0,0 @@ -nextflow_process { - - name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" - script "../main.nf" - process "CUSTOM_DUMPSOFTWAREVERSIONS" - tag "modules" - tag "modules_nfcore" - tag "custom" - tag "dumpsoftwareversions" - tag "custom/dumpsoftwareversions" - - test("Should run without failures") { - when { - process { - """ - def tool1_version = ''' - TOOL1: - tool1: 0.11.9 - '''.stripIndent() - - def tool2_version = ''' - TOOL2: - tool2: 1.9 - '''.stripIndent() - - input[0] = Channel.of(tool1_version, tool2_version).collectFile() - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.versions, - file(process.out.mqc_yml[0]).readLines()[0..10], - file(process.out.yml[0]).readLines()[0..7] - ).match() - } - ) - } - } -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap deleted file mode 100644 index 5f59a936..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap +++ /dev/null @@ -1,33 +0,0 @@ -{ - "Should run without failures": { - "content": [ - [ - "versions.yml:md5,76d454d92244589d32455833f7c1ba6d" - ], - [ - "data: \"\\n\\n \\n \\n \\n \\n \\n \\n \\n\\", - " \\n\\n\\n \\n \\n\\", - " \\ \\n\\n\\n\\n \\n \\", - " \\ \\n \\n\\n\\n\\n\\", - " \\n\\n \\n \\n\\", - " \\ \\n\\n\\n\\n\\n\\n \\n\\", - " \\ \\n \\n\\n\\n\\n\\", - " \\n\\n \\n \\n\\" - ], - [ - "CUSTOM_DUMPSOFTWAREVERSIONS:", - " python: 3.11.7", - " yaml: 5.4.1", - "TOOL1:", - " tool1: 0.11.9", - "TOOL2:", - " tool2: '1.9'", - "Workflow:" - ] - ], - "timestamp": "2024-01-09T23:01:18.710682" - } -} \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml deleted file mode 100644 index 405aa24a..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -custom/dumpsoftwareversions: - - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 1f21c664..70edae4d 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -33,7 +33,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_single") } ) } } @@ -63,7 +63,7 @@ nextflow_process { { assert path(process.out.html[0][1][0]).text.contains("") }, { assert path(process.out.html[0][1][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_paired") } ) } } @@ -89,7 +89,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } ) } } @@ -115,7 +115,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_bam") } ) } } @@ -153,7 +153,7 @@ nextflow_process { { assert path(process.out.html[0][1][2]).text.contains("") }, { assert path(process.out.html[0][1][3]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } ) } } @@ -179,7 +179,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } ) } } @@ -204,7 +204,7 @@ nextflow_process { { assert process.success }, { assert snapshot(process.out.html.collect { file(it[1]).getName() } + process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match() } + process.out.versions ).match("fastqc_stub") } ) } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 5d624bb8..86f7c311 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,5 +1,17 @@ { - "sarscov2 single-end [fastq] - stub": { + "fastqc_versions_interleaved": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:40:07.293713" + }, + "fastqc_stub": { "content": [ [ "test.html", @@ -7,14 +19,70 @@ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], - "timestamp": "2024-01-17T18:40:57.254299" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:31:01.425198" + }, + "fastqc_versions_multiple": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:40:55.797907" + }, + "fastqc_versions_bam": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:40:26.795862" + }, + "fastqc_versions_single": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:39:27.043675" + }, + "fastqc_versions_paired": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:39:47.584191" }, - "versions": { + "fastqc_versions_custom_prefix": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], - "timestamp": "2024-01-17T18:36:50.033627" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:41:14.576531" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 7625b752..2212096a 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.19 + - bioconda::multiqc=1.20 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 1b9f7c43..354f4430 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : - 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_0' : + 'biocontainers/multiqc:1.20--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index d0438eda..f1c4242e 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -3,6 +3,7 @@ nextflow_process { name "Test Process MULTIQC" script "../main.nf" process "MULTIQC" + tag "modules" tag "modules_nfcore" tag "multiqc" @@ -12,7 +13,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = [] input[2] = [] input[3] = [] @@ -25,7 +26,7 @@ nextflow_process { { assert process.success }, { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("multiqc_versions_single") } ) } @@ -36,7 +37,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] @@ -49,7 +50,7 @@ nextflow_process { { assert process.success }, { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("multiqc_versions_config") } ) } } @@ -61,7 +62,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = [] input[2] = [] input[3] = [] @@ -75,7 +76,7 @@ nextflow_process { { assert snapshot(process.out.report.collect { file(it).getName() } + process.out.data.collect { file(it).getName() } + process.out.plots.collect { file(it).getName() } + - process.out.versions ).match() } + process.out.versions ).match("multiqc_stub") } ) } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index d37e7304..c204b488 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -1,21 +1,41 @@ { - "versions": { + "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" ] ], - "timestamp": "2024-01-09T23:02:49.911994" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T09:28:51.744211298" }, - "sarscov2 single-end [fastqc] - stub": { + "multiqc_stub": { "content": [ [ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" ] ], - "timestamp": "2024-01-09T23:03:14.524346" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T09:29:28.847433492" + }, + "multiqc_versions_config": { + "content": [ + [ + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T09:29:13.223621555" } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 458e66e5..ffa9b39e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -88,7 +88,6 @@ params { config_profile_contact = null config_profile_url = null - // Max resource options max_memory = '300.GB' max_cpus = 50 diff --git a/nextflow_schema.json b/nextflow_schema.json index 98c9bc80..5bdc6753 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -16,6 +16,7 @@ "type": "string", "format": "file-path", "exists": true, + "schema": "assets/schema_input.json", "mimetype": "text/csv", "pattern": "^\\S+\\.csv$", "description": "Path to comma-separated file containing information about the samples in the experiment.", diff --git a/pyproject.toml b/pyproject.toml index 7d08e1c8..56110621 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,11 +3,13 @@ [tool.ruff] line-length = 120 target-version = "py38" -select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"] cache-dir = "~/.cache/ruff" -[tool.ruff.isort] +[tool.ruff.lint] +select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"] + +[tool.ruff.lint.isort] known-first-party = ["nf_core"] -[tool.ruff.per-file-ignores] +[tool.ruff.lint.per-file-ignores] "__init__.py" = ["E402", "F401"] diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf deleted file mode 100644 index faf7c5b2..00000000 --- a/subworkflows/local/input_check.nf +++ /dev/null @@ -1,77 +0,0 @@ -// -// Check input files -// - -include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check' - -workflow INPUT_CHECK { - take: - samplesheet - ch_phenotype - - main: - phenotype = params.phenotype && params.module.contains('differential_expression') ? examine_phenotype(ch_phenotype) : Channel.empty() - - SAMPLESHEET_CHECK ( samplesheet ) - .csv - .splitCsv ( header:true, sep:',' ) - .map { create_fastq_channel(it) } - .set { reads } - - emit: - phenotype // Channel: [ pheno ] - reads // channel: [ val(meta), [ reads ] ] - versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ] -} - -// Function to get list of [ meta, [ fastq_1, fastq_2 ] ] -def create_fastq_channel(LinkedHashMap row) { - // create meta map - def meta = [:] - meta.id = row.sample - meta.single_end = row.single_end.toBoolean() - - // add path(s) of the fastq file(s) to the meta map - def fastq_meta = [] - if (!file(row.fastq_1).exists()) { - exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}" - } - if (meta.single_end) { - fastq_meta = [ meta, [ file(row.fastq_1) ] ] - - // Conduct check here, cannot figure out how to outside of this scope i.e accessing meta.single end for an if else from channel. - if(params.tool.split(',').contains('ciriquant')){ - exit 1, "ERROR: Unfortunately CIRIquant does not support single-end reads. Please select one of the other 6 quantification tools." - } - - } else { - if (!file(row.fastq_2).exists()) { - exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}" - } - fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ] - } - return fastq_meta -} - - -def examine_phenotype(pheno){ - - Channel - .fromPath(pheno) - .splitCsv(header: true, sep: ',') - .map{ row -> - - def expected_cols = ['condition'] - - if (!row.keySet().containsAll(expected_cols)) exit 1, "[nf-core/circrna] error: 'condition' is not a column name in the phenotype file.\n\nThe primary response variable must be named 'condition', please refer to the usage documentation online" - - def condition = row.condition.matches('NA') ? 'NA' : row.condition - - if(condition == '') exit 1, "[nf-core/circrna] error: Invalid phenotype file, condition column contains empty cells." - if(condition.matches('NA')) exit 1, "[nf-core/circrna] error: NA value in phenotype condition column." - - } - .toList() - - return Channel.value(file(pheno)) -} diff --git a/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf b/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf new file mode 100644 index 00000000..dc90ad90 --- /dev/null +++ b/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf @@ -0,0 +1,247 @@ +// +// Subworkflow with functionality specific to the nf-core/pipeline pipeline +// + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' +include { paramsSummaryMap } from 'plugin/nf-validation' +include { fromSamplesheet } from 'plugin/nf-validation' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' +include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' +include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' +include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' +include { imNotification } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' +include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' + +/* +======================================================================================== + SUBWORKFLOW TO INITIALISE PIPELINE +======================================================================================== +*/ + +workflow PIPELINE_INITIALISATION { + + take: + version // boolean: Display version and exit + help // boolean: Display help text + validate_params // boolean: Boolean whether to validate parameters against the schema at runtime + monochrome_logs // boolean: Do not use coloured log outputs + nextflow_cli_args // array: List of positional nextflow CLI args + outdir // string: The output directory where the results will be saved + input // string: Path to input samplesheet + + main: + + ch_versions = Channel.empty() + + // + // Print version and exit if required and dump pipeline parameters to JSON file + // + UTILS_NEXTFLOW_PIPELINE ( + version, + true, + outdir, + workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 + ) + + // + // Validate parameters and generate parameter summary to stdout + // + pre_help_text = nfCoreLogo(monochrome_logs) + post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs) + def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " + UTILS_NFVALIDATION_PLUGIN ( + help, + workflow_command, + pre_help_text, + post_help_text, + validate_params, + "nextflow_schema.json" + ) + + // + // Check config provided to the pipeline + // + UTILS_NFCORE_PIPELINE ( + nextflow_cli_args + ) + // + // Custom validation for pipeline parameters + // + validateInputParameters() + + // + // Create channel from input file provided through params.input + // + Channel + .fromSamplesheet("input") + .map { + meta, fastq_1, fastq_2 -> + if (!fastq_2) { + return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] + } else { + return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] + } + } + .groupTuple() + .map { + validateInputSamplesheet(it) + } + .map { + meta, fastqs -> + return [ meta, fastqs.flatten() ] + } + .set { ch_samplesheet } + + emit: + samplesheet = ch_samplesheet + versions = ch_versions +} + +/* +======================================================================================== + SUBWORKFLOW FOR PIPELINE COMPLETION +======================================================================================== +*/ + +workflow PIPELINE_COMPLETION { + + take: + email // string: email address + email_on_fail // string: email address sent on pipeline failure + plaintext_email // boolean: Send plain-text email instead of HTML + outdir // path: Path to output directory where results will be published + monochrome_logs // boolean: Disable ANSI colour codes in log output + hook_url // string: hook URL for notifications + multiqc_report // string: Path to MultiQC report + + main: + + summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + + // + // Completion email and summary + // + workflow.onComplete { + if (email || email_on_fail) { + completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) + } + + completionSummary(monochrome_logs) + + if (hook_url) { + imNotification(summary_params, hook_url) + } + } +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ +// +// Check and validate pipeline parameters +// +def validateInputParameters() { + genomeExistsError() +}// +// Validate channels from input samplesheet +// +def validateInputSamplesheet(input) { + def (metas, fastqs) = input[1..2] + + // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end + def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 + if (!endedness_ok) { + error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") + } + + return [ metas[0], fastqs ] +} +// +// Get attribute from genome config file e.g. fasta +// +def getGenomeAttribute(attribute) { + if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { + if (params.genomes[ params.genome ].containsKey(attribute)) { + return params.genomes[ params.genome ][ attribute ] + } + } + return null +} + +// +// Exit pipeline if incorrect --genome key provided +// +def genomeExistsError() { + if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { + def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + + " Currently, the available genome keys are:\n" + + " ${params.genomes.keySet().join(", ")}\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + error(error_string) + } +}// +// Generate methods description for MultiQC +// +def toolCitationText() { + // TODO nf-core: Optionally add in-text citation tools to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def citation_text = [ + "Tools used in the workflow included:", + "FastQC (Andrews 2010),", + "MultiQC (Ewels et al. 2016)", + "." + ].join(' ').trim() + + return citation_text +} + +def toolBibliographyText() { + // TODO nf-core: Optionally add bibliographic entries to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def reference_text = [ + "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", + "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " + ].join(' ').trim() + + return reference_text +} + +def methodsDescriptionText(mqc_methods_yaml) { + // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file + def meta = [:] + meta.workflow = workflow.toMap() + meta["manifest_map"] = workflow.manifest.toMap() + + // Pipeline DOI + meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" + meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + + // Tool references + meta["tool_citations"] = "" + meta["tool_bibliography"] = "" + + // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! + // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") + // meta["tool_bibliography"] = toolBibliographyText() + + + def methods_text = mqc_methods_yaml.text + + def engine = new groovy.text.SimpleTemplateEngine() + def description_html = engine.createTemplate(methods_text).make(meta) + + return description_html.toString() +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf new file mode 100644 index 00000000..ac31f28f --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -0,0 +1,126 @@ +// +// Subworkflow with functionality that may be useful for any Nextflow pipeline +// + +import org.yaml.snakeyaml.Yaml +import groovy.json.JsonOutput +import nextflow.extension.FilesEx + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow UTILS_NEXTFLOW_PIPELINE { + + take: + print_version // boolean: print version + dump_parameters // boolean: dump parameters + outdir // path: base directory used to publish pipeline results + check_conda_channels // boolean: check conda channels + + main: + + // + // Print workflow version and exit on --version + // + if (print_version) { + log.info "${workflow.manifest.name} ${getWorkflowVersion()}" + System.exit(0) + } + + // + // Dump pipeline parameters to a JSON file + // + if (dump_parameters && outdir) { + dumpParametersToJSON(outdir) + } + + // + // When running with Conda, warn if channels have not been set-up appropriately + // + if (check_conda_channels) { + checkCondaChannels() + } + + emit: + dummy_emit = true +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ + +// +// Generate version string +// +def getWorkflowVersion() { + String version_string = "" + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string +} + +// +// Dump pipeline parameters to a JSON file +// +def dumpParametersToJSON(outdir) { + def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = JsonOutput.toJson(params) + temp_pf.text = JsonOutput.prettyPrint(jsonStr) + + FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + temp_pf.delete() +} + +// +// When running with -profile conda, warn if channels have not been set-up appropriately +// +def checkCondaChannels() { + Yaml parser = new Yaml() + def channels = [] + try { + def config = parser.load("conda config --show channels".execute().text) + channels = config.channels + } catch(NullPointerException | IOException e) { + log.warn "Could not verify conda channel configuration." + return + } + + // Check that all channels are present + // This channel list is ordered by required channel priority. + def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean + + // Check that they are in the right order + def channel_priority_violation = false + def n = required_channels_in_order.size() + for (int i = 0; i < n - 1; i++) { + channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) + } + + if (channels_missing | channel_priority_violation) { + log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " There is a problem with your Conda configuration!\n\n" + + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + + " Please refer to https://bioconda.github.io/\n" + + " The observed channel order is \n" + + " ${channels}\n" + + " but the following channel order is required:\n" + + " ${required_channels_in_order}\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml new file mode 100644 index 00000000..e5c3a0a8 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml @@ -0,0 +1,38 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NEXTFLOW_PIPELINE" +description: Subworkflow with functionality that may be useful for any Nextflow pipeline +keywords: + - utility + - pipeline + - initialise + - version +components: [] +input: + - print_version: + type: boolean + description: | + Print the version of the pipeline and exit + - dump_parameters: + type: boolean + description: | + Dump the parameters of the pipeline to a JSON file + - output_directory: + type: directory + description: Path to output dir to write JSON file to. + pattern: "results/" + - check_conda_channel: + type: boolean + description: | + Check if the conda channel priority is correct. +output: + - dummy_emit: + type: boolean + description: | + Dummy emit to make nf-core subworkflows lint happy +authors: + - "@adamrtalbot" + - "@drpatelh" +maintainers: + - "@adamrtalbot" + - "@drpatelh" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test new file mode 100644 index 00000000..8ed4310c --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test @@ -0,0 +1,54 @@ + +nextflow_function { + + name "Test Functions" + script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf" + config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" + tag 'subworkflows' + tag 'utils_nextflow_pipeline' + tag 'subworkflows/utils_nextflow_pipeline' + + test("Test Function getWorkflowVersion") { + + function "getWorkflowVersion" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function dumpParametersToJSON") { + + function "dumpParametersToJSON" + + when { + function { + """ + // define inputs of the function here. Example: + input[0] = "$outputDir" + """.stripIndent() + } + } + + then { + assertAll( + { assert function.success } + ) + } + } + + test("Test Function checkCondaChannels") { + + function "checkCondaChannels" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap new file mode 100644 index 00000000..db2030f8 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap @@ -0,0 +1,12 @@ +{ + "Test Function getWorkflowVersion": { + "content": [ + "v9.9.9" + ], + "timestamp": "2024-01-19T11:32:36.031083" + }, + "Test Function checkCondaChannels": { + "content": null, + "timestamp": "2024-01-19T11:32:50.456" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test new file mode 100644 index 00000000..f7c54bc6 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -0,0 +1,123 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NEXTFLOW_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" + workflow "UTILS_NEXTFLOW_PIPELINE" + tag 'subworkflows' + tag 'utils_nextflow_pipeline' + tag 'subworkflows/utils_nextflow_pipeline' + + test("Should run no inputs") { + + when { + params { + outdir = "tests/results" + } + workflow { + """ + print_version = false + dump_parameters = false + outdir = null + check_conda_channels = false + + input[0] = print_version + input[1] = dump_parameters + input[2] = outdir + input[3] = check_conda_channels + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should print version") { + + when { + params { + outdir = "tests/results" + } + workflow { + """ + print_version = true + dump_parameters = false + outdir = null + check_conda_channels = false + + input[0] = print_version + input[1] = dump_parameters + input[2] = outdir + input[3] = check_conda_channels + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } + ) + } + } + + test("Should dump params") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + print_version = false + dump_parameters = true + outdir = params.outdir + check_conda_channels = false + + input[0] = false + input[1] = true + input[2] = params.outdir + input[3] = false + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should not create params JSON if no output directory") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + print_version = false + dump_parameters = true + outdir = params.outdir + check_conda_channels = false + + input[0] = false + input[1] = true + input[2] = null + input[3] = false + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config new file mode 100644 index 00000000..53574ffe --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -0,0 +1,9 @@ +manifest { + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" + nextflowVersion = '!>=23.04.0' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml new file mode 100644 index 00000000..f8476112 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nextflow_pipeline: + - subworkflows/nf-core/utils_nextflow_pipeline/** diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf new file mode 100644 index 00000000..a8b55d6f --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -0,0 +1,440 @@ +// +// Subworkflow with utility functions specific to the nf-core pipeline template +// + +import org.yaml.snakeyaml.Yaml +import nextflow.extension.FilesEx + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow UTILS_NFCORE_PIPELINE { + + take: + nextflow_cli_args + + main: + valid_config = checkConfigProvided() + checkProfileProvided(nextflow_cli_args) + + emit: + valid_config +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ + +// +// Warn if a -profile or Nextflow config has not been provided to run the pipeline +// +def checkConfigProvided() { + valid_config = true + if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { + log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + + "Please refer to the quick start section and usage docs for the pipeline.\n " + valid_config = false + } + return valid_config +} + +// +// Exit pipeline if --profile contains spaces +// +def checkProfileProvided(nextflow_cli_args) { + if (workflow.profile.endsWith(',')) { + error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + } + if (nextflow_cli_args[0]) { + log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + } +} + +// +// Citation string for pipeline +// +def workflowCitation() { + return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + + "* The pipeline\n" + + " ${workflow.manifest.doi}\n\n" + + "* The nf-core framework\n" + + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + + "* Software dependencies\n" + + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" +} + +// +// Generate workflow version string +// +def getWorkflowVersion() { + String version_string = "" + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string +} + +// +// Get software versions for pipeline +// +def processVersionsFromYAML(yaml_file) { + Yaml yaml = new Yaml() + versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + return yaml.dumpAsMap(versions).trim() +} + +// +// Get workflow version for pipeline +// +def workflowVersionToYAML() { + return """ + Workflow: + $workflow.manifest.name: ${getWorkflowVersion()} + Nextflow: $workflow.nextflow.version + """.stripIndent().trim() +} + +// +// Get channel of software versions used in pipeline in YAML format +// +def softwareVersionsToYAML(ch_versions) { + return ch_versions + .unique() + .map { processVersionsFromYAML(it) } + .unique() + .mix(Channel.of(workflowVersionToYAML())) +} + +// +// Get workflow summary for MultiQC +// +def paramsSummaryMultiqc(summary_params) { + def summary_section = '' + for (group in summary_params.keySet()) { + def group_params = summary_params.get(group) // This gets the parameters of that particular group + if (group_params) { + summary_section += "

    $group

    \n" + summary_section += "
    \n" + for (param in group_params.keySet()) { + summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" + } + summary_section += "
    \n" + } + } + + String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" + + return yaml_file_text +} + +// +// nf-core logo +// +def nfCoreLogo(monochrome_logs=true) { + Map colors = logColours(monochrome_logs) + String.format( + """\n + ${dashedLine(monochrome_logs)} + ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} + ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} + ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} + ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} + ${colors.green}`._,._,\'${colors.reset} + ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset} + ${dashedLine(monochrome_logs)} + """.stripIndent() + ) +} + +// +// Return dashed line +// +def dashedLine(monochrome_logs=true) { + Map colors = logColours(monochrome_logs) + return "-${colors.dim}----------------------------------------------------${colors.reset}-" +} + +// +// ANSII colours used for terminal logging +// +def logColours(monochrome_logs=true) { + Map colorcodes = [:] + + // Reset / Meta + colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" + colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" + colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" + colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" + colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" + colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" + colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" + + // Regular Colors + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + + // Bold + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + + // Underline + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + + // High Intensity + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + + // Bold High Intensity + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + + return colorcodes +} + +// +// Attach the multiqc report to email +// +def attachMultiqcReport(multiqc_report) { + def mqc_report = null + try { + if (workflow.success) { + mqc_report = multiqc_report.getVal() + if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { + if (mqc_report.size() > 1) { + log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" + } + mqc_report = mqc_report[0] + } + } + } catch (all) { + if (multiqc_report) { + log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" + } + } + return mqc_report +} + +// +// Construct and send completion email +// +def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { + + // Set up the e-mail variables + def subject = "[$workflow.manifest.name] Successful: $workflow.runName" + if (!workflow.success) { + subject = "[$workflow.manifest.name] FAILED: $workflow.runName" + } + + def summary = [:] + for (group in summary_params.keySet()) { + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['Date Started'] = workflow.start + misc_fields['Date Completed'] = workflow.complete + misc_fields['Pipeline script file path'] = workflow.scriptFile + misc_fields['Pipeline script hash ID'] = workflow.scriptId + if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository + if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId + if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build + misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp + + def email_fields = [:] + email_fields['version'] = getWorkflowVersion() + email_fields['runName'] = workflow.runName + email_fields['success'] = workflow.success + email_fields['dateComplete'] = workflow.complete + email_fields['duration'] = workflow.duration + email_fields['exitStatus'] = workflow.exitStatus + email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + email_fields['errorReport'] = (workflow.errorReport ?: 'None') + email_fields['commandLine'] = workflow.commandLine + email_fields['projectDir'] = workflow.projectDir + email_fields['summary'] = summary << misc_fields + + // On success try attach the multiqc report + def mqc_report = attachMultiqcReport(multiqc_report) + + // Check if we are only sending emails on failure + def email_address = email + if (!email && email_on_fail && !workflow.success) { + email_address = email_on_fail + } + + // Render the TXT template + def engine = new groovy.text.GStringTemplateEngine() + def tf = new File("${workflow.projectDir}/assets/email_template.txt") + def txt_template = engine.createTemplate(tf).make(email_fields) + def email_txt = txt_template.toString() + + // Render the HTML template + def hf = new File("${workflow.projectDir}/assets/email_template.html") + def html_template = engine.createTemplate(hf).make(email_fields) + def email_html = html_template.toString() + + // Render the sendmail template + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit + def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] + def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") + def sendmail_template = engine.createTemplate(sf).make(smail_fields) + def sendmail_html = sendmail_template.toString() + + // Send the HTML e-mail + Map colors = logColours(monochrome_logs) + if (email_address) { + try { + if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } + // Try to send HTML e-mail using sendmail + def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") + sendmail_tf.withWriter { w -> w << sendmail_html } + [ 'sendmail', '-t' ].execute() << sendmail_html + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" + } catch (all) { + // Catch failures and try with plaintext + def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] + mail_cmd.execute() << email_html + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" + } + } + + // Write summary e-mail HTML to a file + def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") + output_hf.withWriter { w -> w << email_html } + FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + output_hf.delete() + + // Write summary e-mail TXT to a file + def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") + output_tf.withWriter { w -> w << email_txt } + FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + output_tf.delete() +} + +// +// Print pipeline summary on completion +// +def completionSummary(monochrome_logs=true) { + Map colors = logColours(monochrome_logs) + if (workflow.success) { + if (workflow.stats.ignoredCount == 0) { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" + } else { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + } + } else { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" + } +} + +// +// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack +// +def imNotification(summary_params, hook_url) { + def summary = [:] + for (group in summary_params.keySet()) { + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) misc_fields['repository'] = workflow.repository + if (workflow.commitId) misc_fields['commitid'] = workflow.commitId + if (workflow.revision) misc_fields['revision'] = workflow.revision + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + + def msg_fields = [:] + msg_fields['version'] = getWorkflowVersion() + msg_fields['runName'] = workflow.runName + msg_fields['success'] = workflow.success + msg_fields['dateComplete'] = workflow.complete + msg_fields['duration'] = workflow.duration + msg_fields['exitStatus'] = workflow.exitStatus + msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + msg_fields['errorReport'] = (workflow.errorReport ?: 'None') + msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") + msg_fields['projectDir'] = workflow.projectDir + msg_fields['summary'] = summary << misc_fields + + // Render the JSON template + def engine = new groovy.text.GStringTemplateEngine() + // Different JSON depending on the service provider + // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format + def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" + def hf = new File("${workflow.projectDir}/assets/${json_path}") + def json_template = engine.createTemplate(hf).make(msg_fields) + def json_message = json_template.toString() + + // POST + def post = new URL(hook_url).openConnection(); + post.setRequestMethod("POST") + post.setDoOutput(true) + post.setRequestProperty("Content-Type", "application/json") + post.getOutputStream().write(json_message.getBytes("UTF-8")); + def postRC = post.getResponseCode(); + if (! postRC.equals(200)) { + log.warn(post.getErrorStream().getText()); + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml new file mode 100644 index 00000000..d08d2434 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml @@ -0,0 +1,24 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NFCORE_PIPELINE" +description: Subworkflow with utility functions specific to the nf-core pipeline template +keywords: + - utility + - pipeline + - initialise + - version +components: [] +input: + - nextflow_cli_args: + type: list + description: | + Nextflow CLI positional arguments +output: + - success: + type: boolean + description: | + Dummy output to indicate success +authors: + - "@adamrtalbot" +maintainers: + - "@adamrtalbot" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test new file mode 100644 index 00000000..1dc317f8 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test @@ -0,0 +1,134 @@ + +nextflow_function { + + name "Test Functions" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Test Function checkConfigProvided") { + + function "checkConfigProvided" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function checkProfileProvided") { + + function "checkProfileProvided" + + when { + function { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function workflowCitation") { + + function "workflowCitation" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function nfCoreLogo") { + + function "nfCoreLogo" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function dashedLine") { + + function "dashedLine" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function without logColours") { + + function "logColours" + + when { + function { + """ + input[0] = true + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function with logColours") { + function "logColours" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap new file mode 100644 index 00000000..10f948e6 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -0,0 +1,138 @@ +{ + "Test Function checkProfileProvided": { + "content": null, + "timestamp": "2024-02-09T15:43:55.145717" + }, + "Test Function checkConfigProvided": { + "content": [ + true + ], + "timestamp": "2024-01-19T11:34:13.548431224" + }, + "Test Function nfCoreLogo": { + "content": [ + "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" + ], + "timestamp": "2024-01-19T11:34:38.840454873" + }, + "Test Function workflowCitation": { + "content": [ + "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" + ], + "timestamp": "2024-01-19T11:34:22.24352016" + }, + "Test Function without logColours": { + "content": [ + { + "reset": "", + "bold": "", + "dim": "", + "underlined": "", + "blink": "", + "reverse": "", + "hidden": "", + "black": "", + "red": "", + "green": "", + "yellow": "", + "blue": "", + "purple": "", + "cyan": "", + "white": "", + "bblack": "", + "bred": "", + "bgreen": "", + "byellow": "", + "bblue": "", + "bpurple": "", + "bcyan": "", + "bwhite": "", + "ublack": "", + "ured": "", + "ugreen": "", + "uyellow": "", + "ublue": "", + "upurple": "", + "ucyan": "", + "uwhite": "", + "iblack": "", + "ired": "", + "igreen": "", + "iyellow": "", + "iblue": "", + "ipurple": "", + "icyan": "", + "iwhite": "", + "biblack": "", + "bired": "", + "bigreen": "", + "biyellow": "", + "biblue": "", + "bipurple": "", + "bicyan": "", + "biwhite": "" + } + ], + "timestamp": "2024-01-19T11:35:04.418416984" + }, + "Test Function dashedLine": { + "content": [ + "-\u001b[2m----------------------------------------------------\u001b[0m-" + ], + "timestamp": "2024-01-19T11:34:55.420000755" + }, + "Test Function with logColours": { + "content": [ + { + "reset": "\u001b[0m", + "bold": "\u001b[1m", + "dim": "\u001b[2m", + "underlined": "\u001b[4m", + "blink": "\u001b[5m", + "reverse": "\u001b[7m", + "hidden": "\u001b[8m", + "black": "\u001b[0;30m", + "red": "\u001b[0;31m", + "green": "\u001b[0;32m", + "yellow": "\u001b[0;33m", + "blue": "\u001b[0;34m", + "purple": "\u001b[0;35m", + "cyan": "\u001b[0;36m", + "white": "\u001b[0;37m", + "bblack": "\u001b[1;30m", + "bred": "\u001b[1;31m", + "bgreen": "\u001b[1;32m", + "byellow": "\u001b[1;33m", + "bblue": "\u001b[1;34m", + "bpurple": "\u001b[1;35m", + "bcyan": "\u001b[1;36m", + "bwhite": "\u001b[1;37m", + "ublack": "\u001b[4;30m", + "ured": "\u001b[4;31m", + "ugreen": "\u001b[4;32m", + "uyellow": "\u001b[4;33m", + "ublue": "\u001b[4;34m", + "upurple": "\u001b[4;35m", + "ucyan": "\u001b[4;36m", + "uwhite": "\u001b[4;37m", + "iblack": "\u001b[0;90m", + "ired": "\u001b[0;91m", + "igreen": "\u001b[0;92m", + "iyellow": "\u001b[0;93m", + "iblue": "\u001b[0;94m", + "ipurple": "\u001b[0;95m", + "icyan": "\u001b[0;96m", + "iwhite": "\u001b[0;97m", + "biblack": "\u001b[1;90m", + "bired": "\u001b[1;91m", + "bigreen": "\u001b[1;92m", + "biyellow": "\u001b[1;93m", + "biblue": "\u001b[1;94m", + "bipurple": "\u001b[1;95m", + "bicyan": "\u001b[1;96m", + "biwhite": "\u001b[1;97m" + } + ], + "timestamp": "2024-01-19T11:35:13.436366565" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test new file mode 100644 index 00000000..8940d32d --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test @@ -0,0 +1,29 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NFCORE_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + workflow "UTILS_NFCORE_PIPELINE" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Should run without failures") { + + when { + workflow { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap new file mode 100644 index 00000000..d07ce54c --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap @@ -0,0 +1,15 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + true + ], + "valid_config": [ + true + ] + } + ], + "timestamp": "2024-01-19T11:35:22.538940073" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config new file mode 100644 index 00000000..d0a926bf --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config @@ -0,0 +1,9 @@ +manifest { + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" + nextflowVersion = '!>=23.04.0' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml new file mode 100644 index 00000000..ac8523c9 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nfcore_pipeline: + - subworkflows/nf-core/utils_nfcore_pipeline/** diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf new file mode 100644 index 00000000..2585b65d --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf @@ -0,0 +1,62 @@ +// +// Subworkflow that uses the nf-validation plugin to render help text and parameter summary +// + +/* +======================================================================================== + IMPORT NF-VALIDATION PLUGIN +======================================================================================== +*/ + +include { paramsHelp } from 'plugin/nf-validation' +include { paramsSummaryLog } from 'plugin/nf-validation' +include { validateParameters } from 'plugin/nf-validation' + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow UTILS_NFVALIDATION_PLUGIN { + + take: + print_help // boolean: print help + workflow_command // string: default commmand used to run pipeline + pre_help_text // string: string to be printed before help text and summary log + post_help_text // string: string to be printed after help text and summary log + validate_params // boolean: validate parameters + schema_filename // path: JSON schema file, null to use default value + + main: + + log.debug "Using schema file: ${schema_filename}" + + // Default values for strings + pre_help_text = pre_help_text ?: '' + post_help_text = post_help_text ?: '' + workflow_command = workflow_command ?: '' + + // + // Print help message if needed + // + if (print_help) { + log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text + System.exit(0) + } + + // + // Print parameter summary to stdout + // + log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text + + // + // Validate parameters relative to the parameter JSON schema + // + if (validate_params){ + validateParameters(parameters_schema: schema_filename) + } + + emit: + dummy_emit = true +} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml new file mode 100644 index 00000000..3d4a6b04 --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml @@ -0,0 +1,44 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NFVALIDATION_PLUGIN" +description: Use nf-validation to initiate and validate a pipeline +keywords: + - utility + - pipeline + - initialise + - validation +components: [] +input: + - print_help: + type: boolean + description: | + Print help message and exit + - workflow_command: + type: string + description: | + The command to run the workflow e.g. "nextflow run main.nf" + - pre_help_text: + type: string + description: | + Text to print before the help message + - post_help_text: + type: string + description: | + Text to print after the help message + - validate_params: + type: boolean + description: | + Validate the parameters and error if invalid. + - schema_filename: + type: string + description: | + The filename of the schema to validate against. +output: + - dummy_emit: + type: boolean + description: | + Dummy emit to make nf-core subworkflows lint happy +authors: + - "@adamrtalbot" +maintainers: + - "@adamrtalbot" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test new file mode 100644 index 00000000..517ee54e --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test @@ -0,0 +1,200 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NFVALIDATION_PLUGIN" + script "../main.nf" + workflow "UTILS_NFVALIDATION_PLUGIN" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "plugin/nf-validation" + tag "'plugin/nf-validation'" + tag "utils_nfvalidation_plugin" + tag "subworkflows/utils_nfvalidation_plugin" + + test("Should run nothing") { + + when { + + params { + monochrome_logs = true + test_data = '' + } + + workflow { + """ + help = false + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should run help") { + + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } } + ) + } + } + + test("Should run help with command") { + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = "nextflow run noorg/doesntexist" + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } } + ) + } + } + + test("Should run help with extra text") { + + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = "nextflow run noorg/doesntexist" + pre_help_text = "pre-help-text" + post_help_text = "post-help-text" + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('pre-help-text') } }, + { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } }, + { assert workflow.stdout.any { it.contains('post-help-text') } } + ) + } + } + + test("Should validate params") { + + when { + + params { + monochrome_logs = true + test_data = '' + outdir = 1 + } + workflow { + """ + help = false + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = true + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } } + ) + } + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json new file mode 100644 index 00000000..7626c1c9 --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json @@ -0,0 +1,96 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", + "title": ". pipeline parameters", + "description": "", + "type": "object", + "definitions": { + "input_output_options": { + "title": "Input/output options", + "type": "object", + "fa_icon": "fas fa-terminal", + "description": "Define where the pipeline should find input data and save output data.", + "required": ["outdir"], + "properties": { + "validate_params": { + "type": "boolean", + "description": "Validate parameters?", + "default": true, + "hidden": true + }, + "outdir": { + "type": "string", + "format": "directory-path", + "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", + "fa_icon": "fas fa-folder-open" + }, + "test_data_base": { + "type": "string", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules", + "description": "Base for test data directory", + "hidden": true + }, + "test_data": { + "type": "string", + "description": "Fake test data param", + "hidden": true + } + } + }, + "generic_options": { + "title": "Generic options", + "type": "object", + "fa_icon": "fas fa-file-import", + "description": "Less common options for the pipeline, typically set in a config file.", + "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", + "properties": { + "help": { + "type": "boolean", + "description": "Display help text.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "version": { + "type": "boolean", + "description": "Display version and exit.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "logo": { + "type": "boolean", + "default": true, + "description": "Display nf-core logo in console output.", + "fa_icon": "fas fa-image", + "hidden": true + }, + "singularity_pull_docker_container": { + "type": "boolean", + "description": "Pull Singularity container from Docker?", + "hidden": true + }, + "publish_dir_mode": { + "type": "string", + "default": "copy", + "description": "Method used to save pipeline results to output directory.", + "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", + "fa_icon": "fas fa-copy", + "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], + "hidden": true + }, + "monochrome_logs": { + "type": "boolean", + "description": "Use monochrome_logs", + "hidden": true + } + } + } + }, + "allOf": [ + { + "$ref": "#/definitions/input_output_options" + }, + { + "$ref": "#/definitions/generic_options" + } + ] +} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml new file mode 100644 index 00000000..60b1cfff --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nfvalidation_plugin: + - subworkflows/nf-core/utils_nfvalidation_plugin/** diff --git a/workflows/circrna.nf b/workflows/circrna.nf index f540065b..af4880bd 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -1,6 +1,6 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - PRINT PARAMS SUMMARY + IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ @@ -98,9 +98,6 @@ include { FASTQC_TRIMGALORE } from '../subworkflows/nf-core/fastqc_trimgalore' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// Info required for completion email and summary -def multiqc_report = [] - workflow CIRCRNA { ch_reports = Channel.empty() @@ -230,9 +227,12 @@ workflow CIRCRNA { ch_versions = ch_versions.mix(DIFFERENTIAL_EXPRESSION.out.versions) ch_reports = ch_reports.mix(DIFFERENTIAL_EXPRESSION.out.reports) - CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique().collectFile(name: 'collated_versions.yml') - ) + // + // Collate and save software versions + // + softwareVersionsToYAML(ch_versions) + .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true) + .set { ch_collated_versions } // MODULE: MultiQC workflow_summary = WorkflowCircrna.paramsSummaryMultiqc(workflow, summary_params) @@ -254,31 +254,10 @@ workflow CIRCRNA { ch_multiqc_custom_config.toList(), ch_multiqc_logo.toList() ) - multiqc_report = MULTIQC.out.report.toList() -} -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - COMPLETION EMAIL AND SUMMARY -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -workflow.onComplete { - if (params.email || params.email_on_fail) { - NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report) - } - NfcoreTemplate.dump_parameters(workflow, params) - NfcoreTemplate.summary(workflow, params, log) - if (params.hook_url) { - NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log) - } -} - -workflow.onError { - if (workflow.errorReport.contains("Process requirement exceeds available memory")) { - println("🛑 Default resources exceed availability 🛑 ") - println("💡 See here on how to configure pipeline: https://nf-co.re/docs/usage/configuration#tuning-workflow-resources 💡") - } + emit: + multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + versions = ch_versions // channel: [ path(versions.yml) ] } /* From 499eef1746f1e1f769f34b2ec786e3435512e013 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 29 Feb 2024 09:58:27 +0100 Subject: [PATCH 129/491] Implement pipeline changes necessary for the 2.13 tools update --- main.nf | 16 +-- .../utils_nfcore_circrna_pipeline/main.nf | 35 +++++- workflows/{circrna.nf => circrna/main.nf} | 102 ++++-------------- 3 files changed, 64 insertions(+), 89 deletions(-) rename workflows/{circrna.nf => circrna/main.nf} (69%) diff --git a/main.nf b/main.nf index 66917a46..f3e91b43 100644 --- a/main.nf +++ b/main.nf @@ -29,14 +29,14 @@ include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_circ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta') -params.gtf = WorkflowMain.getGenomeAttribute(params, 'gtf') -params.bwa = WorkflowMain.getGenomeAttribute(params, 'bwa') -params.star = WorkflowMain.getGenomeAttribute(params, 'star') -params.bowtie = WorkflowMain.getGenomeAttribute(params, 'bowtie') -params.bowtie2 = WorkflowMain.getGenomeAttribute(params, 'bowtie2') -params.mature = WorkflowMain.getGenomeAttribute(params, 'mature') -params.species = WorkflowMain.getGenomeAttribute(params, 'species_id') +params.fasta = getGenomeAttribute('fasta') +params.gtf = getGenomeAttribute('gtf') +params.bwa = getGenomeAttribute('bwa') +params.star = getGenomeAttribute('star') +params.bowtie = getGenomeAttribute('bowtie') +params.bowtie2 = getGenomeAttribute('bowtie2') +params.mature = getGenomeAttribute('mature') +params.species = getGenomeAttribute('species_id') /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf b/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf index dc90ad90..f67b0a4e 100644 --- a/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf @@ -190,7 +190,20 @@ def genomeExistsError() { "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" error(error_string) } -}// +} + +def moduleExistsError() { + if (params.module && !checkParameterList(params.module, defineModuleList())) { + def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " Module '${params.modules.join(", ")}' not found in the pipeline.\n" + + " Currently, the available modules are:\n" + + " ${defineModuleList().join(", ")}\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + error(error_string) + } +} + +// // Generate methods description for MultiQC // def toolCitationText() { @@ -245,3 +258,23 @@ def methodsDescriptionText(mqc_methods_yaml) { return description_html.toString() } + +def defineModuleList() { + return [ + 'circrna_discovery', + 'mirna_prediction', + 'differential_expression' + ] +} + +def checkParameterExistence(it, list) { + if (!list.contains(it)) { + log.warn "Unknown parameter: ${it}" + return false + } + return true +} + +def checkParameterList(list, realList) { + return list.every{ checkParameterExistence(it, realList) } +} \ No newline at end of file diff --git a/workflows/circrna.nf b/workflows/circrna/main.nf similarity index 69% rename from workflows/circrna.nf rename to workflows/circrna/main.nf index af4880bd..f1c0b592 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna/main.nf @@ -4,52 +4,6 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' - -def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) -def citation = '\n' + WorkflowMain.citation(workflow) + '\n' -def summary_params = paramsSummaryMap(workflow) - -// Print parameter summary log to screen -log.info logo + paramsSummaryLog(workflow) + citation - -WorkflowCircrna.initialise(params, log) - -// Check modules paramater -def checkParameterExistence(it, list) { - if (!list.contains(it)) { - log.warn "Unknown parameter: ${it}" - return false - } - return true -} - -def checkParameterList(list, realList) { - return list.every{ checkParameterExistence(it, realList) } -} - -def defineModuleList() { - return [ - 'circrna_discovery', - 'mirna_prediction', - 'differential_expression' - ] -} - -moduleList = defineModuleList() -module = params.module ? params.module.split(',').collect{it.trim().toLowerCase()} : [] -if(!checkParameterList(module, moduleList)) { - log.error "error: Unknown module selected, please choose one of the following:\n\n circrna_discovery\n\n mirna_prediction\n\n differential_expression\n\nPlease refer to the help documentation for a description of each module." - System.exit(1) -} - -// Check input path parameters to see if they exist -def checkPathParamList = [ params.input, params.multiqc_config ] -for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } } - -// Check mandatory parameters -if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' } - ch_phenotype = params.phenotype && params.module.contains('differential_expression') ? file(params.phenotype, checkIfExists:true) : Channel.empty() ch_fasta = params.fasta ? file(params.fasta) : 'null' ch_gtf = params.gtf ? file(params.gtf) : 'null' @@ -73,11 +27,12 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil */ // SUBWORKFLOWS: -include { INPUT_CHECK } from '../subworkflows/local/input_check' -include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome' -include { CIRCRNA_DISCOVERY } from '../subworkflows/local/circrna_discovery' -include { MIRNA_PREDICTION } from '../subworkflows/local/mirna_prediction' -include { DIFFERENTIAL_EXPRESSION } from '../subworkflows/local/differential_expression' +include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline' +include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' +include { PREPARE_GENOME } from '../../subworkflows/local/prepare_genome' +include { CIRCRNA_DISCOVERY } from '../../subworkflows/local/circrna_discovery' +include { MIRNA_PREDICTION } from '../../subworkflows/local/mirna_prediction' +include { DIFFERENTIAL_EXPRESSION } from '../../subworkflows/local/differential_expression' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -86,12 +41,11 @@ include { DIFFERENTIAL_EXPRESSION } from '../subworkflows/local/differential_exp */ // MODULES: -include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' -include { CAT_FASTQ } from '../modules/nf-core/cat/fastq/main' +include { MULTIQC } from '../../modules/nf-core/multiqc/main' +include { CAT_FASTQ } from '../../modules/nf-core/cat/fastq/main' // SUBWORKFLOWS: -include { FASTQC_TRIMGALORE } from '../subworkflows/nf-core/fastqc_trimgalore' +include { FASTQC_TRIMGALORE } from '../../subworkflows/nf-core/fastqc_trimgalore' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RUN MAIN WORKFLOW @@ -99,38 +53,26 @@ include { FASTQC_TRIMGALORE } from '../subworkflows/nf-core/fastqc_trimgalore' */ workflow CIRCRNA { + take: + ch_samplesheet + ch_versions - ch_reports = Channel.empty() - ch_versions = Channel.empty() + main: // // 1. Pre-processing // // SUBWORKFLOW: - // Validate input samplesheet & phenotype file - INPUT_CHECK ( - ch_input, - ch_phenotype - ) - .reads - .map { - meta, fastq -> - meta.id = meta.id.split('_')[0..-2].join('_') - [ meta, fastq ] } - .groupTuple(by: [0]) - .branch { - meta, fastq -> - single : fastq.size() == 1 - return [ meta, fastq.flatten() ] - multiple: fastq.size() > 1 - return [ meta, fastq.flatten() ] - } - .set { ch_fastq } - ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) - // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") - // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ - // ! There is currently no tooling to help you write a sample sheet schema + ch_samplesheet + .branch { + meta, fastq -> + single : fastq.size() == 1 + return [ meta, fastq.flatten() ] + multiple: fastq.size() > 1 + return [ meta, fastq.flatten() ] + } + .set { ch_fastq } // MODULE: // Concatenate FastQ files from same sample if required From 6184a4971e28e27bf0540946c4ee9048d8f0f03c Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 29 Feb 2024 10:34:06 +0100 Subject: [PATCH 130/491] Fix some more problems with template update --- main.nf | 16 +++++------ workflows/circrna/main.nf | 56 +++++++++++++++++++++++++-------------- 2 files changed, 43 insertions(+), 29 deletions(-) diff --git a/main.nf b/main.nf index f3e91b43..9cf725ef 100644 --- a/main.nf +++ b/main.nf @@ -48,17 +48,17 @@ params.species = getGenomeAttribute('species_id') // WORKFLOW: Run main analysis pipeline depending on type of input // workflow NFCORE_CIRCRNA { - - take: - samplesheet // channel: samplesheet read in from --input - main: + ch_versions = Channel.empty() + // - // WORKFLOW: Run pipeline + // WORKFLOW: Run nf-core/circrna workflow // + ch_samplesheet = Channel.value(file(params.input, checkIfExists: true)) CIRCRNA ( - samplesheet + ch_samplesheet, + ch_versions ) emit: @@ -91,9 +91,7 @@ workflow { // // WORKFLOW: Run main workflow // - NFCORE_CIRCRNA ( - PIPELINE_INITIALISATION.out.samplesheet - ) + NFCORE_CIRCRNA () // // SUBWORKFLOW: Run completion tasks diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index f1c0b592..84f5723c 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -27,7 +27,10 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil */ // SUBWORKFLOWS: +include { paramsSummaryMap } from 'plugin/nf-validation' include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline' +include { validateInputSamplesheet } from '../../subworkflows/local/utils_nfcore_circrna_pipeline' + include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' include { PREPARE_GENOME } from '../../subworkflows/local/prepare_genome' include { CIRCRNA_DISCOVERY } from '../../subworkflows/local/circrna_discovery' @@ -59,18 +62,37 @@ workflow CIRCRNA { main: + ch_multiqc_files = Channel.empty() + // // 1. Pre-processing // // SUBWORKFLOW: - ch_samplesheet + Channel + .fromSamplesheet("input") + .map { + meta, fastq_1, fastq_2 -> + if (!fastq_2) { + return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] + } else { + return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] + } + } + .groupTuple() + .map { + validateInputSamplesheet(it) + } + .map { + meta, fastqs -> + return [ meta, fastqs.flatten() ] + } .branch { - meta, fastq -> - single : fastq.size() == 1 - return [ meta, fastq.flatten() ] - multiple: fastq.size() > 1 - return [ meta, fastq.flatten() ] + meta, fastqs -> + single : fastqs.size() == 1 + return [ meta, fastqs ] + multiple: fastqs.size() > 1 + return [ meta, fastqs ] } .set { ch_fastq } @@ -108,8 +130,8 @@ workflow CIRCRNA { params.skip_trimming ) ch_versions = ch_versions.mix(FASTQC_TRIMGALORE.out.versions) - ch_reports = ch_reports.mix(FASTQC_TRIMGALORE.out.trim_zip.collect{it[1]}.ifEmpty([])) - ch_reports = ch_reports.mix(FASTQC_TRIMGALORE.out.trim_log.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(FASTQC_TRIMGALORE.out.trim_zip.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(FASTQC_TRIMGALORE.out.trim_log.collect{it[1]}.ifEmpty([])) // // 2. circRNA Discovery @@ -167,7 +189,7 @@ workflow CIRCRNA { ) ch_versions = ch_versions.mix(DIFFERENTIAL_EXPRESSION.out.versions) - ch_reports = ch_reports.mix(DIFFERENTIAL_EXPRESSION.out.reports) + ch_multiqc_files = ch_multiqc_files.mix(DIFFERENTIAL_EXPRESSION.out.reports) // // Collate and save software versions @@ -177,18 +199,12 @@ workflow CIRCRNA { .set { ch_collated_versions } // MODULE: MultiQC - workflow_summary = WorkflowCircrna.paramsSummaryMultiqc(workflow, summary_params) - ch_workflow_summary = Channel.value(workflow_summary) - - methods_description = WorkflowCircrna.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) - ch_methods_description = Channel.value(methods_description) - - ch_multiqc_files = Channel.empty() + ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty() + ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo) : Channel.empty() + summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC_TRIMGALORE.out.fastqc_zip.collect{it[1]}.ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(ch_reports.collect().ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) MULTIQC ( ch_multiqc_files.collect(), From 0d5b03264b96f4e0175c6145f79ee0a0fb688f39 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 29 Feb 2024 10:51:48 +0100 Subject: [PATCH 131/491] Fix linting problems --- subworkflows/local/utils_nfcore_circrna_pipeline/main.nf | 2 +- workflows/circrna/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf b/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf index f67b0a4e..690b335d 100644 --- a/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf @@ -277,4 +277,4 @@ def checkParameterExistence(it, list) { def checkParameterList(list, realList) { return list.every{ checkParameterExistence(it, realList) } -} \ No newline at end of file +} diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 84f5723c..3e95f4ca 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -83,7 +83,7 @@ workflow CIRCRNA { .map { validateInputSamplesheet(it) } - .map { + .map { meta, fastqs -> return [ meta, fastqs.flatten() ] } From 09a630e8dee7c18d16904bcac228b1037d311d79 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 29 Feb 2024 16:09:40 +0000 Subject: [PATCH 132/491] Template update for nf-core/tools version 2.13.1 --- .devcontainer/devcontainer.json | 10 +---- .github/CONTRIBUTING.md | 14 ++++--- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/awsfulltest.yml | 4 +- .github/workflows/awstest.yml | 4 +- .github/workflows/ci.yml | 2 +- .github/workflows/download_pipeline.yml | 2 +- .github/workflows/linting.yml | 2 +- .github/workflows/release-announcements.yml | 2 +- .gitpod.yml | 6 +-- README.md | 3 +- modules.json | 8 ++-- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- .../nf-core/multiqc/tests/main.nf.test.snap | 12 +++--- .../utils_nfcore_circrna_pipeline/main.nf | 10 +++-- .../tests/main.function.nf.test | 2 +- .../tests/main.function.nf.test.snap | 12 +++++- .../tests/main.workflow.nf.test | 20 ++------- .../tests/nextflow.config | 2 +- .../tests/main.function.nf.test.snap | 42 +++++++++++++++---- .../tests/main.workflow.nf.test.snap | 6 ++- .../tests/main.nf.test | 2 +- 23 files changed, 99 insertions(+), 74 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 4ecfbfe3..b290e090 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -10,15 +10,7 @@ "vscode": { // Set *default* container specific settings.json values on container create. "settings": { - "python.defaultInterpreterPath": "/opt/conda/bin/python", - "python.linting.enabled": true, - "python.linting.pylintEnabled": true, - "python.formatting.autopep8Path": "/opt/conda/bin/autopep8", - "python.formatting.yapfPath": "/opt/conda/bin/yapf", - "python.linting.flake8Path": "/opt/conda/bin/flake8", - "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", - "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", - "python.linting.pylintPath": "/opt/conda/bin/pylint" + "python.defaultInterpreterPath": "/opt/conda/bin/python" }, // Add the IDs of extensions you want installed when the container is created. diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 479ec155..d8a9ab91 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -9,9 +9,8 @@ Please use the pre-filled template to save time. However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;) -:::info -If you need help using or modifying nf-core/circrna then the best place to ask is on the nf-core Slack [#circrna](https://nfcore.slack.com/channels/circrna) channel ([join our Slack here](https://nf-co.re/join/slack)). -::: +> [!NOTE] +> If you need help using or modifying nf-core/circrna then the best place to ask is on the nf-core Slack [#circrna](https://nfcore.slack.com/channels/circrna) channel ([join our Slack here](https://nf-co.re/join/slack)). ## Contribution workflow @@ -27,8 +26,11 @@ If you're not used to this workflow with git, you can start with some [docs from ## Tests -You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to -receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir `. +You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: + +```bash +nf-test test --profile debug,test,docker --verbose +``` When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. @@ -90,7 +92,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`. Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. -The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block. +The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. ### Naming schemes diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 9d44ed38..364dd9b5 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/circ - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/circrna/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/circrna _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). -- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). +- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 94521ebc..7b6bd16d 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 + uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -31,7 +31,7 @@ jobs: } profiles: test_full - - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + - uses: actions/upload-artifact@v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 5307e9aa..9590dcae 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 + uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + - uses: actions/upload-artifact@v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 4e5754df..916fd86a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -31,7 +31,7 @@ jobs: uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 with: version: "${{ matrix.NXF_VER }}" diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index f823210d..08622fd5 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -28,7 +28,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 748b4311..073e1876 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -35,7 +35,7 @@ jobs: uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index c3674af2..d468aeaa 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -12,7 +12,7 @@ jobs: - name: get topics and convert to hashtags id: get_topics run: | - curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' > $GITHUB_OUTPUT + curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: diff --git a/.gitpod.yml b/.gitpod.yml index 363d5b1d..105a1821 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -10,13 +10,11 @@ tasks: vscode: extensions: # based on nf-core.nf-core-extensionpack - - codezombiech.gitignore # Language support for .gitignore files - # - cssho.vscode-svgviewer # SVG viewer - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - # - nextflow.nextflow # Nextflow syntax highlighting + # - nextflow.nextflow # Nextflow syntax highlighting - oderwat.indent-rainbow # Highlight indentation level - streetsidesoftware.code-spell-checker # Spelling checker for source code + - charliermarsh.ruff # Code linter Ruff diff --git a/README.md b/README.md index 18919fd1..ab055f20 100644 --- a/README.md +++ b/README.md @@ -7,12 +7,13 @@ [![GitHub Actions CI Status](https://github.com/nf-core/circrna/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/circrna/actions/workflows/ci.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/circrna/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/circrna/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/circrna/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) -[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/circrna) +[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/circrna) [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23circrna-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/circrna)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) diff --git a/modules.json b/modules.json index 8cca7fba..c0226feb 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "ccacf6f5de6df3bc6d73b665c1fd2933d8bbc290", + "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", "installed_by": ["modules"] } } @@ -21,17 +21,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 2212096a..ca39fb67 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.20 + - bioconda::multiqc=1.21 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 354f4430..47ac352f 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_0' : - 'biocontainers/multiqc:1.20--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : + 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index c204b488..bfebd802 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T09:28:51.744211298" + "timestamp": "2024-02-29T08:48:55.657331" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T09:29:28.847433492" + "timestamp": "2024-02-29T08:49:49.071937" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T09:29:13.223621555" + "timestamp": "2024-02-29T08:49:25.457567" } } \ No newline at end of file diff --git a/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf b/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf index dc90ad90..69918616 100644 --- a/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf @@ -1,5 +1,5 @@ // -// Subworkflow with functionality specific to the nf-core/pipeline pipeline +// Subworkflow with functionality specific to the nf-core/circrna pipeline // /* @@ -152,7 +152,9 @@ workflow PIPELINE_COMPLETION { // def validateInputParameters() { genomeExistsError() -}// +} + +// // Validate channels from input samplesheet // def validateInputSamplesheet(input) { @@ -190,7 +192,9 @@ def genomeExistsError() { "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" error(error_string) } -}// +} + +// // Generate methods description for MultiQC // def toolCitationText() { diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test index 8ed4310c..68718e4f 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test @@ -51,4 +51,4 @@ nextflow_function { ) } } -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap index db2030f8..e3f0baf4 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap @@ -3,10 +3,18 @@ "content": [ "v9.9.9" ], - "timestamp": "2024-01-19T11:32:36.031083" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:05.308243" }, "Test Function checkCondaChannels": { "content": null, - "timestamp": "2024-01-19T11:32:50.456" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:12.425833" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test index f7c54bc6..ca964ce8 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -11,9 +11,6 @@ nextflow_workflow { test("Should run no inputs") { when { - params { - outdir = "tests/results" - } workflow { """ print_version = false @@ -39,9 +36,6 @@ nextflow_workflow { test("Should print version") { when { - params { - outdir = "tests/results" - } workflow { """ print_version = true @@ -68,19 +62,16 @@ nextflow_workflow { test("Should dump params") { when { - params { - outdir = "$outputDir" - } workflow { """ print_version = false dump_parameters = true - outdir = params.outdir + outdir = 'results' check_conda_channels = false input[0] = false input[1] = true - input[2] = params.outdir + input[2] = outdir input[3] = false """ } @@ -96,19 +87,16 @@ nextflow_workflow { test("Should not create params JSON if no output directory") { when { - params { - outdir = "$outputDir" - } workflow { """ print_version = false dump_parameters = true - outdir = params.outdir + outdir = null check_conda_channels = false input[0] = false input[1] = true - input[2] = null + input[2] = outdir input[3] = false """ } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index 53574ffe..d0a926bf 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -6,4 +6,4 @@ manifest { nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap index 10f948e6..1037232c 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -1,25 +1,41 @@ { "Test Function checkProfileProvided": { "content": null, - "timestamp": "2024-02-09T15:43:55.145717" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:03.360873" }, "Test Function checkConfigProvided": { "content": [ true ], - "timestamp": "2024-01-19T11:34:13.548431224" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:59.729647" }, "Test Function nfCoreLogo": { "content": [ "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" ], - "timestamp": "2024-01-19T11:34:38.840454873" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:10.562934" }, "Test Function workflowCitation": { "content": [ "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" ], - "timestamp": "2024-01-19T11:34:22.24352016" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:07.019761" }, "Test Function without logColours": { "content": [ @@ -73,13 +89,21 @@ "biwhite": "" } ], - "timestamp": "2024-01-19T11:35:04.418416984" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:17.969323" }, "Test Function dashedLine": { "content": [ "-\u001b[2m----------------------------------------------------\u001b[0m-" ], - "timestamp": "2024-01-19T11:34:55.420000755" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:14.366181" }, "Test Function with logColours": { "content": [ @@ -133,6 +157,10 @@ "biwhite": "\u001b[1;97m" } ], - "timestamp": "2024-01-19T11:35:13.436366565" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:21.714424" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap index d07ce54c..859d1030 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap @@ -10,6 +10,10 @@ ] } ], - "timestamp": "2024-01-19T11:35:22.538940073" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:25.726491" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test index 517ee54e..5784a33f 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test @@ -197,4 +197,4 @@ nextflow_workflow { ) } } -} \ No newline at end of file +} From 93c2881dc80963376e7c131ee8596600a8b8ed5c Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 1 Feb 2024 10:58:58 +0100 Subject: [PATCH 133/491] Implement pandas-based annotation --- conf/modules.config | 5 + .../local/annotation/full_annotation/main.nf | 103 ++++++++++++------ subworkflows/local/circrna_discovery.nf | 84 +++++++------- 3 files changed, 117 insertions(+), 75 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 52b47439..0b64d0de 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -604,6 +604,11 @@ if (!params.skip_trimming) { ] } + withName: INTERSECT_ANNOTATION { + ext.args = "-loj" + ext.suffix = "intersect.bed" + } + withName: FASTA { ext.when = { params.module.split(',').contains('circrna_discovery') } publishDir = [ diff --git a/modules/local/annotation/full_annotation/main.nf b/modules/local/annotation/full_annotation/main.nf index 789c884f..da50da22 100644 --- a/modules/local/annotation/full_annotation/main.nf +++ b/modules/local/annotation/full_annotation/main.nf @@ -1,48 +1,83 @@ process ANNOTATION { - tag "${meta.id}:${meta.tool}" - label 'process_high' + tag "$meta.id" + label 'process_single' - conda "bioconda::ucsc-gtftogenepred=377 bioconda::ucsc-genepredtobed=377 bioconda::bedtools=2.27.0" + conda "bioconda::pandas=1.5.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-d7ee3552d06d8acebbc660507b48487c7369e221:07daadbfe8182aa3c974c7b78924d5c8730b922d-0' : - 'quay.io/biocontainers/mulled-v2-d7ee3552d06d8acebbc660507b48487c7369e221:07daadbfe8182aa3c974c7b78924d5c8730b922d-0' }" + 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : + 'quay.io/biocontainers/pandas:1.5.2' }" input: - tuple val(meta), path(bed) - path gtf - path biotypes - val exon_boundary + tuple val(meta), path(intersection) + val(exon_boundary) + + output: + tuple val(meta), path("${meta.id}.annotation.bed"), emit: bed + + script: + """ + #!/usr/bin/env python + import pandas as pd + import os - output: - tuple val(meta), path("${prefix}.bed"), emit: bed - path("*.log") , emit: log - path "versions.yml" , emit: versions + columns = { + 0: 'chr', + 1: 'start', + 2: 'end', + 3: 'name', + 4: 'score', + 5: 'strand', + 9: 'tx_start', + 10: 'tx_end', + 14: 'attributes' + } - when: - task.ext.when == null || task.ext.when + attributes = ['gene_id', 'transcript_id'] - script: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '377' - """ - grep -vf $biotypes $gtf > filt.gtf - mv $bed circs.bed + exon_boundary = ${exon_boundary} + + df = pd.read_csv("${intersection}", sep="\\t", header=None, usecols=columns.keys()) + df = df.rename(columns=columns) + # Convert attributes to a dictionary + df['attributes'] = df['attributes'].apply(lambda row: dict([[value.strip(r'\\"') for value in entry.strip().split(' ')] for entry in row.split(';') if entry])) + # Keep only the attributes we want + df['attributes'] = df['attributes'].apply(lambda row: {key: row[key] for key in attributes}) + # Convert attributes to columns + df = pd.concat([df.drop(['attributes'], axis=1), df['attributes'].apply(pd.Series)], axis=1) + + df['any_outside'] = (df['start'] < df['tx_start'] - exon_boundary) | (df['end'] > df['tx_end'] + exon_boundary) + # Perfect is inverse of any_outside + df['perfect'] = ~df['any_outside'] + # Drop any_outside + df = df.drop(['any_outside', 'tx_start', 'tx_end'], axis=1) + + df = df.groupby(['chr', 'start', 'end', 'strand']).aggregate({ + 'name': lambda x: x.iloc[0], + 'score': lambda x: x.iloc[0], + 'gene_id': lambda x: list(x), + 'transcript_id': lambda x: list(x), + 'perfect': lambda x: list(x) + }) - annotate_outputs.sh $exon_boundary &> ${prefix}.log - mv master_bed12.bed ${prefix}.bed.tmp + def filter_perfect(row, col): + if any(row['perfect']): + matching_values = [value for value, perfectness in zip(row[col], row['perfect']) if perfectness] + else: + matching_values = row[col] + return ",".join(set(matching_values)) - awk -v FS="\\t" '{print \$11}' ${prefix}.bed.tmp > mature_len.tmp - awk -v FS="," '{for(i=t=0;i mature_length + df['type'] = df['perfect'].apply(lambda x: 'circRNA' if any(x) else 'EI-circRNA') + df['gene_id'] = df.apply(lambda row: filter_perfect(row, 'gene_id'), axis=1) + df['transcript_id'] = df.apply(lambda row: filter_perfect(row, 'transcript_id'), axis=1) + # Drop perfect + df = df.drop(['perfect'], axis=1) - paste ${prefix}.bed.tmp mature_length > ${prefix}.bed + df = df.sort_index() + df = df.reset_index() + bed_order = ['chr', 'start', 'end', 'name', 'score', 'strand', 'type', 'gene_id', 'transcript_id'] + df = df[bed_order] - cat <<-END_VERSIONS > versions.yml - "${task.process}": - awk: \$(awk --version | head -n1 | cut -d' ' -f3 | sed 's/,//g' ) - bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") - ucsc: $VERSION - END_VERSIONS + df.to_csv('${meta.id}.annotation.bed', sep='\\t', index=False, header=False) """ -} +} \ No newline at end of file diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 80ba9a19..1fef8419 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -1,44 +1,45 @@ -include { ANNOTATION } from '../../modules/local/annotation/full_annotation/main' -include { BOWTIE2_ALIGN as FIND_CIRC_ALIGN } from '../../modules/nf-core/bowtie2/align/main' -include { SAMTOOLS_VIEW } from '../../modules/nf-core/samtools/view/main' -include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main' -include { FIND_CIRC_ANCHORS } from '../../modules/local/find_circ/anchors/main' -include { FIND_CIRC } from '../../modules/local/find_circ/find_circ/main' -include { FIND_CIRC_FILTER } from '../../modules/local/find_circ/filter/main' -include { CIRIQUANT_YML } from '../../modules/local/ciriquant/yml/main' -include { CIRIQUANT } from '../../modules/local/ciriquant/ciriquant/main' -include { CIRIQUANT_FILTER } from '../../modules/local/ciriquant/filter/main' -include { CIRCRNA_FINDER_FILTER } from '../../modules/local/circrna_finder/filter/main' -include { SEGEMEHL_ALIGN } from '../../modules/nf-core/segemehl/align/main' -include { SEGEMEHL_FILTER } from '../../modules/local/segemehl/filter/main' -include { STAR_ALIGN as STAR_1ST_PASS } from '../../modules/nf-core/star/align/main' -include { STAR_ALIGN as STAR_2ND_PASS } from '../../modules/nf-core/star/align/main' -include { SJDB as STAR_SJDB } from '../../modules/local/star/sjdb/main' -include { STAR_ALIGN as DCC_1ST_PASS } from '../../modules/nf-core/star/align/main' -include { STAR_ALIGN as DCC_2ND_PASS } from '../../modules/nf-core/star/align/main' -include { SJDB as DCC_SJDB } from '../../modules/local/star/sjdb/main' -include { STAR_ALIGN as DCC_MATE1_1ST_PASS } from '../../modules/nf-core/star/align/main' -include { STAR_ALIGN as DCC_MATE1_2ND_PASS } from '../../modules/nf-core/star/align/main' -include { SJDB as DCC_MATE1_SJDB } from '../../modules/local/star/sjdb/main' -include { STAR_ALIGN as DCC_MATE2_1ST_PASS } from '../../modules/nf-core/star/align/main' -include { STAR_ALIGN as DCC_MATE2_2ND_PASS } from '../../modules/nf-core/star/align/main' -include { SJDB as DCC_MATE2_SJDB } from '../../modules/local/star/sjdb/main' -include { DCC } from '../../modules/local/dcc/dcc/main' -include { DCC_FILTER } from '../../modules/local/dcc/filter/main' -include { MAPSPLICE_ALIGN } from '../../modules/local/mapsplice/align/main' -include { FASTA } from '../../modules/local/fasta/main' -include { MERGE_TOOLS } from '../../modules/local/count_matrix/merge_tools/main' -include { COUNTS_COMBINED } from '../../modules/local/count_matrix/combined/main' -include { COUNTS_SINGLE } from '../../modules/local/count_matrix/single/main' -include { CIRCEXPLORER2_REFERENCE as CIRCEXPLORER2_REF } from '../../modules/local/circexplorer2/reference/main' -include { CIRCEXPLORER2_PARSE as CIRCEXPLORER2_PAR } from '../../modules/nf-core/circexplorer2/parse/main' -include { CIRCEXPLORER2_ANNOTATE as CIRCEXPLORER2_ANN } from '../../modules/nf-core/circexplorer2/annotate/main' -include { CIRCEXPLORER2_FILTER as CIRCEXPLORER2_FLT } from '../../modules/local/circexplorer2/filter/main' +include { ANNOTATION } from '../../modules/local/annotation/full_annotation/main' +include { BEDTOOLS_INTERSECT as INTERSECT_ANNOTATION } from '../../modules/nf-core/bedtools/intersect/main' +include { BOWTIE2_ALIGN as FIND_CIRC_ALIGN } from '../../modules/nf-core/bowtie2/align/main' +include { SAMTOOLS_VIEW } from '../../modules/nf-core/samtools/view/main' +include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main' +include { FIND_CIRC_ANCHORS } from '../../modules/local/find_circ/anchors/main' +include { FIND_CIRC } from '../../modules/local/find_circ/find_circ/main' +include { FIND_CIRC_FILTER } from '../../modules/local/find_circ/filter/main' +include { CIRIQUANT_YML } from '../../modules/local/ciriquant/yml/main' +include { CIRIQUANT } from '../../modules/local/ciriquant/ciriquant/main' +include { CIRIQUANT_FILTER } from '../../modules/local/ciriquant/filter/main' +include { CIRCRNA_FINDER_FILTER } from '../../modules/local/circrna_finder/filter/main' +include { SEGEMEHL_ALIGN } from '../../modules/nf-core/segemehl/align/main' +include { SEGEMEHL_FILTER } from '../../modules/local/segemehl/filter/main' +include { STAR_ALIGN as STAR_1ST_PASS } from '../../modules/nf-core/star/align/main' +include { STAR_ALIGN as STAR_2ND_PASS } from '../../modules/nf-core/star/align/main' +include { SJDB as STAR_SJDB } from '../../modules/local/star/sjdb/main' +include { STAR_ALIGN as DCC_1ST_PASS } from '../../modules/nf-core/star/align/main' +include { STAR_ALIGN as DCC_2ND_PASS } from '../../modules/nf-core/star/align/main' +include { SJDB as DCC_SJDB } from '../../modules/local/star/sjdb/main' +include { STAR_ALIGN as DCC_MATE1_1ST_PASS } from '../../modules/nf-core/star/align/main' +include { STAR_ALIGN as DCC_MATE1_2ND_PASS } from '../../modules/nf-core/star/align/main' +include { SJDB as DCC_MATE1_SJDB } from '../../modules/local/star/sjdb/main' +include { STAR_ALIGN as DCC_MATE2_1ST_PASS } from '../../modules/nf-core/star/align/main' +include { STAR_ALIGN as DCC_MATE2_2ND_PASS } from '../../modules/nf-core/star/align/main' +include { SJDB as DCC_MATE2_SJDB } from '../../modules/local/star/sjdb/main' +include { DCC } from '../../modules/local/dcc/dcc/main' +include { DCC_FILTER } from '../../modules/local/dcc/filter/main' +include { MAPSPLICE_ALIGN } from '../../modules/local/mapsplice/align/main' +include { FASTA } from '../../modules/local/fasta/main' +include { MERGE_TOOLS } from '../../modules/local/count_matrix/merge_tools/main' +include { COUNTS_COMBINED } from '../../modules/local/count_matrix/combined/main' +include { COUNTS_SINGLE } from '../../modules/local/count_matrix/single/main' +include { CIRCEXPLORER2_REFERENCE as CIRCEXPLORER2_REF } from '../../modules/local/circexplorer2/reference/main' +include { CIRCEXPLORER2_PARSE as CIRCEXPLORER2_PAR } from '../../modules/nf-core/circexplorer2/parse/main' +include { CIRCEXPLORER2_ANNOTATE as CIRCEXPLORER2_ANN } from '../../modules/nf-core/circexplorer2/annotate/main' +include { CIRCEXPLORER2_FILTER as CIRCEXPLORER2_FLT } from '../../modules/local/circexplorer2/filter/main' include { CIRCEXPLORER2_REFERENCE as MAPSPLICE_REFERENCE } from '../../modules/local/circexplorer2/reference/main' -include { CIRCEXPLORER2_PARSE as MAPSPLICE_PARSE } from '../../modules/nf-core/circexplorer2/parse/main' -include { CIRCEXPLORER2_ANNOTATE as MAPSPLICE_ANNOTATE } from '../../modules/nf-core/circexplorer2/annotate/main' -include { CIRCEXPLORER2_FILTER as MAPSPLICE_FILTER } from '../../modules/local/circexplorer2/filter/main' +include { CIRCEXPLORER2_PARSE as MAPSPLICE_PARSE } from '../../modules/nf-core/circexplorer2/parse/main' +include { CIRCEXPLORER2_ANNOTATE as MAPSPLICE_ANNOTATE } from '../../modules/nf-core/circexplorer2/annotate/main' +include { CIRCEXPLORER2_FILTER as MAPSPLICE_FILTER } from '../../modules/local/circexplorer2/filter/main' workflow CIRCRNA_DISCOVERY { @@ -217,9 +218,10 @@ workflow CIRCRNA_DISCOVERY { DCC_FILTER.out.results, MAPSPLICE_FILTER.out.results) - ANNOTATION( circrna_filtered, gtf, ch_biotypes.collect(), exon_boundary ) + INTERSECT_ANNOTATION( circrna_filtered.combine(ch_gtf), [[], []]) + ANNOTATION( INTERSECT_ANNOTATION.out.intersect, exon_boundary ) - ch_versions = ch_versions.mix(ANNOTATION.out.versions) + ch_versions = ch_versions.mix(INTERSECT_ANNOTATION.out.versions) // // FASTA WORKFLOW: From cfee6c77ba1195203f5e8749f71a6151820c0ca2 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 1 Feb 2024 12:42:23 +0100 Subject: [PATCH 134/491] Implement handling of intergenic circRNAs --- .../local/annotation/full_annotation/main.nf | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/modules/local/annotation/full_annotation/main.nf b/modules/local/annotation/full_annotation/main.nf index da50da22..22c16b21 100644 --- a/modules/local/annotation/full_annotation/main.nf +++ b/modules/local/annotation/full_annotation/main.nf @@ -39,8 +39,17 @@ process ANNOTATION { df = pd.read_csv("${intersection}", sep="\\t", header=None, usecols=columns.keys()) df = df.rename(columns=columns) + + # Extract circRNAs without match + mask = df['tx_start'] == -1 + df_nomatch = df[mask] + df = df[~mask] + df_nomatch['type'] = 'intergenic-circRNA' + df_nomatch['gene_id'] = 'NaN' + df_nomatch['transcript_id'] = 'NaN' + # Convert attributes to a dictionary - df['attributes'] = df['attributes'].apply(lambda row: dict([[value.strip(r'\\"') for value in entry.strip().split(' ')] for entry in row.split(';') if entry])) + df['attributes'] = df['attributes'].apply(lambda row: dict([[value.strip(r'"') for value in entry.strip().split(' ')] for entry in row.split(';') if entry])) # Keep only the attributes we want df['attributes'] = df['attributes'].apply(lambda row: {key: row[key] for key in attributes}) # Convert attributes to columns @@ -73,10 +82,16 @@ process ANNOTATION { # Drop perfect df = df.drop(['perfect'], axis=1) - df = df.sort_index() df = df.reset_index() + df_nomatch = df_nomatch.reset_index() bed_order = ['chr', 'start', 'end', 'name', 'score', 'strand', 'type', 'gene_id', 'transcript_id'] df = df[bed_order] + df_nomatch = df_nomatch[bed_order] + + df = pd.concat([df, df_nomatch], axis=0) + + # Sort by chr, start, end + df = df.sort_values(['chr', 'start', 'end']) df.to_csv('${meta.id}.annotation.bed', sep='\\t', index=False, header=False) """ From 3e5f72a726c4de3ffea5ad495c6c1d3dbc8196b2 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 1 Feb 2024 13:06:21 +0100 Subject: [PATCH 135/491] Fix linting problems --- modules/local/annotation/full_annotation/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/local/annotation/full_annotation/main.nf b/modules/local/annotation/full_annotation/main.nf index 22c16b21..8cde37dd 100644 --- a/modules/local/annotation/full_annotation/main.nf +++ b/modules/local/annotation/full_annotation/main.nf @@ -10,10 +10,10 @@ process ANNOTATION { input: tuple val(meta), path(intersection) val(exon_boundary) - + output: tuple val(meta), path("${meta.id}.annotation.bed"), emit: bed - + script: """ #!/usr/bin/env python @@ -95,4 +95,4 @@ process ANNOTATION { df.to_csv('${meta.id}.annotation.bed', sep='\\t', index=False, header=False) """ -} \ No newline at end of file +} From 740d17aa3d0bd990a3a9cfc0106d06e7bf564a25 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Feb 2024 19:18:47 +0100 Subject: [PATCH 136/491] Implement handling of "gene" rows in annotation --- .../local/annotation/full_annotation/main.nf | 32 ++++++++++++------- 1 file changed, 21 insertions(+), 11 deletions(-) diff --git a/modules/local/annotation/full_annotation/main.nf b/modules/local/annotation/full_annotation/main.nf index 8cde37dd..e44af433 100644 --- a/modules/local/annotation/full_annotation/main.nf +++ b/modules/local/annotation/full_annotation/main.nf @@ -19,7 +19,7 @@ process ANNOTATION { #!/usr/bin/env python import pandas as pd - import os + import numpy as np columns = { 0: 'chr', @@ -42,16 +42,16 @@ process ANNOTATION { # Extract circRNAs without match mask = df['tx_start'] == -1 - df_nomatch = df[mask] + df_intergenic = df[mask] df = df[~mask] - df_nomatch['type'] = 'intergenic-circRNA' - df_nomatch['gene_id'] = 'NaN' - df_nomatch['transcript_id'] = 'NaN' + df_intergenic['type'] = 'intergenic-circRNA' + df_intergenic['gene_id'] = 'NaN' + df_intergenic['transcript_id'] = 'NaN' # Convert attributes to a dictionary df['attributes'] = df['attributes'].apply(lambda row: dict([[value.strip(r'"') for value in entry.strip().split(' ')] for entry in row.split(';') if entry])) # Keep only the attributes we want - df['attributes'] = df['attributes'].apply(lambda row: {key: row[key] for key in attributes}) + df['attributes'] = df['attributes'].apply(lambda row: {key: row[key] for key in attributes if key in row}) # Convert attributes to columns df = pd.concat([df.drop(['attributes'], axis=1), df['attributes'].apply(pd.Series)], axis=1) @@ -74,21 +74,31 @@ process ANNOTATION { matching_values = [value for value, perfectness in zip(row[col], row['perfect']) if perfectness] else: matching_values = row[col] - return ",".join(set(matching_values)) + valid_values = set([value for value in matching_values if type(value) == str]) + return ",".join(valid_values) if valid_values else "NaN" - df['type'] = df['perfect'].apply(lambda x: 'circRNA' if any(x) else 'EI-circRNA') + def determine_type(row): + if row["no_transcript"]: + return "ciRNA" + if any(row['perfect']): + return "circRNA" + else: + return 'EI-circRNA' + + df['no_transcript'] = df['transcript_id'].apply(lambda x: all([type(value) != str and np.isnan(value) for value in x])) + df['type'] = df.apply(lambda row: determine_type(row), axis=1) df['gene_id'] = df.apply(lambda row: filter_perfect(row, 'gene_id'), axis=1) df['transcript_id'] = df.apply(lambda row: filter_perfect(row, 'transcript_id'), axis=1) # Drop perfect df = df.drop(['perfect'], axis=1) df = df.reset_index() - df_nomatch = df_nomatch.reset_index() + df_intergenic = df_intergenic.reset_index() bed_order = ['chr', 'start', 'end', 'name', 'score', 'strand', 'type', 'gene_id', 'transcript_id'] df = df[bed_order] - df_nomatch = df_nomatch[bed_order] + df_intergenic = df_intergenic[bed_order] - df = pd.concat([df, df_nomatch], axis=0) + df = pd.concat([df, df_intergenic], axis=0) # Sort by chr, start, end df = df.sort_values(['chr', 'start', 'end']) From 686e40fabeea6ba005029ac1d1bff7a6e26fef46 Mon Sep 17 00:00:00 2001 From: Nico Trummer <52698566+nictru@users.noreply.github.com> Date: Wed, 28 Feb 2024 19:47:31 +0100 Subject: [PATCH 137/491] Remove quay.io prefix from container definition Co-authored-by: Maxime U Garcia --- modules/local/annotation/full_annotation/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/annotation/full_annotation/main.nf b/modules/local/annotation/full_annotation/main.nf index e44af433..bfa58786 100644 --- a/modules/local/annotation/full_annotation/main.nf +++ b/modules/local/annotation/full_annotation/main.nf @@ -5,7 +5,7 @@ process ANNOTATION { conda "bioconda::pandas=1.5.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : - 'quay.io/biocontainers/pandas:1.5.2' }" + 'biocontainers/pandas:1.5.2' }" input: tuple val(meta), path(intersection) From 49f47ca2f9369a921a7961248d087682ed04491d Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Wed, 28 Feb 2024 20:19:54 +0100 Subject: [PATCH 138/491] Implement capture of versions in annotation --- bin/annotation.py | 97 +++++++++++++++++++ .../local/annotation/full_annotation/main.nf | 97 ++----------------- subworkflows/local/circrna_discovery.nf | 1 + 3 files changed, 107 insertions(+), 88 deletions(-) create mode 100755 bin/annotation.py diff --git a/bin/annotation.py b/bin/annotation.py new file mode 100755 index 00000000..2d5992ff --- /dev/null +++ b/bin/annotation.py @@ -0,0 +1,97 @@ +#!/usr/bin/env python + +import pandas as pd +import numpy as np +import argparse + +parser = argparse.ArgumentParser(description='Annotate circRNAs') +parser.add_argument('--input', type=str, help='Path to the input file') +parser.add_argument('--exon_boundary', type=int, help='Exon boundary') +parser.add_argument('--output', type=str, help='Path to the output file') + +args = parser.parse_args() + + +columns = { + 0: 'chr', + 1: 'start', + 2: 'end', + 3: 'name', + 4: 'score', + 5: 'strand', + 9: 'tx_start', + 10: 'tx_end', + 14: 'attributes' +} + +attributes = ['gene_id', 'transcript_id'] + +exon_boundary = args.exon_boundary + +df = pd.read_csv(args.input, sep="\\t", header=None, usecols=columns.keys()) +df = df.rename(columns=columns) + +# Extract circRNAs without match +mask = df['tx_start'] == -1 +df_intergenic = df[mask] +df = df[~mask] +df_intergenic['type'] = 'intergenic-circRNA' +df_intergenic['gene_id'] = 'NaN' +df_intergenic['transcript_id'] = 'NaN' + +# Convert attributes to a dictionary +df['attributes'] = df['attributes'].apply(lambda row: dict([[value.strip(r'"') for value in entry.strip().split(' ')] for entry in row.split(';') if entry])) +# Keep only the attributes we want +df['attributes'] = df['attributes'].apply(lambda row: {key: row[key] for key in attributes if key in row}) +# Convert attributes to columns +df = pd.concat([df.drop(['attributes'], axis=1), df['attributes'].apply(pd.Series)], axis=1) + +df['any_outside'] = (df['start'] < df['tx_start'] - exon_boundary) | (df['end'] > df['tx_end'] + exon_boundary) +# Perfect is inverse of any_outside +df['perfect'] = ~df['any_outside'] +# Drop any_outside +df = df.drop(['any_outside', 'tx_start', 'tx_end'], axis=1) + +df = df.groupby(['chr', 'start', 'end', 'strand']).aggregate({ + 'name': lambda x: x.iloc[0], + 'score': lambda x: x.iloc[0], + 'gene_id': lambda x: list(x), + 'transcript_id': lambda x: list(x), + 'perfect': lambda x: list(x) +}) + +def filter_perfect(row, col): + if any(row['perfect']): + matching_values = [value for value, perfectness in zip(row[col], row['perfect']) if perfectness] + else: + matching_values = row[col] + valid_values = set([value for value in matching_values if type(value) == str]) + return ",".join(valid_values) if valid_values else "NaN" + +def determine_type(row): + if row["no_transcript"]: + return "ciRNA" + if any(row['perfect']): + return "circRNA" + else: + return 'EI-circRNA' + +df['no_transcript'] = df['transcript_id'].apply(lambda x: all([type(value) != str and np.isnan(value) for value in x])) +df['type'] = df.apply(lambda row: determine_type(row), axis=1) +df['gene_id'] = df.apply(lambda row: filter_perfect(row, 'gene_id'), axis=1) +df['transcript_id'] = df.apply(lambda row: filter_perfect(row, 'transcript_id'), axis=1) +# Drop perfect +df = df.drop(['perfect'], axis=1) + +df = df.reset_index() +df_intergenic = df_intergenic.reset_index() +bed_order = ['chr', 'start', 'end', 'name', 'score', 'strand', 'type', 'gene_id', 'transcript_id'] +df = df[bed_order] +df_intergenic = df_intergenic[bed_order] + +df = pd.concat([df, df_intergenic], axis=0) + +# Sort by chr, start, end +df = df.sort_values(['chr', 'start', 'end']) + +df.to_csv(args.output, sep='\\t', index=False, header=False) \ No newline at end of file diff --git a/modules/local/annotation/full_annotation/main.nf b/modules/local/annotation/full_annotation/main.nf index bfa58786..1df42646 100644 --- a/modules/local/annotation/full_annotation/main.nf +++ b/modules/local/annotation/full_annotation/main.nf @@ -13,96 +13,17 @@ process ANNOTATION { output: tuple val(meta), path("${meta.id}.annotation.bed"), emit: bed + path "versions.yml", emit: versions script: """ - #!/usr/bin/env python - - import pandas as pd - import numpy as np - - columns = { - 0: 'chr', - 1: 'start', - 2: 'end', - 3: 'name', - 4: 'score', - 5: 'strand', - 9: 'tx_start', - 10: 'tx_end', - 14: 'attributes' - } - - attributes = ['gene_id', 'transcript_id'] - - exon_boundary = ${exon_boundary} - - df = pd.read_csv("${intersection}", sep="\\t", header=None, usecols=columns.keys()) - df = df.rename(columns=columns) - - # Extract circRNAs without match - mask = df['tx_start'] == -1 - df_intergenic = df[mask] - df = df[~mask] - df_intergenic['type'] = 'intergenic-circRNA' - df_intergenic['gene_id'] = 'NaN' - df_intergenic['transcript_id'] = 'NaN' - - # Convert attributes to a dictionary - df['attributes'] = df['attributes'].apply(lambda row: dict([[value.strip(r'"') for value in entry.strip().split(' ')] for entry in row.split(';') if entry])) - # Keep only the attributes we want - df['attributes'] = df['attributes'].apply(lambda row: {key: row[key] for key in attributes if key in row}) - # Convert attributes to columns - df = pd.concat([df.drop(['attributes'], axis=1), df['attributes'].apply(pd.Series)], axis=1) - - df['any_outside'] = (df['start'] < df['tx_start'] - exon_boundary) | (df['end'] > df['tx_end'] + exon_boundary) - # Perfect is inverse of any_outside - df['perfect'] = ~df['any_outside'] - # Drop any_outside - df = df.drop(['any_outside', 'tx_start', 'tx_end'], axis=1) - - df = df.groupby(['chr', 'start', 'end', 'strand']).aggregate({ - 'name': lambda x: x.iloc[0], - 'score': lambda x: x.iloc[0], - 'gene_id': lambda x: list(x), - 'transcript_id': lambda x: list(x), - 'perfect': lambda x: list(x) - }) - - def filter_perfect(row, col): - if any(row['perfect']): - matching_values = [value for value, perfectness in zip(row[col], row['perfect']) if perfectness] - else: - matching_values = row[col] - valid_values = set([value for value in matching_values if type(value) == str]) - return ",".join(valid_values) if valid_values else "NaN" - - def determine_type(row): - if row["no_transcript"]: - return "ciRNA" - if any(row['perfect']): - return "circRNA" - else: - return 'EI-circRNA' - - df['no_transcript'] = df['transcript_id'].apply(lambda x: all([type(value) != str and np.isnan(value) for value in x])) - df['type'] = df.apply(lambda row: determine_type(row), axis=1) - df['gene_id'] = df.apply(lambda row: filter_perfect(row, 'gene_id'), axis=1) - df['transcript_id'] = df.apply(lambda row: filter_perfect(row, 'transcript_id'), axis=1) - # Drop perfect - df = df.drop(['perfect'], axis=1) - - df = df.reset_index() - df_intergenic = df_intergenic.reset_index() - bed_order = ['chr', 'start', 'end', 'name', 'score', 'strand', 'type', 'gene_id', 'transcript_id'] - df = df[bed_order] - df_intergenic = df_intergenic[bed_order] - - df = pd.concat([df, df_intergenic], axis=0) - - # Sort by chr, start, end - df = df.sort_values(['chr', 'start', 'end']) - - df.to_csv('${meta.id}.annotation.bed', sep='\\t', index=False, header=False) + ./annotation.py --input ${intersection} --exon_boundary ${exon_boundary} --output ${meta.id}.annotation.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //g') + pandas: \$(python -c "import pandas; print(pandas.__version__)") + numpy: \$(python -c "import numpy; print(numpy.__version__)") + END_VERSIONS """ } diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 1fef8419..90b60726 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -222,6 +222,7 @@ workflow CIRCRNA_DISCOVERY { ANNOTATION( INTERSECT_ANNOTATION.out.intersect, exon_boundary ) ch_versions = ch_versions.mix(INTERSECT_ANNOTATION.out.versions) + ch_versions = ch_versions.mix(ANNOTATION.out.versions) // // FASTA WORKFLOW: From fb6a1d95ef92624ef80f45066f2c3f0e34de90db Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 1 Mar 2024 12:31:05 +0100 Subject: [PATCH 139/491] Fix linting --- bin/annotation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/annotation.py b/bin/annotation.py index 2d5992ff..e88bda5c 100755 --- a/bin/annotation.py +++ b/bin/annotation.py @@ -94,4 +94,4 @@ def determine_type(row): # Sort by chr, start, end df = df.sort_values(['chr', 'start', 'end']) -df.to_csv(args.output, sep='\\t', index=False, header=False) \ No newline at end of file +df.to_csv(args.output, sep='\\t', index=False, header=False) From cf46f11bee9150c760dedd4823a4dc079dad48fd Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 1 Mar 2024 12:59:51 +0100 Subject: [PATCH 140/491] Fix problem with annotation.py script calling --- modules/local/annotation/full_annotation/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/annotation/full_annotation/main.nf b/modules/local/annotation/full_annotation/main.nf index 1df42646..f06546ac 100644 --- a/modules/local/annotation/full_annotation/main.nf +++ b/modules/local/annotation/full_annotation/main.nf @@ -17,7 +17,7 @@ process ANNOTATION { script: """ - ./annotation.py --input ${intersection} --exon_boundary ${exon_boundary} --output ${meta.id}.annotation.bed + annotation.py --input ${intersection} --exon_boundary ${exon_boundary} --output ${meta.id}.annotation.bed cat <<-END_VERSIONS > versions.yml "${task.process}": From 2de5b60ee5f8c6bab7f3ef7d8aa313ba5b66b3cc Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 1 Mar 2024 13:18:10 +0100 Subject: [PATCH 141/491] Fix problem with escape characters in dedicated python script --- bin/annotation.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/annotation.py b/bin/annotation.py index e88bda5c..ab9dc01d 100755 --- a/bin/annotation.py +++ b/bin/annotation.py @@ -28,7 +28,7 @@ exon_boundary = args.exon_boundary -df = pd.read_csv(args.input, sep="\\t", header=None, usecols=columns.keys()) +df = pd.read_csv(args.input, sep="\t", header=None, usecols=columns.keys()) df = df.rename(columns=columns) # Extract circRNAs without match @@ -94,4 +94,4 @@ def determine_type(row): # Sort by chr, start, end df = df.sort_values(['chr', 'start', 'end']) -df.to_csv(args.output, sep='\\t', index=False, header=False) +df.to_csv(args.output, sep='\t', index=False, header=False) From 82e1b2849346df5e67b06c4a94b6e6f367eeb455 Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Fri, 1 Mar 2024 17:48:01 +0100 Subject: [PATCH 142/491] add dumpsoftwareversions --- modules.json | 33 ------ .../dumpsoftwareversions/environment.yml | 7 ++ .../custom/dumpsoftwareversions/main.nf | 24 +++++ .../custom/dumpsoftwareversions/meta.yml | 37 +++++++ .../templates/dumpsoftwareversions.py | 101 ++++++++++++++++++ .../dumpsoftwareversions/tests/main.nf.test | 43 ++++++++ .../tests/main.nf.test.snap | 33 ++++++ .../dumpsoftwareversions/tests/tags.yml | 2 + 8 files changed, 247 insertions(+), 33 deletions(-) create mode 100644 modules/nf-core/custom/dumpsoftwareversions/environment.yml create mode 100644 modules/nf-core/custom/dumpsoftwareversions/main.nf create mode 100644 modules/nf-core/custom/dumpsoftwareversions/meta.yml create mode 100755 modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml diff --git a/modules.json b/modules.json index d82ffc55..9cfb49d2 100644 --- a/modules.json +++ b/modules.json @@ -167,39 +167,6 @@ } } }, - "subworkflows": { - "nf-core": { - "bam_sort_stats_samtools": { - "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": ["subworkflows"] - }, - "bam_stats_samtools": { - "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": ["bam_sort_stats_samtools"] - } - } - }, - "subworkflows": { - "nf-core": { - "utils_nextflow_pipeline": { - "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", - "installed_by": ["subworkflows"] - }, - "utils_nfcore_pipeline": { - "branch": "master", - "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8", - "installed_by": ["subworkflows"] - }, - "utils_nfvalidation_plugin": { - "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", - "installed_by": ["subworkflows"] - } - } - }, "subworkflows": { "nf-core": { "utils_nextflow_pipeline": { diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml new file mode 100644 index 00000000..9b3272bc --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -0,0 +1,7 @@ +name: custom_dumpsoftwareversions +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.19 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf new file mode 100644 index 00000000..f2187611 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -0,0 +1,24 @@ +process CUSTOM_DUMPSOFTWAREVERSIONS { + label 'process_single' + + // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : + 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" + + input: + path versions + + output: + path "software_versions.yml" , emit: yml + path "software_versions_mqc.yml", emit: mqc_yml + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + template 'dumpsoftwareversions.py' +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml new file mode 100644 index 00000000..5f15a5fd --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -0,0 +1,37 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: custom_dumpsoftwareversions +description: Custom module used to dump software versions within the nf-core pipeline template +keywords: + - custom + - dump + - version +tools: + - custom: + description: Custom module used to dump software versions within the nf-core pipeline template + homepage: https://github.com/nf-core/tools + documentation: https://github.com/nf-core/tools + licence: ["MIT"] +input: + - versions: + type: file + description: YML file containing software versions + pattern: "*.yml" +output: + - yml: + type: file + description: Standard YML file containing software versions + pattern: "software_versions.yml" + - mqc_yml: + type: file + description: MultiQC custom content YML file containing software versions + pattern: "software_versions_mqc.yml" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@drpatelh" + - "@grst" +maintainers: + - "@drpatelh" + - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py new file mode 100755 index 00000000..da033408 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -0,0 +1,101 @@ +#!/usr/bin/env python + + +"""Provide functions to merge multiple versions.yml files.""" + + +import yaml +import platform +from textwrap import dedent + + +def _make_versions_html(versions): + """Generate a tabular HTML output of all versions for MultiQC.""" + html = [ + dedent( + """\\ + +
    Process Name \\", - " \\ Software Version
    CUSTOM_DUMPSOFTWAREVERSIONSpython3.11.7
    yaml5.4.1
    TOOL1tool10.11.9
    TOOL2tool21.9
    WorkflowNextflow
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    + + + + + + + + """ + ) + ] + for process, tmp_versions in sorted(versions.items()): + html.append("") + for i, (tool, version) in enumerate(sorted(tmp_versions.items())): + html.append( + dedent( + f"""\\ + + + + + + """ + ) + ) + html.append("") + html.append("
    Process Name Software Version
    {process if (i == 0) else ''}{tool}{version}
    ") + return "\\n".join(html) + + +def main(): + """Load all version files and generate merged output.""" + versions_this_module = {} + versions_this_module["${task.process}"] = { + "python": platform.python_version(), + "yaml": yaml.__version__, + } + + with open("$versions") as f: + versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module + + # aggregate versions by the module name (derived from fully-qualified process name) + versions_by_module = {} + for process, process_versions in versions_by_process.items(): + module = process.split(":")[-1] + try: + if versions_by_module[module] != process_versions: + raise AssertionError( + "We assume that software versions are the same between all modules. " + "If you see this error-message it means you discovered an edge-case " + "and should open an issue in nf-core/tools. " + ) + except KeyError: + versions_by_module[module] = process_versions + + versions_by_module["Workflow"] = { + "Nextflow": "$workflow.nextflow.version", + "$workflow.manifest.name": "$workflow.manifest.version", + } + + versions_mqc = { + "id": "software_versions", + "section_name": "${workflow.manifest.name} Software Versions", + "section_href": "https://github.com/${workflow.manifest.name}", + "plot_type": "html", + "description": "are collected at run time from the software output.", + "data": _make_versions_html(versions_by_module), + } + + with open("software_versions.yml", "w") as f: + yaml.dump(versions_by_module, f, default_flow_style=False) + with open("software_versions_mqc.yml", "w") as f: + yaml.dump(versions_mqc, f, default_flow_style=False) + + with open("versions.yml", "w") as f: + yaml.dump(versions_this_module, f, default_flow_style=False) + + +if __name__ == "__main__": + main() diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test new file mode 100644 index 00000000..b1e1630b --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -0,0 +1,43 @@ +nextflow_process { + + name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" + script "../main.nf" + process "CUSTOM_DUMPSOFTWAREVERSIONS" + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "dumpsoftwareversions" + tag "custom/dumpsoftwareversions" + + test("Should run without failures") { + when { + process { + """ + def tool1_version = ''' + TOOL1: + tool1: 0.11.9 + '''.stripIndent() + + def tool2_version = ''' + TOOL2: + tool2: 1.9 + '''.stripIndent() + + input[0] = Channel.of(tool1_version, tool2_version).collectFile() + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.mqc_yml[0]).readLines()[0..10], + file(process.out.yml[0]).readLines()[0..7] + ).match() + } + ) + } + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap new file mode 100644 index 00000000..5f59a936 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -0,0 +1,33 @@ +{ + "Should run without failures": { + "content": [ + [ + "versions.yml:md5,76d454d92244589d32455833f7c1ba6d" + ], + [ + "data: \"\\n\\n \\n \\n \\n \\n \\n \\n \\n\\", + " \\n\\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n \\n \\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n\\n\\n \\n\\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\" + ], + [ + "CUSTOM_DUMPSOFTWAREVERSIONS:", + " python: 3.11.7", + " yaml: 5.4.1", + "TOOL1:", + " tool1: 0.11.9", + "TOOL2:", + " tool2: '1.9'", + "Workflow:" + ] + ], + "timestamp": "2024-01-09T23:01:18.710682" + } +} \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml new file mode 100644 index 00000000..405aa24a --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml @@ -0,0 +1,2 @@ +custom/dumpsoftwareversions: + - modules/nf-core/custom/dumpsoftwareversions/** From abd9aa7fc8005a412e3c16733a21fef64382b233 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sun, 3 Mar 2024 08:30:51 +0100 Subject: [PATCH 143/491] Fix script references --- modules/local/count_matrix/single/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/count_matrix/single/main.nf b/modules/local/count_matrix/single/main.nf index 856ffa7e..20e1b975 100644 --- a/modules/local/count_matrix/single/main.nf +++ b/modules/local/count_matrix/single/main.nf @@ -29,12 +29,12 @@ process COUNTS_SINGLE { mv \$b \${sample_name}.bed done - python ${workflow.projectDir}/bin/circRNA_counts_matrix.py > matrix.txt + circRNA_counts_matrix.py > matrix.txt ## handle non-canon chromosomes here (https://stackoverflow.com/questions/71479919/joining-columns-based-on-number-of-fields) n_samps=\$(ls *.bed | wc -l) canon=\$(awk -v a="\$n_samps" 'BEGIN {print a + 4}') awk -v n="\$canon" '{ for (i = 2; i <= NF - n + 1; ++i) { \$1 = \$1"-"\$i; \$i=""; } } 1' matrix.txt | awk -v OFS="\\t" '\$1=\$1' > circRNA_matrix.txt - Rscript ${workflow.projectDir}/bin/reformat_count_matrix.R + reformat_count_matrix.R cat <<-END_VERSIONS > versions.yml "${task.process}": From 5a68987e2ae64d226963d0a6faf14c81d70efeba Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 18 Mar 2024 08:58:54 +0100 Subject: [PATCH 144/491] Improve channel structure --- main.nf | 11 +++++- modules/local/targetscan/database/main.nf | 6 +-- modules/local/targetscan/predict/main.nf | 2 +- subworkflows/local/circrna_discovery.nf | 29 +++++++------- subworkflows/local/differential_expression.nf | 17 +++----- subworkflows/local/prepare_genome.nf | 39 +++++++------------ workflows/circrna/main.nf | 24 +++++------- 7 files changed, 56 insertions(+), 72 deletions(-) diff --git a/main.nf b/main.nf index 9cf725ef..1e202b27 100644 --- a/main.nf +++ b/main.nf @@ -55,9 +55,18 @@ workflow NFCORE_CIRCRNA { // // WORKFLOW: Run nf-core/circrna workflow // - ch_samplesheet = Channel.value(file(params.input, checkIfExists: true)) + ch_samplesheet = Channel.fromSamplesheet("input") + ch_phenotype = Channel.value([[id: "phenotype"], file(params.phenotype, checkIfExists:true)]) + ch_fasta = Channel.value([[id: "fasta"], file(params.fasta, checkIfExists:true)]) + ch_gtf = Channel.value([[id: "gtf"], file(params.gtf, checkIfExists:true)]) + ch_mature = Channel.value([[id: "mature"], file(params.mature, checkIfExists:true)]) + CIRCRNA ( ch_samplesheet, + ch_phenotype, + ch_fasta, + ch_gtf, + ch_mature, ch_versions ) diff --git a/modules/local/targetscan/database/main.nf b/modules/local/targetscan/database/main.nf index 44e54e40..8ba3ef71 100644 --- a/modules/local/targetscan/database/main.nf +++ b/modules/local/targetscan/database/main.nf @@ -1,5 +1,5 @@ process TARGETSCAN_DATABASE { - tag "$mature" + tag "$meta.id" label 'process_low' conda "conda-forge::sed=4.7" @@ -8,10 +8,10 @@ process TARGETSCAN_DATABASE { 'nf-core/ubuntu:20.04' }" input: - path(mature) + tuple val(meta), path(mature) output: - path("mature.txt") , emit: mature_txt + tuple val(meta), path("mature.txt") , emit: mature_txt path "versions.yml" , emit: versions when: diff --git a/modules/local/targetscan/predict/main.nf b/modules/local/targetscan/predict/main.nf index e8e5567f..12d3511e 100644 --- a/modules/local/targetscan/predict/main.nf +++ b/modules/local/targetscan/predict/main.nf @@ -9,7 +9,7 @@ process TARGETSCAN { input: tuple val(meta), path(fasta) - path(mature_txt) + tuple val(meta2), path(mature_txt) output: tuple val(meta), path("${prefix}.txt"), emit: txt diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 90b60726..a0a20433 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -45,8 +45,8 @@ workflow CIRCRNA_DISCOVERY { take: reads - fasta - gtf + ch_fasta + ch_gtf bowtie_index bowtie2_index bwa_index @@ -61,11 +61,8 @@ workflow CIRCRNA_DISCOVERY { main: ch_versions = Channel.empty() - ch_fasta = Channel.value(fasta) - ch_gtf = Channel.value(gtf) - fasta_tuple = Channel.value([[id: "fasta"], fasta]) - gtf_tuple = Channel.value([[id: "gtf"], gtf]) - + fasta = ch_fasta.map{meta, fasta -> fasta} + gtf = ch_gtf.map{meta, gtf -> gtf} // // SEGEMEHL WORKFLOW: @@ -86,10 +83,10 @@ workflow CIRCRNA_DISCOVERY { seq_center = params.seq_center ?: '' seq_platform = '' - STAR_1ST_PASS( reads, star_index.first(), gtf_tuple, star_ignore_sjdbgtf, seq_platform, seq_center) + STAR_1ST_PASS( reads, star_index, ch_gtf, star_ignore_sjdbgtf, seq_platform, seq_center) sjdb = STAR_1ST_PASS.out.tab.map{ meta, tab -> return tab }.collect().map{[[id: "star_sjdb"], it]} STAR_SJDB( sjdb, bsj_reads ) - STAR_2ND_PASS( reads, star_index.first(), STAR_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) + STAR_2ND_PASS( reads, star_index, STAR_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) ch_versions = ch_versions.mix(STAR_1ST_PASS.out.versions) ch_versions = ch_versions.mix(STAR_2ND_PASS.out.versions) @@ -125,7 +122,7 @@ workflow CIRCRNA_DISCOVERY { FIND_CIRC_ALIGN( reads, bowtie2_index.collect(), false, true ) SAMTOOLS_INDEX( FIND_CIRC_ALIGN.out.aligned ) - SAMTOOLS_VIEW( FIND_CIRC_ALIGN.out.aligned.join( SAMTOOLS_INDEX.out.bai ), fasta_tuple, [] ) + SAMTOOLS_VIEW( FIND_CIRC_ALIGN.out.aligned.join( SAMTOOLS_INDEX.out.bai ), ch_fasta, [] ) FIND_CIRC_ANCHORS( SAMTOOLS_VIEW.out.bam ) FIND_CIRC( FIND_CIRC_ANCHORS.out.anchors, bowtie2_index.collect(), fasta ) find_circ_filter = FIND_CIRC.out.bed.map{ meta, bed -> [ meta + [tool: "find_circ"], bed ] } @@ -156,14 +153,14 @@ workflow CIRCRNA_DISCOVERY { // mate1 = reads.filter{ meta, reads -> !meta.single_end }.map{ meta, reads -> return [ [id: meta.id, single_end: true], reads[0] ] } - DCC_MATE1_1ST_PASS( mate1, star_index.first(), gtf_tuple, star_ignore_sjdbgtf, seq_platform, seq_center ) + DCC_MATE1_1ST_PASS( mate1, star_index, ch_gtf, star_ignore_sjdbgtf, seq_platform, seq_center ) DCC_MATE1_SJDB( DCC_MATE1_1ST_PASS.out.tab.map{ meta, tab -> return tab }.collect().map{[[id: "mate1_sjdb"], it]}, bsj_reads ) - DCC_MATE1_2ND_PASS( mate1, star_index.first(), DCC_MATE1_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) + DCC_MATE1_2ND_PASS( mate1, star_index, DCC_MATE1_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) mate2 = reads.filter{ meta, reads -> !meta.single_end }.map{ meta, reads -> return [ [id: meta.id, single_end: true], reads[1] ] } - DCC_MATE2_1ST_PASS( mate2, star_index.first(), gtf_tuple, star_ignore_sjdbgtf, seq_platform, seq_center ) + DCC_MATE2_1ST_PASS( mate2, star_index, ch_gtf, star_ignore_sjdbgtf, seq_platform, seq_center ) DCC_MATE2_SJDB( DCC_MATE2_1ST_PASS.out.tab.map{ meta, tab -> return tab }.collect().map{[[id: "mate2_sjdb"], it]}, bsj_reads ) - DCC_MATE2_2ND_PASS( mate2, star_index.first(), DCC_MATE2_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) + DCC_MATE2_2ND_PASS( mate2, star_index, DCC_MATE2_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) dcc_stage = STAR_2ND_PASS.out.junction.map{ meta, junction -> return [ meta.id, meta, junction]} .join( @@ -194,7 +191,7 @@ workflow CIRCRNA_DISCOVERY { // MAPSPLICE_REFERENCE( gtf ) - MAPSPLICE_ALIGN( reads, bowtie_index.collect(), chromosomes, ch_gtf ) + MAPSPLICE_ALIGN( reads, bowtie_index.collect(), chromosomes, gtf ) MAPSPLICE_PARSE( MAPSPLICE_ALIGN.out.raw_fusions ) MAPSPLICE_ANNOTATE( MAPSPLICE_PARSE.out.junction, fasta, MAPSPLICE_REFERENCE.out.txt ) mapsplice_filter = MAPSPLICE_ANNOTATE.out.txt.map{ meta, txt -> [ meta + [tool: "mapsplice"], txt ] } @@ -218,7 +215,7 @@ workflow CIRCRNA_DISCOVERY { DCC_FILTER.out.results, MAPSPLICE_FILTER.out.results) - INTERSECT_ANNOTATION( circrna_filtered.combine(ch_gtf), [[], []]) + INTERSECT_ANNOTATION( circrna_filtered.combine(gtf), [[], []]) ANNOTATION( INTERSECT_ANNOTATION.out.intersect, exon_boundary ) ch_versions = ch_versions.mix(INTERSECT_ANNOTATION.out.versions) diff --git a/subworkflows/local/differential_expression.nf b/subworkflows/local/differential_expression.nf index 2964c3fb..f341fd3f 100644 --- a/subworkflows/local/differential_expression.nf +++ b/subworkflows/local/differential_expression.nf @@ -12,8 +12,8 @@ workflow DIFFERENTIAL_EXPRESSION { take: reads - gtf - fasta + ch_gtf + ch_fasta hisat2_index splice_sites phenotype @@ -25,22 +25,17 @@ workflow DIFFERENTIAL_EXPRESSION { main: ch_versions = Channel.empty() - qc_reports = Channel.empty() - ch_fasta = Channel.fromPath(fasta) - ch_gtf = Channel.fromPath(gtf) + qc_reports = Channel.empty() - ch_fasta.map{ it -> [ [id: it.simpleName], [it] ] - }.set{ fasta_tuple } - - ch_gtf.map{ it -> [ [id: it.simpleName], [it] ] - }.set{ gtf_tuple } + fasta = ch_fasta.map{ meta, fasta -> fasta } + gtf = ch_gtf.map{ meta, gtf -> gtf } // // LINEAR RNA ALIGNEMT WORKFLOW: // HISAT2_ALIGN( reads, hisat2_index, splice_sites ) - BAM_SORT_STATS_SAMTOOLS( HISAT2_ALIGN.out.bam, fasta_tuple ) + BAM_SORT_STATS_SAMTOOLS( HISAT2_ALIGN.out.bam, ch_fasta ) STRINGTIE_STRINGTIE( BAM_SORT_STATS_SAMTOOLS.out.bam, gtf ) STRINGTIE_PREPDE( STRINGTIE_STRINGTIE.out.transcript_gtf.map{ meta, gtf -> return [ gtf ] }.collect() ) diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 96045cfc..5d82d65d 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -11,8 +11,8 @@ include { GAWK as CLEAN_FASTA } from '../../modules/nf-core/gawk/main' workflow PREPARE_GENOME { take: - fasta - gtf + ch_fasta + ch_gtf main: ch_versions = Channel.empty() @@ -20,53 +20,40 @@ workflow PREPARE_GENOME { // MapSplice cannot deal with extra field in the fasta headers // this removes all additional fields in the headers of the input fasta file if( params.tool.contains('mapsplice') && params.module.contains('circrna_discovery') ) { - - CLEAN_FASTA(Channel.value([[id: "${fasta.baseName}" + ".clean_headers" ], fasta]), []) - - ch_fasta = CLEAN_FASTA.out.output.map{ it.last() } - } - - else { - - ch_fasta = Channel.fromPath(fasta) - + CLEAN_FASTA(ch_fasta, []) + ch_fasta = CLEAN_FASTA.out.output } - - ch_gtf = Channel.fromPath(gtf) - fasta_tuple = Channel.value([[id: "fasta"], fasta]) - gtf_tuple = Channel.value([[id: "gtf"], gtf]) - // MapSplice & find_circ requires reference genome to be split per chromosome: if( ( params.tool.contains('mapsplice') || params.tool.contains('find_circ') ) && params.module.contains('circrna_discovery') ){ directory = file("${params.outdir}/references/chromosomes") if ( !directory.exists() ) { directory.mkdirs() - ch_fasta.splitFasta( record: [id:true] ) + ch_fasta.map{meta, fasta -> fasta}.splitFasta( record: [id:true] ) .map{ record -> record.id.toString() } .set{ ID } - ch_fasta.splitFasta( file: true ) + ch_fasta.map{meta, fasta -> fasta}.splitFasta( file: true ) .merge( ID ).map{ file, id -> file.copyTo(directory + "/${id}.fa") } } stage_chromosomes = Channel.value(directory) } - BOWTIE_BUILD(ch_fasta) + BOWTIE_BUILD(ch_fasta.map{ meta, fasta -> fasta }) - BOWTIE2_BUILD(fasta_tuple) + BOWTIE2_BUILD(ch_fasta) - BWA_INDEX (fasta_tuple) + BWA_INDEX (ch_fasta) - HISAT2_EXTRACTSPLICESITES(gtf_tuple) + HISAT2_EXTRACTSPLICESITES(ch_gtf) - HISAT2_BUILD(fasta_tuple, gtf_tuple, HISAT2_EXTRACTSPLICESITES.out.txt) + HISAT2_BUILD(ch_fasta, ch_gtf, HISAT2_EXTRACTSPLICESITES.out.txt) - STAR_GENOMEGENERATE(fasta_tuple, gtf_tuple) + STAR_GENOMEGENERATE(ch_fasta, ch_gtf) - SEGEMEHL_INDEX(fasta) + SEGEMEHL_INDEX(ch_fasta.map{ meta, fasta -> fasta}) // TODO: Add support for meta // Collect versions ch_versions = ch_versions.mix(BOWTIE_BUILD.out.versions) diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 3e95f4ca..e51d850e 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -4,11 +4,6 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -ch_phenotype = params.phenotype && params.module.contains('differential_expression') ? file(params.phenotype, checkIfExists:true) : Channel.empty() -ch_fasta = params.fasta ? file(params.fasta) : 'null' -ch_gtf = params.gtf ? file(params.gtf) : 'null' -ch_mature = params.mature && params.module.contains('mirna_prediction') ? file(params.mature) : Channel.empty() - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CONFIG FILES @@ -58,6 +53,10 @@ include { FASTQC_TRIMGALORE } from '../../subworkflows/nf-core/fastqc_trimgalore workflow CIRCRNA { take: ch_samplesheet + ch_phenotype + ch_fasta + ch_gtf + ch_mature ch_versions main: @@ -69,8 +68,7 @@ workflow CIRCRNA { // // SUBWORKFLOW: - Channel - .fromSamplesheet("input") + ch_samplesheet .map { meta, fastq_1, fastq_2 -> if (!fastq_2) { @@ -98,13 +96,11 @@ workflow CIRCRNA { // MODULE: // Concatenate FastQ files from same sample if required - CAT_FASTQ ( - ch_fastq.multiple - ) - .reads - .mix(ch_fastq.single) - .set { ch_cat_fastq } - ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null)) + CAT_FASTQ (ch_fastq.multiple) + .reads + .mix(ch_fastq.single) + .set { ch_cat_fastq } + ch_versions = ch_versions.mix(CAT_FASTQ.out.versions) // SUBORKFLOW: // Prepare index files &/or use iGenomes if chosen. From 0a782bea722662ecfced07254c1e82eeb37e8d7e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 18 Mar 2024 09:23:14 +0100 Subject: [PATCH 145/491] Implement seqkit_split --- conf/modules.config | 10 ++++++ modules/local/seqkit/split/environment.yml | 7 +++++ modules/local/seqkit/split/main.nf | 36 ++++++++++++++++++++++ subworkflows/local/prepare_genome.nf | 21 ++----------- 4 files changed, 56 insertions(+), 18 deletions(-) create mode 100644 modules/local/seqkit/split/environment.yml create mode 100644 modules/local/seqkit/split/main.nf diff --git a/conf/modules.config b/conf/modules.config index 65671920..8c1f48bd 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -78,6 +78,16 @@ if (!params.skip_trimming) { ] } + withName: SEQKIT_SPLIT { + ext.args = "-i" + publishDir = [ + path: { "${params.outdir}/references/chromosomes" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + enabled: params.save_reference + ] + } + withName: BOWTIE_BUILD { ext.when = { params.fasta && !params.bowtie && params.tool.split(',').contains('mapsplice') && params.module.split(',').contains('circrna_discovery') } publishDir = [ diff --git a/modules/local/seqkit/split/environment.yml b/modules/local/seqkit/split/environment.yml new file mode 100644 index 00000000..6eaa568f --- /dev/null +++ b/modules/local/seqkit/split/environment.yml @@ -0,0 +1,7 @@ +name: seqkit_split +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::seqkit=2.1.0 \ No newline at end of file diff --git a/modules/local/seqkit/split/main.nf b/modules/local/seqkit/split/main.nf new file mode 100644 index 00000000..c1be1899 --- /dev/null +++ b/modules/local/seqkit/split/main.nf @@ -0,0 +1,36 @@ +process SEQKIT_SPLIT { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0' : + 'biocontainers/seqkit:2.1.0--h9ee0642_0' }" + + input: + tuple val(meta), path(fasta) + + output: + tuple val(meta), path("${prefix}/*"), emit: split + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + """ + seqkit \\ + split \\ + $args \\ + --threads $task.cpus \\ + $fasta \\ + --out-dir ${prefix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + seqkit: \$(echo \$(seqkit 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS + """ +} \ No newline at end of file diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 5d82d65d..b27e226d 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -1,4 +1,4 @@ - +include { SEQKIT_SPLIT } from '../../modules/local/seqkit/split/main' include { BOWTIE_BUILD } from '../../modules/nf-core/bowtie/build/main' include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build/main' include { BWA_INDEX } from '../../modules/nf-core/bwa/index/main' @@ -24,22 +24,7 @@ workflow PREPARE_GENOME { ch_fasta = CLEAN_FASTA.out.output } - // MapSplice & find_circ requires reference genome to be split per chromosome: - if( ( params.tool.contains('mapsplice') || params.tool.contains('find_circ') ) && params.module.contains('circrna_discovery') ){ - directory = file("${params.outdir}/references/chromosomes") - - if ( !directory.exists() ) { - directory.mkdirs() - ch_fasta.map{meta, fasta -> fasta}.splitFasta( record: [id:true] ) - .map{ record -> record.id.toString() } - .set{ ID } - - ch_fasta.map{meta, fasta -> fasta}.splitFasta( file: true ) - .merge( ID ).map{ file, id -> file.copyTo(directory + "/${id}.fa") } - } - - stage_chromosomes = Channel.value(directory) - } + SEQKIT_SPLIT(ch_fasta) BOWTIE_BUILD(ch_fasta.map{ meta, fasta -> fasta }) @@ -68,7 +53,7 @@ workflow PREPARE_GENOME { bowtie = BOWTIE_BUILD.out.index bowtie2 = BOWTIE2_BUILD.out.index bwa = BWA_INDEX.out.index - chromosomes = ( params.tool.contains('mapsplice') || params.tool.contains('find_circ') ) ? stage_chromosomes : 'null' + chromosomes = SEQKIT_SPLIT.out.split hisat2 = HISAT2_BUILD.out.index.collect() star = STAR_GENOMEGENERATE.out.index.collect() segemehl = SEGEMEHL_INDEX.out.index From 09642064ad1520eb0ba4885faaefb39278f7c78f Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 18 Mar 2024 09:41:52 +0100 Subject: [PATCH 146/491] Update seqkit version --- conf/modules.config | 2 +- modules/local/mapsplice/align/main.nf | 8 ++++---- modules/local/seqkit/split/environment.yml | 2 +- modules/local/seqkit/split/main.nf | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 8c1f48bd..a6ccdf5c 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -79,7 +79,7 @@ if (!params.skip_trimming) { } withName: SEQKIT_SPLIT { - ext.args = "-i" + ext.args = "-i --by-id-prefix \"\"" publishDir = [ path: { "${params.outdir}/references/chromosomes" }, mode: params.publish_dir_mode, diff --git a/modules/local/mapsplice/align/main.nf b/modules/local/mapsplice/align/main.nf index b62e4db2..7dcbbbd3 100644 --- a/modules/local/mapsplice/align/main.nf +++ b/modules/local/mapsplice/align/main.nf @@ -10,7 +10,7 @@ process MAPSPLICE_ALIGN { input: tuple val(meta), path(reads) path bowtie_index - path chromosomes + tuple val(meta2), path(chromosomes, stageAs: 'chromosomes/*') path gtf output: @@ -32,7 +32,7 @@ process MAPSPLICE_ALIGN { $handleGzip_R1 mapsplice.py \\ - -c $chromosomes \\ + -c chromosomes \\ -x $gtf_prefix \\ -1 ${read1} \\ -p ${task.cpus} \\ @@ -46,7 +46,7 @@ process MAPSPLICE_ALIGN { mapsplice: $VERSION END_VERSIONS """ - }else{ + } else { def handleGzip_R1 = reads[0].getExtension() == 'gz' ? "gzip -d -f ${reads[0]}" : '' def handleGzip_R2 = reads[1].getExtension() == 'gz' ? "gzip -d -f ${reads[1]}" : '' def read1 = reads[0].getExtension() == 'gz' ? reads[0].toString() - ~/.gz/ : reads[0] @@ -56,7 +56,7 @@ process MAPSPLICE_ALIGN { $handleGzip_R2 mapsplice.py \\ - -c $chromosomes \\ + -c chromosomes \\ -x $gtf_prefix \\ -1 ${read1} \\ -2 ${read2} \\ diff --git a/modules/local/seqkit/split/environment.yml b/modules/local/seqkit/split/environment.yml index 6eaa568f..fb5b8b63 100644 --- a/modules/local/seqkit/split/environment.yml +++ b/modules/local/seqkit/split/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::seqkit=2.1.0 \ No newline at end of file + - bioconda::seqkit=2.8.0 \ No newline at end of file diff --git a/modules/local/seqkit/split/main.nf b/modules/local/seqkit/split/main.nf index c1be1899..5d70f47b 100644 --- a/modules/local/seqkit/split/main.nf +++ b/modules/local/seqkit/split/main.nf @@ -4,8 +4,8 @@ process SEQKIT_SPLIT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0' : - 'biocontainers/seqkit:2.1.0--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/seqkit:2.8.0--h9ee0642_0' : + 'biocontainers/seqkit:2.8.0--h9ee0642_0' }" input: tuple val(meta), path(fasta) From c4a3e8e62224c236f73da02c6e836867e0bd1fc7 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 18 Mar 2024 10:04:22 +0100 Subject: [PATCH 147/491] Update modules --- modules.json | 52 +- modules/nf-core/bedtools/intersect/meta.yml | 4 +- modules/nf-core/bedtools/sort/meta.yml | 4 +- modules/nf-core/bwa/index/tests/main.nf.test | 4 +- modules/nf-core/cat/cat/main.nf | 11 +- modules/nf-core/cat/cat/tests/main.nf.test | 23 +- modules/nf-core/cat/fastq/environment.yml | 2 +- modules/nf-core/cat/fastq/main.nf | 1 - modules/nf-core/cat/fastq/tests/main.nf.test | 63 ++- .../nf-core/cat/fastq/tests/main.nf.test.snap | 185 +++++-- .../dumpsoftwareversions/environment.yml | 2 +- .../custom/dumpsoftwareversions/main.nf | 4 +- .../nf-core/hisat2/align/tests/main.nf.test | 144 +++--- .../nf-core/hisat2/build/tests/main.nf.test | 29 +- .../extractsplicesites/tests/main.nf.test | 14 +- .../tests/main.nf.test.snap | 29 +- .../nf-core/samtools/flagstat/environment.yml | 3 +- modules/nf-core/samtools/flagstat/main.nf | 4 +- .../samtools/flagstat/tests/main.nf.test | 12 +- .../samtools/flagstat/tests/main.nf.test.snap | 20 +- .../nf-core/samtools/idxstats/environment.yml | 3 +- modules/nf-core/samtools/idxstats/main.nf | 4 +- .../samtools/idxstats/tests/main.nf.test | 14 +- .../samtools/idxstats/tests/main.nf.test.snap | 20 +- .../nf-core/samtools/index/environment.yml | 3 +- modules/nf-core/samtools/index/main.nf | 4 +- .../nf-core/samtools/index/tests/main.nf.test | 36 +- .../samtools/index/tests/main.nf.test.snap | 54 +- modules/nf-core/samtools/sort/environment.yml | 3 +- modules/nf-core/samtools/sort/main.nf | 32 +- modules/nf-core/samtools/sort/meta.yml | 32 +- .../nf-core/samtools/sort/tests/main.nf.test | 71 ++- .../samtools/sort/tests/main.nf.test.snap | 128 ++++- .../samtools/sort/tests/nextflow.config | 3 +- .../nf-core/samtools/stats/environment.yml | 3 +- modules/nf-core/samtools/stats/main.nf | 4 +- .../nf-core/samtools/stats/tests/main.nf.test | 53 +- .../samtools/stats/tests/main.nf.test.snap | 32 +- modules/nf-core/samtools/view/environment.yml | 3 +- modules/nf-core/samtools/view/main.nf | 4 +- .../nf-core/samtools/view/tests/main.nf.test | 193 ++++---- .../samtools/view/tests/main.nf.test.snap | 466 +++++++++++++++--- modules/nf-core/star/align/environment.yml | 1 + modules/nf-core/star/align/tests/main.nf.test | 141 ++---- .../star/genomegenerate/environment.yml | 3 +- .../star/genomegenerate/tests/main.nf.test | 40 +- .../genomegenerate/tests/main.nf.test.snap | 80 ++- .../stringtie/stringtie/tests/main.nf.test | 64 +-- .../stringtie/stringtie/tests/nextflow.config | 5 + modules/nf-core/trimgalore/environment.yml | 3 + modules/nf-core/trimgalore/tests/main.nf.test | 20 +- .../trimgalore/tests/main.nf.test.snap | 154 +----- .../nf-core/bam_sort_stats_samtools/main.nf | 2 +- .../tests/main.nf.test | 28 +- .../tests/main.nf.test.snap | 36 +- 55 files changed, 1461 insertions(+), 891 deletions(-) create mode 100644 modules/nf-core/stringtie/stringtie/tests/nextflow.config diff --git a/modules.json b/modules.json index 9cfb49d2..c7beb988 100644 --- a/modules.json +++ b/modules.json @@ -7,12 +7,12 @@ "nf-core": { "bedtools/intersect": { "branch": "master", - "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", + "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", "installed_by": ["modules"] }, "bedtools/sort": { "branch": "master", - "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", + "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", "installed_by": ["modules"] }, "bowtie/align": { @@ -37,17 +37,17 @@ }, "bwa/index": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "6278bf9afd4a4b2d00fa6052250e73da3d91546f", "installed_by": ["modules"] }, "cat/cat": { "branch": "master", - "git_sha": "d593e8f6b7d1bbbb2acf43a4b9efeeac8d6720f2", + "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8", "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", - "git_sha": "e8940f18cfbbdcdcde38f4b3633df5ed4e48da10", + "git_sha": "0997b47c93c06b49aa7b3fefda87e728312cf2ca", "installed_by": ["modules"] }, "circexplorer2/annotate": { @@ -67,12 +67,12 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", + "git_sha": "de45447d060b8c8b98575bc637a4a575fd0638e1", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "617777a807a1770f73deb38c80004bac06807eef", + "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c", "installed_by": ["modules"] }, "gawk": { @@ -82,22 +82,22 @@ }, "hisat2/align": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", "installed_by": ["modules"] }, "hisat2/build": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", "installed_by": ["modules"] }, "hisat2/extractsplicesites": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", "installed_by": ["modules"] }, "miranda": { "branch": "master", - "git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "multiqc": { @@ -107,32 +107,32 @@ }, "samtools/flagstat": { "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": ["bam_stats_samtools"] }, "samtools/idxstats": { "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": ["bam_sort_stats_samtools", "modules"] }, "samtools/sort": { "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", + "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", "installed_by": ["bam_sort_stats_samtools", "modules"] }, "samtools/stats": { "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": ["bam_stats_samtools"] }, "samtools/view": { "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", + "git_sha": "0bd7d2333a88483aa0476acea172e9f5f6dd83bb", "installed_by": ["modules"] }, "segemehl/align": { @@ -147,28 +147,38 @@ }, "star/align": { "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", + "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", "installed_by": ["modules"] }, "star/genomegenerate": { "branch": "master", - "git_sha": "d87a6e2156c2099c09280fa70776eaf0a824817a", + "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", "installed_by": ["modules"] }, "stringtie/stringtie": { "branch": "master", - "git_sha": "b0dcb44b018d9b2bcb35b1abb7bcd34061bc5a6d", + "git_sha": "b1b959609bda44341120aed1766329909f54b8d0", "installed_by": ["modules"] }, "trimgalore": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "a98418419ae6c9df3cf6cf108d1e1aba71037d5a", "installed_by": ["modules"] } } }, "subworkflows": { "nf-core": { + "bam_sort_stats_samtools": { + "branch": "master", + "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", + "installed_by": ["subworkflows"] + }, + "bam_stats_samtools": { + "branch": "master", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "installed_by": ["bam_sort_stats_samtools", "subworkflows"] + }, "utils_nextflow_pipeline": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", diff --git a/modules/nf-core/bedtools/intersect/meta.yml b/modules/nf-core/bedtools/intersect/meta.yml index 8d9a08aa..0939cb54 100644 --- a/modules/nf-core/bedtools/intersect/meta.yml +++ b/modules/nf-core/bedtools/intersect/meta.yml @@ -48,12 +48,12 @@ output: description: File containing software versions pattern: "versions.yml" authors: - - "@Emiller88" + - "@edmundmiller" - "@sruthipsuresh" - "@drpatelh" - "@sidorov-si" maintainers: - - "@Emiller88" + - "@edmundmiller" - "@sruthipsuresh" - "@drpatelh" - "@sidorov-si" diff --git a/modules/nf-core/bedtools/sort/meta.yml b/modules/nf-core/bedtools/sort/meta.yml index 9ad70b11..7c915f5f 100644 --- a/modules/nf-core/bedtools/sort/meta.yml +++ b/modules/nf-core/bedtools/sort/meta.yml @@ -41,13 +41,13 @@ output: description: File containing software versions pattern: "versions.yml" authors: - - "@Emiller88" + - "@edmundmiller" - "@sruthipsuresh" - "@drpatelh" - "@chris-cheshire" - "@adamrtalbot" maintainers: - - "@Emiller88" + - "@edmundmiller" - "@sruthipsuresh" - "@drpatelh" - "@chris-cheshire" diff --git a/modules/nf-core/bwa/index/tests/main.nf.test b/modules/nf-core/bwa/index/tests/main.nf.test index 5fc8d496..af33e73c 100644 --- a/modules/nf-core/bwa/index/tests/main.nf.test +++ b/modules/nf-core/bwa/index/tests/main.nf.test @@ -15,7 +15,7 @@ nextflow_process { """ input[0] = [ [id: 'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -29,5 +29,5 @@ nextflow_process { } } - + } diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index 970ab760..adbdbd7b 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -22,6 +22,8 @@ process CAT_CAT { def args2 = task.ext.args2 ?: '' def file_list = files_in.collect { it.toString() } + // choose appropriate concatenation tool depending on input and output format + // | input | output | command1 | command2 | // |-----------|------------|----------|----------| // | gzipped | gzipped | cat | | @@ -30,7 +32,7 @@ process CAT_CAT { // | ungzipped | gzipped | cat | pigz | // Use input file ending as default - prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}" + prefix = task.ext.prefix ?: "${meta.id}${getFileSuffix(file_list[0])}" out_zip = prefix.endsWith('.gz') in_zip = file_list[0].endsWith('.gz') command1 = (in_zip && !out_zip) ? 'zcat' : 'cat' @@ -68,3 +70,10 @@ process CAT_CAT { END_VERSIONS """ } + +// for .gz files also include the second to last extension if it is present. E.g., .fasta.gz +def getFileSuffix(filename) { + def match = filename =~ /^.*?((\.\w{1,5})?(\.\w{1,5}\.gz$))/ + return match ? match[0][1] : filename.substring(filename.lastIndexOf('.')) +} + diff --git a/modules/nf-core/cat/cat/tests/main.nf.test b/modules/nf-core/cat/cat/tests/main.nf.test index ed5a4f12..fcee2d19 100644 --- a/modules/nf-core/cat/cat/tests/main.nf.test +++ b/modules/nf-core/cat/cat/tests/main.nf.test @@ -19,8 +19,8 @@ nextflow_process { [ [ id:'genome', single_end:true ], [ - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) ] ] """ @@ -45,8 +45,8 @@ nextflow_process { [ [ id:'test', single_end:true ], [ - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) ] ] """ @@ -72,8 +72,8 @@ nextflow_process { [ [ id:'test', single_end:true ], [ - file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) ] ] """ @@ -102,8 +102,8 @@ nextflow_process { [ [ id:'test', single_end:true ], [ - file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) ] ] """ @@ -131,8 +131,8 @@ nextflow_process { [ [ id:'test', single_end:true ], [ - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) ] ] """ @@ -160,7 +160,7 @@ nextflow_process { [ [ id:'test', single_end:true ], [ - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] ] """ @@ -176,4 +176,3 @@ nextflow_process { } } } - diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index bff93add..8c69b121 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - conda-forge::sed=4.7 + - conda-forge::coreutils=8.30 diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 3d963784..f132b2ad 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -76,5 +76,4 @@ process CAT_FASTQ { """ } } - } diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test index f5f94182..dab2e14c 100644 --- a/modules/nf-core/cat/fastq/tests/main.nf.test +++ b/modules/nf-core/cat/fastq/tests/main.nf.test @@ -16,11 +16,11 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test', single_end:true ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true) ] - ] + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) """ } } @@ -28,8 +28,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.reads).match() }, - { assert path(process.out.versions.get(0)).getText().contains("cat") } + { assert snapshot(process.out).match() } ) } } @@ -42,13 +41,13 @@ nextflow_process { } process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) ] - ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)] + ]) """ } } @@ -56,8 +55,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.reads).match() }, - { assert path(process.out.versions.get(0)).getText().contains("cat") } + { assert snapshot(process.out).match() } ) } } @@ -70,11 +68,11 @@ nextflow_process { } process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] - ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) """ } } @@ -82,8 +80,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.reads).match() }, - { assert path(process.out.versions.get(0)).getText().contains("cat") } + { assert snapshot(process.out).match() } ) } } @@ -96,13 +93,13 @@ nextflow_process { } process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] - ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) """ } } @@ -110,8 +107,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.reads).match() }, - { assert path(process.out.versions.get(0)).getText().contains("cat") } + { assert snapshot(process.out).match() } ) } } @@ -124,10 +120,10 @@ nextflow_process { } process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)] - ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) """ } } @@ -135,8 +131,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.reads).match() }, - { assert path(process.out.versions.get(0)).getText().contains("cat") } + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test.snap b/modules/nf-core/cat/fastq/tests/main.nf.test.snap index 7f44e3e0..43dfe28f 100644 --- a/modules/nf-core/cat/fastq/tests/main.nf.test.snap +++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap @@ -1,78 +1,169 @@ { "test_cat_fastq_single_end": { "content": [ - [ - [ - { - "id": "test", - "single_end": true - }, - "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22" + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" ] - ] + } ], - "timestamp": "2024-01-12T14:02:54.278243" + "timestamp": "2024-01-17T17:30:39.816981" }, "test_cat_fastq_single_end_same_name": { "content": [ - [ - [ - { - "id": "test", - "single_end": true - }, - "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22" + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" ] - ] + } ], - "timestamp": "2024-01-12T14:03:01.765432" + "timestamp": "2024-01-17T17:32:35.229332" }, "test_cat_fastq_single_end_single_file": { "content": [ - [ - [ - { - "id": "test", - "single_end": true - }, - "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" ] - ] + } ], - "timestamp": "2024-01-12T14:03:08.858654" + "timestamp": "2024-01-17T17:34:00.058829" }, "test_cat_fastq_paired_end_same_name": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, + { + "0": [ [ - "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", - "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" ] - ] + } ], - "timestamp": "2024-01-12T14:03:05.494631" + "timestamp": "2024-01-17T17:33:33.031555" }, "test_cat_fastq_paired_end": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ [ - "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", - "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" ] - ] + } ], - "timestamp": "2024-01-12T14:02:58.35062" + "timestamp": "2024-01-17T17:32:02.270935" } } \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml index 9b3272bc..b48ced26 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.19 + - bioconda::multiqc=1.20 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index f2187611..105f9265 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -4,8 +4,8 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : - 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_0' : + 'biocontainers/multiqc:1.20--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/hisat2/align/tests/main.nf.test b/modules/nf-core/hisat2/align/tests/main.nf.test index 79e137c9..3a520e9a 100644 --- a/modules/nf-core/hisat2/align/tests/main.nf.test +++ b/modules/nf-core/hisat2/align/tests/main.nf.test @@ -7,6 +7,8 @@ nextflow_process { tag "modules_nfcore" tag "hisat2" tag "hisat2/align" + tag "hisat2/build" + tag "hisat2/extractsplicesites" test("Single-End") { @@ -15,26 +17,28 @@ nextflow_process { script "../../extractsplicesites/main.nf" process { """ - input[0] = [ [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) - ] + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ]) """ - } + } } run("HISAT2_BUILD") { script "../../build/main.nf" process { """ - input[0] = [ [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - input[1] = [ [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) - ] + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[1] = Channel.of([ [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ]) input[2] = HISAT2_EXTRACTSPLICESITES.out.txt """ - } + } } } @@ -44,12 +48,10 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test', single_end:true ], // meta map - [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ] - ] + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) input[1] = HISAT2_BUILD.out.index input[2] = HISAT2_EXTRACTSPLICESITES.out.txt """ @@ -58,10 +60,10 @@ nextflow_process { then { assertAll( - { assert process.success }, - { assert snapshot(process.out.summary).match("se_summary") }, - { assert snapshot(process.out.fastq).match("se_fastq") }, - { assert snapshot(process.out.versions).match("se_versions") } + { assert process.success }, + { assert snapshot(process.out.summary).match("se_summary") }, + { assert snapshot(process.out.fastq).match("se_fastq") }, + { assert snapshot(process.out.versions).match("se_versions") } ) } } @@ -73,26 +75,28 @@ nextflow_process { script "../../extractsplicesites/main.nf" process { """ - input[0] = [ [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) - ] + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ]) """ - } + } } run("HISAT2_BUILD") { script "../../build/main.nf" process { """ - input[0] = [ [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - input[1] = [ [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) - ] + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[1] = Channel.of([ [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ]) input[2] = HISAT2_EXTRACTSPLICESITES.out.txt """ - } + } } } @@ -102,13 +106,11 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) - ] - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) input[1] = HISAT2_BUILD.out.index input[2] = HISAT2_EXTRACTSPLICESITES.out.txt """ @@ -117,10 +119,10 @@ nextflow_process { then { assertAll( - { assert process.success }, - { assert snapshot(process.out.summary).match("pe_summary") }, - { assert snapshot(process.out.fastq).match("pe_fastq") }, - { assert snapshot(process.out.versions).match("pe_versions") } + { assert process.success }, + { assert snapshot(process.out.summary).match("pe_summary") }, + { assert snapshot(process.out.fastq).match("pe_fastq") }, + { assert snapshot(process.out.versions).match("pe_versions") } ) } } @@ -132,13 +134,14 @@ nextflow_process { script "../../build/main.nf" process { """ - input[0] = [ [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) input[1] = [[:],[]] input[2] = [[:],[]] """ - } + } } } @@ -148,12 +151,10 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test', single_end:true ], // meta map - [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ] - ] + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + ]) input[1] = HISAT2_BUILD.out.index input[2] = [[:],[]] """ @@ -162,10 +163,10 @@ nextflow_process { then { assertAll( - { assert process.success }, - { assert snapshot(process.out.summary).match("se_no_ss_summary") }, - { assert snapshot(process.out.fastq).match("se_no_ss_fastq") }, - { assert snapshot(process.out.versions).match("se_no_ss_versions") } + { assert process.success }, + { assert snapshot(process.out.summary).match("se_no_ss_summary") }, + { assert snapshot(process.out.fastq).match("se_no_ss_fastq") }, + { assert snapshot(process.out.versions).match("se_no_ss_versions") } ) } } @@ -177,13 +178,14 @@ nextflow_process { script "../../build/main.nf" process { """ - input[0] = [ [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) input[1] = [[:],[]] input[2] = [[:],[]] """ - } + } } } @@ -193,13 +195,11 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) - ] - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) input[1] = HISAT2_BUILD.out.index input[2] = [[:],[]] """ @@ -208,10 +208,10 @@ nextflow_process { then { assertAll( - { assert process.success }, - { assert snapshot(process.out.summary).match("pe_no_ss_summary") }, - { assert snapshot(process.out.fastq).match("pe_no_ss_fastq") }, - { assert snapshot(process.out.versions).match("pe_no_ss_versions") } + { assert process.success }, + { assert snapshot(process.out.summary).match("pe_no_ss_summary") }, + { assert snapshot(process.out.fastq).match("pe_no_ss_fastq") }, + { assert snapshot(process.out.versions).match("pe_no_ss_versions") } ) } } diff --git a/modules/nf-core/hisat2/build/tests/main.nf.test b/modules/nf-core/hisat2/build/tests/main.nf.test index c5fc1763..5b31debc 100644 --- a/modules/nf-core/hisat2/build/tests/main.nf.test +++ b/modules/nf-core/hisat2/build/tests/main.nf.test @@ -7,6 +7,7 @@ nextflow_process { tag "modules_nfcore" tag "hisat2" tag "hisat2/build" + tag "hisat2/extractsplicesites" test("Should run without failures") { @@ -15,11 +16,12 @@ nextflow_process { script "../../extractsplicesites/main.nf" process { """ - input[0] = [ [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) - ] + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ]) """ - } + } } } @@ -29,12 +31,13 @@ nextflow_process { } process { """ - input[0] = [ [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - input[1] = [ [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) - ] + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[1] = Channel.of([ [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ]) input[2] = HISAT2_EXTRACTSPLICESITES.out.txt """ } @@ -42,11 +45,9 @@ nextflow_process { then { assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert process.success }, + { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test b/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test index a7a22e9b..72eb6d53 100644 --- a/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test +++ b/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test @@ -16,20 +16,20 @@ nextflow_process { } process { """ - input[0] = [ [id:'test'], - file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) - ] + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ]) """ } } then { assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert process.success }, + { assert path("${process.out.txt[0][1]}").exists() }, + { assert snapshot(process.out.versions).match() } ) } - } - } diff --git a/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test.snap b/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test.snap index 3cef6905..17f1c8eb 100644 --- a/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test.snap +++ b/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test.snap @@ -1,31 +1,10 @@ { "Should run without failures": { "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "genome.splice_sites.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - "versions.yml:md5,eeea7231fe197810659b8bad4133aff2" - ], - "txt": [ - [ - { - "id": "test" - }, - "genome.splice_sites.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,eeea7231fe197810659b8bad4133aff2" - ] - } + [ + "versions.yml:md5,eeea7231fe197810659b8bad4133aff2" + ] ], - "timestamp": "2023-10-16T14:25:01.248332036" + "timestamp": "2024-01-18T20:56:30.71763" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index 5efae053..bd57cb54 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -4,4 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.18 + - bioconda::samtools=1.19.2 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index f1893d7c..eb5f5252 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FLAGSTAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : - 'biocontainers/samtools:1.18--h50ea8bc_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : + 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test b/modules/nf-core/samtools/flagstat/tests/main.nf.test index c8dd8dc9..24c3c04b 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test @@ -16,11 +16,11 @@ nextflow_process { } process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) - ] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) """ } } @@ -28,8 +28,8 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.flagstat).match() }, - { assert path(process.out.versions.get(0)).getText().contains("samtools") } + { assert snapshot(process.out.flagstat).match("flagstat") }, + { assert snapshot(process.out.versions).match("versions") } ) } } diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap index 880019f2..a76fc27e 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "BAM": { + "flagstat": { "content": [ [ [ @@ -11,6 +11,22 @@ ] ] ], - "timestamp": "2023-11-14T15:49:22.577133" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:31:37.783927" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,fd0030ce49ab3a92091ad80260226452" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:11:44.299617452" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index 2401db0f..174973b8 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -4,4 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.18 + - bioconda::samtools=1.19.2 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index 00d916bb..a544026f 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_IDXSTATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : - 'biocontainers/samtools:1.18--h50ea8bc_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : + 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test b/modules/nf-core/samtools/idxstats/tests/main.nf.test index f6c92150..a2dcb27c 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test @@ -8,7 +8,7 @@ nextflow_process { tag "samtools" tag "samtools/idxstats" - test("BAM") { + test("bam") { when { params { @@ -16,11 +16,11 @@ nextflow_process { } process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) - ] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) """ } } @@ -28,8 +28,8 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.idxstats).match() }, - { assert path(process.out.versions.get(0)).getText().contains("samtools") } + { assert snapshot(process.out.idxstats).match("idxstats") }, + { assert snapshot(process.out.versions).match("versions") } ) } } diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap index 4c6c12bd..a7050bdc 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap @@ -1,5 +1,17 @@ { - "BAM": { + "versions": { + "content": [ + [ + "versions.yml:md5,613dde56f108418039ffcdeeddba397a" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:16:50.147462763" + }, + "idxstats": { "content": [ [ [ @@ -11,6 +23,10 @@ ] ] ], - "timestamp": "2023-11-14T15:52:19.875194" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:36:41.561026" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 296ed99e..a5e50649 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -4,4 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.18 + - bioconda::samtools=1.19.2 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 8ad18fdc..dc14f98d 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : - 'biocontainers/samtools:1.18--h50ea8bc_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : + 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test index c76a9169..bb7756d1 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -8,7 +8,7 @@ nextflow_process { tag "samtools" tag "samtools/index" - test("sarscov2 [BAI]") { + test("bai") { when { params { @@ -16,10 +16,10 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) """ } } @@ -28,12 +28,12 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot(process.out.bai).match("bai") }, - { assert path(process.out.versions.get(0)).getText().contains("samtools") } + { assert snapshot(process.out.versions).match("bai_versions") } ) } } - test("homo_sapiens [CRAI]") { + test("crai") { when { params { @@ -41,10 +41,10 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true) - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true) + ]) """ } } @@ -53,12 +53,12 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot(process.out.crai).match("crai") }, - { assert path(process.out.versions.get(0)).getText().contains("samtools") } + { assert snapshot(process.out.versions).match("crai_versions") } ) } } - test("homo_sapiens [CSI]") { + test("csi") { config "./csi.nextflow.config" @@ -68,10 +68,10 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) """ } } @@ -80,7 +80,7 @@ nextflow_process { assertAll ( { assert process.success }, { assert path(process.out.csi.get(0).get(1)).exists() }, - { assert path(process.out.versions.get(0)).getText().contains("samtools") } + { assert snapshot(process.out.versions).match("csi_versions") } ) } } diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index b3baee7f..3dc8e7de 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -1,28 +1,74 @@ { + "crai_versions": { + "content": [ + [ + "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:12:00.324667957" + }, + "csi_versions": { + "content": [ + [ + "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:12:07.885103162" + }, "crai": { "content": [ [ [ { - "id": "test" + "id": "test", + "single_end": false }, "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" ] ] ], - "timestamp": "2023-11-15T15:17:37.30801" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:41:38.446424" }, "bai": { "content": [ [ [ { - "id": "test" + "id": "test", + "single_end": false }, "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" ] ] ], - "timestamp": "2023-11-15T15:17:30.869234" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:40:46.579747" + }, + "bai_versions": { + "content": [ + [ + "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:11:51.641425452" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index cd50868c..4d898e48 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -4,4 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.18 + - bioconda::samtools=1.19.2 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 4a666d42..fc374f98 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -4,15 +4,18 @@ process SAMTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : - 'biocontainers/samtools:1.18--h50ea8bc_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : + 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" input: - tuple val(meta), path(bam) + tuple val(meta) , path(bam) + tuple val(meta2), path(fasta) output: - tuple val(meta), path("*.bam"), emit: bam - tuple val(meta), path("*.csi"), emit: csi, optional: true + tuple val(meta), path("*.bam"), emit: bam, optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true + tuple val(meta), path("*.crai"), emit: crai, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true path "versions.yml" , emit: versions when: @@ -21,14 +24,24 @@ process SAMTOOLS_SORT { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + def extension = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt cram") ? "cram" : + "bam" + def reference = fasta ? "--reference ${fasta}" : "" if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + samtools cat \\ + --threads $task.cpus \\ + ${bam} \\ + | \\ samtools sort \\ $args \\ - -@ $task.cpus \\ - -o ${prefix}.bam \\ - -T $prefix \\ - $bam + -T ${prefix} \\ + --threads $task.cpus \\ + ${reference} \\ + -o ${prefix}.${extension} \\ + - cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -40,6 +53,7 @@ process SAMTOOLS_SORT { def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.bam + touch ${prefix}.bam.csi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml index 2200de72..341a7d0e 100644 --- a/modules/nf-core/samtools/sort/meta.yml +++ b/modules/nf-core/samtools/sort/meta.yml @@ -23,8 +23,18 @@ input: e.g. [ id:'test', single_end:false ] - bam: type: file - description: BAM/CRAM/SAM file + description: BAM/CRAM/SAM file(s) pattern: "*.{bam,cram,sam}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta,fna}" + optional: true output: - meta: type: map @@ -33,19 +43,29 @@ output: e.g. [ id:'test', single_end:false ] - bam: type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - versions: + description: Sorted BAM file + pattern: "*.{bam}" + - cram: type: file - description: File containing software versions - pattern: "versions.yml" + description: Sorted CRAM file + pattern: "*.{cram}" + - crai: + type: file + description: CRAM index file (optional) + pattern: "*.crai" - csi: type: file description: BAM index file (optional) pattern: "*.csi" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" + - "@matthdsm" maintainers: - "@drpatelh" - "@ewels" + - "@matthdsm" diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index abb80978..8360e2b1 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -8,22 +8,21 @@ nextflow_process { tag "samtools" tag "samtools/sort" - test("test_samtools_sort") { + test("bam") { config "./nextflow.config" when { - params { - outdir = "$outputDir" - } process { """ - input[0] = [ - [ id:'test', single_end:false ], - [ - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) """ } } @@ -34,13 +33,39 @@ nextflow_process { { assert snapshot(process.out).match() } ) } + } + + test("cram") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } } - test("test_samtools_sort_stub") { + test("bam_stub") { config "./nextflow.config" - options "-stub-run" + options "-stub" when { params { @@ -48,12 +73,14 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test', single_end:false ], - [ - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) """ } } @@ -61,13 +88,9 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot( - file(process.out.bam[0][1]).name, - process.out.versions - ).match() } + { assert snapshot(file(process.out.bam[0][1]).name).match("bam_stub_bam") }, + { assert snapshot(process.out.versions).match("bam_stub_versions") } ) } - } - } diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index ff722259..38477656 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "test_samtools_sort": { + "cram": { "content": [ { "0": [ @@ -8,14 +8,26 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,ea6a0fef94eb534e901f107a05a33a06" + "test.sorted.bam:md5,bc0b7c25da26384a006ed84cc9e4da23" ] ], "1": [ ], "2": [ - "versions.yml:md5,33b6a403dc19a0d28e4219ccab0a1d80" + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,8d4e836c2fed6c0bf874d5e8cdba5831" + ] + ], + "4": [ + "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" ], "bam": [ [ @@ -23,26 +35,120 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,ea6a0fef94eb534e901f107a05a33a06" + "test.sorted.bam:md5,bc0b7c25da26384a006ed84cc9e4da23" ] ], - "csi": [ + "crai": [ + + ], + "cram": [ + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,8d4e836c2fed6c0bf874d5e8cdba5831" + ] ], "versions": [ - "versions.yml:md5,33b6a403dc19a0d28e4219ccab0a1d80" + "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" ] } ], - "timestamp": "2023-12-04T11:11:22.005628301" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-04T15:08:00.830294" + }, + "bam_stub_bam": { + "content": [ + "test.sorted.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:21:04.364044" }, - "test_samtools_sort_stub": { + "bam_stub_versions": { "content": [ - "test.sorted.bam", [ - "versions.yml:md5,33b6a403dc19a0d28e4219ccab0a1d80" + "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" ] ], - "timestamp": "2023-12-04T17:47:22.314445935" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:15:00.20800281" + }, + "bam": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,bc0b7c25da26384a006ed84cc9e4da23" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,8d4e836c2fed6c0bf874d5e8cdba5831" + ] + ], + "4": [ + "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,bc0b7c25da26384a006ed84cc9e4da23" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,8d4e836c2fed6c0bf874d5e8cdba5831" + ] + ], + "versions": [ + "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-04T15:07:48.773803" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/tests/nextflow.config b/modules/nf-core/samtools/sort/tests/nextflow.config index d0f35086..f642771f 100644 --- a/modules/nf-core/samtools/sort/tests/nextflow.config +++ b/modules/nf-core/samtools/sort/tests/nextflow.config @@ -1,7 +1,8 @@ process { withName: SAMTOOLS_SORT { - ext.prefix = { "${meta.id}.sorted" } + ext.prefix = { "${meta.id}.sorted" } + ext.args = "--write-index" } } diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index b89ce647..67bb0ca4 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -4,4 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.18 + - bioconda::samtools=1.19.2 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 7539140a..52b00f4b 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_STATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : - 'biocontainers/samtools:1.18--h50ea8bc_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : + 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test b/modules/nf-core/samtools/stats/tests/main.nf.test index 20c3efe1..e3d5cb14 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test +++ b/modules/nf-core/samtools/stats/tests/main.nf.test @@ -8,71 +8,58 @@ nextflow_process { tag "samtools" tag "samtools/stats" - test("SAMTOOLS STATS Should run without failures") { + test("bam") { when { params { - outdir = "$outputDir" } process { """ - // define inputs of the process here. - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) - - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) input[1] = [[],[]] """ - } } then { assertAll( - {assert process.success}, - {assert snapshot(process.out).match()} + {assert process.success}, + {assert snapshot(process.out).match()} ) } - } - test("SAMTOOLS CRAM Should run without failures") { + test("cram") { when { params { - outdir = "$outputDir" } process { """ - // define inputs of the process here - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true) - - ] - input[1] = [ - [ id:'genome' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) """ } - - } then { assertAll( - {assert process.success}, - {assert snapshot(process.out).match()} + {assert process.success}, + {assert snapshot(process.out).match()} ) } - } - - } diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap index 025c83a5..1b7c9ba4 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "SAMTOOLS STATS Should run without failures": { + "cram": { "content": [ { "0": [ @@ -8,11 +8,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,045a48208b1c6f5b8af4347fe31f4def" + "test.stats:md5,01812900aa4027532906c5d431114233" ] ], "1": [ - "versions.yml:md5,650a365c6635001436008350ae83337c" + "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9" ], "stats": [ [ @@ -20,17 +20,21 @@ "id": "test", "single_end": false }, - "test.stats:md5,045a48208b1c6f5b8af4347fe31f4def" + "test.stats:md5,01812900aa4027532906c5d431114233" ] ], "versions": [ - "versions.yml:md5,650a365c6635001436008350ae83337c" + "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9" ] } ], - "timestamp": "2023-12-04T11:07:28.26821485" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:15:25.562429714" }, - "SAMTOOLS CRAM Should run without failures": { + "bam": { "content": [ { "0": [ @@ -39,11 +43,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,dfbfa130d4a6925ddd1931dcd8354a43" + "test.stats:md5,5d8681bf541199898c042bf400391d59" ] ], "1": [ - "versions.yml:md5,650a365c6635001436008350ae83337c" + "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9" ], "stats": [ [ @@ -51,14 +55,18 @@ "id": "test", "single_end": false }, - "test.stats:md5,dfbfa130d4a6925ddd1931dcd8354a43" + "test.stats:md5,5d8681bf541199898c042bf400391d59" ] ], "versions": [ - "versions.yml:md5,650a365c6635001436008350ae83337c" + "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9" ] } ], - "timestamp": "2023-12-04T11:07:50.356233402" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:15:07.857611509" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml index 99aa69d0..b0676f33 100644 --- a/modules/nf-core/samtools/view/environment.yml +++ b/modules/nf-core/samtools/view/environment.yml @@ -4,4 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.18 + - bioconda::samtools=1.19.2 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index 0b5a2912..5a8989d6 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_VIEW { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : - 'biocontainers/samtools:1.18--h50ea8bc_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : + 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/samtools/view/tests/main.nf.test b/modules/nf-core/samtools/view/tests/main.nf.test index 89ed3555..45a0defb 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test +++ b/modules/nf-core/samtools/view/tests/main.nf.test @@ -9,16 +9,16 @@ nextflow_process { tag "samtools" tag "samtools/view" - test("sarscov2 - [bam, []], [], []") { + test("bam") { when { process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), [] - ] + ]) input[1] = [[],[]] input[2] = [] """ @@ -28,34 +28,31 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.bam[0][1]).name, - process.out.cram, - process.out.sam, - process.out.bai, - process.out.crai, - process.out.csi, - process.out.versions - ).match() } + { assert snapshot(file(process.out.bam[0][1]).name).match("bam_bam") }, + { assert snapshot(process.out.bai).match("bam_bai") }, + { assert snapshot(process.out.crai).match("bam_crai") }, + { assert snapshot(process.out.cram).match("bam_cram") }, + { assert snapshot(process.out.csi).match("bam_csi") }, + { assert snapshot(process.out.sam).match("bam_sam") }, + { assert snapshot(process.out.versions).match("bam_versions") } ) } - } - test("homo_sapiens - [cram, crai], fasta, []") { + test("cram") { when { process { """ - input[0] = [ - [ id: 'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) - ] - input[1] = [ - [ id:'genome' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) input[2] = [] """ } @@ -64,36 +61,33 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.cram[0][1]).name, - process.out.bam, - process.out.sam, - process.out.bai, - process.out.crai, - process.out.csi, - process.out.versions - ).match() } + { assert snapshot(file(process.out.cram[0][1]).name).match("cram_cram") }, + { assert snapshot(process.out.bai).match("cram_bai") }, + { assert snapshot(process.out.bam).match("cram_bam") }, + { assert snapshot(process.out.crai).match("cram_crai") }, + { assert snapshot(process.out.csi).match("cram_csi") }, + { assert snapshot(process.out.sam).match("cram_sam") }, + { assert snapshot(process.out.versions).match("cram_versions") } ) } - } - test("homo_sapiens - [cram, []], fasta, [] - bam output") { + test("cram_to_bam") { config "./bam.config" when { process { """ - input[0] = [ - [ id: 'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), [] - ] - input[1] = [ - [ id:'genome' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - ] + ]) + input[1] = Channel.of([ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) input[2] = [] """ } @@ -102,36 +96,33 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.bam[0][1]).name, - process.out.cram, - process.out.sam, - process.out.bai, - process.out.crai, - process.out.csi, - process.out.versions - ).match() } + { assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_bam") }, + { assert snapshot(process.out.bai).match("cram_to_bam_bai") }, + { assert snapshot(process.out.crai).match("cram_to_bam_crai") }, + { assert snapshot(process.out.cram).match("cram_to_bam_cram") }, + { assert snapshot(process.out.csi).match("cram_to_bam_csi") }, + { assert snapshot(process.out.sam).match("cram_to_bam_sam") }, + { assert snapshot(process.out.versions).match("cram_to_bam_versions") } ) } - } - test("homo_sapiens - [cram, []], fasta, [] - bam & index output") { + test("cram_to_bam_index") { config "./bam_index.config" when { process { """ - input[0] = [ - [ id: 'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), [] - ] - input[1] = [ - [ id:'genome' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - ] + ]) + input[1] = Channel.of([ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) input[2] = [] """ } @@ -140,36 +131,33 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.bam[0][1]).name, - process.out.cram, - process.out.sam, - file(process.out.csi[0][1]).name, - process.out.crai, - process.out.bai, - process.out.versions - ).match() } + { assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_index_bam") }, + { assert snapshot(file(process.out.csi[0][1]).name).match("cram_to_bam_index_csi") }, + { assert snapshot(process.out.bai).match("cram_to_bam_index_bai") }, + { assert snapshot(process.out.crai).match("cram_to_bam_index_crai") }, + { assert snapshot(process.out.cram).match("cram_to_bam_index_cram") }, + { assert snapshot(process.out.sam).match("cram_to_bam_index_sam") }, + { assert snapshot(process.out.versions).match("cram_to_bam_index_versions") } ) } - } - test("homo_sapiens - [cram, []], fasta, qname - bam & index output") { + test("cram_to_bam_index_qname") { config "./bam_index.config" when { process { """ - input[0] = [ - [ id: 'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), [] - ] - input[1] = [ - [ id:'genome' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - ] + ]) + input[1] = Channel.of([ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) input[2] = Channel.of("testN:2817", "testN:2814").collectFile(name: "readnames.list", newLine: true) """ } @@ -178,21 +166,18 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.bam[0][1]).name, - process.out.cram, - process.out.sam, - file(process.out.csi[0][1]).name, - process.out.crai, - process.out.bai, - process.out.versions - ).match() } + { assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_index_qname_bam") }, + { assert snapshot(file(process.out.csi[0][1]).name).match("cram_to_bam_index_qname_csi") }, + { assert snapshot(process.out.bai).match("cram_to_bam_index_qname_bai") }, + { assert snapshot(process.out.crai).match("cram_to_bam_index_qname_crai") }, + { assert snapshot(process.out.cram).match("cram_to_bam_index_qname_cram") }, + { assert snapshot(process.out.sam).match("cram_to_bam_index_qname_sam") }, + { assert snapshot(process.out.versions).match("cram_to_bam_index_qname_versions") } ) } - } - test("sarscov2 - [bam, []], [], [] - stub") { + test("bam_stub") { options "-stub" config "./bam_index.config" @@ -200,11 +185,11 @@ nextflow_process { when { process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), [] - ] + ]) input[1] = [[],[]] input[2] = [] """ @@ -214,18 +199,14 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.bam[0][1]).name, - process.out.cram, - process.out.sam, - file(process.out.csi[0][1]).name, - process.out.crai, - process.out.bai, - process.out.versions - ).match() } + { assert snapshot(file(process.out.bam[0][1]).name).match("bam_stub_bam") }, + { assert snapshot(file(process.out.csi[0][1]).name).match("bam_stub_csi") }, + { assert snapshot(process.out.bai).match("bam_stub_bai") }, + { assert snapshot(process.out.crai).match("bam_stub_crai") }, + { assert snapshot(process.out.cram).match("bam_stub_cram") }, + { assert snapshot(process.out.sam).match("bam_stub_sam") }, + { assert snapshot(process.out.versions).match("bam_stub_versions") } ) } - } - } diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap index 83427491..f55943a7 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap @@ -1,140 +1,488 @@ { - "homo_sapiens - [cram, []], fasta, [] - bam output": { + "bam_bam": { + "content": [ + "test.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:51.256068" + }, + "cram_to_bam_index_csi": { + "content": [ + "test.bam.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:12.958617" + }, + "bam_stub_bam": { + "content": [ + "test.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:32.065301" + }, + "bam_bai": { "content": [ - "test.bam", [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:51.258578" + }, + "bam_stub_bai": { + "content": [ [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:32.071284" + }, + "bam_stub_versions": { + "content": [ [ - - ], + "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:13:09.713353823" + }, + "cram_to_bam_index_cram": { + "content": [ [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:12.972288" + }, + "cram_to_bam_sam": { + "content": [ [ - ], - [ - "versions.yml:md5,06b9049228b111e7bed5c52fe8a98d9b" ] ], - "timestamp": "2023-12-04T17:41:17.563069206" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:04.999247" }, - "sarscov2 - [bam, []], [], []": { + "cram_to_bam_index_sam": { "content": [ - "test.bam", [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:12.976457" + }, + "cram_crai": { + "content": [ [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:56.497581" + }, + "cram_csi": { + "content": [ [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:56.50038" + }, + "cram_to_bam_cram": { + "content": [ [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:04.992239" + }, + "cram_to_bam_index_qname_csi": { + "content": [ + "test.bam.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.325496" + }, + "bam_stub_sam": { + "content": [ [ - ], - [ - "versions.yml:md5,06b9049228b111e7bed5c52fe8a98d9b" ] ], - "timestamp": "2023-12-04T17:41:03.206994564" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:32.079529" }, - "homo_sapiens - [cram, []], fasta, qname - bam & index output": { + "cram_cram": { + "content": [ + "test.cram" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:56.490286" + }, + "bam_csi": { "content": [ - "test.bam", [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:51.262882" + }, + "cram_to_bam_crai": { + "content": [ [ - ], - "test.bam.csi", + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:04.989247" + }, + "cram_to_bam_index_crai": { + "content": [ [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:12.967681" + }, + "cram_to_bam_index_qname_versions": { + "content": [ [ - - ], + "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:13:03.935041046" + }, + "cram_to_bam_bam": { + "content": [ + "test.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:04.982361" + }, + "cram_to_bam_index_bam": { + "content": [ + "test.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:12.95456" + }, + "cram_to_bam_index_versions": { + "content": [ [ - "versions.yml:md5,06b9049228b111e7bed5c52fe8a98d9b" + "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1" ] ], - "timestamp": "2023-12-04T17:44:39.165289759" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:12:55.910685496" }, - "homo_sapiens - [cram, []], fasta, [] - bam & index output": { + "cram_to_bam_bai": { "content": [ - "test.bam", [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:04.98601" + }, + "cram_to_bam_versions": { + "content": [ [ - - ], - "test.bam.csi", + "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:12:47.715221169" + }, + "cram_bam": { + "content": [ [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:56.495512" + }, + "bam_stub_cram": { + "content": [ [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:32.076908" + }, + "cram_to_bam_index_qname_bai": { + "content": [ [ - "versions.yml:md5,06b9049228b111e7bed5c52fe8a98d9b" + ] ], - "timestamp": "2023-12-04T17:44:32.25731224" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.328458" }, - "sarscov2 - [bam, []], [], [] - stub": { + "cram_to_bam_index_qname_crai": { "content": [ - "test.bam", [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.330789" + }, + "cram_bai": { + "content": [ [ - ], - "test.csi", + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:56.493129" + }, + "bam_stub_crai": { + "content": [ [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:32.074313" + }, + "cram_to_bam_index_qname_bam": { + "content": [ + "test.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.322874" + }, + "bam_versions": { + "content": [ + [ + "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:12:31.692607421" + }, + "cram_to_bam_index_qname_cram": { + "content": [ [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.333248" + }, + "bam_crai": { + "content": [ [ - "versions.yml:md5,06b9049228b111e7bed5c52fe8a98d9b" + ] ], - "timestamp": "2023-12-04T17:44:45.81037195" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:51.259774" }, - "homo_sapiens - [cram, crai], fasta, []": { + "bam_cram": { "content": [ - "test.cram", [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:51.261287" + }, + "cram_to_bam_csi": { + "content": [ [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:04.995454" + }, + "cram_sam": { + "content": [ [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:56.502625" + }, + "cram_versions": { + "content": [ + [ + "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:12:39.913411036" + }, + "bam_sam": { + "content": [ [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:51.264651" + }, + "cram_to_bam_index_bai": { + "content": [ [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:12.962863" + }, + "cram_to_bam_index_qname_sam": { + "content": [ [ - "versions.yml:md5,06b9049228b111e7bed5c52fe8a98d9b" + ] ], - "timestamp": "2023-12-04T17:41:10.730011823" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.337634" + }, + "bam_stub_csi": { + "content": [ + "test.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:32.068596" } } \ No newline at end of file diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml index 36fcd022..8bd58cff 100644 --- a/modules/nf-core/star/align/environment.yml +++ b/modules/nf-core/star/align/environment.yml @@ -6,4 +6,5 @@ channels: dependencies: - bioconda::star=2.7.10a - bioconda::samtools=1.18 + - bioconda::htslib=1.18 - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/align/tests/main.nf.test b/modules/nf-core/star/align/tests/main.nf.test index 4c878474..6ecd7786 100644 --- a/modules/nf-core/star/align/tests/main.nf.test +++ b/modules/nf-core/star/align/tests/main.nf.test @@ -7,39 +7,40 @@ nextflow_process { tag "modules_nfcore" tag "star" tag "star/align" + tag "star/genomegenerate" - test("homo_sapiens - single_end") { - config "./nextflow.config" - - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test_fasta' ], - [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] - ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] - ]) - """ - } + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ } } + } + + test("homo_sapiens - single_end") { + config "./nextflow.config" when { process { """ input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map - [ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ] ]) input[1] = STAR_GENOMEGENERATE.out.index input[2] = Channel.of([ [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] ]) input[3] = false input[4] = 'illumina' @@ -74,38 +75,20 @@ nextflow_process { test("homo_sapiens - paired_end") { config "./nextflow.config" - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test_fasta' ], - [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] - ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] - ]) - """ - } - } - } - when { process { """ input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) ] ]) input[1] = STAR_GENOMEGENERATE.out.index input[2] = Channel.of([ [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] ]) input[3] = false input[4] = 'illumina' @@ -140,38 +123,20 @@ nextflow_process { test("homo_sapiens - paired_end - arriba") { config "./nextflow.arriba.config" - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test_fasta' ], - [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] - ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] - ]) - """ - } - } - } - when { process { """ input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) ] ]) input[1] = STAR_GENOMEGENERATE.out.index input[2] = Channel.of([ [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] ]) input[3] = false input[4] = 'illumina' @@ -206,38 +171,20 @@ nextflow_process { test("homo_sapiens - paired_end - starfusion") { config "./nextflow.starfusion.config" - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test_fasta' ], - [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] - ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] - ]) - """ - } - } - } - when { process { """ input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) ] ]) input[1] = STAR_GENOMEGENERATE.out.index input[2] = Channel.of([ [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] ]) input[3] = false input[4] = 'illumina' @@ -272,40 +219,22 @@ nextflow_process { test("homo_sapiens - paired_end - multiple") { config "./nextflow.config" - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test_fasta' ], - [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] - ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] - ]) - """ - } - } - } - when { process { """ input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) ] ]) input[1] = STAR_GENOMEGENERATE.out.index input[2] = Channel.of([ [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] ]) input[3] = false input[4] = 'illumina' diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml index 93e4476a..791f255e 100644 --- a/modules/nf-core/star/genomegenerate/environment.yml +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -1,11 +1,10 @@ name: star_genomegenerate - channels: - conda-forge - bioconda - defaults - dependencies: - bioconda::samtools=1.18 + - bioconda::htslib=1.18 - bioconda::star=2.7.10a - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test b/modules/nf-core/star/genomegenerate/tests/main.nf.test index af0c9421..c17c8ba4 100644 --- a/modules/nf-core/star/genomegenerate/tests/main.nf.test +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test @@ -8,18 +8,18 @@ nextflow_process { tag "star" tag "star/genomegenerate" - test("homo_sapiens") { + test("fasta_gtf") { when { process { """ input[0] = Channel.of([ [ id:'test_fasta' ], - [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] ]) input[1] = Channel.of([ [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] ]) """ } @@ -28,14 +28,13 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_with_gtf") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_gtf_index") }, + { assert snapshot(process.out.versions).match("fasta_gtf_versions") } ) } - } - test("homo_sapiens-stub") { + test("fasta_gtf_stub") { options '-stub' @@ -44,11 +43,11 @@ nextflow_process { """ input[0] = Channel.of([ [ id:'test_fasta' ], - [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] ]) input[1] = Channel.of([ [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] ]) """ } @@ -57,21 +56,20 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_with_gtf") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_gtf_stub_index") }, + { assert snapshot(process.out.versions).match("fasta_gtf_stub_versions") } ) } - } - test("homo_sapiens-without_gtf") { + test("fasta") { when { process { """ input[0] = Channel.of([ [ id:'test_fasta' ], - [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] ]) input[1] = Channel.of([ [], [] ]) """ @@ -81,14 +79,14 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_without_gtf") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_index") }, + { assert snapshot(process.out.versions).match("fasta_versions") } ) } } - test("homo_sapiens-without_gtf-stub") { + test("fasta_stub") { options '-stub' @@ -97,7 +95,7 @@ nextflow_process { """ input[0] = Channel.of([ [ id:'test_fasta' ], - [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] ]) input[1] = Channel.of([ [], [] ]) """ @@ -107,11 +105,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_without_gtf") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_stub_index") }, + { assert snapshot(process.out.versions).match("fasta_stub_versions") } ) } } -} \ No newline at end of file +} diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap index 9de08c74..5653d6e6 100644 --- a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap @@ -1,22 +1,90 @@ { - "versions": { + "fasta_gtf_versions": { "content": [ [ "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" ] ], - "timestamp": "2023-12-19T11:05:51.741109" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-01T15:54:31.798555" }, - "index_with_gtf": { + "fasta_stub_versions": { + "content": [ + [ + "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-01T15:55:07.521209" + }, + "fasta_gtf_stub_index": { + "content": [ + "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-01T15:54:46.478098" + }, + "fasta_gtf_stub_versions": { + "content": [ + [ + "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-01T15:54:46.491657" + }, + "fasta_index": { + "content": [ + "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-01T15:54:57.552329" + }, + "fasta_versions": { + "content": [ + [ + "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-01T15:54:57.560541" + }, + "fasta_gtf_index": { "content": [ "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]" ], - "timestamp": "2023-12-19T11:38:14.551548" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-01T15:54:31.786814" }, - "index_without_gtf": { + "fasta_stub_index": { "content": [ "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]" ], - "timestamp": "2023-12-19T11:38:22.382905" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-01T15:55:07.517472" } } \ No newline at end of file diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test b/modules/nf-core/stringtie/stringtie/tests/main.nf.test index 68786b74..00efe8f1 100644 --- a/modules/nf-core/stringtie/stringtie/tests/main.nf.test +++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test @@ -10,13 +10,15 @@ nextflow_process { test("sarscov2 [bam] - forward strandedness") { + config "./nextflow.config" + when { process { """ input[0] = [ [ id:'test', strandedness:'forward' ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] - ] + [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ] + ] input[1] = [] """ } @@ -24,24 +26,26 @@ nextflow_process { then { assertAll( - { assert process.success }, - { assert snapshot(process.out.transcript_gtf).match("fs_transcript_gtf") }, - { assert snapshot(process.out.abundance).match("fs_abundance") }, - { assert snapshot(process.out.versions).match("fs_versions") } + { assert process.success }, + { assert snapshot(process.out.transcript_gtf).match("fs_transcript_gtf") }, + { assert snapshot(process.out.abundance).match("fs_abundance") }, + { assert snapshot(process.out.versions).match("fs_versions") } ) } } test("sarscov2 [bam] - forward strandedness + reference annotation") { + config "./nextflow.config" + when { process { """ input[0] = [ - [ id:'test', strandedness:'forward' ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] - ] - input[1] = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) + [ id:'test', strandedness:'forward' ], // meta map + [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ] + ] + input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true) """ } } @@ -49,23 +53,25 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.transcript_gtf).match("fs_gtf_transcript_gtf") }, - { assert snapshot(process.out.abundance).match("fs_gtf_abundance") }, - { assert snapshot(process.out.ballgown).match("fs_gtf_ballgown") }, - { assert snapshot(process.out.versions).match("fs_gtf_versions") } + { assert snapshot(process.out.transcript_gtf).match("fs_gtf_transcript_gtf") }, + { assert snapshot(process.out.abundance).match("fs_gtf_abundance") }, + { assert snapshot(process.out.ballgown).match("fs_gtf_ballgown") }, + { assert snapshot(process.out.versions).match("fs_gtf_versions") } ) } } test("sarscov2 [bam] - reverse strandedness") { + config "./nextflow.config" + when { process { """ input[0] = [ [ id:'test', strandedness:'reverse' ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] - ] + [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ] + ] input[1] = [] """ } @@ -73,35 +79,37 @@ nextflow_process { then { assertAll( - { assert process.success }, - { assert snapshot(process.out.transcript_gtf).match("rs_transcript_gtf") }, - { assert snapshot(process.out.abundance).match("rs_abundance") }, - { assert snapshot(process.out.versions).match("rs_versions") } + { assert process.success }, + { assert snapshot(process.out.transcript_gtf).match("rs_transcript_gtf") }, + { assert snapshot(process.out.abundance).match("rs_abundance") }, + { assert snapshot(process.out.versions).match("rs_versions") } ) } } test("sarscov2 [bam] - reverse strandedness + reference annotation") { + config "./nextflow.config" + when { process { """ input[0] = [ [ id:'test', strandedness:'reverse' ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] - ] - input[1] = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) + [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ] + ] + input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true) """ } } then { assertAll( - { assert process.success }, - { assert snapshot(process.out.transcript_gtf).match("rs_gtf_transcript_gtf") }, - { assert snapshot(process.out.abundance).match("rs_gtf_abundance") }, - { assert snapshot(process.out.ballgown).match("rs_gtf_ballgown") }, - { assert snapshot(process.out.versions).match("rs_gtf_versions") } + { assert process.success }, + { assert snapshot(process.out.transcript_gtf).match("rs_gtf_transcript_gtf") }, + { assert snapshot(process.out.abundance).match("rs_gtf_abundance") }, + { assert snapshot(process.out.ballgown).match("rs_gtf_ballgown") }, + { assert snapshot(process.out.versions).match("rs_gtf_versions") } ) } } diff --git a/modules/nf-core/stringtie/stringtie/tests/nextflow.config b/modules/nf-core/stringtie/stringtie/tests/nextflow.config new file mode 100644 index 00000000..e3aaa099 --- /dev/null +++ b/modules/nf-core/stringtie/stringtie/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'STRINGTIE_STRINGTIE' { + ext.args = '' + } +} diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml index 6cd0f51b..0981320c 100644 --- a/modules/nf-core/trimgalore/environment.yml +++ b/modules/nf-core/trimgalore/environment.yml @@ -1,7 +1,10 @@ name: trimgalore + channels: - conda-forge - bioconda - defaults + dependencies: + - bioconda::cutadapt=3.4 - bioconda::trim-galore=0.6.7 diff --git a/modules/nf-core/trimgalore/tests/main.nf.test b/modules/nf-core/trimgalore/tests/main.nf.test index bc6812cc..43904ac3 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test +++ b/modules/nf-core/trimgalore/tests/main.nf.test @@ -10,13 +10,10 @@ nextflow_process { test("test_trimgalore_single_end") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = [ [ id:'test', single_end:true ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] + [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] ] """ } @@ -41,7 +38,8 @@ nextflow_process { { report1_lines.each { report1_line -> { assert path(process.out.log.get(0).get(1)).getText().contains(report1_line) } } - } + }, + { assert snapshot(process.out.versions).match() } ) } } @@ -49,15 +47,14 @@ nextflow_process { test("test_trimgalore_paired_end") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = [ [ id:'test', single_end:false ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] + [ + file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] + ] """ } } @@ -98,7 +95,8 @@ nextflow_process { { report2_lines.each { report2_line -> { assert path(process.out.log.get(0).get(1).get(1)).getText().contains(report2_line) } } - } + }, + { assert snapshot(process.out.versions).match() } ) } } diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap index 84feacca..082c5500 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test.snap +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -1,148 +1,26 @@ { "test_trimgalore_single_end": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test_trimmed.fq.gz:md5,e0a7516b8ea8d6467d6306acb2cd13c4" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastq.gz_trimming_report.txt:md5,a1ab3958205f1ddf48af623242b5b429" - ] - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - - ], - "5": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" - ], - "html": [ - - ], - "log": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastq.gz_trimming_report.txt:md5,a1ab3958205f1ddf48af623242b5b429" - ] - ], - "reads": [ - [ - { - "id": "test", - "single_end": true - }, - "test_trimmed.fq.gz:md5,e0a7516b8ea8d6467d6306acb2cd13c4" - ] - ], - "unpaired": [ - - ], - "versions": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" - ], - "zip": [ - - ] - } + [ + "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + ] ], - "timestamp": "2023-10-17T15:24:57.782141441" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-29T16:33:20.401347" }, "test_trimgalore_paired_end": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_1_val_1.fq.gz:md5,e0a7516b8ea8d6467d6306acb2cd13c4", - "test_2_val_2.fq.gz:md5,f3d61189e6d10202da7b8686f1dbb71b" - ] - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_1.fastq.gz_trimming_report.txt:md5,315d40465412f9909bbaabf52269274d", - "test_2.fastq.gz_trimming_report.txt:md5,34436303da1c78811103427a2fb57f7b" - ] - ] - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - - ], - "5": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" - ], - "html": [ - - ], - "log": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_1.fastq.gz_trimming_report.txt:md5,315d40465412f9909bbaabf52269274d", - "test_2.fastq.gz_trimming_report.txt:md5,34436303da1c78811103427a2fb57f7b" - ] - ] - ], - "reads": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_1_val_1.fq.gz:md5,e0a7516b8ea8d6467d6306acb2cd13c4", - "test_2_val_2.fq.gz:md5,f3d61189e6d10202da7b8686f1dbb71b" - ] - ] - ], - "unpaired": [ - - ], - "versions": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" - ], - "zip": [ - - ] - } + [ + "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + ] ], - "timestamp": "2023-10-17T15:25:08.513589909" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-29T16:33:28.960497" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf index fc1c652b..b716375b 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf +++ b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf @@ -15,7 +15,7 @@ workflow BAM_SORT_STATS_SAMTOOLS { ch_versions = Channel.empty() - SAMTOOLS_SORT ( ch_bam ) + SAMTOOLS_SORT ( ch_bam, ch_fasta ) ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions.first()) SAMTOOLS_INDEX ( SAMTOOLS_SORT.out.bam ) diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test index 59b749d8..75b5b934 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test @@ -24,12 +24,14 @@ nextflow_workflow { } workflow { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) - ] - input[1] = [ [ id:'genome' ], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) """ } } @@ -54,12 +56,14 @@ nextflow_workflow { } workflow { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - input[1] = [ [ id:'genome' ], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) """ } } diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap index 77afbf17..6645a092 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap @@ -11,6 +11,10 @@ ] ] ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, "timestamp": "2023-10-22T20:25:03.687121177" }, "test_bam_sort_stats_samtools_paired_end_idxstats": { @@ -25,6 +29,10 @@ ] ] ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, "timestamp": "2023-10-22T20:25:03.709648916" }, "test_bam_sort_stats_samtools_single_end_stats": { @@ -35,11 +43,15 @@ "id": "test", "single_end": false }, - "test.stats:md5,f281507081517414eb1a04b2d9c855b2" + "test.stats:md5,cb0bf2b79de52fdf0c61e80efcdb0bb4" ] ] ], - "timestamp": "2023-12-04T11:06:50.951881479" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:44:38.553256801" }, "test_bam_sort_stats_samtools_paired_end_stats": { "content": [ @@ -49,11 +61,15 @@ "id": "test", "single_end": false }, - "test.stats:md5,e32e7e49dce1fbe327a89e0fb7bc01b1" + "test.stats:md5,d7796222a087b9bb97f631f1c21b9c95" ] ] ], - "timestamp": "2023-12-04T11:06:59.253905951" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:44:48.355870518" }, "test_bam_sort_stats_samtools_single_end_idxstats": { "content": [ @@ -67,7 +83,11 @@ ] ] ], - "timestamp": "2023-10-22T20:25:58.451364604" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-01-18T17:10:02.84631" }, "test_bam_sort_stats_samtools_single_end_flagstats": { "content": [ @@ -81,6 +101,10 @@ ] ] ], - "timestamp": "2023-10-22T20:25:58.416859285" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-01-18T17:10:02.829756" } } \ No newline at end of file From 72dd514cc90d19797bf3869b9427d879677582f6 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 18 Mar 2024 11:39:50 +0100 Subject: [PATCH 148/491] Fix some common problems in CIRIquant and HISAT2_ALIGN --- modules/local/ciriquant/yml/main.nf | 6 +++--- nextflow.config | 1 + subworkflows/local/circrna_discovery.nf | 2 +- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/modules/local/ciriquant/yml/main.nf b/modules/local/ciriquant/yml/main.nf index 25bc0b01..4eb2d06f 100644 --- a/modules/local/ciriquant/yml/main.nf +++ b/modules/local/ciriquant/yml/main.nf @@ -7,8 +7,8 @@ process CIRIQUANT_YML { 'quay.io/biocontainers/ciriquant:1.1.2--pyhdfd78af_2' }" input: - path gtf - path fasta + tuple val(meta), path(gtf) + tuple val(meta2), path(fasta) path bwa path hisat2 @@ -19,7 +19,7 @@ process CIRIQUANT_YML { task.ext.when == null || task.ext.when script: - hisat2_prefix = fasta.toString() - ~/.(fa|fasta)$/ + hisat2_prefix = meta2.id fasta_path = fasta.toRealPath() gtf_path = gtf.toRealPath() bwa_path = bwa.toRealPath() diff --git a/nextflow.config b/nextflow.config index ffa9b39e..018a60da 100644 --- a/nextflow.config +++ b/nextflow.config @@ -206,6 +206,7 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.runOptions = '--no-mount tmp --writable-tmpfs' } gitpod { executor.name = 'local' diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index a0a20433..73ac5e62 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -141,7 +141,7 @@ workflow CIRCRNA_DISCOVERY { // only need path to bwa, only need path to hisat2. // do not want to upset the collect declr for all indices just for this. - CIRIQUANT_YML( gtf, fasta, bwa_index.map{ meta, index -> return index }, hisat2_index.map{ meta, index -> return index } ) + CIRIQUANT_YML( ch_gtf, ch_fasta, bwa_index.map{ meta, index -> return index }, hisat2_index.map{ meta, index -> return index } ) CIRIQUANT( reads, CIRIQUANT_YML.out.yml.collect() ) CIRIQUANT_FILTER( CIRIQUANT.out.gtf.map{ meta, gtf -> [ meta + [tool: "ciriquant"], gtf ] }, bsj_reads ) From 6fc9ae8c4db439c07b544a7c5e8880ca6ddb8f58 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 18 Mar 2024 11:42:08 +0100 Subject: [PATCH 149/491] Fix miranda channel structure --- subworkflows/local/mirna_prediction.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index b9a4cfc7..cdd6f86d 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -8,7 +8,7 @@ workflow MIRNA_PREDICTION{ take: circrna_fasta circrna_bed12 - mature + ch_mature main: ch_versions = Channel.empty() @@ -17,7 +17,7 @@ workflow MIRNA_PREDICTION{ // TARGETSCAN WORKFLOW: // - TARGETSCAN_DATABASE( mature ) + TARGETSCAN_DATABASE( ch_mature ) TARGETSCAN( circrna_fasta, TARGETSCAN_DATABASE.out.mature_txt ) ch_versions = ch_versions.mix(TARGETSCAN_DATABASE.out.versions) @@ -27,7 +27,7 @@ workflow MIRNA_PREDICTION{ // MIRANDA WORKFLOW: // - MIRANDA( circrna_fasta, mature ) + MIRANDA( circrna_fasta, ch_mature.map{meta, mature -> mature} ) ch_versions = ch_versions.mix(MIRANDA.out.versions) From 4e50b0b67262f7e01ebc61e7dfb92218fe37ae4e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 18 Mar 2024 11:54:17 +0100 Subject: [PATCH 150/491] Fix linting --- modules/local/seqkit/split/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/seqkit/split/main.nf b/modules/local/seqkit/split/main.nf index 5d70f47b..1fbc0c8d 100644 --- a/modules/local/seqkit/split/main.nf +++ b/modules/local/seqkit/split/main.nf @@ -33,4 +33,4 @@ process SEQKIT_SPLIT { seqkit: \$(echo \$(seqkit 2>&1) | sed 's/^.*Version: //; s/ .*\$//') END_VERSIONS """ -} \ No newline at end of file +} From 919f5fa92d4f49568e01516437947ac7eebdec40 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 18 Mar 2024 12:11:31 +0100 Subject: [PATCH 151/491] Add some meta inputs --- modules/local/circtest/test/main.nf | 2 +- modules/local/deseq2/differential_expression/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/circtest/test/main.nf b/modules/local/circtest/test/main.nf index 1d1e4df3..643f2c56 100644 --- a/modules/local/circtest/test/main.nf +++ b/modules/local/circtest/test/main.nf @@ -9,7 +9,7 @@ process CIRCTEST { input: path(circ_csv) path(linear_csv) - path(phenotype) + tuple val(meta), path(phenotype) output: path "*" , emit: results diff --git a/modules/local/deseq2/differential_expression/main.nf b/modules/local/deseq2/differential_expression/main.nf index 67631ed5..86ee474c 100644 --- a/modules/local/deseq2/differential_expression/main.nf +++ b/modules/local/deseq2/differential_expression/main.nf @@ -8,7 +8,7 @@ process DESEQ2_DIFFERENTIAL_EXPRESSION { input: path(gene_matrix) - path(phenotype) + tuple val(meta), path(phenotype) path(circrna_matrix) val(species) path(biomart_keys) From 50a6ca2d2a1913e43e6e4e65fe53707c89d2dd52 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 18 Mar 2024 12:16:45 +0100 Subject: [PATCH 152/491] Prettier --- modules/local/seqkit/split/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/seqkit/split/environment.yml b/modules/local/seqkit/split/environment.yml index fb5b8b63..d557b8b3 100644 --- a/modules/local/seqkit/split/environment.yml +++ b/modules/local/seqkit/split/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::seqkit=2.8.0 \ No newline at end of file + - bioconda::seqkit=2.8.0 From 30552fa2dec7d0a6a3edcb6530582edce59507cb Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 07:59:24 +0100 Subject: [PATCH 153/491] Unify species_id parameter --- conf/test.config | 2 +- main.nf | 18 ++++++++++-------- nextflow.config | 1 + nextflow_schema.json | 2 +- workflows/circrna/main.nf | 3 ++- 5 files changed, 15 insertions(+), 11 deletions(-) diff --git a/conf/test.config b/conf/test.config index c0444832..0c75023b 100644 --- a/conf/test.config +++ b/conf/test.config @@ -30,5 +30,5 @@ params { module = "circrna_discovery,mirna_prediction,differential_expression" outdir = "results/" bsj_reads = 2 - species = "cel" + species_id = "cel" } diff --git a/main.nf b/main.nf index 1e202b27..544e9738 100644 --- a/main.nf +++ b/main.nf @@ -29,14 +29,14 @@ include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_circ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -params.fasta = getGenomeAttribute('fasta') -params.gtf = getGenomeAttribute('gtf') -params.bwa = getGenomeAttribute('bwa') -params.star = getGenomeAttribute('star') -params.bowtie = getGenomeAttribute('bowtie') -params.bowtie2 = getGenomeAttribute('bowtie2') -params.mature = getGenomeAttribute('mature') -params.species = getGenomeAttribute('species_id') +params.fasta = getGenomeAttribute('fasta') +params.gtf = getGenomeAttribute('gtf') +params.bwa = getGenomeAttribute('bwa') +params.star = getGenomeAttribute('star') +params.bowtie = getGenomeAttribute('bowtie') +params.bowtie2 = getGenomeAttribute('bowtie2') +params.mature = getGenomeAttribute('mature') +params.species_id = getGenomeAttribute('species_id') /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -60,6 +60,7 @@ workflow NFCORE_CIRCRNA { ch_fasta = Channel.value([[id: "fasta"], file(params.fasta, checkIfExists:true)]) ch_gtf = Channel.value([[id: "gtf"], file(params.gtf, checkIfExists:true)]) ch_mature = Channel.value([[id: "mature"], file(params.mature, checkIfExists:true)]) + ch_species = Channel.value(params.species_id) CIRCRNA ( ch_samplesheet, @@ -67,6 +68,7 @@ workflow NFCORE_CIRCRNA { ch_fasta, ch_gtf, ch_mature, + ch_species, ch_versions ) diff --git a/nextflow.config b/nextflow.config index 018a60da..4c3bfcd5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -31,6 +31,7 @@ params { hisat2_build_memory = '200.GB' segemehl = null save_reference = true + species_id = null // Trimming min_trimmed_reads = 10000 diff --git a/nextflow_schema.json b/nextflow_schema.json index 5bdc6753..912bd12b 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -212,7 +212,7 @@ "fa_icon": "fas fa-wheelchair", "default": null }, - "species": { + "species_id": { "type": "string", "fa_icon": "fas fa-dog", "description": "String identifying species.", diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index e51d850e..f090f857 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -57,6 +57,7 @@ workflow CIRCRNA { ch_fasta ch_gtf ch_mature + ch_species ch_versions main: @@ -179,7 +180,7 @@ workflow CIRCRNA { ch_phenotype, CIRCRNA_DISCOVERY.out.dea_matrix, CIRCRNA_DISCOVERY.out.clr_matrix, - params.species, + ch_species, ch_ensembl_database_map, params.exon_boundary ) From b4929ee2373d97322a75f2bda4e7381d7968fc72 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 08:14:49 +0100 Subject: [PATCH 154/491] Simplify handling of tool indices --- conf/modules.config | 16 +++++++------- subworkflows/local/circrna_discovery.nf | 6 ++--- subworkflows/local/prepare_genome.nf | 29 +++++++++++++------------ workflows/circrna/main.nf | 15 ++++++------- 4 files changed, 33 insertions(+), 33 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index a6ccdf5c..875f83ee 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -89,7 +89,7 @@ if (!params.skip_trimming) { } withName: BOWTIE_BUILD { - ext.when = { params.fasta && !params.bowtie && params.tool.split(',').contains('mapsplice') && params.module.split(',').contains('circrna_discovery') } + ext.when = { !params.bowtie && params.tool.split(',').contains('mapsplice') && params.module.split(',').contains('circrna_discovery') } publishDir = [ path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, @@ -99,7 +99,7 @@ if (!params.skip_trimming) { } withName: BOWTIE2_BUILD { - ext.when = { params.fasta && !params.bowtie2 && params.tool.split(',').contains('find_circ') && params.module.split(',').contains('circrna_discovery') } + ext.when = { !params.bowtie2 && params.tool.split(',').contains('find_circ') && params.module.split(',').contains('circrna_discovery') } publishDir = [ path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, @@ -109,7 +109,7 @@ if (!params.skip_trimming) { } withName: BWA_INDEX { - ext.when = { params.fasta && !params.bwa && params.tool.split(',').contains('ciriquant') && params.module.split(',').contains('circrna_discovery') } + ext.when = { !params.bwa && params.tool.split(',').contains('ciriquant') && params.module.split(',').contains('circrna_discovery') } publishDir = [ path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, @@ -119,7 +119,7 @@ if (!params.skip_trimming) { } withName: HISAT2_EXTRACTSPLICESITES { - ext.when = { params.fasta && params.gtf && ( params.module.split(',').contains('differential_expression') || params.tool.split(',').contains('ciriquant') ) } + ext.when = { params.module.split(',').contains('differential_expression') || params.tool.split(',').contains('ciriquant') } publishDir = [ path: { "${params.outdir}/references/index/hisat2" }, mode: params.publish_dir_mode, @@ -129,7 +129,7 @@ if (!params.skip_trimming) { } withName: HISAT2_BUILD { - ext.when = { params.fasta && params.gtf && ( params.module.split(',').contains('differential_expression') || params.tool.split(',').contains('ciriquant') ) } + ext.when = { params.module.split(',').contains('differential_expression') || params.tool.split(',').contains('ciriquant') } publishDir = [ path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, @@ -139,7 +139,7 @@ if (!params.skip_trimming) { } withName: STAR_GENOMEGENERATE { - ext.when = { params.fasta && params.gtf && !params.star && params.module.split(',').contains('circrna_discovery') && ( params.tool.split(',').contains('circexplorer2') || params.tool.split(',').contains('dcc') || params.tool.split(',').contains('circrna_finder') ) } + ext.when = { !params.star && params.module.split(',').contains('circrna_discovery') && ( params.tool.split(',').contains('circexplorer2') || params.tool.split(',').contains('dcc') || params.tool.split(',').contains('circrna_finder') ) } ext.args = [ "", params.sjdboverhang ? "--sjdbOverhang ${params.sjdboverhang}" : '', ].join(' ').trim() @@ -152,7 +152,7 @@ if (!params.skip_trimming) { } withName: SEGEMEHL_INDEX { - ext.when = { params.fasta && !params.segemehl && params.tool.split(',').contains('segemehl') && params.module.split(',').contains('circrna_discovery') } + ext.when = { !params.segemehl && params.tool.split(',').contains('segemehl') && params.module.split(',').contains('circrna_discovery') } publishDir = [ path: { "${params.outdir}/references/index/segemehl" }, mode: params.publish_dir_mode, @@ -164,7 +164,7 @@ if (!params.skip_trimming) { // circRNA withName: SEGEMEHL_ALIGN { - ext.when = { params.fasta && params.tool.split(',').contains('segemehl') && params.module.split(',').contains('circrna_discovery') } + ext.when = { params.tool.split(',').contains('segemehl') && params.module.split(',').contains('circrna_discovery') } ext.args = [ "", "-b", "-S" diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 73ac5e62..b51c821f 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -120,11 +120,11 @@ workflow CIRCRNA_DISCOVERY { // FIND_CIRC WORKFLOW: // - FIND_CIRC_ALIGN( reads, bowtie2_index.collect(), false, true ) + FIND_CIRC_ALIGN( reads, bowtie2_index, false, true ) SAMTOOLS_INDEX( FIND_CIRC_ALIGN.out.aligned ) SAMTOOLS_VIEW( FIND_CIRC_ALIGN.out.aligned.join( SAMTOOLS_INDEX.out.bai ), ch_fasta, [] ) FIND_CIRC_ANCHORS( SAMTOOLS_VIEW.out.bam ) - FIND_CIRC( FIND_CIRC_ANCHORS.out.anchors, bowtie2_index.collect(), fasta ) + FIND_CIRC( FIND_CIRC_ANCHORS.out.anchors, bowtie2_index, fasta ) find_circ_filter = FIND_CIRC.out.bed.map{ meta, bed -> [ meta + [tool: "find_circ"], bed ] } FIND_CIRC_FILTER( find_circ_filter, bsj_reads ) @@ -191,7 +191,7 @@ workflow CIRCRNA_DISCOVERY { // MAPSPLICE_REFERENCE( gtf ) - MAPSPLICE_ALIGN( reads, bowtie_index.collect(), chromosomes, gtf ) + MAPSPLICE_ALIGN( reads, bowtie_index, chromosomes, gtf ) MAPSPLICE_PARSE( MAPSPLICE_ALIGN.out.raw_fusions ) MAPSPLICE_ANNOTATE( MAPSPLICE_PARSE.out.junction, fasta, MAPSPLICE_REFERENCE.out.txt ) mapsplice_filter = MAPSPLICE_ANNOTATE.out.txt.map{ meta, txt -> [ meta + [tool: "mapsplice"], txt ] } diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index b27e226d..8c7a5994 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -19,7 +19,7 @@ workflow PREPARE_GENOME { // MapSplice cannot deal with extra field in the fasta headers // this removes all additional fields in the headers of the input fasta file - if( params.tool.contains('mapsplice') && params.module.contains('circrna_discovery') ) { + if( params.module.contains('circrna_discovery') && params.tool.contains('mapsplice') ) { CLEAN_FASTA(ch_fasta, []) ch_fasta = CLEAN_FASTA.out.output } @@ -41,22 +41,23 @@ workflow PREPARE_GENOME { SEGEMEHL_INDEX(ch_fasta.map{ meta, fasta -> fasta}) // TODO: Add support for meta // Collect versions - ch_versions = ch_versions.mix(BOWTIE_BUILD.out.versions) - ch_versions = ch_versions.mix(BOWTIE2_BUILD.out.versions) - ch_versions = ch_versions.mix(BWA_INDEX.out.versions) - ch_versions = ch_versions.mix(HISAT2_EXTRACTSPLICESITES.out.versions) - ch_versions = ch_versions.mix(HISAT2_BUILD.out.versions) - ch_versions = ch_versions.mix(SEGEMEHL_INDEX.out.versions) - ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions) + ch_versions = ch_versions.mix(BOWTIE_BUILD.out.versions, + BOWTIE2_BUILD.out.versions, + BWA_INDEX.out.versions, + HISAT2_EXTRACTSPLICESITES.out.versions, + HISAT2_BUILD.out.versions, + SEGEMEHL_INDEX.out.versions, + STAR_GENOMEGENERATE.out.versions) emit: - bowtie = BOWTIE_BUILD.out.index - bowtie2 = BOWTIE2_BUILD.out.index - bwa = BWA_INDEX.out.index + bowtie = params.bowtie ?: BOWTIE_BUILD.out.index + segemehl = params.segemehl ?: SEGEMEHL_INDEX.out.index + bowtie2 = params.bowtie2 ? Channel.value([[id: "bowtie2"], file(params.bowtie2, checkIfExists: true)]) : BOWTIE2_BUILD.out.index.collect() + bwa = params.bwa ? Channel.value([[id: "bwa"], file(params.bwa, checkIfExists: true)]) : BWA_INDEX.out.index.collect() + hisat2 = params.hisat2 ? Channel.value([[id: "hisat2"], file(params.hisat2, checkIfExists: true)]) : HISAT2_BUILD.out.index.collect() + star = params.star ? Channel.value([[id: "star"], file(params.star, checkIfExists: true)]) : STAR_GENOMEGENERATE.out.index.collect() chromosomes = SEQKIT_SPLIT.out.split - hisat2 = HISAT2_BUILD.out.index.collect() - star = STAR_GENOMEGENERATE.out.index.collect() - segemehl = SEGEMEHL_INDEX.out.index splice_sites = HISAT2_EXTRACTSPLICESITES.out.txt.collect() + versions = ch_versions } diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index f090f857..4a614505 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -110,14 +110,13 @@ workflow CIRCRNA { ch_gtf ) - // Stage the indices via newly created indices, iGenomes or empty list if tool not selected. - bowtie_index = params.fasta ? params.bowtie ? Channel.fromPath(params.bowtie) : PREPARE_GENOME.out.bowtie : [] - bowtie2_index = params.fasta ? params.bowtie2 ? Channel.fromPath(params.bowtie2).map{ it -> [[id:'bowtie2'], it] } : PREPARE_GENOME.out.bowtie2 : [] - bwa_index = params.fasta ? params.bwa ? Channel.fromPath(params.bwa).map{ it -> [[id:'bwa'], it] } : PREPARE_GENOME.out.bwa : [] - chromosomes = params.fasta && ( params.tool.contains('mapsplice') || params.tool.contains('find_circ') ) ? PREPARE_GENOME.out.chromosomes : [] - hisat2_index = params.fasta ? params.hisat2 && ( params.tool.contains('ciriquant') || params.module.contains('differential_expression') ) ? Channel.fromPath(params.hisat2).map{ [[id:"hisat2"], it]} : PREPARE_GENOME.out.hisat2 : [] - star_index = params.fasta ? params.star ? Channel.fromPath(params.star).map{[[id:'star'], it]}: PREPARE_GENOME.out.star : [] - segemehl_index = params.fasta ? params.segemehl ? Channel.fromPath(params.segemehl) : PREPARE_GENOME.out.segemehl : [] + bowtie_index = PREPARE_GENOME.out.bowtie + bowtie2_index = PREPARE_GENOME.out.bowtie2 + bwa_index = PREPARE_GENOME.out.bwa + chromosomes = PREPARE_GENOME.out.chromosomes + hisat2_index = PREPARE_GENOME.out.hisat2 + star_index = PREPARE_GENOME.out.star + segemehl_index = PREPARE_GENOME.out.segemehl ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) // MODULE: Run FastQC, trimgalore! From f741c75c47a2c64e07e1e16d3ea302f6f6b074f1 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 08:27:50 +0100 Subject: [PATCH 155/491] Add defaults for previously undefined parameters --- nextflow.config | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/nextflow.config b/nextflow.config index 4c3bfcd5..628468c4 100644 --- a/nextflow.config +++ b/nextflow.config @@ -27,6 +27,10 @@ params { genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false + bowtie = null + bowtie2 = null + bwa = null + star = null hisat2 = null hisat2_build_memory = '200.GB' segemehl = null From c2089ca697f581c5d313faef959aa62458aac34d Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 08:39:45 +0100 Subject: [PATCH 156/491] Linting --- subworkflows/local/prepare_genome.nf | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 8c7a5994..0118cf2d 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -42,12 +42,12 @@ workflow PREPARE_GENOME { // Collect versions ch_versions = ch_versions.mix(BOWTIE_BUILD.out.versions, - BOWTIE2_BUILD.out.versions, - BWA_INDEX.out.versions, - HISAT2_EXTRACTSPLICESITES.out.versions, - HISAT2_BUILD.out.versions, - SEGEMEHL_INDEX.out.versions, - STAR_GENOMEGENERATE.out.versions) + BOWTIE2_BUILD.out.versions, + BWA_INDEX.out.versions, + HISAT2_EXTRACTSPLICESITES.out.versions, + HISAT2_BUILD.out.versions, + SEGEMEHL_INDEX.out.versions, + STAR_GENOMEGENERATE.out.versions) emit: bowtie = params.bowtie ?: BOWTIE_BUILD.out.index From e691f5c800cf3ea934717df4156bb7f82be94563 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 17:11:41 +0100 Subject: [PATCH 157/491] Fix indent --- conf/test.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test.config b/conf/test.config index 0c75023b..af8b601e 100644 --- a/conf/test.config +++ b/conf/test.config @@ -30,5 +30,5 @@ params { module = "circrna_discovery,mirna_prediction,differential_expression" outdir = "results/" bsj_reads = 2 - species_id = "cel" + species_id = "cel" } From 0ee988b0ba81a5201485d5b1eb1879690893f45b Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 30 Mar 2024 08:01:36 +0100 Subject: [PATCH 158/491] Make some parameters non-required when according modules are disabled --- main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/main.nf b/main.nf index 544e9738..a360b046 100644 --- a/main.nf +++ b/main.nf @@ -56,11 +56,11 @@ workflow NFCORE_CIRCRNA { // WORKFLOW: Run nf-core/circrna workflow // ch_samplesheet = Channel.fromSamplesheet("input") - ch_phenotype = Channel.value([[id: "phenotype"], file(params.phenotype, checkIfExists:true)]) ch_fasta = Channel.value([[id: "fasta"], file(params.fasta, checkIfExists:true)]) ch_gtf = Channel.value([[id: "gtf"], file(params.gtf, checkIfExists:true)]) - ch_mature = Channel.value([[id: "mature"], file(params.mature, checkIfExists:true)]) - ch_species = Channel.value(params.species_id) + ch_mature = params.module.split(',').contains('mirna_prediction') ? Channel.value([[id: "mature"], file(params.mature, checkIfExists:true)]) : Channel.empty() + ch_phenotype = params.module.split(',').contains('differential_expression') ? Channel.value([[id: "phenotype"], file(params.phenotype, checkIfExists:true)]) : Channel.empty() + ch_species = params.module.split(',').contains('differential_expression') ? Channel.value(params.species_id) : Channel.empty() CIRCRNA ( ch_samplesheet, From 30af2097d27ebad532dbc1264d5e607f70596ef0 Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Thu, 11 Apr 2024 15:06:18 +0200 Subject: [PATCH 159/491] fix hisast2 index bug in yml file --- modules/local/ciriquant/yml/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/ciriquant/yml/main.nf b/modules/local/ciriquant/yml/main.nf index 4eb2d06f..42de10dc 100644 --- a/modules/local/ciriquant/yml/main.nf +++ b/modules/local/ciriquant/yml/main.nf @@ -19,7 +19,7 @@ process CIRIQUANT_YML { task.ext.when == null || task.ext.when script: - hisat2_prefix = meta2.id + hisat2_prefix = fasta.toString() - ~/.(fa|fasta)$/ fasta_path = fasta.toRealPath() gtf_path = gtf.toRealPath() bwa_path = bwa.toRealPath() From a860bf8d8e96a63443d9314fade2524cf6c2af8a Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Thu, 11 Apr 2024 15:07:01 +0200 Subject: [PATCH 160/491] fix bug to make dir --- modules/local/ciriquant/ciriquant/main.nf | 3 +++ 1 file changed, 3 insertions(+) diff --git a/modules/local/ciriquant/ciriquant/main.nf b/modules/local/ciriquant/ciriquant/main.nf index 3ad0c34a..31d80e3a 100644 --- a/modules/local/ciriquant/ciriquant/main.nf +++ b/modules/local/ciriquant/ciriquant/main.nf @@ -24,6 +24,9 @@ process CIRIQUANT { prefix = task.ext.prefix ?: "${meta.id}" def VERSION = '2.1.0' """ + mkdir -p ${prefix} + mkdir -p ${prefix}/circ + touch ${prefix}/circ/${prefix}.ciri CIRIquant \\ -t ${task.cpus} \\ -1 ${reads[0]} \\ From 63cfd78d1ca4c1d61cb81aaafaefecc3662f1aed Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Thu, 11 Apr 2024 15:55:51 +0200 Subject: [PATCH 161/491] cleaner way to set hisat2_prefix --- modules/local/ciriquant/yml/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/ciriquant/yml/main.nf b/modules/local/ciriquant/yml/main.nf index 42de10dc..89c7048f 100644 --- a/modules/local/ciriquant/yml/main.nf +++ b/modules/local/ciriquant/yml/main.nf @@ -19,7 +19,7 @@ process CIRIQUANT_YML { task.ext.when == null || task.ext.when script: - hisat2_prefix = fasta.toString() - ~/.(fa|fasta)$/ + hisat2_prefix = fasta.baseName fasta_path = fasta.toRealPath() gtf_path = gtf.toRealPath() bwa_path = bwa.toRealPath() From cf0a05519a95a40994d6037644e2ef87c6cf4d31 Mon Sep 17 00:00:00 2001 From: MariekeVromman <74721287+MariekeVromman@users.noreply.github.com> Date: Thu, 11 Apr 2024 16:03:41 +0200 Subject: [PATCH 162/491] revert back changes for testing --- modules/local/ciriquant/ciriquant/main.nf | 3 --- 1 file changed, 3 deletions(-) diff --git a/modules/local/ciriquant/ciriquant/main.nf b/modules/local/ciriquant/ciriquant/main.nf index 31d80e3a..3ad0c34a 100644 --- a/modules/local/ciriquant/ciriquant/main.nf +++ b/modules/local/ciriquant/ciriquant/main.nf @@ -24,9 +24,6 @@ process CIRIQUANT { prefix = task.ext.prefix ?: "${meta.id}" def VERSION = '2.1.0' """ - mkdir -p ${prefix} - mkdir -p ${prefix}/circ - touch ${prefix}/circ/${prefix}.ciri CIRIquant \\ -t ${task.cpus} \\ -1 ${reads[0]} \\ From 1c9d74e396c2e27cf5021b89577f1370858a81a7 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 15 Apr 2024 13:51:13 +0200 Subject: [PATCH 163/491] Add parameter for setting STAR limitSjdbInsertNsj --- conf/modules.config | 8 ++++++++ nextflow.config | 1 + nextflow_schema.json | 5 +++++ 3 files changed, 14 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index 875f83ee..bf2cf087 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -197,6 +197,7 @@ if (!params.skip_trimming) { "--outReadsUnmapped None", "--readFilesCommand zcat", "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}", + "--limitSjdbInsertNsj ${params.limitSjdbInsertNsj}", "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}", "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() @@ -228,6 +229,7 @@ if (!params.skip_trimming) { "--readFilesCommand zcat", "--sjdbFileChrStartEnd dataset.SJ.out.tab", "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}", + "--limitSjdbInsertNsj ${params.limitSjdbInsertNsj}", "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}", "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() @@ -395,6 +397,7 @@ if (!params.skip_trimming) { "--outReadsUnmapped None", "--readFilesCommand zcat", "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}", + "--limitSjdbInsertNsj ${params.limitSjdbInsertNsj}", "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}", "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() @@ -426,6 +429,7 @@ if (!params.skip_trimming) { "--readFilesCommand zcat", "--sjdbFileChrStartEnd dataset.SJ.out.tab", "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}", + "--limitSjdbInsertNsj ${params.limitSjdbInsertNsj}", "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}", "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() @@ -447,6 +451,7 @@ if (!params.skip_trimming) { "--outReadsUnmapped None", "--readFilesCommand zcat", "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}", + "--limitSjdbInsertNsj ${params.limitSjdbInsertNsj}", "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}", "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() @@ -479,6 +484,7 @@ if (!params.skip_trimming) { "--readFilesCommand zcat", "--sjdbFileChrStartEnd dataset.SJ.out.tab", "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}", + "--limitSjdbInsertNsj ${params.limitSjdbInsertNsj}", "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}", "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() @@ -500,6 +506,7 @@ if (!params.skip_trimming) { "--outReadsUnmapped None", "--readFilesCommand zcat", "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}", + "--limitSjdbInsertNsj ${params.limitSjdbInsertNsj}", "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}", "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() @@ -532,6 +539,7 @@ if (!params.skip_trimming) { "--readFilesCommand zcat", "--sjdbFileChrStartEnd dataset.SJ.out.tab", "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}", + "--limitSjdbInsertNsj ${params.limitSjdbInsertNsj}", "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}", "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() diff --git a/nextflow.config b/nextflow.config index 628468c4..257145b9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -54,6 +54,7 @@ params { alignSJDBoverhangMin = 10 chimSegmentMin = 10 sjdboverhang = 100 + limitSjdbInsertNsj = 1000000 //> MAPSPLICE seglen = 25 diff --git a/nextflow_schema.json b/nextflow_schema.json index 912bd12b..3cf5fd34 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -125,6 +125,11 @@ "description": "Minimum overhang for annotated junctions", "default": 10 }, + "limitSjdbInsertNsj": { + "type": "integer", + "description": "Maximum number of junction to be inserted to the genome on the fly at the mapping stage, including those from annotations and those detected in the 1st step of the 2-pass run", + "default": 1000000 + }, "chimSegmentMin": { "type": "integer", "description": "Minimum length of chimeric segment length. Must be set to a positive value to detect circular junctions.", From e14ceae239324ca5b5fe4b9c5ab4c1612b6ec1b7 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 19 Apr 2024 10:23:12 +0200 Subject: [PATCH 164/491] Remove problematic ciriquant-yml process --- modules/local/ciriquant/ciriquant/main.nf | 20 ++++++++++-- modules/local/ciriquant/yml/main.nf | 40 ----------------------- subworkflows/local/circrna_discovery.nf | 4 +-- 3 files changed, 19 insertions(+), 45 deletions(-) delete mode 100644 modules/local/ciriquant/yml/main.nf diff --git a/modules/local/ciriquant/ciriquant/main.nf b/modules/local/ciriquant/ciriquant/main.nf index 3ad0c34a..acf435a6 100644 --- a/modules/local/ciriquant/ciriquant/main.nf +++ b/modules/local/ciriquant/ciriquant/main.nf @@ -9,7 +9,10 @@ process CIRIQUANT { input: tuple val(meta), path(reads) - path yml + tuple val(meta2), path(gtf) + tuple val(meta3), path(fasta) + tuple val(meta4), path(bwa) + tuple val(meta5), path(hisat2) output: tuple val(meta), path("${prefix}/${prefix}.gtf"), emit: gtf @@ -24,11 +27,24 @@ process CIRIQUANT { prefix = task.ext.prefix ?: "${meta.id}" def VERSION = '2.1.0' """ + BWA=`which bwa` + HISAT2=`which hisat2` + STRINGTIE=`which stringtie` + SAMTOOLS=`which samtools` + + BWA_FILE=`ls ${bwa}/*.bwt` + BWA_PREFIX=`basename \$BWA_FILE .bwt` + + HISAT2_FILE=`ls ${hisat2}/*.1.ht2` + HISAT2_PREFIX=`basename \$HISAT2_FILE .1.ht2` + + printf "name: ciriquant\\ntools:\\n bwa: \$BWA\\n hisat2: \$HISAT2\\n stringtie: \$STRINGTIE\\n samtools: \$SAMTOOLS\\n\\nreference:\\n fasta: ${fasta}\\n gtf: ${gtf}\\n bwa_index: ${bwa}/\$BWA_PREFIX\\n hisat_index: ${hisat2}/\$HISAT2_PREFIX" > config.yml + CIRIquant \\ -t ${task.cpus} \\ -1 ${reads[0]} \\ -2 ${reads[1]} \\ - --config $yml \\ + --config config.yml \\ --no-gene \\ -o ${prefix} \\ -p ${prefix} diff --git a/modules/local/ciriquant/yml/main.nf b/modules/local/ciriquant/yml/main.nf deleted file mode 100644 index 89c7048f..00000000 --- a/modules/local/ciriquant/yml/main.nf +++ /dev/null @@ -1,40 +0,0 @@ -process CIRIQUANT_YML { - label 'process_single' - - conda "bioconda::ciriquant=1.1.2" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ciriquant:1.1.2--pyhdfd78af_2' : - 'quay.io/biocontainers/ciriquant:1.1.2--pyhdfd78af_2' }" - - input: - tuple val(meta), path(gtf) - tuple val(meta2), path(fasta) - path bwa - path hisat2 - - output: - path "travis.yml" , emit: yml - - when: - task.ext.when == null || task.ext.when - - script: - hisat2_prefix = fasta.baseName - fasta_path = fasta.toRealPath() - gtf_path = gtf.toRealPath() - bwa_path = bwa.toRealPath() - hisat2_path = hisat2.toRealPath() - """ - BWA=`which bwa` - HISAT2=`which hisat2` - STRINGTIE=`which stringtie` - SAMTOOLS=`which samtools` - - # Get first file in bwa index directory - BWA_FILE=`ls ${bwa_path}/*.bwt` - BWA_FILE=`basename \$BWA_FILE .bwt` - - touch travis.yml - printf "name: ciriquant\ntools:\n bwa: \$BWA\n hisat2: \$HISAT2\n stringtie: \$STRINGTIE\n samtools: \$SAMTOOLS\n\nreference:\n fasta: ${fasta_path}\n gtf: ${gtf_path}\n bwa_index: ${bwa_path}/\$BWA_FILE\n hisat_index: ${hisat2_path}/${hisat2_prefix}" >> travis.yml - """ -} diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index b51c821f..0708ee37 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -7,7 +7,6 @@ include { SAMTOOLS_INDEX } from '../../modules/n include { FIND_CIRC_ANCHORS } from '../../modules/local/find_circ/anchors/main' include { FIND_CIRC } from '../../modules/local/find_circ/find_circ/main' include { FIND_CIRC_FILTER } from '../../modules/local/find_circ/filter/main' -include { CIRIQUANT_YML } from '../../modules/local/ciriquant/yml/main' include { CIRIQUANT } from '../../modules/local/ciriquant/ciriquant/main' include { CIRIQUANT_FILTER } from '../../modules/local/ciriquant/filter/main' include { CIRCRNA_FINDER_FILTER } from '../../modules/local/circrna_finder/filter/main' @@ -141,8 +140,7 @@ workflow CIRCRNA_DISCOVERY { // only need path to bwa, only need path to hisat2. // do not want to upset the collect declr for all indices just for this. - CIRIQUANT_YML( ch_gtf, ch_fasta, bwa_index.map{ meta, index -> return index }, hisat2_index.map{ meta, index -> return index } ) - CIRIQUANT( reads, CIRIQUANT_YML.out.yml.collect() ) + CIRIQUANT( reads, ch_gtf, ch_fasta, bwa_index, hisat2_index ) CIRIQUANT_FILTER( CIRIQUANT.out.gtf.map{ meta, gtf -> [ meta + [tool: "ciriquant"], gtf ] }, bsj_reads ) ch_versions = ch_versions.mix(CIRIQUANT.out.versions) From ff100b332a75525d56cb0a7b343525bc2044dc03 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Wed, 28 Feb 2024 19:56:01 +0100 Subject: [PATCH 165/491] Implement common quantification --- conf/modules.config | 9 ++++ modules.json | 5 +++ modules/local/psirc/combine/main.nf | 39 +++++++++++++++++ modules/local/psirc/index/main.nf | 17 ++++++++ modules/local/psirc/quant/main.nf | 23 ++++++++++ .../quantification/transcriptome/main.nf | 42 +++++++++++++++++++ .../nf-core/bedtools/getfasta/environment.yml | 7 ++++ modules/nf-core/bedtools/getfasta/main.nf | 37 ++++++++++++++++ modules/nf-core/bedtools/getfasta/meta.yml | 36 ++++++++++++++++ subworkflows/local/quantification.nf | 34 +++++++++++++++ workflows/circrna/main.nf | 8 ++++ 11 files changed, 257 insertions(+) create mode 100644 modules/local/psirc/combine/main.nf create mode 100644 modules/local/psirc/index/main.nf create mode 100644 modules/local/psirc/quant/main.nf create mode 100644 modules/local/quantification/transcriptome/main.nf create mode 100644 modules/nf-core/bedtools/getfasta/environment.yml create mode 100644 modules/nf-core/bedtools/getfasta/main.nf create mode 100644 modules/nf-core/bedtools/getfasta/meta.yml create mode 100644 subworkflows/local/quantification.nf diff --git a/conf/modules.config b/conf/modules.config index bf2cf087..d0d87018 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -667,6 +667,15 @@ if (!params.skip_trimming) { ] } + withName: COUNTS_TO_BED { + ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$4, \".\", \$4 }'" + ext.suffix = "bed" + } + + withName: TRANSCRIPTOME_FASTA { + ext.args = "-nameOnly" + } + withName: TARGETSCAN_DATABASE { ext.when = { params.module.split(',').contains('mirna_prediction') } publishDir = [ diff --git a/modules.json b/modules.json index c7beb988..8aec025c 100644 --- a/modules.json +++ b/modules.json @@ -5,6 +5,11 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { + "bedtools/getfasta": { + "branch": "master", + "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", + "installed_by": ["modules"] + }, "bedtools/intersect": { "branch": "master", "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", diff --git a/modules/local/psirc/combine/main.nf b/modules/local/psirc/combine/main.nf new file mode 100644 index 00000000..30481139 --- /dev/null +++ b/modules/local/psirc/combine/main.nf @@ -0,0 +1,39 @@ +process PSIRC_COMBINE { + label 'process_single' + + conda "conda-forge::mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6==fccb0c41a243c639e11dd1be7b74f563e624fcca-0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0': + 'biocontainers/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0' }" + + input: + path(files) + + output: + path("counts.tsv"), emit: est_counts + path("tpm.tsv"), emit: tpm + + + script: + """ + #!/usr/bin/env python + + import os + import pandas as pd + + files = "${files}".split(" ") + + counts_df = pd.DataFrame() + tpm_df = pd.DataFrame() + + for f in files: + sample_name = os.path.basename(f)[:-len(".tsv")] + df = pd.read_csv(f, sep="\\t", index_col=0) + + counts_df[sample_name] = df["est_counts"] + tpm_df[sample_name] = df["tpm"] + + counts_df.to_csv("counts.tsv", sep="\\t") + tpm_df.to_csv("tpm.tsv", sep="\\t") + """ +} diff --git a/modules/local/psirc/index/main.nf b/modules/local/psirc/index/main.nf new file mode 100644 index 00000000..bda903d1 --- /dev/null +++ b/modules/local/psirc/index/main.nf @@ -0,0 +1,17 @@ +process PSIRC_INDEX { + tag "${meta.id}" + label 'process_single' + + container "registry.hub.docker.com/bigdatainbiomedicine/psirc" + + input: + tuple val(meta), path(fasta) + + output: + tuple val(meta), path("psirc.index") + + script: + """ + psirc-quant index -i psirc.index --make-unique $fasta + """ +} diff --git a/modules/local/psirc/quant/main.nf b/modules/local/psirc/quant/main.nf new file mode 100644 index 00000000..87ddbb36 --- /dev/null +++ b/modules/local/psirc/quant/main.nf @@ -0,0 +1,23 @@ +process PSIRC_QUANT { + tag "${meta.id}" + label 'process_medium' + + container "registry.hub.docker.com/bigdatainbiomedicine/psirc" + + input: + tuple val(meta), path(reads) + tuple val(meta2), path(index) + + output: + tuple val(meta), path("output/${meta.id}.tsv"), emit: abundance_tsv + tuple val(meta), path("output/${meta.id}.h5"), emit: abundance_h5 + + script: + def single_end = meta.single_end ? "--single -l 76 -s 20" : "" + """ + psirc-quant quant -t $task.cpus -i $index -o output $single_end $reads + + mv output/abundance.tsv output/${meta.id}.tsv + mv output/abundance.h5 output/${meta.id}.h5 + """ +} diff --git a/modules/local/quantification/transcriptome/main.nf b/modules/local/quantification/transcriptome/main.nf new file mode 100644 index 00000000..a21d1429 --- /dev/null +++ b/modules/local/quantification/transcriptome/main.nf @@ -0,0 +1,42 @@ +process EXTRACT_TRANSCRIPTOME { + tag "$meta.id" + label 'process_single' + + conda "bioconda::pandas=1.5.2" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : + 'quay.io/biocontainers/pandas:1.5.2' }" + + input: + tuple val(meta), path(gtf) + + output: + tuple val(meta), path("${meta.id}.transcriptome.bed"), emit: bed + + script: + """ + #!/usr/bin/env python + + import pandas as pd + + columns = ["seqname", "source", "feature", "start", "end", "score", "strand", "frame", "attributes"] + + df = pd.read_csv("${gtf}", sep="\\t", comment="#", names=columns, header=None) + + # Keep only transcript features + df = df[df['feature'] == 'transcript'] + + # Convert attributes to a dictionary + df['attributes'] = df['attributes'].apply(lambda row: dict([[value.strip(r'"') for value in entry.strip().split(' ')] for entry in row.split(';') if entry])) + + # Extract gene_id and transcript_id + df['gene_id'] = df['attributes'].apply(lambda row: row['gene_id']) + df['transcript_id'] = df['attributes'].apply(lambda row: row['transcript_id']) + df['name'] = df['gene_id'] + ":" + df['transcript_id'] + + # Format as bed + df = df[['seqname', 'start', 'end', 'name', 'score', 'strand']] + + df.to_csv("${meta.id}.transcriptome.bed", sep="\\t", index=False, header=False) + """ +} diff --git a/modules/nf-core/bedtools/getfasta/environment.yml b/modules/nf-core/bedtools/getfasta/environment.yml new file mode 100644 index 00000000..a89401f2 --- /dev/null +++ b/modules/nf-core/bedtools/getfasta/environment.yml @@ -0,0 +1,7 @@ +name: bedtools_getfasta +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/getfasta/main.nf b/modules/nf-core/bedtools/getfasta/main.nf new file mode 100644 index 00000000..50549c7d --- /dev/null +++ b/modules/nf-core/bedtools/getfasta/main.nf @@ -0,0 +1,37 @@ +process BEDTOOLS_GETFASTA { + tag "$bed" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_0' : + 'biocontainers/bedtools:2.31.1--hf5e1c6e_0' }" + + input: + path bed + path fasta + + output: + path "*.fa" , emit: fasta + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${bed.baseName}" + """ + bedtools \\ + getfasta \\ + $args \\ + -fi $fasta \\ + -bed $bed \\ + -fo ${prefix}.fa + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ +} diff --git a/modules/nf-core/bedtools/getfasta/meta.yml b/modules/nf-core/bedtools/getfasta/meta.yml new file mode 100644 index 00000000..25fb19a1 --- /dev/null +++ b/modules/nf-core/bedtools/getfasta/meta.yml @@ -0,0 +1,36 @@ +name: bedtools_getfasta +description: extract sequences in a FASTA file based on intervals defined in a feature file. +keywords: + - bed + - fasta + - getfasta +tools: + - bedtools: + description: | + A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. + documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html + licence: ["MIT"] +input: + - bed: + type: file + description: Bed feature file + pattern: "*.{bed}" + - fasta: + type: file + description: Input fasta file + pattern: "*.{fa,fasta}" +output: + - fasta: + type: file + description: Output fasta file with extracted sequences + pattern: "*.{fa}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@joseespinosa" + - "@drpatelh" +maintainers: + - "@joseespinosa" + - "@drpatelh" diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf new file mode 100644 index 00000000..e7502fec --- /dev/null +++ b/subworkflows/local/quantification.nf @@ -0,0 +1,34 @@ +include { EXTRACT_TRANSCRIPTOME } from '../../modules/local/quantification/transcriptome/main' +include { BEDTOOLS_GETFASTA as TRANSCRIPTOME_FASTA } from '../../modules/nf-core/bedtools/getfasta/main' +include { GAWK as COUNTS_TO_BED } from '../../modules/nf-core/gawk/main' +include { CAT_CAT as CAT_TRANSCRIPTOME } from '../../modules/nf-core/cat/cat/main' +include { PSIRC_INDEX } from '../../modules/local/psirc/index/main' +include { PSIRC_QUANT } from '../../modules/local/psirc/quant/main' +include { PSIRC_COMBINE } from '../../modules/local/psirc/combine/main' + +workflow QUANTIFICATION { + take: + ch_gtf + ch_fasta + counts + reads + + main: + EXTRACT_TRANSCRIPTOME(ch_gtf) + COUNTS_TO_BED(counts.map{counts -> [[id: "counts"], counts]}, []) + + CAT_TRANSCRIPTOME( + EXTRACT_TRANSCRIPTOME.out.bed.map{meta, bed -> bed}.mix( + COUNTS_TO_BED.out.output.map{meta, bed -> bed} + ).collect().map(beds -> [[id: "transcriptome"], beds]) + ) + + TRANSCRIPTOME_FASTA( + CAT_TRANSCRIPTOME.out.file_out.map{meta, bed -> bed}, + ch_fasta.map{meta, fasta -> fasta} + ) + + PSIRC_INDEX(TRANSCRIPTOME_FASTA.out.fasta.map{fasta -> [[id: "transcriptome"], fasta]}) + PSIRC_QUANT(reads, PSIRC_INDEX.out.collect()) + PSIRC_COMBINE( PSIRC_QUANT.out.abundance_tsv.map{ meta, data -> data }.collect() ) +} diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 4a614505..0fa1446c 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -29,6 +29,7 @@ include { validateInputSamplesheet } from '../../subworkflows/local/util include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' include { PREPARE_GENOME } from '../../subworkflows/local/prepare_genome' include { CIRCRNA_DISCOVERY } from '../../subworkflows/local/circrna_discovery' +include { QUANTIFICATION } from '../../subworkflows/local/quantification' include { MIRNA_PREDICTION } from '../../subworkflows/local/mirna_prediction' include { DIFFERENTIAL_EXPRESSION } from '../../subworkflows/local/differential_expression' @@ -152,6 +153,13 @@ workflow CIRCRNA { ch_versions = ch_versions.mix(CIRCRNA_DISCOVERY.out.versions) + QUANTIFICATION( + ch_gtf, + ch_fasta, + CIRCRNA_DISCOVERY.out.dea_matrix, + FASTQC_TRIMGALORE.out.reads + ) + // // 3. miRNA prediction // From 27b17a2708ff87df2df6b94d43a760006af8f944 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 07:36:20 +0100 Subject: [PATCH 166/491] Add marking of circRNAs in quantification --- conf/modules.config | 8 ++++++++ subworkflows/local/quantification.nf | 6 +++++- 2 files changed, 13 insertions(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index d0d87018..cfc67d5a 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -676,6 +676,14 @@ if (!params.skip_trimming) { ext.args = "-nameOnly" } + withName: MARK_CIRCULAR { + // GAWK process that marks FASTA headers. + // Leaves headers starting with "ENS" and non-header lines as is. + // Adds "\tC" to the end of the header for all other headers + ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (!/^>/ || /^>ENS/) { print } else { print \$1 \"\\tC\" } }'" + ext.suffix = "marked.fasta" + } + withName: TARGETSCAN_DATABASE { ext.when = { params.module.split(',').contains('mirna_prediction') } publishDir = [ diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index e7502fec..33b32cca 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -2,6 +2,7 @@ include { EXTRACT_TRANSCRIPTOME } from '../../modules/local/q include { BEDTOOLS_GETFASTA as TRANSCRIPTOME_FASTA } from '../../modules/nf-core/bedtools/getfasta/main' include { GAWK as COUNTS_TO_BED } from '../../modules/nf-core/gawk/main' include { CAT_CAT as CAT_TRANSCRIPTOME } from '../../modules/nf-core/cat/cat/main' +include { GAWK as MARK_CIRCULAR } from '../../modules/nf-core/gawk/main' include { PSIRC_INDEX } from '../../modules/local/psirc/index/main' include { PSIRC_QUANT } from '../../modules/local/psirc/quant/main' include { PSIRC_COMBINE } from '../../modules/local/psirc/combine/main' @@ -27,8 +28,11 @@ workflow QUANTIFICATION { CAT_TRANSCRIPTOME.out.file_out.map{meta, bed -> bed}, ch_fasta.map{meta, fasta -> fasta} ) + ch_transcriptome_fasta = TRANSCRIPTOME_FASTA.out.fasta.map{fasta -> [[id: "transcriptome"], fasta]} - PSIRC_INDEX(TRANSCRIPTOME_FASTA.out.fasta.map{fasta -> [[id: "transcriptome"], fasta]}) + MARK_CIRCULAR(ch_transcriptome_fasta, []) + + PSIRC_INDEX(MARK_CIRCULAR.out.output) PSIRC_QUANT(reads, PSIRC_INDEX.out.collect()) PSIRC_COMBINE( PSIRC_QUANT.out.abundance_tsv.map{ meta, data -> data }.collect() ) } From 1d81d4b99c8f427cbb37c1b3e331b8bdf2b87907 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 08:29:23 +0100 Subject: [PATCH 167/491] Increase resources for PSIRC --- modules/local/psirc/index/main.nf | 2 +- modules/local/psirc/quant/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/psirc/index/main.nf b/modules/local/psirc/index/main.nf index bda903d1..daca0402 100644 --- a/modules/local/psirc/index/main.nf +++ b/modules/local/psirc/index/main.nf @@ -1,6 +1,6 @@ process PSIRC_INDEX { tag "${meta.id}" - label 'process_single' + label 'process_high' container "registry.hub.docker.com/bigdatainbiomedicine/psirc" diff --git a/modules/local/psirc/quant/main.nf b/modules/local/psirc/quant/main.nf index 87ddbb36..88ecef04 100644 --- a/modules/local/psirc/quant/main.nf +++ b/modules/local/psirc/quant/main.nf @@ -1,6 +1,6 @@ process PSIRC_QUANT { tag "${meta.id}" - label 'process_medium' + label 'process_high' container "registry.hub.docker.com/bigdatainbiomedicine/psirc" From eb3b3669d8d289aad63483a65a3ba0db838a8446 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 11:01:11 +0100 Subject: [PATCH 168/491] Implement separation of circular and linear counts --- modules/local/psirc/combine/main.nf | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/modules/local/psirc/combine/main.nf b/modules/local/psirc/combine/main.nf index 30481139..4aa23e6a 100644 --- a/modules/local/psirc/combine/main.nf +++ b/modules/local/psirc/combine/main.nf @@ -10,8 +10,13 @@ process PSIRC_COMBINE { path(files) output: - path("counts.tsv"), emit: est_counts - path("tpm.tsv"), emit: tpm + path("linear_counts.tsv"), emit: linear_counts + path("circular_counts.tsv"), emit: circular_counts + path("counts.tsv"), emit: counts + + path("linear_tpm.tsv"), emit: linear_tpm + path("circular_tpm.tsv"), emit: circular_tpm + path("tpm.tsv"), emit: tpm script: @@ -33,7 +38,13 @@ process PSIRC_COMBINE { counts_df[sample_name] = df["est_counts"] tpm_df[sample_name] = df["tpm"] - counts_df.to_csv("counts.tsv", sep="\\t") - tpm_df.to_csv("tpm.tsv", sep="\\t") + for name, df in [("counts", counts_df), ("tpm", tpm_df)]: + is_linear = df.index.str.startswith("ENS") + linear_df = df[is_linear] + circular_df = df[~is_linear] + + linear_df.to_csv(f"linear_{name}.tsv", sep="\\t") + circular_df.to_csv(f"circular_{name}.tsv", sep="\\t") + df.to_csv(f"{name}.tsv", sep="\\t") """ } From 7176cceafe580e1a49e6dab6e8cfc6229bc40f88 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 12:33:38 +0100 Subject: [PATCH 169/491] Implement aggregation of annotations --- conf/modules.config | 13 ++ modules.json | 5 + .../local/annotation/full_annotation/main.nf | 7 +- modules/nf-core/gnu/sort/environment.yml | 7 + modules/nf-core/gnu/sort/main.nf | 51 +++++++ modules/nf-core/gnu/sort/meta.yml | 41 ++++++ modules/nf-core/gnu/sort/tests/main.nf.test | 120 ++++++++++++++++ .../nf-core/gnu/sort/tests/main.nf.test.snap | 136 ++++++++++++++++++ .../gnu/sort/tests/sort_complex.config | 6 + .../gnu/sort/tests/sort_simple_bed.config | 6 + .../gnu/sort/tests/sort_simple_genome.config | 6 + modules/nf-core/gnu/sort/tests/tags.yml | 2 + subworkflows/local/circrna_discovery.nf | 4 + 13 files changed, 402 insertions(+), 2 deletions(-) create mode 100644 modules/nf-core/gnu/sort/environment.yml create mode 100644 modules/nf-core/gnu/sort/main.nf create mode 100644 modules/nf-core/gnu/sort/meta.yml create mode 100644 modules/nf-core/gnu/sort/tests/main.nf.test create mode 100644 modules/nf-core/gnu/sort/tests/main.nf.test.snap create mode 100644 modules/nf-core/gnu/sort/tests/sort_complex.config create mode 100644 modules/nf-core/gnu/sort/tests/sort_simple_bed.config create mode 100644 modules/nf-core/gnu/sort/tests/sort_simple_genome.config create mode 100644 modules/nf-core/gnu/sort/tests/tags.yml diff --git a/conf/modules.config b/conf/modules.config index cfc67d5a..5504f876 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -625,6 +625,7 @@ if (!params.skip_trimming) { } withName: ANNOTATION { + ext.prefix = { "${meta.id}.${meta.tool}.annotated" } publishDir = [ path: { "${params.outdir}/circrna_discovery/${meta.tool}/${meta.id}" }, mode: params.publish_dir_mode, @@ -637,6 +638,18 @@ if (!params.skip_trimming) { ext.suffix = "intersect.bed" } + withName: COMBINE_ANNOTATIONS { + ext.args = "-k 1,1 -k2,2n -k3,3n -u" + ext.suffix = "combined.bed" + } + + withName: REMOVE_SCORE { + // AWK command to replace the 5th column with a dot + // input and output are both BED files + ext.args = "-v FS='\\t' -v OFS='\\t' '{ \$5=\".\"; print }'" + ext.suffix = "noscore.bed" + } + withName: FASTA { ext.when = { params.module.split(',').contains('circrna_discovery') } publishDir = [ diff --git a/modules.json b/modules.json index 8aec025c..ed44f1c4 100644 --- a/modules.json +++ b/modules.json @@ -85,6 +85,11 @@ "git_sha": "dc3527855e7358c6d8400828754c0caa5f11698f", "installed_by": ["modules"] }, + "gnu/sort": { + "branch": "master", + "git_sha": "ca199cfe5aa4f1ea3c41302158f0af2cfaa58957", + "installed_by": ["modules"] + }, "hisat2/align": { "branch": "master", "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", diff --git a/modules/local/annotation/full_annotation/main.nf b/modules/local/annotation/full_annotation/main.nf index f06546ac..bf17b2cc 100644 --- a/modules/local/annotation/full_annotation/main.nf +++ b/modules/local/annotation/full_annotation/main.nf @@ -12,12 +12,15 @@ process ANNOTATION { val(exon_boundary) output: - tuple val(meta), path("${meta.id}.annotation.bed"), emit: bed + tuple val(meta), path("${outfile}"), emit: bed path "versions.yml", emit: versions script: + prefix = task.ext.prefix ?: "${meta.id}.annotation" + suffix = task.ext.suffix ?: "bed" + outfile = "${prefix}.${suffix}" """ - annotation.py --input ${intersection} --exon_boundary ${exon_boundary} --output ${meta.id}.annotation.bed + annotation.py --input ${intersection} --exon_boundary ${exon_boundary} --output ${outfile} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/gnu/sort/environment.yml b/modules/nf-core/gnu/sort/environment.yml new file mode 100644 index 00000000..5c4eb9d1 --- /dev/null +++ b/modules/nf-core/gnu/sort/environment.yml @@ -0,0 +1,7 @@ +name: gnu_sort +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::coreutils=8.25 diff --git a/modules/nf-core/gnu/sort/main.nf b/modules/nf-core/gnu/sort/main.nf new file mode 100644 index 00000000..d0560ee2 --- /dev/null +++ b/modules/nf-core/gnu/sort/main.nf @@ -0,0 +1,51 @@ +process GNU_SORT { + tag "${meta.id}" + label "process_low" + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/coreutils:8.25--1' : + 'biocontainers/coreutils:8.25--1' }" + + input: + tuple val(meta), path(input) + + output: + tuple val(meta), file( "${output_file}" ) , emit: sorted + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + suffix = task.ext.suffix ?: "${input.extension}" + output_file = "${prefix}.${suffix}" + def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + if ("$input" == "$output_file") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + sort ${args} ${input} > ${output_file} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + coreutils: $VERSION + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + suffix = task.ext.suffix ?: "${input.extension}" + output_file = "${prefix}.${suffix}" + def VERSION = "9.1" + + if ("$input" == "$output_file") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + touch ${output_file} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + coreutils: $VERSION + END_VERSIONS + """ +} diff --git a/modules/nf-core/gnu/sort/meta.yml b/modules/nf-core/gnu/sort/meta.yml new file mode 100644 index 00000000..9d961750 --- /dev/null +++ b/modules/nf-core/gnu/sort/meta.yml @@ -0,0 +1,41 @@ +name: "gnu_sort" +description: | + Writes a sorted concatenation of file/s +keywords: + - GNU + - sort + - merge compare +tools: + - sort: + description: "Writes a sorted concatenation of file/s" + homepage: "https://github.com/vgl-hub/gfastats" + documentation: "https://www.gnu.org/software/coreutils/manual/html_node/sort-invocation.html" + licence: ["GPL"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Draft assembly file + pattern: "*.{txt,bed,interval,genome,bins}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sorted: + type: file + description: The sorted txt file generated by sort + pattern: "*.{txt,bed,interval,genome,bins}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@DLBPointon" +maintainers: + - "@DLBPointon" diff --git a/modules/nf-core/gnu/sort/tests/main.nf.test b/modules/nf-core/gnu/sort/tests/main.nf.test new file mode 100644 index 00000000..e4030187 --- /dev/null +++ b/modules/nf-core/gnu/sort/tests/main.nf.test @@ -0,0 +1,120 @@ +nextflow_process { + + name "Test Process GNU_SORT" + script "modules/nf-core/gnu/sort/main.nf" + process "GNU_SORT" + + tag "modules" + tag "modules_nfcore" + tag "gnu" + tag "gnu/sort" + + test("unsorted_genome_sort") { + config "./sort_simple_bed.config" + + when { + process { + """ + input[0] = [ + [id:'genome_test'], + file(params.test_data['generic']['unsorted_data']['unsorted_text']['genome_file'], + checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.sorted[0][1]).name + ).match("genome_sort") + } + ) + } + + } + + test("unsorted_intervals_sort") { + config "./sort_simple_bed.config" + when { + process { + """ + input[0] = [ + [id:'test'], + file(params.test_data['generic']['unsorted_data']['unsorted_text']['intervals'], + checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.sorted[0][1]).name + ).match("interval_sort") + } + ) + } + + } + + test("unsorted_csv_sort") { + config "./sort_complex.config" + + when { + process { + """ + input[0] = [ + [id:'test'], + file(params.test_data['generic']['unsorted_data']['unsorted_text']['numbers_csv'], + checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.sorted[0][1]).name + ).match("csv_sort") + } + ) + } + + } + + test("unsorted_csv_sort_stub") { + config "./sort_complex.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [id:'test'], + file(params.test_data['generic']['unsorted_data']['unsorted_text']['numbers_csv'], + checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + + } + +} diff --git a/modules/nf-core/gnu/sort/tests/main.nf.test.snap b/modules/nf-core/gnu/sort/tests/main.nf.test.snap new file mode 100644 index 00000000..fc20d872 --- /dev/null +++ b/modules/nf-core/gnu/sort/tests/main.nf.test.snap @@ -0,0 +1,136 @@ +{ + "unsorted_csv_sort": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.csv.sorted:md5,0b52d1b4c4a0c6e972c6f94aafd75a1d" + ] + ], + "1": [ + "versions.yml:md5,8ebec31a85721157399cb4faab6e0d26" + ], + "sorted": [ + [ + { + "id": "test" + }, + "test.csv.sorted:md5,0b52d1b4c4a0c6e972c6f94aafd75a1d" + ] + ], + "versions": [ + "versions.yml:md5,8ebec31a85721157399cb4faab6e0d26" + ] + } + ], + "timestamp": "2024-02-22T13:57:33.598003" + }, + "interval_sort": { + "content": [ + "test.bed.sorted" + ], + "timestamp": "2024-02-22T13:57:25.5442" + }, + "unsorted_csv_sort_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.csv.sorted:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,8ebec31a85721157399cb4faab6e0d26" + ], + "sorted": [ + [ + { + "id": "test" + }, + "test.csv.sorted:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,8ebec31a85721157399cb4faab6e0d26" + ] + } + ], + "timestamp": "2024-02-22T13:57:41.490986" + }, + "csv_sort": { + "content": [ + "test.csv.sorted" + ], + "timestamp": "2024-02-22T13:57:33.62444" + }, + "unsorted_genome_sort": { + "content": [ + { + "0": [ + [ + { + "id": "genome_test" + }, + "genome_test.bed.sorted:md5,fd97f7efafdbbfa71d9b560f10b4b048" + ] + ], + "1": [ + "versions.yml:md5,8ebec31a85721157399cb4faab6e0d26" + ], + "sorted": [ + [ + { + "id": "genome_test" + }, + "genome_test.bed.sorted:md5,fd97f7efafdbbfa71d9b560f10b4b048" + ] + ], + "versions": [ + "versions.yml:md5,8ebec31a85721157399cb4faab6e0d26" + ] + } + ], + "timestamp": "2024-02-22T13:57:17.281092" + }, + "genome_sort": { + "content": [ + "genome_test.bed.sorted" + ], + "timestamp": "2024-02-22T13:57:17.340463" + }, + "unsorted_intervals_sort": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed.sorted:md5,abbce903ef263d38b2f71856387799ab" + ] + ], + "1": [ + "versions.yml:md5,8ebec31a85721157399cb4faab6e0d26" + ], + "sorted": [ + [ + { + "id": "test" + }, + "test.bed.sorted:md5,abbce903ef263d38b2f71856387799ab" + ] + ], + "versions": [ + "versions.yml:md5,8ebec31a85721157399cb4faab6e0d26" + ] + } + ], + "timestamp": "2024-02-22T13:57:25.514206" + } +} \ No newline at end of file diff --git a/modules/nf-core/gnu/sort/tests/sort_complex.config b/modules/nf-core/gnu/sort/tests/sort_complex.config new file mode 100644 index 00000000..103eaaf6 --- /dev/null +++ b/modules/nf-core/gnu/sort/tests/sort_complex.config @@ -0,0 +1,6 @@ +process { + withName: GNU_SORT { + ext.args = { "-t ';' -g -k 1,1 -k 2,2" } + ext.suffix = { "csv.sorted" } + } +} \ No newline at end of file diff --git a/modules/nf-core/gnu/sort/tests/sort_simple_bed.config b/modules/nf-core/gnu/sort/tests/sort_simple_bed.config new file mode 100644 index 00000000..d7d52e0f --- /dev/null +++ b/modules/nf-core/gnu/sort/tests/sort_simple_bed.config @@ -0,0 +1,6 @@ +process { + withName: GNU_SORT { + ext.args = { "-k1,1 -k2,2n" } + ext.suffix = { "bed.sorted" } + } +} \ No newline at end of file diff --git a/modules/nf-core/gnu/sort/tests/sort_simple_genome.config b/modules/nf-core/gnu/sort/tests/sort_simple_genome.config new file mode 100644 index 00000000..4dcec385 --- /dev/null +++ b/modules/nf-core/gnu/sort/tests/sort_simple_genome.config @@ -0,0 +1,6 @@ +process { + withName: GNU_SORT { + ext.args = { "-k1,1 -k2,2n" } + ext.suffix = { "genome.sorted" } + } +} \ No newline at end of file diff --git a/modules/nf-core/gnu/sort/tests/tags.yml b/modules/nf-core/gnu/sort/tests/tags.yml new file mode 100644 index 00000000..ac40e376 --- /dev/null +++ b/modules/nf-core/gnu/sort/tests/tags.yml @@ -0,0 +1,2 @@ +gnu/sort: + - "modules/nf-core/gnu/sort/**" diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 0708ee37..c45ac4ff 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -1,5 +1,7 @@ include { ANNOTATION } from '../../modules/local/annotation/full_annotation/main' +include { GNU_SORT as COMBINE_ANNOTATIONS } from '../../modules/nf-core/gnu/sort/main' +include { GAWK as REMOVE_SCORE } from '../../modules/nf-core/gawk/main' include { BEDTOOLS_INTERSECT as INTERSECT_ANNOTATION } from '../../modules/nf-core/bedtools/intersect/main' include { BOWTIE2_ALIGN as FIND_CIRC_ALIGN } from '../../modules/nf-core/bowtie2/align/main' include { SAMTOOLS_VIEW } from '../../modules/nf-core/samtools/view/main' @@ -215,6 +217,8 @@ workflow CIRCRNA_DISCOVERY { INTERSECT_ANNOTATION( circrna_filtered.combine(gtf), [[], []]) ANNOTATION( INTERSECT_ANNOTATION.out.intersect, exon_boundary ) + COMBINE_ANNOTATIONS(ANNOTATION.out.bed.map{ meta, bed -> bed}.collect().map{[[id: "annotation"], it]}) + REMOVE_SCORE( COMBINE_ANNOTATIONS.out.sorted, []) ch_versions = ch_versions.mix(INTERSECT_ANNOTATION.out.versions) ch_versions = ch_versions.mix(ANNOTATION.out.versions) From b7d63010b623ddb8b7ee5306d67142e38ba2f050 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 13:57:15 +0100 Subject: [PATCH 170/491] Update quantification subworkflow --- modules.json | 10 + modules/local/psirc/quant/main.nf | 10 +- .../quantification/transcriptome/main.nf | 58 +- .../nf-core/custom/tx2gene/environment.yml | 9 + modules/nf-core/custom/tx2gene/main.nf | 36 ++ modules/nf-core/custom/tx2gene/meta.yml | 65 ++ .../custom/tx2gene/templates/tx2gene.py | 187 ++++++ .../nf-core/custom/tx2gene/tests/main.nf.test | 81 +++ .../custom/tx2gene/tests/main.nf.test.snap | 60 ++ modules/nf-core/custom/tx2gene/tests/tags.yml | 2 + .../nf-core/tximeta/tximport/environment.yml | 9 + modules/nf-core/tximeta/tximport/main.nf | 47 ++ modules/nf-core/tximeta/tximport/meta.yml | 120 ++++ .../tximeta/tximport/templates/tximport.r | 220 +++++++ .../tximeta/tximport/tests/main.nf.test | 193 ++++++ .../tximeta/tximport/tests/main.nf.test.snap | 594 ++++++++++++++++++ .../nf-core/tximeta/tximport/tests/tags.yml | 2 + subworkflows/local/quantification.nf | 35 +- 18 files changed, 1688 insertions(+), 50 deletions(-) create mode 100644 modules/nf-core/custom/tx2gene/environment.yml create mode 100644 modules/nf-core/custom/tx2gene/main.nf create mode 100644 modules/nf-core/custom/tx2gene/meta.yml create mode 100755 modules/nf-core/custom/tx2gene/templates/tx2gene.py create mode 100644 modules/nf-core/custom/tx2gene/tests/main.nf.test create mode 100644 modules/nf-core/custom/tx2gene/tests/main.nf.test.snap create mode 100644 modules/nf-core/custom/tx2gene/tests/tags.yml create mode 100644 modules/nf-core/tximeta/tximport/environment.yml create mode 100644 modules/nf-core/tximeta/tximport/main.nf create mode 100644 modules/nf-core/tximeta/tximport/meta.yml create mode 100755 modules/nf-core/tximeta/tximport/templates/tximport.r create mode 100644 modules/nf-core/tximeta/tximport/tests/main.nf.test create mode 100644 modules/nf-core/tximeta/tximport/tests/main.nf.test.snap create mode 100644 modules/nf-core/tximeta/tximport/tests/tags.yml diff --git a/modules.json b/modules.json index ed44f1c4..439ea7a3 100644 --- a/modules.json +++ b/modules.json @@ -75,6 +75,11 @@ "git_sha": "de45447d060b8c8b98575bc637a4a575fd0638e1", "installed_by": ["modules"] }, + "custom/tx2gene": { + "branch": "master", + "git_sha": "ec155021a9104441bf6a9bae3b55d1b5b0bfdb3a", + "installed_by": ["modules"] + }, "fastqc": { "branch": "master", "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c", @@ -174,6 +179,11 @@ "branch": "master", "git_sha": "a98418419ae6c9df3cf6cf108d1e1aba71037d5a", "installed_by": ["modules"] + }, + "tximeta/tximport": { + "branch": "master", + "git_sha": "c275c3baac6df8f0c7c500760a0cf014ce7b525d", + "installed_by": ["modules"] } } }, diff --git a/modules/local/psirc/quant/main.nf b/modules/local/psirc/quant/main.nf index 88ecef04..df4e8b54 100644 --- a/modules/local/psirc/quant/main.nf +++ b/modules/local/psirc/quant/main.nf @@ -9,15 +9,13 @@ process PSIRC_QUANT { tuple val(meta2), path(index) output: - tuple val(meta), path("output/${meta.id}.tsv"), emit: abundance_tsv - tuple val(meta), path("output/${meta.id}.h5"), emit: abundance_h5 + tuple val(meta), path("${meta.id}/abundance.tsv"), emit: abundance_tsv + tuple val(meta), path("${meta.id}/abundance.h5"), emit: abundance_h5 + tuple val(meta), path("${meta.id}"), emit: directory script: def single_end = meta.single_end ? "--single -l 76 -s 20" : "" """ - psirc-quant quant -t $task.cpus -i $index -o output $single_end $reads - - mv output/abundance.tsv output/${meta.id}.tsv - mv output/abundance.h5 output/${meta.id}.h5 + psirc-quant quant -t $task.cpus -i $index -o $meta.id $single_end $reads """ } diff --git a/modules/local/quantification/transcriptome/main.nf b/modules/local/quantification/transcriptome/main.nf index a21d1429..4d4d3028 100644 --- a/modules/local/quantification/transcriptome/main.nf +++ b/modules/local/quantification/transcriptome/main.nf @@ -1,42 +1,38 @@ -process EXTRACT_TRANSCRIPTOME { +process TRANSCRIPTOME { tag "$meta.id" - label 'process_single' + label 'process_low' - conda "bioconda::pandas=1.5.2" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : - 'quay.io/biocontainers/pandas:1.5.2' }" + 'https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0' : + 'biocontainers/gffread:0.12.1--h8b12597_0' }" input: - tuple val(meta), path(gtf) + tuple val(meta), path(gff) + tuple val(meta2), path(genome) output: - tuple val(meta), path("${meta.id}.transcriptome.bed"), emit: bed + tuple val(meta), path("$outfile"), emit: transcriptome + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def extension = task.ext.extension ?: "fasta" + outfile = "${prefix}.${extension}" """ - #!/usr/bin/env python - - import pandas as pd - - columns = ["seqname", "source", "feature", "start", "end", "score", "strand", "frame", "attributes"] - - df = pd.read_csv("${gtf}", sep="\\t", comment="#", names=columns, header=None) - - # Keep only transcript features - df = df[df['feature'] == 'transcript'] - - # Convert attributes to a dictionary - df['attributes'] = df['attributes'].apply(lambda row: dict([[value.strip(r'"') for value in entry.strip().split(' ')] for entry in row.split(';') if entry])) - - # Extract gene_id and transcript_id - df['gene_id'] = df['attributes'].apply(lambda row: row['gene_id']) - df['transcript_id'] = df['attributes'].apply(lambda row: row['transcript_id']) - df['name'] = df['gene_id'] + ":" + df['transcript_id'] - - # Format as bed - df = df[['seqname', 'start', 'end', 'name', 'score', 'strand']] - - df.to_csv("${meta.id}.transcriptome.bed", sep="\\t", index=False, header=False) + gffread \\ + -g $genome \\ + -w $outfile \\ + $args \\ + $gff + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gffread: \$(gffread --version 2>&1) + END_VERSIONS """ -} +} \ No newline at end of file diff --git a/modules/nf-core/custom/tx2gene/environment.yml b/modules/nf-core/custom/tx2gene/environment.yml new file mode 100644 index 00000000..a859dc88 --- /dev/null +++ b/modules/nf-core/custom/tx2gene/environment.yml @@ -0,0 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +name: "custom_tx2gene" +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - python=3.9.5 diff --git a/modules/nf-core/custom/tx2gene/main.nf b/modules/nf-core/custom/tx2gene/main.nf new file mode 100644 index 00000000..99c00aa0 --- /dev/null +++ b/modules/nf-core/custom/tx2gene/main.nf @@ -0,0 +1,36 @@ +process CUSTOM_TX2GENE { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/python:3.9--1' : + 'biocontainers/python:3.9--1' }" + + input: + tuple val(meta), path(gtf) + tuple val(meta2), path ("quants/*") + val quant_type + val id + val extra + + output: + tuple val(meta), path("*tx2gene.tsv"), emit: tx2gene + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + template 'tx2gene.py' + + stub: + """ + touch ${meta.id}.tx2gene.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //g') + END_VERSIONS + """ +} diff --git a/modules/nf-core/custom/tx2gene/meta.yml b/modules/nf-core/custom/tx2gene/meta.yml new file mode 100644 index 00000000..d991bf1b --- /dev/null +++ b/modules/nf-core/custom/tx2gene/meta.yml @@ -0,0 +1,65 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "custom_tx2gene" +description: Make a transcript/gene mapping from a GTF and cross-reference with transcript quantifications. +keywords: + - gene + - gtf + - pseudoalignment + - transcript +tools: + - "custom": + description: | + "Custom module to create a transcript to gene mapping from a GTF and + check it against transcript quantifications" + tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tx2gene/main.nf" + licence: ["MIT"] + +input: + - meta: + type: map + description: | + Groovy Map containing reference information related to the GTF file + e.g. `[ id:'yeast' ]` + - gtf: + type: file + description: An annotation file of the reference genome in GTF format + pattern: "*.gtf" + - meta2: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - quants: + type: directory + description: Paths to subdirectories corresponding to + sample-wise runs of Salmon or Kallisto + - quant_type: + type: string + description: Quantification type, 'kallisto' or 'salmon' + - id: + type: string + description: Gene ID attribute in the GTF file (default= gene_id) + - extra: + type: string + description: Extra gene attribute in the GTF file (default= gene_name) + +output: + - meta: + type: map + description: | + Groovy Map containing reference information related to the GTF file + e.g. `[ id:'yeast' ]` + - tx2gene: + type: file + description: A transcript/ gene mapping table in TSV format + pattern: "*.tx2gene.tsv" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@pinin4fjords" +maintainers: + - "@pinin4fjords" diff --git a/modules/nf-core/custom/tx2gene/templates/tx2gene.py b/modules/nf-core/custom/tx2gene/templates/tx2gene.py new file mode 100755 index 00000000..7fd0de64 --- /dev/null +++ b/modules/nf-core/custom/tx2gene/templates/tx2gene.py @@ -0,0 +1,187 @@ +#!/usr/bin/env python3 + +# Written by Lorena Pantano with subsequent reworking by Jonathan Manning. Released under the MIT license. + +import logging +import argparse +import glob +import os +import platform +import re +from collections import Counter, defaultdict, OrderedDict +from collections.abc import Set +from typing import Dict + +# Configure logging +logging.basicConfig(format="%(name)s - %(asctime)s %(levelname)s: %(message)s") +logger = logging.getLogger(__name__) +logger.setLevel(logging.INFO) + +def format_yaml_like(data: dict, indent: int = 0) -> str: + """Formats a dictionary to a YAML-like string. + + Args: + data (dict): The dictionary to format. + indent (int): The current indentation level. + + Returns: + str: A string formatted as YAML. + """ + yaml_str = "" + for key, value in data.items(): + spaces = " " * indent + if isinstance(value, dict): + yaml_str += f"{spaces}{key}:\\n{format_yaml_like(value, indent + 1)}" + else: + yaml_str += f"{spaces}{key}: {value}\\n" + return yaml_str + +def read_top_transcripts(quant_dir: str, file_pattern: str) -> Set[str]: + """ + Read the top 100 transcripts from the quantification file. + + Parameters: + quant_dir (str): Directory where quantification files are located. + file_pattern (str): Pattern to match quantification files. + + Returns: + set: A set containing the top 100 transcripts. + """ + try: + # Find the quantification file within the directory + quant_file_path = glob.glob(os.path.join(quant_dir, "*", file_pattern))[0] + with open(quant_file_path, "r") as file_handle: + # Read the file and extract the top 100 transcripts + return {line.split()[0] for i, line in enumerate(file_handle) if i > 0 and i <= 100} + except IndexError: + # Log an error and raise a FileNotFoundError if the quant file does not exist + logger.error("No quantification files found.") + raise FileNotFoundError("Quantification file not found.") + + +def discover_transcript_attribute(gtf_file: str, transcripts: Set[str]) -> str: + """ + Discover the attribute in the GTF that corresponds to transcripts, prioritizing 'transcript_id'. + + Parameters: + gtf_file (str): Path to the GTF file. + transcripts (Set[str]): A set of transcripts to match in the GTF file. + + Returns: + str: The attribute name that corresponds to transcripts in the GTF file. + """ + + votes = Counter() + with open(gtf_file) as inh: + # Read GTF file, skipping header lines + for line in filter(lambda x: not x.startswith("#"), inh): + cols = line.split("\\t") + + # Use regular expression to correctly split the attributes string + attributes_str = cols[8] + attributes = dict(re.findall(r'(\\S+) "(.*?)(? Dict[str, str]: + """ + Parse the attributes column of a GTF file. + + :param attributes_text: The attributes column as a string. + :return: A dictionary of the attributes. + """ + # Split the attributes string by semicolon and strip whitespace + attributes = attributes_text.strip().split(";") + attr_dict = OrderedDict() + + # Iterate over each attribute pair + for attribute in attributes: + # Split the attribute into key and value, ensuring there are two parts + parts = attribute.strip().split(" ", 1) + if len(parts) == 2: + key, value = parts + # Remove any double quotes from the value + value = value.replace('"', "") + attr_dict[key] = value + + return attr_dict + + +def map_transcripts_to_gene( + quant_type: str, gtf_file: str, quant_dir: str, gene_id: str, extra_id_field: str, output_file: str +) -> bool: + """ + Map transcripts to gene names and write the output to a file. + + Parameters: + quant_type (str): The quantification method used (e.g., 'salmon'). + gtf_file (str): Path to the GTF file. + quant_dir (str): Directory where quantification files are located. + gene_id (str): The gene ID attribute in the GTF file. + extra_id_field (str): Additional ID field in the GTF file. + output_file (str): The output file path. + + Returns: + bool: True if the operation was successful, False otherwise. + """ + # Read the top transcripts based on quantification type + transcripts = read_top_transcripts(quant_dir, "quant.sf" if quant_type == "salmon" else "abundance.tsv") + # Discover the attribute that corresponds to transcripts in the GTF + transcript_attribute = discover_transcript_attribute(gtf_file, transcripts) + + # Open GTF and output file to write the mappings + # Initialize the set to track seen combinations + seen = set() + + with open(gtf_file) as inh, open(output_file, "w") as output_handle: + output_handle.write(f"{transcript_attribute}\\t{gene_id}\\t{extra_id_field}\\n") + # Parse each line of the GTF, mapping transcripts to genes + for line in filter(lambda x: not x.startswith("#"), inh): + cols = line.split("\\t") + attr_dict = parse_attributes(cols[8]) + if gene_id in attr_dict and transcript_attribute in attr_dict: + # Create a unique identifier for the transcript-gene combination + transcript_gene_pair = (attr_dict[transcript_attribute], attr_dict[gene_id]) + + # Check if the combination has already been seen + if transcript_gene_pair not in seen: + # If it's a new combination, write it to the output and add to the seen set + extra_id = attr_dict.get(extra_id_field, attr_dict[gene_id]) + output_handle.write(f"{attr_dict[transcript_attribute]}\\t{attr_dict[gene_id]}\\t{extra_id}\\n") + seen.add(transcript_gene_pair) + + return True + + +# Main function to parse arguments and call the mapping function +if __name__ == "__main__": + if '${task.ext.prefix}' != "null": + prefix = "${task.ext.prefix}." + elif '$meta.id' != "null": + prefix = '${meta.id}.' + else: + prefix = '' + + if not map_transcripts_to_gene('$quant_type', '$gtf', 'quants', '$id', '$extra', f"{prefix}tx2gene.tsv"): + logger.error("Failed to map transcripts to genes.") + + # Write the versions + versions_this_module = {} + versions_this_module["${task.process}"] = {"python": platform.python_version()} + with open("versions.yml", "w") as f: + f.write(format_yaml_like(versions_this_module)) diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test b/modules/nf-core/custom/tx2gene/tests/main.nf.test new file mode 100644 index 00000000..b1559279 --- /dev/null +++ b/modules/nf-core/custom/tx2gene/tests/main.nf.test @@ -0,0 +1,81 @@ +nextflow_process { + + name "Test Process CUSTOM_TX2GENE" + script "../main.nf" + process "CUSTOM_TX2GENE" + + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "custom/tx2gene" + tag "untar" + + setup { + + run("UNTAR") { + script "../../../untar/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz', checkIfExists: true) + ]) + """ + } + } + } + + test("saccharomyces_cerevisiae - gtf") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/genome_gfp.gtf', checkIfExists: true) + ]) + input[1] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] } + input[2] = 'kallisto' + input[3] = 'gene_id' + input[4] = 'gene_name' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.tx2gene).match('tx2gene') }, + { assert snapshot(process.out.versions).match('versions') } + ) + } + } + + test("saccharomyces_cerevisiae - gtf - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/genome_gfp.gtf', checkIfExists: true) + ]) + input[1] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] } + input[2] = 'kallisto' + input[3] = 'gene_id' + input[4] = 'gene_name' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.tx2gene).match('tx2gene - stub') }, + { assert snapshot(process.out.versions).match('versions - stub') } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap new file mode 100644 index 00000000..1e76e10d --- /dev/null +++ b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap @@ -0,0 +1,60 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,fb8145d7fbc6043ba031249b23ecda50" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-26T13:14:18.218251" + }, + "tx2gene": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-26T13:14:18.21054" + }, + "tx2gene - stub": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.tx2gene.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-26T13:14:25.915434" + }, + "versions - stub": { + "content": [ + [ + "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-26T13:14:25.919243" + } +} \ No newline at end of file diff --git a/modules/nf-core/custom/tx2gene/tests/tags.yml b/modules/nf-core/custom/tx2gene/tests/tags.yml new file mode 100644 index 00000000..493fbc3b --- /dev/null +++ b/modules/nf-core/custom/tx2gene/tests/tags.yml @@ -0,0 +1,2 @@ +custom/tx2gene: + - "modules/nf-core/custom/tx2gene/**" diff --git a/modules/nf-core/tximeta/tximport/environment.yml b/modules/nf-core/tximeta/tximport/environment.yml new file mode 100644 index 00000000..24b20222 --- /dev/null +++ b/modules/nf-core/tximeta/tximport/environment.yml @@ -0,0 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +name: "tximeta_tximport" +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - "bioconda::bioconductor-tximeta=1.20.1" diff --git a/modules/nf-core/tximeta/tximport/main.nf b/modules/nf-core/tximeta/tximport/main.nf new file mode 100644 index 00000000..b0cce853 --- /dev/null +++ b/modules/nf-core/tximeta/tximport/main.nf @@ -0,0 +1,47 @@ +process TXIMETA_TXIMPORT { + label "process_medium" + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bioconductor-tximeta%3A1.20.1--r43hdfd78af_0' : + 'biocontainers/bioconductor-tximeta:1.20.1--r43hdfd78af_0' }" + + input: + tuple val(meta), path("quants/*") + tuple val(meta2), path(tx2gene) + val quant_type + + output: + tuple val(meta), path("*gene_tpm.tsv") , emit: tpm_gene + tuple val(meta), path("*gene_counts.tsv") , emit: counts_gene + tuple val(meta), path("*gene_counts_length_scaled.tsv"), emit: counts_gene_length_scaled + tuple val(meta), path("*gene_counts_scaled.tsv") , emit: counts_gene_scaled + tuple val(meta), path("*gene_lengths.tsv") , emit: lengths_gene + tuple val(meta), path("*transcript_tpm.tsv") , emit: tpm_transcript + tuple val(meta), path("*transcript_counts.tsv") , emit: counts_transcript + tuple val(meta), path("*transcript_lengths.tsv") , emit: lengths_transcript + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + template 'tximport.r' + + stub: + """ + touch ${meta.id}.gene_tpm.tsv + touch ${meta.id}.gene_counts.tsv + touch ${meta.id}.gene_counts_length_scaled.tsv + touch ${meta.id}.gene_counts_scaled.tsv + touch ${meta.id}.gene_lengths.tsv + touch ${meta.id}.transcript_tpm.tsv + touch ${meta.id}.transcript_counts.tsv + touch ${meta.id}.transcript_lengths.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bioconductor-tximeta: \$(Rscript -e "library(tximeta); cat(as.character(packageVersion('tximeta')))") + END_VERSIONS + """ +} diff --git a/modules/nf-core/tximeta/tximport/meta.yml b/modules/nf-core/tximeta/tximport/meta.yml new file mode 100644 index 00000000..9ee5fd36 --- /dev/null +++ b/modules/nf-core/tximeta/tximport/meta.yml @@ -0,0 +1,120 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "tximeta_tximport" +description: | + Import transcript-level abundances and estimated counts for gene-level + analysis packages +keywords: + - gene + - kallisto + - pseudoalignment + - salmon + - transcript +tools: + - "tximeta": + description: "Transcript Quantification Import with Automatic Metadata" + homepage: "https://bioconductor.org/packages/release/bioc/html/tximeta.html" + documentation: "https://bioconductor.org/packages/release/bioc/vignettes/tximeta/inst/doc/tximeta.html" + tool_dev_url: "https://github.com/thelovelab/tximeta" + doi: "10.1371/journal.pcbi.1007664" + licence: ["GPL-2"] + +input: + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - quants: + type: directory + description: Paths to subdirectories corresponding to + sample-wise runs of Salmon or Kallisto + - meta2: + type: map + description: | + Groovy Map containing reference information related to the species + reference e.g. `[ id:'yeast' ]` + - tx2gene: + type: file + description: A transcript to gene mapping table such as those generated + by custom/tx2gene + pattern: "*.{csv,tsv}" + - meta3: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - coldata: + type: file + description: | + Optional 'coldata' file equivalent to a sample sheet where the first + column corresponds to the sample names (directory names in the input + salmon/ kallisto results) + pattern: "*.{csv,tsv}" + - quant_type: + type: string + description: Quantification type, 'kallisto' or 'salmon' + +output: + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - tpm_gene: + type: file + description: | + Abundance (TPM) values derived from tximport output after + summarizeToGene(), without a 'countsFromAbundance' specification + pattern: "*gene_tpm.tsv" + - counts_gene: + type: file + description: | + Count values derived from tximport output after + summarizeToGene(), without a 'countsFromAbundance' specification + pattern: "*gene_counts.tsv" + - counts_gene_length_scaled: + type: file + description: | + Count values derived from tximport output after summarizeToGene(), with + a 'countsFromAbundance' specification of 'lengthScaledTPM' + pattern: "*gene_counts_length_scaled.tsv" + - counts_gene_scaled: + type: file + description: | + Count values derived from tximport output after summarizeToGene(), with + a 'countsFromAbundance' specification of 'scaledTPM' + pattern: "*gene_counts_scaled.tsv" + - lengths_gene: + type: file + description: | + Length values derived from tximport output after summarizeToGene(), + without a 'countsFromAbundance' specification + pattern: "*gene_lengths.tsv" + - tpm_transcript: + type: file + description: | + Abundance (TPM) values derived from tximport output without + summarizeToGene(), without a 'countsFromAbundance' specification + pattern: "*transcript_tpm.tsv" + - counts_transcript: + type: file + description: | + Count values derived from tximport output without + summarizeToGene(), without a 'countsFromAbundance' specification + pattern: "*transcript_counts.tsv" + - lengths_transcript: + type: file + description: | + Length values derived from tximport output without summarizeToGene(), + without a 'countsFromAbundance' specification + pattern: "*gene_lengths.tsv" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@pinin4fjords" +maintainers: + - "@pinin4fjords" diff --git a/modules/nf-core/tximeta/tximport/templates/tximport.r b/modules/nf-core/tximeta/tximport/templates/tximport.r new file mode 100755 index 00000000..92f1a9e8 --- /dev/null +++ b/modules/nf-core/tximeta/tximport/templates/tximport.r @@ -0,0 +1,220 @@ +#!/usr/bin/env Rscript --vanilla + +# Script for importing and processing transcript-level quantifications. +# Written by Lorena Pantano, later modified by Jonathan Manning, and released +# under the MIT license. + +# Loading required libraries +library(SummarizedExperiment) +library(tximport) + +################################################ +################################################ +## Functions ## +################################################ +################################################ + +#' Build a table from a SummarizedExperiment object +#' +#' This function takes a SummarizedExperiment object and a specific slot name to extract +#' assay data. It then combines the first two columns of the rowData with the specified +#' assay data slot into a new data table. +#' +#' @param se.obj A SummarizedExperiment object from which to build the table. +#' @param slot The name of the slot in the assays list from which to extract data. +#' +#' @return A data frame combining the first two columns of the rowData with the assay data from the specified slot. + +build_table <- function(se.obj, slot) { + cbind(rowData(se.obj)[,1:2], assays(se.obj)[[slot]]) +} + +#' Write a table to a file from a SummarizedExperiment object with given parameters +#' +#' This function generates a table from a SummarizedExperiment object using specified parameters +#' and writes the resulting table to a file. The file name is constructed using a prefix and a +#' suffix from the parameters, and the table is written with tab separation, without quoting text, +#' and without row names. +#' +#' @param params A list containing the parameters needed for file generation and table writing. +#' The list should include: +#' - `obj`: A SummarizedExperiment object from which to build the table. +#' - `slot`: The name of the slot in the assays list from which to extract data. +#' - `suffix`: Suffix to use for generating the file name. +#' +#' @return NULL The function is called for its side effect of writing a file and does not return anything. + +write_se_table <- function(params, prefix) { + file_name <- paste0(prefix, ".", params\$suffix) + write.table(build_table(params\$obj, params\$slot), file_name, + sep="\t", quote=FALSE, row.names = FALSE) +} + +#' Read Transcript Metadata from a Given Path +#' +#' This function reads transcript metadata from a specified file path. The file is expected to +#' be a tab-separated values file without headers, containing transcript information. The function +#' checks if the file is empty and stops execution with an error message if so. It reads the file +#' into a data frame, expecting columns for transcript IDs, gene IDs, and gene names. Additional +#' processing is done to ensure compatibility with a predefined data structure (e.g., `txi[[1]]`), +#' including adding missing entries and reordering based on the transcript IDs found in `txi[[1]]`. +#' +#' @param tinfo_path The file path to the transcript information file. +#' +#' @return A list containing three elements: +#' - `transcript`: A data frame with transcript IDs, gene IDs, and gene names, indexed by transcript IDs. +#' - `gene`: A data frame with unique gene IDs and gene names. +#' - `tx2gene`: A data frame mapping transcript IDs to gene IDs. + +read_transcript_info <- function(tinfo_path){ + info <- file.info(tinfo_path) + if (info\$size == 0) { + stop("tx2gene file is empty") + } + + transcript_info <- read.csv(tinfo_path, sep="\t", header = TRUE, + col.names = c("tx", "gene_id", "gene_name")) + + extra <- setdiff(rownames(txi[[1]]), as.character(transcript_info[["tx"]])) + transcript_info <- rbind(transcript_info, data.frame(tx=extra, gene_id=extra, gene_name=extra)) + transcript_info <- transcript_info[match(rownames(txi[[1]]), transcript_info[["tx"]]), ] + rownames(transcript_info) <- transcript_info[["tx"]] + + list(transcript = transcript_info, + gene = unique(transcript_info[,2:3]), + tx2gene = transcript_info[,1:2]) +} + +#' Create a SummarizedExperiment Object +#' +#' Constructs a SummarizedExperiment object using provided matrices for counts, abundance, and length, +#' along with metadata for columns and rows. This function facilitates the organization of experimental +#' data (e.g., RNA-seq or other high-throughput data) in a structured format that is convenient for +#' further analyses and visualization. +#' +#' @param counts A matrix or DataFrame containing counts data, with rows as features (e.g., genes) and +#' columns as samples. +#' @param abundance A matrix or DataFrame containing abundance data (e.g., TPM or FPKM) with the same +#' dimensions and row/column names as the counts data. +#' @param length A matrix or DataFrame containing feature lengths, matching the dimensions and row/column +#' names of the counts data. +#' @param col_data A DataFrame containing sample-level metadata, with rows corresponding to columns in the +#' counts, abundance, and length matrices. +#' @param row_data A DataFrame containing feature-level metadata, with rows corresponding to features in +#' the counts, abundance, and length matrices. +#' +#' @return A SummarizedExperiment object containing the supplied data and metadata. + +create_summarized_experiment <- function(counts, abundance, length, col_data, row_data) { + SummarizedExperiment(assays = list(counts = counts, abundance = abundance, length = length), + colData = col_data, + rowData = row_data) +} + +################################################ +################################################ +## Main script starts here ## +################################################ +################################################ + +# Define pattern for file names based on quantification type +pattern <- ifelse('$quant_type' == "kallisto", "abundance.tsv", "quant.sf") +fns <- list.files('quants', pattern = pattern, recursive = T, full.names = T) +names <- basename(dirname(fns)) +names(fns) <- names +dropInfReps <- '$quant_type' == "kallisto" + +# Import transcript-level quantifications +txi <- tximport(fns, type = '$quant_type', txOut = TRUE, dropInfReps = dropInfReps) + +# Read transcript and sample data +transcript_info <- read_transcript_info('$tx2gene') + +# Make coldata just to appease the summarizedexperiment +coldata <- data.frame(files = fns, names = names) +rownames(coldata) <- coldata[["names"]] + +# Create initial SummarizedExperiment object +se <- create_summarized_experiment(txi[["counts"]], txi[["abundance"]], txi[["length"]], + DataFrame(coldata), transcript_info\$transcript) + +# Setting parameters for writing tables +params <- list( + list(obj = se, slot = "abundance", suffix = "transcript_tpm.tsv"), + list(obj = se, slot = "counts", suffix = "transcript_counts.tsv"), + list(obj = se, slot = "length", suffix = "transcript_lengths.tsv") +) + +# Process gene-level data if tx2gene mapping is available +if ("tx2gene" %in% names(transcript_info) && !is.null(transcript_info\$tx2gene)) { + tx2gene <- transcript_info\$tx2gene + gi <- summarizeToGene(txi, tx2gene = tx2gene) + gi.ls <- summarizeToGene(txi, tx2gene = tx2gene, countsFromAbundance = "lengthScaledTPM") + gi.s <- summarizeToGene(txi, tx2gene = tx2gene, countsFromAbundance = "scaledTPM") + + gene_info <- transcript_info\$gene[match(rownames(gi[[1]]), transcript_info\$gene[["gene_id"]]),] + rownames(gene_info) <- gene_info[["tx"]] + + col_data_frame <- DataFrame(coldata) + + # Create gene-level SummarizedExperiment objects + gse <- create_summarized_experiment(gi[["counts"]], gi[["abundance"]], gi[["length"]], + col_data_frame, gene_info) + gse.ls <- create_summarized_experiment(gi.ls[["counts"]], gi.ls[["abundance"]], gi.ls[["length"]], + col_data_frame, gene_info) + gse.s <- create_summarized_experiment(gi.s[["counts"]], gi.s[["abundance"]], gi.s[["length"]], + col_data_frame, gene_info) + + params <- c(params, list( + list(obj = gse, slot = "length", suffix = "gene_lengths.tsv"), + list(obj = gse, slot = "abundance", suffix = "gene_tpm.tsv"), + list(obj = gse, slot = "counts", suffix = "gene_counts.tsv"), + list(obj = gse.ls, slot = "abundance", suffix = "gene_tpm_length_scaled.tsv"), + list(obj = gse.ls, slot = "counts", suffix = "gene_counts_length_scaled.tsv"), + list(obj = gse.s, slot = "abundance", suffix = "gene_tpm_scaled.tsv"), + list(obj = gse.s, slot = "counts", suffix = "gene_counts_scaled.tsv") + )) +} + +# Writing tables for each set of parameters + +prefix <- '' +if ('$task.ext.prefix' != 'null'){ + prefix = '$task.ext.prefix' +} else if ('$meta.id' != 'null'){ + prefix = '$meta.id' +} + +done <- lapply(params, write_se_table, prefix) + +################################################ +################################################ +## R SESSION INFO ## +################################################ +################################################ + +sink(paste(prefix, "R_sessionInfo.log", sep = '.')) +citation("tximeta") +print(sessionInfo()) +sink() + +################################################ +################################################ +## VERSIONS FILE ## +################################################ +################################################ + +r.version <- strsplit(version[['version.string']], ' ')[[1]][3] +tximeta.version <- as.character(packageVersion('tximeta')) + +writeLines( + c( + '"${task.process}":', + paste(' bioconductor-tximeta:', tximeta.version) + ), +'versions.yml') + +################################################ +################################################ +################################################ +################################################ diff --git a/modules/nf-core/tximeta/tximport/tests/main.nf.test b/modules/nf-core/tximeta/tximport/tests/main.nf.test new file mode 100644 index 00000000..5cf6af83 --- /dev/null +++ b/modules/nf-core/tximeta/tximport/tests/main.nf.test @@ -0,0 +1,193 @@ +nextflow_process { + + name "Test Process TXIMETA_TXIMPORT" + script "../main.nf" + process "TXIMETA_TXIMPORT" + + tag "modules" + tag "modules_nfcore" + tag "custom/tx2gene" + tag "tximeta" + tag "tximeta/tximport" + tag "untar" + + test("saccharomyces_cerevisiae - kallisto - gtf") { + + setup { + + run("UNTAR") { + script "../../../untar/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz', checkIfExists: true) + ]) + """ + } + } + run("CUSTOM_TX2GENE") { + script "../../../custom/tx2gene/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/genome_gfp.gtf', checkIfExists: true) + ]) + input[1] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] } + input[2] = 'kallisto' + input[3] = 'gene_id' + input[4] = 'gene_name' + """ + } + } + } + + when { + process { + """ + input[0] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] } + input[1] = CUSTOM_TX2GENE.out.tx2gene + input[2] = 'kallisto' + """ + } + } + + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.counts_gene).match('counts_gene_kallisto') }, + { assert snapshot(process.out.counts_gene_length_scaled).match('counts_gene_length_scaled_kallisto') }, + { assert snapshot(process.out.counts_gene_scaled).match('counts_gene_scaled_kallisto') }, + { assert snapshot(process.out.counts_transcript).match('counts_transcript_kallisto') }, + { assert snapshot(process.out.lengths_gene).match('lengths_gene_kallisto') }, + { assert snapshot(process.out.lengths_transcript).match('lengths_transcript_kallisto') }, + { assert snapshot(process.out.tpm_gene).match('tpm_gene_kallisto') }, + { assert snapshot(process.out.tpm_transcript).match('tpm_transcript_kallisto') }, + { assert snapshot(process.out.versions).match('versions_kallisto') } + ) + } + } + + test("saccharomyces_cerevisiae - kallisto - gtf - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ [], [] ]) + input[1] = Channel.of([ [], [] ]) + input[2] = 'kallisto' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.counts_gene).match('counts_gene_kallisto - stub') }, + { assert snapshot(process.out.counts_gene_length_scaled).match('counts_gene_length_scaled_kallisto - stub') }, + { assert snapshot(process.out.counts_gene_scaled).match('counts_gene_scaled_kallisto - stub') }, + { assert snapshot(process.out.counts_transcript).match('counts_transcript_kallisto - stub') }, + { assert snapshot(process.out.lengths_gene).match('lengths_gene_kallisto - stub') }, + { assert snapshot(process.out.lengths_transcript).match('lengths_transcript_kallisto - stub') }, + { assert snapshot(process.out.tpm_gene).match('tpm_gene_kallisto - stub') }, + { assert snapshot(process.out.tpm_transcript).match('tpm_transcript_kallisto - stub') }, + { assert snapshot(process.out.versions).match('versions_kallisto - stub') } + ) + } + + } + test("saccharomyces_cerevisiae - salmon - gtf") { + + setup { + + run("UNTAR") { + script "../../../untar/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/salmon_results.tar.gz', checkIfExists: true) + ]) + """ + } + } + run("CUSTOM_TX2GENE") { + script "../../../custom/tx2gene/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/genome_gfp.gtf', checkIfExists: true) + ]) + input[1] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] } + input[2] = 'salmon' + input[3] = 'gene_id' + input[4] = 'gene_name' + """ + } + } + } + + when { + process { + """ + input[0] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] } + input[1] = CUSTOM_TX2GENE.out.tx2gene + input[2] = 'salmon' + """ + } + } + + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.counts_gene).match('counts_gene_salmon') }, + { assert snapshot(process.out.counts_gene_length_scaled).match('counts_gene_length_scaled_salmon') }, + { assert snapshot(process.out.counts_gene_scaled).match('counts_gene_scaled_salmon') }, + { assert snapshot(process.out.counts_transcript).match('counts_transcript_salmon') }, + { assert snapshot(process.out.lengths_gene).match('lengths_gene_salmon') }, + { assert snapshot(process.out.lengths_transcript).match('lengths_transcript_salmon') }, + { assert snapshot(process.out.tpm_gene).match('tpm_gene_salmon') }, + { assert snapshot(process.out.tpm_transcript).match('tpm_transcript_salmon') }, + { assert snapshot(process.out.versions).match('versions_salmon') } + ) + } + + } + + test("saccharomyces_cerevisiae - salmon - gtf - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ [], [] ]) + input[1] = Channel.of([ [], [] ]) + input[2] = 'salmon' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.counts_gene).match('counts_gene_salmon - stub') }, + { assert snapshot(process.out.counts_gene_length_scaled).match('counts_gene_length_scaled_salmon - stub') }, + { assert snapshot(process.out.counts_gene_scaled).match('counts_gene_scaled_salmon - stub') }, + { assert snapshot(process.out.counts_transcript).match('counts_transcript_salmon - stub') }, + { assert snapshot(process.out.lengths_gene).match('lengths_gene_salmon - stub') }, + { assert snapshot(process.out.lengths_transcript).match('lengths_transcript_salmon - stub') }, + { assert snapshot(process.out.tpm_gene).match('tpm_gene_salmon - stub') }, + { assert snapshot(process.out.tpm_transcript).match('tpm_transcript_salmon - stub') }, + { assert snapshot(process.out.versions).match('versions_salmon - stub') } + ) + } + } +} + diff --git a/modules/nf-core/tximeta/tximport/tests/main.nf.test.snap b/modules/nf-core/tximeta/tximport/tests/main.nf.test.snap new file mode 100644 index 00000000..fe972d09 --- /dev/null +++ b/modules/nf-core/tximeta/tximport/tests/main.nf.test.snap @@ -0,0 +1,594 @@ +{ + "tpm_transcript_salmon - stub": { + "content": [ + [ + [ + [ + + ], + "[].transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-11T11:35:54.169267" + }, + "lengths_gene_kallisto - stub": { + "content": [ + [ + [ + [ + + ], + "[].gene_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-11T11:35:20.838048" + }, + "counts_gene_scaled_salmon - stub": { + "content": [ + [ + [ + [ + + ], + "[].gene_counts_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-11T11:35:54.139493" + }, + "counts_gene_kallisto - stub": { + "content": [ + [ + [ + [ + + ], + 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b/subworkflows/local/quantification.nf index 33b32cca..2757838d 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -1,11 +1,13 @@ -include { EXTRACT_TRANSCRIPTOME } from '../../modules/local/quantification/transcriptome/main' -include { BEDTOOLS_GETFASTA as TRANSCRIPTOME_FASTA } from '../../modules/nf-core/bedtools/getfasta/main' +include { TRANSCRIPTOME as LINEAR_TRANSCRIPTOME } from '../../modules/local/quantification/transcriptome/main' +include { BEDTOOLS_GETFASTA as CIRCULAR_TRANSCRIPTOME } from '../../modules/nf-core/bedtools/getfasta/main' include { GAWK as COUNTS_TO_BED } from '../../modules/nf-core/gawk/main' include { CAT_CAT as CAT_TRANSCRIPTOME } from '../../modules/nf-core/cat/cat/main' include { GAWK as MARK_CIRCULAR } from '../../modules/nf-core/gawk/main' include { PSIRC_INDEX } from '../../modules/local/psirc/index/main' include { PSIRC_QUANT } from '../../modules/local/psirc/quant/main' include { PSIRC_COMBINE } from '../../modules/local/psirc/combine/main' +include { CUSTOM_TX2GENE } from '../../modules/nf-core/custom/tx2gene/main' +include { TXIMETA_TXIMPORT } from '../../modules/nf-core/tximeta/tximport/main' workflow QUANTIFICATION { take: @@ -15,24 +17,31 @@ workflow QUANTIFICATION { reads main: - EXTRACT_TRANSCRIPTOME(ch_gtf) + LINEAR_TRANSCRIPTOME(ch_gtf, ch_fasta) COUNTS_TO_BED(counts.map{counts -> [[id: "counts"], counts]}, []) - CAT_TRANSCRIPTOME( - EXTRACT_TRANSCRIPTOME.out.bed.map{meta, bed -> bed}.mix( - COUNTS_TO_BED.out.output.map{meta, bed -> bed} - ).collect().map(beds -> [[id: "transcriptome"], beds]) + CIRCULAR_TRANSCRIPTOME( + COUNTS_TO_BED.out.output.map{meta, bed -> bed}, + ch_fasta.map{meta, fasta -> fasta} ) - TRANSCRIPTOME_FASTA( - CAT_TRANSCRIPTOME.out.file_out.map{meta, bed -> bed}, - ch_fasta.map{meta, fasta -> fasta} + CAT_TRANSCRIPTOME( + LINEAR_TRANSCRIPTOME.out.transcriptome.map{meta, fasta -> fasta}.mix( + CIRCULAR_TRANSCRIPTOME.out.fasta + ).collect().map(fastas -> [[id: "transcriptome"], fastas]) ) - ch_transcriptome_fasta = TRANSCRIPTOME_FASTA.out.fasta.map{fasta -> [[id: "transcriptome"], fasta]} - MARK_CIRCULAR(ch_transcriptome_fasta, []) + MARK_CIRCULAR(CAT_TRANSCRIPTOME.out.file_out, []) PSIRC_INDEX(MARK_CIRCULAR.out.output) PSIRC_QUANT(reads, PSIRC_INDEX.out.collect()) - PSIRC_COMBINE( PSIRC_QUANT.out.abundance_tsv.map{ meta, data -> data }.collect() ) + // PSIRC_COMBINE( PSIRC_QUANT.out.abundance_tsv.map{ meta, data -> data }.collect() ) + + CUSTOM_TX2GENE( + ch_gtf, + PSIRC_QUANT.out.directory, + "kallisto", + "gene_id", + "gene_name" + ) } From be0453a89e8f787230509b9769a764835c950728 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 14:50:29 +0100 Subject: [PATCH 171/491] Simplify count merging processes --- bin/circRNA_counts_matrix.py | 50 ------- bin/consolidate_algorithms_intersection.R | 134 ------------------ bin/counts_combined.py | 30 ++++ bin/merge_tools.py | 24 ++++ modules/local/count_matrix/combined/main.nf | 31 ++-- .../local/count_matrix/merge_tools/main.nf | 36 ++--- modules/local/count_matrix/single/main.nf | 4 +- subworkflows/local/circrna_discovery.nf | 29 ++-- subworkflows/local/differential_expression.nf | 10 +- workflows/circrna/main.nf | 6 +- 10 files changed, 95 insertions(+), 259 deletions(-) delete mode 100755 bin/circRNA_counts_matrix.py delete mode 100755 bin/consolidate_algorithms_intersection.R create mode 100755 bin/counts_combined.py create mode 100755 bin/merge_tools.py diff --git a/bin/circRNA_counts_matrix.py b/bin/circRNA_counts_matrix.py deleted file mode 100755 index 3f6e24f6..00000000 --- a/bin/circRNA_counts_matrix.py +++ /dev/null @@ -1,50 +0,0 @@ -#!/usr/bin/env python - -import sys, glob -from collections import defaultdict - -""" -Script to parse circRNA quantification bed files, creating a count matrix suitable for statistical analyses -requires python 2.7 -Author: Declan Bennett @declan93 -License: MIT -""" - - -par = sys.argv -hld = defaultdict(list) -samps = defaultdict(list) - -path = "./" -files = [f for f in glob.glob("*.bed")] - -for fi in files: - name = fi.strip("./").split(".bed")[0] - with open(fi) as IN: - for li in IN: - fds = li.strip().split() - k = "_".join(fds[0:4]) - if k in samps: - samps[k].append((name, fds[4])) - else: - samps[k] = [(name, fds[4])] - - -def Diff(list1, list2): - return list(list(set(list1) - set(list2)) + list(set(list2) - set(list1))) - - -tmp = [x.replace(".bed", "") for x in files] -print("Chr\tStart\tStop\tStrand\t" + "\t".join([x for x in tmp])) - -for k, v in samps.items(): - disj = Diff(tmp, [a_tuple[0] for a_tuple in v]) - for val in disj: - v.append((val, "0")) - li = [] - for h in tmp: - for x in v: - if x[0] == h: - li.append(x[1]) - print("\t".join(k.split("_")) + "\t" + "\t".join(li)) -sys.exit() diff --git a/bin/consolidate_algorithms_intersection.R b/bin/consolidate_algorithms_intersection.R deleted file mode 100755 index 1fbd27b4..00000000 --- a/bin/consolidate_algorithms_intersection.R +++ /dev/null @@ -1,134 +0,0 @@ -#!/usr/bin/env Rscript - -## Script to consolidate circRNAs across multiple tools. Allow user -## to apply 'max' or 'mean' aggregate function to those called by multiple -## tools. -## Author: Barry Digby -## License: MIT - -get_args <- function(){ - - argp <- arg_parser( - description="Script to take tool outputs and bring forward circRNAs called by at least n tools", - hide.opts=TRUE) - - argp <- add_argument( - parser=argp, - arg="samples", - short="s", - help="csv file listing tool output files that are not empty", - default="samples.csv") - - argp <- add_argument( - parser=argp, - arg="n_tools", - short="n", - help="number of tools circrna must be called by") - - argp <- add_argument( - parser=argp, - arg="duplicates_fun", - short="d", - help="how to handle counts for duplicate circRNAs [mean, max]") - - argv <- parse_args( - parser=argp, - argv=commandArgs(trailingOnly=TRUE)) - - return(argv) -} - -giveError <- function(message){ - cat(paste("\n", message, sep="")) - quit() -} - -usage <- function(){giveError("Usage: consolidate_algorithms.R samples.csv ${params.n_tools}")} - -## script body - -stage_data <- function(samples, n_tools, duplicates_fun){ - - inputdata <- list() - - samples <- read.csv(samples, sep="\t", header=F, stringsAsFactors=FALSE) - inputdata$samples <- samples - inputdata$n_tools <- n_tools - inputdata$duplicates_fun <- duplicates_fun - - return(inputdata) -} - - -## read in files and make circRNA IDs. - -main <- function(inputdata){ - - samples <- inputdata$samples - n_tools <- inputdata$n_tools - duplicates_fun <- inputdata$duplicates_fun - - ## intit lists - dflist <- list() - idlist <- list() - - # loop over samples, append to counts mat and IDs to respective lists - for(i in 1:nrow(samples)){ - file_handle <- file.path(paste("./", samples$V1[i], sep="")) - df <- read.table(file_handle, sep="\t", header=F, stringsAsFactors=FALSE) - dflist[[i]] <- read.table(file_handle, sep="\t", header=F, stringsAsFactors=FALSE) - idlist[[i]] <- with(df, paste0(V1, sep="-", V2, sep=":", V3, sep="-", V4)) - } - - # place all ids in a vector - vec <- unlist(idlist) - - # make table to get ID ocurrence count - tab <- table(vec) - - # now filter by ocurrence i.e must have been in "n" tools - filt_id <- names(tab)[tab >= n_tools] - - # make matser df, append ID - mat <- do.call("rbind", dflist) - mat$ID <- with(mat, paste0(V1, sep="-", V2, sep=":", V3, sep="-", V4)) - - # extract circrnas called by n tools - mat <- subset(mat, mat$ID %in% filt_id) - print(head(mat)) - # handle duplicate circRNA counts: - if(duplicates_fun == "max"){ - - # Take the max value for duplicate circRNAs - mat <- mat[order(mat$ID, -abs(mat$V5)),] - mat <- mat[!duplicated(mat$ID),] - mat <- subset(mat, select=-c(ID)) - }else{ - - # Remove duplicates like above to generate row indices - tmp <- mat[order(mat$ID, -abs(mat$V5)),] - tmp <- tmp[!duplicated(tmp$ID),] - # Now Take average values, append back to tmp. - mat <- setNames(aggregate(mat$V5, list(mat$ID), FUN=mean), c("ID", "V5")) - stopifnot(nrow(tmp)==nrow(mat)) - tmp <- subset(tmp, select=c(V1,V2,V3,V4)) - mat <- cbind(tmp,mat) - # round up to nearest integer - mat$V5 <- ceiling(mat$V5) - mat <- subset(mat, select=-c(ID)) - } - - write.table(mat, "combined_counts.bed", sep="\t", row.names = F, col.names = F, quote = F) - -} - -## error messages, library load -options(error=function()traceback(2)) -suppressPackageStartupMessages(library("argparser")) - -## initiate script -arg <- get_args() - -inputdata <- stage_data(arg$samples, arg$n_tools, arg$duplicates_fun) - -x <- main(inputdata) diff --git a/bin/counts_combined.py b/bin/counts_combined.py new file mode 100755 index 00000000..cb40c588 --- /dev/null +++ b/bin/counts_combined.py @@ -0,0 +1,30 @@ +#!/usr/bin/env python3 + +import argparse +import pandas as pd +import os + +parser = argparse.ArgumentParser(description='Merge counts across tools for a single sample') +parser.add_argument('--beds', type=str, nargs='+', help='List of bed files to merge') +parser.add_argument('--out_bed', type=str, help='Output bed file') +parser.add_argument('--out_tsv', type=str, help='Output tsv file') + +args = parser.parse_args() + +columns = ['chr', 'start', 'end', 'strand', 'count', 'tools'] +dfs = {os.path.basename(bed).split('.')[0]: pd.read_csv(bed, + sep='\t', + header=None, + names=columns, + index_col=[0, 1, 2, 3]) + .drop('tools', axis=1) for bed in args.beds} + +dfs = [df.rename(columns={'count': sample}) for sample, df in dfs.items()] + +df = pd.concat(dfs, axis=1) +df = df.fillna(0).astype(int) + +df.to_csv(args.out_bed, sep='\t') + +df.index = df.index.map(lambda x: f'{x[0]}:{x[1]}-{x[2]}:{x[3]}') +df.to_csv(args.out_tsv, sep='\t') \ No newline at end of file diff --git a/bin/merge_tools.py b/bin/merge_tools.py new file mode 100755 index 00000000..4246d0fd --- /dev/null +++ b/bin/merge_tools.py @@ -0,0 +1,24 @@ +#!/usr/bin/env python3 + +import argparse +import pandas as pd + +parser = argparse.ArgumentParser(description='Merge counts across tools for a single sample') +parser.add_argument('--beds', type=str, nargs='+', help='List of bed files to merge') +parser.add_argument('--tool_filter', type=int, help='Minimum number of tools to keep a circRNA') +parser.add_argument('--duplicates_fun', type=str, help='Function to apply to duplicates', choices=['sum', 'mean', 'max', 'min']) +parser.add_argument('--output', type=str, help='Output file') + +args = parser.parse_args() + +columns = ['chr', 'start', 'end', 'strand', 'count'] +dfs = [pd.read_csv(bed, sep='\t', header=None, names=columns) for bed in args.beds] +df = pd.concat(dfs) + +df['tool_count'] = 1 + +df = df.groupby(['chr', 'start', 'end', 'strand']).agg({'count': args.duplicates_fun, + 'tool_count': 'sum'}).reset_index() +df = df[df['tool_count'] >= args.tool_filter] + +df.to_csv(args.output, sep='\t', index=False, header=False) diff --git a/modules/local/count_matrix/combined/main.nf b/modules/local/count_matrix/combined/main.nf index 0c4719ab..5b3bc28a 100644 --- a/modules/local/count_matrix/combined/main.nf +++ b/modules/local/count_matrix/combined/main.nf @@ -1,37 +1,28 @@ process COUNTS_COMBINED { - label 'process_low' + label "process_single" - conda "conda-forge::r-base=3.6.3 conda-forge::python=2.7.15 conda-forge::r-argparser=0.6 conda-forge::r-dplyr=1.0.5" + conda "conda-forge::mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6==fccb0c41a243c639e11dd1be7b74f563e624fcca-0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-5fbffedf7f529cf3c5093b976deb4290f5e1267a:3456f1432b1c9dad42815275abe2d6cb6f26fd94-0' : - 'quay.io/biocontainers/mulled-v2-5fbffedf7f529cf3c5093b976deb4290f5e1267a:3456f1432b1c9dad42815275abe2d6cb6f26fd94-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0': + 'biocontainers/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0' }" input: - path(bed) + path(beds) output: - path("circRNA_matrix.txt"), emit: dea_matrix - path("count_matrix.txt") , emit: clr_matrix + path("merged_counts.bed") , emit: counts_bed + path("merged_counts.tsv") , emit: counts_tsv path "versions.yml" , emit: versions - when: - task.ext.when == null || task.ext.when - script: - def args = task.ext.args ?: '' """ - circRNA_counts_matrix.py > matrix.txt - ## handle non-canon chromosomes here (https://stackoverflow.com/questions/71479919/joining-columns-based-on-number-of-fields) - n_samps=\$(ls *.bed | wc -l) - canon=\$(awk -v a="\$n_samps" 'BEGIN {print a + 4}') - awk -v n="\$canon" '{ for (i = 2; i <= NF - n + 1; ++i) { \$1 = \$1"-"\$i; \$i=""; } } 1' matrix.txt | awk -v OFS="\\t" '\$1=\$1' > circRNA_matrix.txt - reformat_count_matrix.R + counts_combined.py --beds ${beds} --out_bed merged_counts.bed --out_tsv merged_counts.tsv cat <<-END_VERSIONS > versions.yml "${task.process}": - awk: \$(awk --version | head -n 1 | cut -d' ' -f3 | sed 's/,//g') - r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//') - dplyr: \$(Rscript -e "library(dplyr); cat(as.character(packageVersion('dplyr')))") + python: \$(python --version | sed 's/Python //g') + pandas: \$(python -c "import pandas; print(pandas.__version__)") + numpy: \$(python -c "import numpy; print(numpy.__version__)") END_VERSIONS """ } diff --git a/modules/local/count_matrix/merge_tools/main.nf b/modules/local/count_matrix/merge_tools/main.nf index 106df47b..55bdcde0 100644 --- a/modules/local/count_matrix/merge_tools/main.nf +++ b/modules/local/count_matrix/merge_tools/main.nf @@ -1,45 +1,31 @@ process MERGE_TOOLS { tag "$meta.id" - label 'process_low' + label "process_single" - conda "conda-forge::r-base=3.6.3 conda-forge::python=2.7.15 conda-forge::r-argparser=0.6 conda-forge::r-dplyr=1.0.5" + conda "conda-forge::mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6==fccb0c41a243c639e11dd1be7b74f563e624fcca-0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-5fbffedf7f529cf3c5093b976deb4290f5e1267a:3456f1432b1c9dad42815275abe2d6cb6f26fd94-0' : - 'quay.io/biocontainers/mulled-v2-5fbffedf7f529cf3c5093b976deb4290f5e1267a:3456f1432b1c9dad42815275abe2d6cb6f26fd94-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0': + 'biocontainers/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0' }" input: - tuple val(meta), path(bed) + tuple val(meta), path(beds) val(tool_filter) val(duplicates_fun) output: - tuple val(meta), path("${prefix}.bed"), emit: merged - path "versions.yml" , emit: versions + tuple val(meta), path("${meta.id}.merged.bed"), emit: merged - when: - task.ext.when == null || task.ext.when + path "versions.yml" , emit: versions script: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" """ - ## make list of files for R to read - ls *.bed > samples.csv - - ## Add catch for empty bed file and delete - check_empty.sh - - ## Use intersection of "n" (params.tool_filter) circRNAs called by tools - ## remove duplicate IDs, keep highest count. - consolidate_algorithms_intersection.R samples.csv $tool_filter $duplicates_fun - mv combined_counts.bed ${prefix}.bed + merge_tools.py --beds ${beds} --tool_filter ${tool_filter} --duplicates_fun ${duplicates_fun} --output ${meta.id}.merged.bed cat <<-END_VERSIONS > versions.yml "${task.process}": - r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//') - argparser: \$(Rscript -e "library(arparser); cat(as.character(packageVersion('argparser')))") - dplyr: \$(Rscript -e "library(dplyr); cat(as.character(packageVersion('dplyr')))") - python: \$(python --version | sed -e 's/Python //g') + python: \$(python --version | sed 's/Python //g') + pandas: \$(python -c "import pandas; print(pandas.__version__)") + numpy: \$(python -c "import numpy; print(numpy.__version__)") END_VERSIONS """ } diff --git a/modules/local/count_matrix/single/main.nf b/modules/local/count_matrix/single/main.nf index 20e1b975..a7c01833 100644 --- a/modules/local/count_matrix/single/main.nf +++ b/modules/local/count_matrix/single/main.nf @@ -11,8 +11,8 @@ process COUNTS_SINGLE { tuple val(meta), path(bed) output: - path("circRNA_matrix.txt"), emit: dea_matrix - path("count_matrix.txt") , emit: clr_matrix + path("circRNA_matrix.txt"), emit: counts_bed + path("count_matrix.txt") , emit: counts_tsv path "versions.yml" , emit: versions when: diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index c45ac4ff..5e88dcaf 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -244,31 +244,20 @@ workflow CIRCRNA_DISCOVERY { tools_selected = params.tool.split(',').collect{it.trim().toLowerCase()} - if( tools_selected.size() > 1){ + MERGE_TOOLS( ch_matrix.map{ meta, bed -> [ [id: meta.id], bed ] }.groupTuple(), + tools_selected.size() > 1 ? tool_filter : 1, duplicates_fun ) - MERGE_TOOLS( ch_matrix.map{ meta, bed -> [ [id: meta.id], bed ] }.groupTuple(), tool_filter, duplicates_fun ) + COUNTS_COMBINED( MERGE_TOOLS.out.merged.map{ meta, bed -> bed }.collect() ) - COUNTS_COMBINED( MERGE_TOOLS.out.merged.map{ meta, bed -> return [ bed ] }.collect() ) - - dea_matrix = COUNTS_COMBINED.out.dea_matrix - clr_matrix = COUNTS_COMBINED.out.clr_matrix - ch_versions = ch_versions.mix(MERGE_TOOLS.out.versions) - ch_versions = ch_versions.mix(COUNTS_COMBINED.out.versions) - - }else{ - - COUNTS_SINGLE( ch_matrix.map{ meta, bed -> [ [tool: meta.tool], bed ] }.groupTuple() ) - - dea_matrix = COUNTS_SINGLE.out.dea_matrix - clr_matrix = COUNTS_SINGLE.out.clr_matrix - ch_versions = ch_versions.mix(COUNTS_SINGLE.out.versions) - - } + counts_bed = COUNTS_COMBINED.out.counts_bed + counts_tsv = COUNTS_COMBINED.out.counts_tsv + ch_versions = ch_versions.mix(MERGE_TOOLS.out.versions) + ch_versions = ch_versions.mix(COUNTS_COMBINED.out.versions) emit: circrna_bed12 = ANNOTATION.out.bed fasta = FASTA.out.analysis_fasta versions = ch_versions - dea_matrix - clr_matrix + counts_bed + counts_tsv } diff --git a/subworkflows/local/differential_expression.nf b/subworkflows/local/differential_expression.nf index f341fd3f..f4454af6 100644 --- a/subworkflows/local/differential_expression.nf +++ b/subworkflows/local/differential_expression.nf @@ -17,8 +17,8 @@ workflow DIFFERENTIAL_EXPRESSION { hisat2_index splice_sites phenotype - dea_matrix - clr_matrix + counts_bed + counts_tsv species ensembl_map exon_boundary @@ -49,7 +49,7 @@ workflow DIFFERENTIAL_EXPRESSION { // Circular, Linear Differential Expression // - DESEQ2_DIFFERENTIAL_EXPRESSION( STRINGTIE_PREPDE.out.gene_matrix, phenotype, dea_matrix, species, ensembl_map ) + DESEQ2_DIFFERENTIAL_EXPRESSION( STRINGTIE_PREPDE.out.gene_matrix, phenotype, counts_bed, species, ensembl_map ) // // CircRNA - Host Gene Ratio tests @@ -57,8 +57,8 @@ workflow DIFFERENTIAL_EXPRESSION { ch_biotypes = Channel.fromPath("${projectDir}/bin/unwanted_biotypes.txt") - PARENT_GENE( clr_matrix, gtf, ch_biotypes.collect(), exon_boundary ) - PREPARE_CLR_TEST( STRINGTIE_PREPDE.out.gene_matrix, clr_matrix, PARENT_GENE.out.circ_host_map, gtf ) + PARENT_GENE( counts_tsv, gtf, ch_biotypes.collect(), exon_boundary ) + PREPARE_CLR_TEST( STRINGTIE_PREPDE.out.gene_matrix, counts_tsv, PARENT_GENE.out.circ_host_map, gtf ) CIRCTEST( PREPARE_CLR_TEST.out.circular, PREPARE_CLR_TEST.out.linear, phenotype ) ch_versions = ch_versions.mix(HISAT2_ALIGN.out.versions) diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 0fa1446c..ffbb2c51 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -156,7 +156,7 @@ workflow CIRCRNA { QUANTIFICATION( ch_gtf, ch_fasta, - CIRCRNA_DISCOVERY.out.dea_matrix, + CIRCRNA_DISCOVERY.out.counts_bed, FASTQC_TRIMGALORE.out.reads ) @@ -185,8 +185,8 @@ workflow CIRCRNA { hisat2_index, PREPARE_GENOME.out.splice_sites, ch_phenotype, - CIRCRNA_DISCOVERY.out.dea_matrix, - CIRCRNA_DISCOVERY.out.clr_matrix, + CIRCRNA_DISCOVERY.out.counts_bed, + CIRCRNA_DISCOVERY.out.counts_tsv, ch_species, ch_ensembl_database_map, params.exon_boundary From be5f1341a1fa051de40abe6b42865ad4ad376d9f Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 15:36:03 +0100 Subject: [PATCH 172/491] Use tximport --- conf/modules.config | 4 ++-- modules/local/psirc/quant/main.nf | 2 -- subworkflows/local/quantification.nf | 6 ++++++ 3 files changed, 8 insertions(+), 4 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 5504f876..47097587 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -685,8 +685,8 @@ if (!params.skip_trimming) { ext.suffix = "bed" } - withName: TRANSCRIPTOME_FASTA { - ext.args = "-nameOnly" + withName: CIRCULAR_TRANSCRIPTOME { + ext.args = "-s" } withName: MARK_CIRCULAR { diff --git a/modules/local/psirc/quant/main.nf b/modules/local/psirc/quant/main.nf index df4e8b54..aa949e3e 100644 --- a/modules/local/psirc/quant/main.nf +++ b/modules/local/psirc/quant/main.nf @@ -9,8 +9,6 @@ process PSIRC_QUANT { tuple val(meta2), path(index) output: - tuple val(meta), path("${meta.id}/abundance.tsv"), emit: abundance_tsv - tuple val(meta), path("${meta.id}/abundance.h5"), emit: abundance_h5 tuple val(meta), path("${meta.id}"), emit: directory script: diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index 2757838d..a1739611 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -44,4 +44,10 @@ workflow QUANTIFICATION { "gene_id", "gene_name" ) + + TXIMETA_TXIMPORT( + PSIRC_QUANT.out.directory, + CUSTOM_TX2GENE.out.tx2gene, + "kallisto" + ) } From 9723eaf2d302f0e33e136be9b8babdf8786a4d4d Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 17:07:22 +0100 Subject: [PATCH 173/491] Finalize quantification --- bin/combine_quantification.py | 51 +++++++++++++++++++ conf/modules.config | 17 ++++--- modules/local/psirc/combine/main.nf | 50 ------------------ .../combine_quantification/main.nf | 35 +++++++++++++ subworkflows/local/circrna_discovery.nf | 5 +- subworkflows/local/quantification.nf | 35 ++++++++----- workflows/circrna/main.nf | 3 +- 7 files changed, 124 insertions(+), 72 deletions(-) create mode 100755 bin/combine_quantification.py delete mode 100644 modules/local/psirc/combine/main.nf create mode 100644 modules/local/quantification/combine_quantification/main.nf diff --git a/bin/combine_quantification.py b/bin/combine_quantification.py new file mode 100755 index 00000000..d26ade6c --- /dev/null +++ b/bin/combine_quantification.py @@ -0,0 +1,51 @@ +#!/usr/bin/env python3 + +import argparse +import pandas as pd +import os + +parser = argparse.ArgumentParser(description='Merge quantification files into a single file') +parser.add_argument('--inputs', type=str, nargs='+', help='List input files to merge') +parser.add_argument('--tx2gene', type=str, help='Path to tx2gene file') +parser.add_argument('--circ_annotation', type=str, help='Path to circRNA annotation file') +parser.add_argument('--out_linear', type=str, help='Path to output linear RNA quantification file') +parser.add_argument('--out_circular', type=str, help='Path to output circRNA quantification file') +parser.add_argument('--out_combined', type=str, help='Path to output combined quantification file') + +args = parser.parse_args() + +df_annotation = pd.read_csv(args.circ_annotation, + sep='\t', header=None, + names=['chr', 'start', 'end', 'name', 'score', 'strand', 'type', 'gene', 'transcript'], + index_col=['name']) + +df_tx2gene = pd.read_csv(args.tx2gene, sep='\t') + +dfs = [pd.read_csv(f, sep='\t', index_col=["gene_id", "gene_name"]) for f in args.inputs] +df_combined = pd.concat(dfs, axis=1, sort=True) + +# Split linear and circular +linear_mask = df_combined.index.get_level_values(0) \ + .isin(df_tx2gene["gene_id"]) +df_linear = df_combined[linear_mask].copy() +df_circular = df_combined[~linear_mask].copy() + +df_linear.to_csv(args.out_linear, sep='\t') + +# Perform annotation +df_annotation["annotation"] = df_annotation.apply(lambda row: 'intergenic' if row['type'] == 'intergenic-circRNA' else row['gene'], axis=1) +annotation_dict = df_annotation["annotation"].to_dict() + +df_circular.reset_index(inplace=True) +df_circular["gene_name"] = df_circular['gene_id'].map(annotation_dict) +df_circular.set_index(["gene_id", "gene_name"], inplace=True) + +df_circular.to_csv(args.out_circular, sep='\t') + +# Save combined +df_linear["type"] = "gene" +df_circular["type"] = "circRNA" + +df_combined = pd.concat([df_linear, df_circular], axis=0, sort=True) + +df_combined.to_csv(args.out_combined, sep='\t') \ No newline at end of file diff --git a/conf/modules.config b/conf/modules.config index 47097587..4bfcba71 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -643,11 +643,9 @@ if (!params.skip_trimming) { ext.suffix = "combined.bed" } - withName: REMOVE_SCORE { - // AWK command to replace the 5th column with a dot - // input and output are both BED files - ext.args = "-v FS='\\t' -v OFS='\\t' '{ \$5=\".\"; print }'" - ext.suffix = "noscore.bed" + withName: REMOVE_SCORE_STRAND { + ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3, \".\", \".\", \$7, \$8, \$9 }'" + ext.suffix = "tidy.bed" } withName: FASTA { @@ -681,12 +679,17 @@ if (!params.skip_trimming) { } withName: COUNTS_TO_BED { - ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$4, \".\", \$4 }'" + ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3, \".\", \".\" }'" ext.suffix = "bed" } + withName: UNIQUE_REGIONS { + ext.args = "-k 1,1 -k2,2n -k3,3n -u" + ext.suffix = "unique.bed" + } + withName: CIRCULAR_TRANSCRIPTOME { - ext.args = "-s" + ext.args = "-nameOnly" } withName: MARK_CIRCULAR { diff --git a/modules/local/psirc/combine/main.nf b/modules/local/psirc/combine/main.nf deleted file mode 100644 index 4aa23e6a..00000000 --- a/modules/local/psirc/combine/main.nf +++ /dev/null @@ -1,50 +0,0 @@ -process PSIRC_COMBINE { - label 'process_single' - - conda "conda-forge::mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6==fccb0c41a243c639e11dd1be7b74f563e624fcca-0" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0': - 'biocontainers/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0' }" - - input: - path(files) - - output: - path("linear_counts.tsv"), emit: linear_counts - path("circular_counts.tsv"), emit: circular_counts - path("counts.tsv"), emit: counts - - path("linear_tpm.tsv"), emit: linear_tpm - path("circular_tpm.tsv"), emit: circular_tpm - path("tpm.tsv"), emit: tpm - - - script: - """ - #!/usr/bin/env python - - import os - import pandas as pd - - files = "${files}".split(" ") - - counts_df = pd.DataFrame() - tpm_df = pd.DataFrame() - - for f in files: - sample_name = os.path.basename(f)[:-len(".tsv")] - df = pd.read_csv(f, sep="\\t", index_col=0) - - counts_df[sample_name] = df["est_counts"] - tpm_df[sample_name] = df["tpm"] - - for name, df in [("counts", counts_df), ("tpm", tpm_df)]: - is_linear = df.index.str.startswith("ENS") - linear_df = df[is_linear] - circular_df = df[~is_linear] - - linear_df.to_csv(f"linear_{name}.tsv", sep="\\t") - circular_df.to_csv(f"circular_{name}.tsv", sep="\\t") - df.to_csv(f"{name}.tsv", sep="\\t") - """ -} diff --git a/modules/local/quantification/combine_quantification/main.nf b/modules/local/quantification/combine_quantification/main.nf new file mode 100644 index 00000000..35193372 --- /dev/null +++ b/modules/local/quantification/combine_quantification/main.nf @@ -0,0 +1,35 @@ +process COMBINE_QUANTIFICATION { + label "process_single" + + conda "conda-forge::mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6==fccb0c41a243c639e11dd1be7b74f563e624fcca-0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0': + 'biocontainers/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0' }" + + input: + tuple val(meta), path(inputs) + tuple val(meta2), path(tx2gene) + tuple val(meta3), path(circ_annotation) + + output: + path("${meta.id}.linear.tsv") , emit: linear + path("${meta.id}.circular.tsv") , emit: circular + path "versions.yml" , emit: versions + + script: + """ + combine_quantification.py --inputs ${inputs} \\ + --tx2gene ${tx2gene} \\ + --circ_annotation ${circ_annotation} \\ + --out_linear ${meta.id}.linear.tsv \\ + --out_circular ${meta.id}.circular.tsv \\ + --out_combined ${meta.id}.combined.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //g') + pandas: \$(python -c "import pandas; print(pandas.__version__)") + numpy: \$(python -c "import numpy; print(numpy.__version__)") + END_VERSIONS + """ +} diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 5e88dcaf..62275d50 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -1,7 +1,7 @@ include { ANNOTATION } from '../../modules/local/annotation/full_annotation/main' include { GNU_SORT as COMBINE_ANNOTATIONS } from '../../modules/nf-core/gnu/sort/main' -include { GAWK as REMOVE_SCORE } from '../../modules/nf-core/gawk/main' +include { GAWK as REMOVE_SCORE_STRAND } from '../../modules/nf-core/gawk/main' include { BEDTOOLS_INTERSECT as INTERSECT_ANNOTATION } from '../../modules/nf-core/bedtools/intersect/main' include { BOWTIE2_ALIGN as FIND_CIRC_ALIGN } from '../../modules/nf-core/bowtie2/align/main' include { SAMTOOLS_VIEW } from '../../modules/nf-core/samtools/view/main' @@ -218,7 +218,7 @@ workflow CIRCRNA_DISCOVERY { INTERSECT_ANNOTATION( circrna_filtered.combine(gtf), [[], []]) ANNOTATION( INTERSECT_ANNOTATION.out.intersect, exon_boundary ) COMBINE_ANNOTATIONS(ANNOTATION.out.bed.map{ meta, bed -> bed}.collect().map{[[id: "annotation"], it]}) - REMOVE_SCORE( COMBINE_ANNOTATIONS.out.sorted, []) + REMOVE_SCORE_STRAND( COMBINE_ANNOTATIONS.out.sorted, []) ch_versions = ch_versions.mix(INTERSECT_ANNOTATION.out.versions) ch_versions = ch_versions.mix(ANNOTATION.out.versions) @@ -257,6 +257,7 @@ workflow CIRCRNA_DISCOVERY { emit: circrna_bed12 = ANNOTATION.out.bed fasta = FASTA.out.analysis_fasta + annotation = REMOVE_SCORE_STRAND.out.output versions = ch_versions counts_bed counts_tsv diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index a1739611..25e66c5a 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -1,13 +1,14 @@ -include { TRANSCRIPTOME as LINEAR_TRANSCRIPTOME } from '../../modules/local/quantification/transcriptome/main' +include { TRANSCRIPTOME as LINEAR_TRANSCRIPTOME } from '../../modules/local/quantification/transcriptome/main' include { BEDTOOLS_GETFASTA as CIRCULAR_TRANSCRIPTOME } from '../../modules/nf-core/bedtools/getfasta/main' -include { GAWK as COUNTS_TO_BED } from '../../modules/nf-core/gawk/main' -include { CAT_CAT as CAT_TRANSCRIPTOME } from '../../modules/nf-core/cat/cat/main' -include { GAWK as MARK_CIRCULAR } from '../../modules/nf-core/gawk/main' -include { PSIRC_INDEX } from '../../modules/local/psirc/index/main' -include { PSIRC_QUANT } from '../../modules/local/psirc/quant/main' -include { PSIRC_COMBINE } from '../../modules/local/psirc/combine/main' -include { CUSTOM_TX2GENE } from '../../modules/nf-core/custom/tx2gene/main' -include { TXIMETA_TXIMPORT } from '../../modules/nf-core/tximeta/tximport/main' +include { GAWK as COUNTS_TO_BED } from '../../modules/nf-core/gawk/main' +include { GNU_SORT as UNIQUE_REGIONS } from '../../modules/nf-core/gnu/sort/main' +include { CAT_CAT as CAT_TRANSCRIPTOME } from '../../modules/nf-core/cat/cat/main' +include { GAWK as MARK_CIRCULAR } from '../../modules/nf-core/gawk/main' +include { PSIRC_INDEX } from '../../modules/local/psirc/index/main' +include { PSIRC_QUANT } from '../../modules/local/psirc/quant/main' +include { CUSTOM_TX2GENE } from '../../modules/nf-core/custom/tx2gene/main' +include { TXIMETA_TXIMPORT } from '../../modules/nf-core/tximeta/tximport/main' +include { COMBINE_QUANTIFICATION } from '../../modules/local/quantification/combine_quantification/main' workflow QUANTIFICATION { take: @@ -15,13 +16,15 @@ workflow QUANTIFICATION { ch_fasta counts reads + circ_annotation main: LINEAR_TRANSCRIPTOME(ch_gtf, ch_fasta) COUNTS_TO_BED(counts.map{counts -> [[id: "counts"], counts]}, []) + UNIQUE_REGIONS(COUNTS_TO_BED.out.output) CIRCULAR_TRANSCRIPTOME( - COUNTS_TO_BED.out.output.map{meta, bed -> bed}, + UNIQUE_REGIONS.out.sorted.map{meta, bed -> bed}, ch_fasta.map{meta, fasta -> fasta} ) @@ -35,11 +38,10 @@ workflow QUANTIFICATION { PSIRC_INDEX(MARK_CIRCULAR.out.output) PSIRC_QUANT(reads, PSIRC_INDEX.out.collect()) - // PSIRC_COMBINE( PSIRC_QUANT.out.abundance_tsv.map{ meta, data -> data }.collect() ) CUSTOM_TX2GENE( ch_gtf, - PSIRC_QUANT.out.directory, + PSIRC_QUANT.out.directory.map{meta, quant -> quant}.collect().map{[[id: "quant"], it]}, "kallisto", "gene_id", "gene_name" @@ -50,4 +52,13 @@ workflow QUANTIFICATION { CUSTOM_TX2GENE.out.tx2gene, "kallisto" ) + + ch_counts = TXIMETA_TXIMPORT.out.counts_gene + ch_tpm = TXIMETA_TXIMPORT.out.tpm_gene + + COMBINE_QUANTIFICATION( + ch_counts.map{meta, counts -> counts}.collect().map{[[id: "counts"], it]}, + CUSTOM_TX2GENE.out.tx2gene, + circ_annotation + ) } diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index ffbb2c51..3db9ee32 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -157,7 +157,8 @@ workflow CIRCRNA { ch_gtf, ch_fasta, CIRCRNA_DISCOVERY.out.counts_bed, - FASTQC_TRIMGALORE.out.reads + FASTQC_TRIMGALORE.out.reads, + CIRCRNA_DISCOVERY.out.annotation ) // From 9c1ef11da2e3b04ae02520945654143e8314d7fc Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 17:09:49 +0100 Subject: [PATCH 174/491] Implement quantification aggregation for TPMs --- .../quantification/combine_quantification/main.nf | 1 + subworkflows/local/quantification.nf | 11 +++++++++-- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/modules/local/quantification/combine_quantification/main.nf b/modules/local/quantification/combine_quantification/main.nf index 35193372..975ae48f 100644 --- a/modules/local/quantification/combine_quantification/main.nf +++ b/modules/local/quantification/combine_quantification/main.nf @@ -14,6 +14,7 @@ process COMBINE_QUANTIFICATION { output: path("${meta.id}.linear.tsv") , emit: linear path("${meta.id}.circular.tsv") , emit: circular + path("${meta.id}.combined.tsv") , emit: combined path "versions.yml" , emit: versions script: diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index 25e66c5a..a06c1360 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -8,7 +8,8 @@ include { PSIRC_INDEX } from '../../modules/loca include { PSIRC_QUANT } from '../../modules/local/psirc/quant/main' include { CUSTOM_TX2GENE } from '../../modules/nf-core/custom/tx2gene/main' include { TXIMETA_TXIMPORT } from '../../modules/nf-core/tximeta/tximport/main' -include { COMBINE_QUANTIFICATION } from '../../modules/local/quantification/combine_quantification/main' +include { COMBINE_QUANTIFICATION as COMBINE_COUNTS } from '../../modules/local/quantification/combine_quantification/main' +include { COMBINE_QUANTIFICATION as COMBINE_TPM } from '../../modules/local/quantification/combine_quantification/main' workflow QUANTIFICATION { take: @@ -56,9 +57,15 @@ workflow QUANTIFICATION { ch_counts = TXIMETA_TXIMPORT.out.counts_gene ch_tpm = TXIMETA_TXIMPORT.out.tpm_gene - COMBINE_QUANTIFICATION( + COMBINE_COUNTS( ch_counts.map{meta, counts -> counts}.collect().map{[[id: "counts"], it]}, CUSTOM_TX2GENE.out.tx2gene, circ_annotation ) + + COMBINE_TPM( + ch_tpm.map{meta, tpm -> tpm}.collect().map{[[id: "tpm"], it]}, + CUSTOM_TX2GENE.out.tx2gene, + circ_annotation + ) } From d384c65614ddb18b9ce6121babc28a243d54ca6f Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 17:18:39 +0100 Subject: [PATCH 175/491] Override publishdir of quantification results --- conf/modules.config | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index 4bfcba71..e070d457 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -700,6 +700,22 @@ if (!params.skip_trimming) { ext.suffix = "marked.fasta" } + withName: COMBINE_COUNTS { + publishDir = [ + path: { "${params.outdir}/quantification/" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: COMBINE_TPM { + publishDir = [ + path: { "${params.outdir}/quantification/" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + withName: TARGETSCAN_DATABASE { ext.when = { params.module.split(',').contains('mirna_prediction') } publishDir = [ From 4ef2321313939df1ff3c11a721cc089cac33a0c4 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 17:19:53 +0100 Subject: [PATCH 176/491] Emit Quantification results --- subworkflows/local/quantification.nf | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index a06c1360..edf44ea1 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -68,4 +68,13 @@ workflow QUANTIFICATION { CUSTOM_TX2GENE.out.tx2gene, circ_annotation ) + + emit: + counts_linear = COMBINE_COUNTS.out.linear + counts_circular = COMBINE_COUNTS.out.circular + counts_combined = COMBINE_COUNTS.out.combined + + tpm_linear = COMBINE_TPM.out.linear + tpm_circular = COMBINE_TPM.out.circular + tpm_combined = COMBINE_TPM.out.combined } From 047421af5e8a90cd6e68178b068809eebc5ca255 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 17:21:25 +0100 Subject: [PATCH 177/491] Align indentation --- subworkflows/local/quantification.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index edf44ea1..d6256a6e 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -70,11 +70,11 @@ workflow QUANTIFICATION { ) emit: - counts_linear = COMBINE_COUNTS.out.linear + counts_linear = COMBINE_COUNTS.out.linear counts_circular = COMBINE_COUNTS.out.circular counts_combined = COMBINE_COUNTS.out.combined - tpm_linear = COMBINE_TPM.out.linear - tpm_circular = COMBINE_TPM.out.circular - tpm_combined = COMBINE_TPM.out.combined + tpm_linear = COMBINE_TPM.out.linear + tpm_circular = COMBINE_TPM.out.circular + tpm_combined = COMBINE_TPM.out.combined } From 9261572a615f9beb7fb4df9da2ce195402f67d71 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 17:40:35 +0100 Subject: [PATCH 178/491] Remove traces of old count combination --- bin/DEA.R | 4 +- bin/prepare_circ_test.R | 2 +- bin/reformat_count_matrix.R | 16 ------- conf/modules.config | 16 ------- modules/local/count_matrix/single/main.nf | 48 ------------------- .../deseq2/differential_expression/main.nf | 2 +- subworkflows/local/circrna_discovery.nf | 1 - 7 files changed, 4 insertions(+), 85 deletions(-) delete mode 100755 bin/reformat_count_matrix.R delete mode 100644 modules/local/count_matrix/single/main.nf diff --git a/bin/DEA.R b/bin/DEA.R index 83f3cccf..bd10c931 100755 --- a/bin/DEA.R +++ b/bin/DEA.R @@ -28,7 +28,7 @@ get_args <- function(){ arg="circRNA", short="c", help="circRNA counts matrix", - default="circRNA_matrix.txt") + default="merged_counts.bed") argp <- add_argument( parser=argp, @@ -57,7 +57,7 @@ giveError <- function(message){ quit() } -usage <- function(){giveError("USAGE: DEA.R ")} +usage <- function(){giveError("USAGE: DEA.R ")} stage_data <- function(gene_counts, phenotype, circRNA, species, map){ diff --git a/bin/prepare_circ_test.R b/bin/prepare_circ_test.R index f95b8f9c..95057f19 100755 --- a/bin/prepare_circ_test.R +++ b/bin/prepare_circ_test.R @@ -3,7 +3,7 @@ ## Author: Barry Digby ## License: MIT -circ_mat = read.table("count_matrix.txt", header=T, sep="\t", check.names = FALSE, stringsAsFactors = F, row.names = "ID") +circ_mat = read.table("merged_counts.tsv", header=T, sep="\t", check.names = FALSE, stringsAsFactors = F, row.names = "ID") gene_mat = read.table("gene_count_matrix.csv", sep=",", header=T, row.names="gene_id", stringsAsFactors = F) map = read.table("circrna_host-gene.txt", header = F, sep="\t", stringsAsFactors = F) diff --git a/bin/reformat_count_matrix.R b/bin/reformat_count_matrix.R deleted file mode 100755 index 3c635b29..00000000 --- a/bin/reformat_count_matrix.R +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env Rscript - -## Author: Barry Digby -## License: MIT - -library(dplyr) -mat <- read.table("circRNA_matrix.txt", sep="\t", header=T, stringsAsFactors=F, check.names=F) -mat$ID <- with(mat, paste0(Chr, sep=":", Start, sep="-", Stop, sep=":", Strand)) -mat <- mat[,-c(1:4)] -mat1 <- mat %>% select(ID, everything()) -ID <- as.data.frame(mat1$ID) -mat <- as.data.frame(subset(mat1, select=-c(ID))) -mat <- mat[, order(names(mat))] -mat1 <- cbind(ID, mat) -colnames(mat1)[1] <- "ID" -write.table(mat1, "count_matrix.txt", sep="\t", row.names=F, col.names=T, quote=F) diff --git a/conf/modules.config b/conf/modules.config index e070d457..fc6a6ba9 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -658,24 +658,8 @@ if (!params.skip_trimming) { ] } - withName: COUNTS_SINGLE { - ext.when = { params.module.split(',').contains('circrna_discovery') } - publishDir = [ - path: { "${params.outdir}/circrna_discovery/" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - pattern: "*.txt" - ] - } - withName: COUNTS_COMBINED { ext.when = { params.module.split(',').contains('circrna_discovery') } - publishDir = [ - path: { "${params.outdir}/circrna_discovery/" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - pattern: "count_matrix.txt" - ] } withName: COUNTS_TO_BED { diff --git a/modules/local/count_matrix/single/main.nf b/modules/local/count_matrix/single/main.nf deleted file mode 100644 index a7c01833..00000000 --- a/modules/local/count_matrix/single/main.nf +++ /dev/null @@ -1,48 +0,0 @@ -process COUNTS_SINGLE { - tag "${meta.tool}" - label 'process_low' - - conda "conda-forge::r-base=3.6.3 conda-forge::python=2.7.15 conda-forge::r-argparser=0.6 conda-forge::r-dplyr=1.0.5" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-5fbffedf7f529cf3c5093b976deb4290f5e1267a:3456f1432b1c9dad42815275abe2d6cb6f26fd94-0' : - 'quay.io/biocontainers/mulled-v2-5fbffedf7f529cf3c5093b976deb4290f5e1267a:3456f1432b1c9dad42815275abe2d6cb6f26fd94-0' }" - - input: - tuple val(meta), path(bed) - - output: - path("circRNA_matrix.txt"), emit: counts_bed - path("count_matrix.txt") , emit: counts_tsv - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def tool_name = "${meta.tool}" - """ - # Strip tool name from BED files (no consolidation prior to this step for 1 tool) - for b in *.bed; do - basename=\${b%".bed"}; - sample_name=\${basename%"_${tool_name}"}; - mv \$b \${sample_name}.bed - done - - circRNA_counts_matrix.py > matrix.txt - ## handle non-canon chromosomes here (https://stackoverflow.com/questions/71479919/joining-columns-based-on-number-of-fields) - n_samps=\$(ls *.bed | wc -l) - canon=\$(awk -v a="\$n_samps" 'BEGIN {print a + 4}') - awk -v n="\$canon" '{ for (i = 2; i <= NF - n + 1; ++i) { \$1 = \$1"-"\$i; \$i=""; } } 1' matrix.txt | awk -v OFS="\\t" '\$1=\$1' > circRNA_matrix.txt - reformat_count_matrix.R - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - awk: \$(awk --version | head -n 1 | cut -d' ' -f3 | sed 's/,//g') - r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//') - argparser: \$(Rscript -e "library(arparser); cat(as.character(packageVersion('argparser')))") - dplyr: \$(Rscript -e "library(dplyr); cat(as.character(packageVersion('dplyr')))") - python: \$(python --version | sed -e 's/Python //g') - END_VERSIONS - """ -} diff --git a/modules/local/deseq2/differential_expression/main.nf b/modules/local/deseq2/differential_expression/main.nf index 86ee474c..249bcba4 100644 --- a/modules/local/deseq2/differential_expression/main.nf +++ b/modules/local/deseq2/differential_expression/main.nf @@ -30,7 +30,7 @@ process DESEQ2_DIFFERENTIAL_EXPRESSION { tail -n +2 $phenotype | LC_COLLATE=C sort > sorted_pheno cat header sorted_pheno > tmp && rm phenotype.csv && mv tmp phenotype.csv - DEA.R $gene_matrix $phenotype $circrna_matrix $species ensembl_database_map.txt + DEA.R -g $gene_matrix -p $phenotype -c $circrna_matrix -s $species -m ensembl_database_map.txt mv boxplots/ circRNA/ mv *.RData DESeq2_QC/ diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 62275d50..49733e7f 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -32,7 +32,6 @@ include { MAPSPLICE_ALIGN } from '../../modules/l include { FASTA } from '../../modules/local/fasta/main' include { MERGE_TOOLS } from '../../modules/local/count_matrix/merge_tools/main' include { COUNTS_COMBINED } from '../../modules/local/count_matrix/combined/main' -include { COUNTS_SINGLE } from '../../modules/local/count_matrix/single/main' include { CIRCEXPLORER2_REFERENCE as CIRCEXPLORER2_REF } from '../../modules/local/circexplorer2/reference/main' include { CIRCEXPLORER2_PARSE as CIRCEXPLORER2_PAR } from '../../modules/nf-core/circexplorer2/parse/main' include { CIRCEXPLORER2_ANNOTATE as CIRCEXPLORER2_ANN } from '../../modules/nf-core/circexplorer2/annotate/main' From 8a8efa7f1ab41f53bb3d110ae6de44d52ae9c29e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 17:57:09 +0100 Subject: [PATCH 179/491] Fix compatibility issues with DGEA --- bin/DEA.R | 4 ++-- bin/counts_combined.py | 1 + modules/local/deseq2/differential_expression/main.nf | 2 +- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/bin/DEA.R b/bin/DEA.R index bd10c931..b40dbfa7 100755 --- a/bin/DEA.R +++ b/bin/DEA.R @@ -69,9 +69,9 @@ stage_data <- function(gene_counts, phenotype, circRNA, species, map){ circ <- read.table(circRNA, sep ="\t", header = T, stringsAsFactors=FALSE) # Merge circRNA genomic loci to ID - circ$circ <- with(circ, paste0(Chr, sep=":", Start, sep="-", Stop, sep=":", Strand)) + circ$circ <- with(circ, paste0(chr, sep=":", start, sep="-", end, sep=":", strand)) rownames(circ) <- circ$circ - circ <- subset(circ, select=-c(Chr, Start, Stop, Strand, circ)) + circ <- subset(circ, select=-c(chr, start, end, strand, circ)) # R converts '-' to '.' in colnames here and results in failures. # If you need to make this 'smarter' check that colnames contains '.', diff --git a/bin/counts_combined.py b/bin/counts_combined.py index cb40c588..7ae67065 100755 --- a/bin/counts_combined.py +++ b/bin/counts_combined.py @@ -27,4 +27,5 @@ df.to_csv(args.out_bed, sep='\t') df.index = df.index.map(lambda x: f'{x[0]}:{x[1]}-{x[2]}:{x[3]}') +df.index.name = 'ID' df.to_csv(args.out_tsv, sep='\t') \ No newline at end of file diff --git a/modules/local/deseq2/differential_expression/main.nf b/modules/local/deseq2/differential_expression/main.nf index 249bcba4..86ee474c 100644 --- a/modules/local/deseq2/differential_expression/main.nf +++ b/modules/local/deseq2/differential_expression/main.nf @@ -30,7 +30,7 @@ process DESEQ2_DIFFERENTIAL_EXPRESSION { tail -n +2 $phenotype | LC_COLLATE=C sort > sorted_pheno cat header sorted_pheno > tmp && rm phenotype.csv && mv tmp phenotype.csv - DEA.R -g $gene_matrix -p $phenotype -c $circrna_matrix -s $species -m ensembl_database_map.txt + DEA.R $gene_matrix $phenotype $circrna_matrix $species ensembl_database_map.txt mv boxplots/ circRNA/ mv *.RData DESeq2_QC/ From f80e0cb5eecd3e902e9d7afd80e9a3158be3b864 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 18:25:36 +0100 Subject: [PATCH 180/491] Add version captures --- subworkflows/local/circrna_discovery.nf | 11 +- subworkflows/local/differential_expression.nf | 1 - subworkflows/local/prepare_genome.nf | 5 +- subworkflows/local/quantification.nf | 131 +++++++++++------- workflows/circrna/main.nf | 10 +- 5 files changed, 97 insertions(+), 61 deletions(-) diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 49733e7f..907cc2c7 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -17,9 +17,6 @@ include { SEGEMEHL_FILTER } from '../../modules/l include { STAR_ALIGN as STAR_1ST_PASS } from '../../modules/nf-core/star/align/main' include { STAR_ALIGN as STAR_2ND_PASS } from '../../modules/nf-core/star/align/main' include { SJDB as STAR_SJDB } from '../../modules/local/star/sjdb/main' -include { STAR_ALIGN as DCC_1ST_PASS } from '../../modules/nf-core/star/align/main' -include { STAR_ALIGN as DCC_2ND_PASS } from '../../modules/nf-core/star/align/main' -include { SJDB as DCC_SJDB } from '../../modules/local/star/sjdb/main' include { STAR_ALIGN as DCC_MATE1_1ST_PASS } from '../../modules/nf-core/star/align/main' include { STAR_ALIGN as DCC_MATE1_2ND_PASS } from '../../modules/nf-core/star/align/main' include { SJDB as DCC_MATE1_SJDB } from '../../modules/local/star/sjdb/main' @@ -89,6 +86,7 @@ workflow CIRCRNA_DISCOVERY { STAR_2ND_PASS( reads, star_index, STAR_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) ch_versions = ch_versions.mix(STAR_1ST_PASS.out.versions) + ch_versions = ch_versions.mix(STAR_SJDB.out.versions) ch_versions = ch_versions.mix(STAR_2ND_PASS.out.versions) // @@ -144,6 +142,7 @@ workflow CIRCRNA_DISCOVERY { CIRIQUANT( reads, ch_gtf, ch_fasta, bwa_index, hisat2_index ) CIRIQUANT_FILTER( CIRIQUANT.out.gtf.map{ meta, gtf -> [ meta + [tool: "ciriquant"], gtf ] }, bsj_reads ) + ch_versions = ch_versions.mix(CIRIQUANT_YML.out.versions) ch_versions = ch_versions.mix(CIRIQUANT.out.versions) ch_versions = ch_versions.mix(CIRIQUANT_FILTER.out.versions) @@ -200,6 +199,7 @@ workflow CIRCRNA_DISCOVERY { ch_versions = ch_versions.mix(MAPSPLICE_ALIGN.out.versions) ch_versions = ch_versions.mix(MAPSPLICE_PARSE.out.versions) ch_versions = ch_versions.mix(MAPSPLICE_ANNOTATE.out.versions) + ch_versions = ch_versions.mix(MAPSPLICE_FILTER.out.versions) // // ANNOTATION WORKFLOW: @@ -221,6 +221,8 @@ workflow CIRCRNA_DISCOVERY { ch_versions = ch_versions.mix(INTERSECT_ANNOTATION.out.versions) ch_versions = ch_versions.mix(ANNOTATION.out.versions) + ch_versions = ch_versions.mix(COMBINE_ANNOTATIONS.out.versions) + ch_versions = ch_versions.mix(REMOVE_SCORE_STRAND.out.versions) // // FASTA WORKFLOW: @@ -257,7 +259,8 @@ workflow CIRCRNA_DISCOVERY { circrna_bed12 = ANNOTATION.out.bed fasta = FASTA.out.analysis_fasta annotation = REMOVE_SCORE_STRAND.out.output - versions = ch_versions counts_bed counts_tsv + + versions = ch_versions } diff --git a/subworkflows/local/differential_expression.nf b/subworkflows/local/differential_expression.nf index f4454af6..d4199b86 100644 --- a/subworkflows/local/differential_expression.nf +++ b/subworkflows/local/differential_expression.nf @@ -1,5 +1,4 @@ include { HISAT2_ALIGN } from '../../modules/nf-core/hisat2/align/main' -include { SAMTOOLS_SORT } from '../../modules/nf-core/samtools/sort/main' include { STRINGTIE_STRINGTIE } from '../../modules/nf-core/stringtie/stringtie/main' include { STRINGTIE_PREPDE } from '../../modules/local/stringtie/prepde/main' include { PARENT_GENE } from '../../modules/local/annotation/parent_gene/main' diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 0118cf2d..5d3b0755 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -22,6 +22,8 @@ workflow PREPARE_GENOME { if( params.module.contains('circrna_discovery') && params.tool.contains('mapsplice') ) { CLEAN_FASTA(ch_fasta, []) ch_fasta = CLEAN_FASTA.out.output + + ch_versions = ch_versions.mix(CLEAN_FASTA.out.versions) } SEQKIT_SPLIT(ch_fasta) @@ -41,7 +43,8 @@ workflow PREPARE_GENOME { SEGEMEHL_INDEX(ch_fasta.map{ meta, fasta -> fasta}) // TODO: Add support for meta // Collect versions - ch_versions = ch_versions.mix(BOWTIE_BUILD.out.versions, + ch_versions = ch_versions.mix(SEQKIT_SPLIT.out.versions, + BOWTIE_BUILD.out.versions, BOWTIE2_BUILD.out.versions, BWA_INDEX.out.versions, HISAT2_EXTRACTSPLICESITES.out.versions, diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index d6256a6e..e5db420d 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -13,61 +13,84 @@ include { COMBINE_QUANTIFICATION as COMBINE_TPM } from '../../modules/loca workflow QUANTIFICATION { take: - ch_gtf - ch_fasta - counts - reads - circ_annotation + ch_gtf + ch_fasta + counts + reads + circ_annotation main: - LINEAR_TRANSCRIPTOME(ch_gtf, ch_fasta) - COUNTS_TO_BED(counts.map{counts -> [[id: "counts"], counts]}, []) - UNIQUE_REGIONS(COUNTS_TO_BED.out.output) - - CIRCULAR_TRANSCRIPTOME( - UNIQUE_REGIONS.out.sorted.map{meta, bed -> bed}, - ch_fasta.map{meta, fasta -> fasta} - ) - - CAT_TRANSCRIPTOME( - LINEAR_TRANSCRIPTOME.out.transcriptome.map{meta, fasta -> fasta}.mix( - CIRCULAR_TRANSCRIPTOME.out.fasta - ).collect().map(fastas -> [[id: "transcriptome"], fastas]) - ) - - MARK_CIRCULAR(CAT_TRANSCRIPTOME.out.file_out, []) - - PSIRC_INDEX(MARK_CIRCULAR.out.output) - PSIRC_QUANT(reads, PSIRC_INDEX.out.collect()) - - CUSTOM_TX2GENE( - ch_gtf, - PSIRC_QUANT.out.directory.map{meta, quant -> quant}.collect().map{[[id: "quant"], it]}, - "kallisto", - "gene_id", - "gene_name" - ) - - TXIMETA_TXIMPORT( - PSIRC_QUANT.out.directory, - CUSTOM_TX2GENE.out.tx2gene, - "kallisto" - ) - - ch_counts = TXIMETA_TXIMPORT.out.counts_gene - ch_tpm = TXIMETA_TXIMPORT.out.tpm_gene - - COMBINE_COUNTS( - ch_counts.map{meta, counts -> counts}.collect().map{[[id: "counts"], it]}, - CUSTOM_TX2GENE.out.tx2gene, - circ_annotation - ) - - COMBINE_TPM( - ch_tpm.map{meta, tpm -> tpm}.collect().map{[[id: "tpm"], it]}, - CUSTOM_TX2GENE.out.tx2gene, - circ_annotation - ) + ch_versions = Channel.empty() + + LINEAR_TRANSCRIPTOME(ch_gtf, ch_fasta) + COUNTS_TO_BED(counts.map{counts -> [[id: "counts"], counts]}, []) + UNIQUE_REGIONS(COUNTS_TO_BED.out.output) + + CIRCULAR_TRANSCRIPTOME( + UNIQUE_REGIONS.out.sorted.map{meta, bed -> bed}, + ch_fasta.map{meta, fasta -> fasta} + ) + + CAT_TRANSCRIPTOME( + LINEAR_TRANSCRIPTOME.out.transcriptome.map{meta, fasta -> fasta}.mix( + CIRCULAR_TRANSCRIPTOME.out.fasta + ).collect().map(fastas -> [[id: "transcriptome"], fastas]) + ) + + MARK_CIRCULAR(CAT_TRANSCRIPTOME.out.file_out, []) + + ch_versions = ch_versions.mix( + LINEAR_TRANSCRIPTOME.out.versions, + COUNTS_TO_BED.out.versions, + UNIQUE_REGIONS.out.versions, + CIRCULAR_TRANSCRIPTOME.out.versions, + CAT_TRANSCRIPTOME.out.versions, + MARK_CIRCULAR.out.versions + ) + + PSIRC_INDEX(MARK_CIRCULAR.out.output) + PSIRC_QUANT(reads, PSIRC_INDEX.out.collect()) + + CUSTOM_TX2GENE( + ch_gtf, + PSIRC_QUANT.out.directory.map{meta, quant -> quant}.collect().map{[[id: "quant"], it]}, + "kallisto", + "gene_id", + "gene_name" + ) + + TXIMETA_TXIMPORT( + PSIRC_QUANT.out.directory, + CUSTOM_TX2GENE.out.tx2gene, + "kallisto" + ) + + ch_versions = ch_versions.mix( + PSIRC_INDEX.out.versions, + PSIRC_QUANT.out.versions, + CUSTOM_TX2GENE.out.versions, + TXIMETA_TXIMPORT.out.versions + ) + + ch_counts = TXIMETA_TXIMPORT.out.counts_gene + ch_tpm = TXIMETA_TXIMPORT.out.tpm_gene + + COMBINE_COUNTS( + ch_counts.map{meta, counts -> counts}.collect().map{[[id: "counts"], it]}, + CUSTOM_TX2GENE.out.tx2gene, + circ_annotation + ) + + COMBINE_TPM( + ch_tpm.map{meta, tpm -> tpm}.collect().map{[[id: "tpm"], it]}, + CUSTOM_TX2GENE.out.tx2gene, + circ_annotation + ) + + ch_versions = ch_versions.mix( + COMBINE_COUNTS.out.versions, + COMBINE_TPM.out.versions + ) emit: counts_linear = COMBINE_COUNTS.out.linear @@ -77,4 +100,6 @@ workflow QUANTIFICATION { tpm_linear = COMBINE_TPM.out.linear tpm_circular = COMBINE_TPM.out.circular tpm_combined = COMBINE_TPM.out.combined + + versions = ch_versions } diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 3db9ee32..7c7d522f 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -153,6 +153,10 @@ workflow CIRCRNA { ch_versions = ch_versions.mix(CIRCRNA_DISCOVERY.out.versions) + // + // 3. Quantification + // + QUANTIFICATION( ch_gtf, ch_fasta, @@ -161,8 +165,10 @@ workflow CIRCRNA { CIRCRNA_DISCOVERY.out.annotation ) + ch_versions = ch_versions.mix(QUANTIFICATION.out.versions) + // - // 3. miRNA prediction + // 4. miRNA prediction // MIRNA_PREDICTION( @@ -174,7 +180,7 @@ workflow CIRCRNA { ch_versions = ch_versions.mix(MIRNA_PREDICTION.out.versions) // - // 4. Differential expression tests + // 5. Differential expression tests // ch_ensembl_database_map = params.module.contains('differential_expression') ? 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ze0bja?;rz*-n{wO;fJC@jXxek2%6jjg&t+h?u4R^znhIPhXYmv%KQxB2Vj#-Ku3zq zyGE#O`Pz0JrD23oET8&=NEQc5PJ;wCju&6XW@wPJ*5%o|Ilj>;e1&?VT{w_|9@_=V z7eia;A9HgSyYXRMO-fFV&yav;?xAB;d8IqmK^hNZL9pu5RD`2y#@?S-Yll|FGUzX$bx Date: Tue, 19 Mar 2024 18:26:57 +0100 Subject: [PATCH 182/491] Update modules --- modules.json | 4 +- .../nf-core/bedtools/sort/tests/main.nf.test | 58 +++++ .../bedtools/sort/tests/main.nf.test.snap | 68 ++++++ .../bedtools/sort/tests/nextflow.config | 8 + modules/nf-core/bedtools/sort/tests/tags.yml | 2 + modules/nf-core/bowtie2/align/main.nf | 26 ++- .../bowtie2/align/tests/cram_crai.config | 5 + .../nf-core/bowtie2/align/tests/main.nf.test | 162 +++++++++---- .../bowtie2/align/tests/main.nf.test.snap | 216 +++++++++++------- 9 files changed, 409 insertions(+), 140 deletions(-) create mode 100644 modules/nf-core/bedtools/sort/tests/main.nf.test create mode 100644 modules/nf-core/bedtools/sort/tests/main.nf.test.snap create mode 100644 modules/nf-core/bedtools/sort/tests/nextflow.config create mode 100644 modules/nf-core/bedtools/sort/tests/tags.yml create mode 100644 modules/nf-core/bowtie2/align/tests/cram_crai.config diff --git a/modules.json b/modules.json index 439ea7a3..751a3f5c 100644 --- a/modules.json +++ b/modules.json @@ -17,7 +17,7 @@ }, "bedtools/sort": { "branch": "master", - "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", + "git_sha": "571a5feac4c9ce0a8df0bc15b94230e7f3e8db47", "installed_by": ["modules"] }, "bowtie/align": { @@ -32,7 +32,7 @@ }, "bowtie2/align": { "branch": "master", - "git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde", + "git_sha": "0fe30831abbc2ed115e46e92330edf38f56edc3d", "installed_by": ["modules"] }, "bowtie2/build": { diff --git a/modules/nf-core/bedtools/sort/tests/main.nf.test b/modules/nf-core/bedtools/sort/tests/main.nf.test new file mode 100644 index 00000000..b1f36dd9 --- /dev/null +++ b/modules/nf-core/bedtools/sort/tests/main.nf.test @@ -0,0 +1,58 @@ +nextflow_process { + + name "Test Process BEDTOOLS_SORT" + script "../main.nf" + config "./nextflow.config" + process "BEDTOOLS_SORT" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/sort" + + test("test_bedtools_sort") { + + when { + process { + """ + input[0] = [ [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + + test("test_bedtools_sort_with_genome") { + + when { + process { + """ + input[0] = [ [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/sort/tests/main.nf.test.snap b/modules/nf-core/bedtools/sort/tests/main.nf.test.snap new file mode 100644 index 00000000..f10e8b98 --- /dev/null +++ b/modules/nf-core/bedtools/sort/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "test_bedtools_sort_with_genome": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_out.testtext:md5,fe4053cf4de3aebbdfc3be2efb125a74" + ] + ], + "1": [ + "versions.yml:md5,cdbae2c7ebc41e534aaf0835779061f8" + ], + "sorted": [ + [ + { + "id": "test" + }, + "test_out.testtext:md5,fe4053cf4de3aebbdfc3be2efb125a74" + ] + ], + "versions": [ + "versions.yml:md5,cdbae2c7ebc41e534aaf0835779061f8" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-19T10:13:11.830452" + }, + "test_bedtools_sort": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_out.testtext:md5,fe4053cf4de3aebbdfc3be2efb125a74" + ] + ], + "1": [ + "versions.yml:md5,cdbae2c7ebc41e534aaf0835779061f8" + ], + "sorted": [ + [ + { + "id": "test" + }, + "test_out.testtext:md5,fe4053cf4de3aebbdfc3be2efb125a74" + ] + ], + "versions": [ + "versions.yml:md5,cdbae2c7ebc41e534aaf0835779061f8" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-19T10:16:40.535947" + } +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/sort/tests/nextflow.config b/modules/nf-core/bedtools/sort/tests/nextflow.config new file mode 100644 index 00000000..f203c99c --- /dev/null +++ b/modules/nf-core/bedtools/sort/tests/nextflow.config @@ -0,0 +1,8 @@ +process { + + withName: BEDTOOLS_SORT { + ext.prefix = { "${meta.id}_out" } + ext.suffix = "testtext" + } + +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/sort/tests/tags.yml b/modules/nf-core/bedtools/sort/tests/tags.yml new file mode 100644 index 00000000..47c85eea --- /dev/null +++ b/modules/nf-core/bedtools/sort/tests/tags.yml @@ -0,0 +1,2 @@ +bedtools/sort: + - "modules/nf-core/bedtools/sort/**" diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf index 8c405ee3..96a7027d 100644 --- a/modules/nf-core/bowtie2/align/main.nf +++ b/modules/nf-core/bowtie2/align/main.nf @@ -10,13 +10,18 @@ process BOWTIE2_ALIGN { input: tuple val(meta) , path(reads) tuple val(meta2), path(index) + tuple val(meta3), path(fasta) val save_unaligned val sort_bam output: - tuple val(meta), path("*.{bam,sam}"), emit: aligned + tuple val(meta), path("*.sam") , emit: sam , optional:true + tuple val(meta), path("*.bam") , emit: bam , optional:true + tuple val(meta), path("*.cram") , emit: cram , optional:true + tuple val(meta), path("*.csi") , emit: csi , optional:true + tuple val(meta), path("*.crai") , emit: crai , optional:true tuple val(meta), path("*.log") , emit: log - tuple val(meta), path("*fastq.gz") , emit: fastq, optional:true + tuple val(meta), path("*fastq.gz") , emit: fastq , optional:true path "versions.yml" , emit: versions when: @@ -39,7 +44,10 @@ process BOWTIE2_ALIGN { def samtools_command = sort_bam ? 'sort' : 'view' def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/ - def extension = (args2 ==~ extension_pattern) ? (args2 =~ extension_pattern)[0][2].toLowerCase() : "bam" + def extension_matcher = (args2 =~ extension_pattern) + def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam" + def reference = fasta && extension=="cram" ? "--reference ${fasta}" : "" + if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output" """ INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/\\.rev.1.bt2\$//"` @@ -53,7 +61,7 @@ process BOWTIE2_ALIGN { $unaligned \\ $args \\ 2> >(tee ${prefix}.bowtie2.log >&2) \\ - | samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.${extension} - + | samtools $samtools_command $args2 --threads $task.cpus ${reference} -o ${prefix}.${extension} - if [ -f ${prefix}.unmapped.fastq.1.gz ]; then mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz @@ -82,9 +90,19 @@ process BOWTIE2_ALIGN { } else { create_unmapped = save_unaligned ? "touch ${prefix}.unmapped_1.fastq.gz && touch ${prefix}.unmapped_2.fastq.gz" : "" } + def reference = fasta && extension=="cram" ? "--reference ${fasta}" : "" + if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output" + + def create_index = "" + if (extension == "cram") { + create_index = "touch ${prefix}.crai" + } else if (extension == "bam") { + create_index = "touch ${prefix}.csi" + } """ touch ${prefix}.${extension} + ${create_index} touch ${prefix}.bowtie2.log ${create_unmapped} diff --git a/modules/nf-core/bowtie2/align/tests/cram_crai.config b/modules/nf-core/bowtie2/align/tests/cram_crai.config new file mode 100644 index 00000000..03f1d5e5 --- /dev/null +++ b/modules/nf-core/bowtie2/align/tests/cram_crai.config @@ -0,0 +1,5 @@ +process { + withName: BOWTIE2_ALIGN { + ext.args2 = '--output-fmt cram --write-index' + } +} diff --git a/modules/nf-core/bowtie2/align/tests/main.nf.test b/modules/nf-core/bowtie2/align/tests/main.nf.test index a478d17b..03aeaf9e 100644 --- a/modules/nf-core/bowtie2/align/tests/main.nf.test +++ b/modules/nf-core/bowtie2/align/tests/main.nf.test @@ -6,9 +6,10 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "bowtie2" + tag "bowtie2/build" tag "bowtie2/align" - test("sarscov2 - fastq, index, false, false - bam") { + test("sarscov2 - fastq, index, fasta, false, false - bam") { setup { run("BOWTIE2_BUILD") { @@ -32,8 +33,9 @@ nextflow_process { file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = false //save_unaligned - input[3] = false //sort + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[3] = false //save_unaligned + input[4] = false //sort """ } } @@ -42,7 +44,7 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - file(process.out.aligned[0][1]).name, + file(process.out.bam[0][1]).name, process.out.log, process.out.fastq, process.out.versions @@ -52,7 +54,7 @@ nextflow_process { } - test("sarscov2 - fastq, index, false, false - sam") { + test("sarscov2 - fastq, index, fasta, false, false - sam") { config "./sam.config" setup { @@ -77,8 +79,9 @@ nextflow_process { file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = false //save_unaligned - input[3] = false //sort + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[3] = false //save_unaligned + input[4] = false //sort """ } } @@ -87,7 +90,7 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - file(process.out.aligned[0][1]).readLines()[0..4], + file(process.out.sam[0][1]).readLines()[0..4], process.out.log, process.out.fastq, process.out.versions @@ -97,7 +100,7 @@ nextflow_process { } - test("sarscov2 - fastq, index, false, false - sam2") { + test("sarscov2 - fastq, index, fasta, false, false - sam2") { config "./sam2.config" setup { @@ -122,8 +125,9 @@ nextflow_process { file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = false //save_unaligned - input[3] = false //sort + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[3] = false //save_unaligned + input[4] = false //sort """ } } @@ -132,7 +136,7 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - file(process.out.aligned[0][1]).readLines()[0..4], + file(process.out.sam[0][1]).readLines()[0..4], process.out.log, process.out.fastq, process.out.versions @@ -142,7 +146,7 @@ nextflow_process { } - test("sarscov2 - fastq, index, false, true - bam") { + test("sarscov2 - fastq, index, fasta, false, true - bam") { setup { run("BOWTIE2_BUILD") { @@ -166,8 +170,9 @@ nextflow_process { file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = false //save_unaligned - input[3] = true //sort + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[3] = false //save_unaligned + input[4] = false //sort """ } } @@ -176,7 +181,7 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - file(process.out.aligned[0][1]).name, + file(process.out.bam[0][1]).name, process.out.log, process.out.fastq, process.out.versions @@ -186,7 +191,7 @@ nextflow_process { } - test("sarscov2 - [fastq1, fastq2], index, false, false - bam") { + test("sarscov2 - [fastq1, fastq2], index, fasta, false, false - bam") { setup { run("BOWTIE2_BUILD") { @@ -213,8 +218,9 @@ nextflow_process { ] ] input[1] = BOWTIE2_BUILD.out.index - input[2] = false //save_unaligned - input[3] = false //sort + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[3] = false //save_unaligned + input[4] = false //sort """ } } @@ -223,7 +229,7 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - file(process.out.aligned[0][1]).name, + file(process.out.bam[0][1]).name, process.out.log, process.out.fastq, process.out.versions @@ -233,7 +239,7 @@ nextflow_process { } - test("sarscov2 - [fastq1, fastq2], index, false, true - bam") { + test("sarscov2 - [fastq1, fastq2], index, fasta, false, true - bam") { setup { run("BOWTIE2_BUILD") { @@ -260,8 +266,9 @@ nextflow_process { ] ] input[1] = BOWTIE2_BUILD.out.index - input[2] = false //save_unaligned - input[3] = true //sort + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[3] = false //save_unaligned + input[4] = false //sort """ } } @@ -270,7 +277,7 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - file(process.out.aligned[0][1]).name, + file(process.out.bam[0][1]).name, process.out.log, process.out.fastq, process.out.versions @@ -280,7 +287,7 @@ nextflow_process { } - test("sarscov2 - fastq, large_index, false, false - bam") { + test("sarscov2 - fastq, large_index, fasta, false, false - bam") { config "./large_index.config" setup { @@ -305,8 +312,9 @@ nextflow_process { file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = false //save_unaligned - input[3] = false //sort + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[3] = false //save_unaligned + input[4] = false //sort """ } } @@ -315,7 +323,7 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - file(process.out.aligned[0][1]).name, + file(process.out.bam[0][1]).name, process.out.log, process.out.fastq, process.out.versions @@ -325,7 +333,7 @@ nextflow_process { } - test("sarscov2 - [fastq1, fastq2], large_index, false, false - bam") { + test("sarscov2 - [fastq1, fastq2], large_index, fasta, false, false - bam") { config "./large_index.config" setup { @@ -353,8 +361,9 @@ nextflow_process { ] ] input[1] = BOWTIE2_BUILD.out.index - input[2] = false //save_unaligned - input[3] = false //sort + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[3] = false //save_unaligned + input[4] = false //sort """ } } @@ -363,7 +372,7 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - file(process.out.aligned[0][1]).name, + file(process.out.bam[0][1]).name, process.out.log, process.out.fastq, process.out.versions @@ -373,7 +382,7 @@ nextflow_process { } - test("sarscov2 - [fastq1, fastq2], index, true, false - bam") { + test("sarscov2 - [fastq1, fastq2], index, fasta, true, false - bam") { setup { run("BOWTIE2_BUILD") { @@ -400,8 +409,9 @@ nextflow_process { ] ] input[1] = BOWTIE2_BUILD.out.index - input[2] = true //save_unaligned - input[3] = false //sort + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[3] = false //save_unaligned + input[4] = false //sort """ } } @@ -410,7 +420,7 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - file(process.out.aligned[0][1]).name, + file(process.out.bam[0][1]).name, process.out.log, process.out.fastq, process.out.versions @@ -420,7 +430,7 @@ nextflow_process { } - test("sarscov2 - fastq, index, true, false - bam") { + test("sarscov2 - fastq, index, fasta, true, false - bam") { setup { run("BOWTIE2_BUILD") { @@ -444,8 +454,9 @@ nextflow_process { file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = true //save_unaligned - input[3] = false //sort + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[3] = false //save_unaligned + input[4] = false //sort """ } } @@ -454,7 +465,7 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - file(process.out.aligned[0][1]).name, + file(process.out.bam[0][1]).name, process.out.log, process.out.fastq, process.out.versions @@ -465,7 +476,54 @@ nextflow_process { } - test("sarscov2 - [fastq1, fastq2], index, false, false - stub") { + test("sarscov2 - [fastq1, fastq2], index, fasta, true, true - cram") { + + config "./cram_crai.config" + setup { + run("BOWTIE2_BUILD") { + script "../../build/main.nf" + process { + """ + input[0] = [ + [ id:'test'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + input[1] = BOWTIE2_BUILD.out.index + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[3] = false //save_unaligned + input[4] = true //sort + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.cram[0][1]).name, + file(process.out.crai[0][1]).name + ).match() } + ) + } + + } + + test("sarscov2 - [fastq1, fastq2], index, fasta, false, false - stub") { options "-stub" setup { @@ -493,8 +551,9 @@ nextflow_process { ] ] input[1] = BOWTIE2_BUILD.out.index - input[2] = false //save_unaligned - input[3] = false //sort + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[3] = false //save_unaligned + input[4] = false //sort """ } } @@ -503,7 +562,8 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - file(process.out.aligned[0][1]).name, + file(process.out.bam[0][1]).name, + file(process.out.csi[0][1]).name, file(process.out.log[0][1]).name, process.out.fastq, process.out.versions @@ -513,7 +573,7 @@ nextflow_process { } - test("sarscov2 - fastq, index, true, false - stub") { + test("sarscov2 - fastq, index, fasta, true, false - stub") { options "-stub" setup { @@ -538,8 +598,9 @@ nextflow_process { file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = true //save_unaligned - input[3] = false //sort + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[3] = false //save_unaligned + input[4] = false //sort """ } } @@ -548,14 +609,15 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - file(process.out.aligned[0][1]).name, + file(process.out.bam[0][1]).name, + file(process.out.csi[0][1]).name, file(process.out.log[0][1]).name, - file(process.out.fastq[0][1]).name, + process.out.fastq, process.out.versions ).match() } ) } } - + } diff --git a/modules/nf-core/bowtie2/align/tests/main.nf.test.snap b/modules/nf-core/bowtie2/align/tests/main.nf.test.snap index 883dc7ec..028e7da6 100644 --- a/modules/nf-core/bowtie2/align/tests/main.nf.test.snap +++ b/modules/nf-core/bowtie2/align/tests/main.nf.test.snap @@ -1,34 +1,38 @@ { - "sarscov2 - fastq, index, false, false - sam2": { + "sarscov2 - [fastq1, fastq2], large_index, fasta, false, false - bam": { "content": [ - [ - "ERR5069949.2151832\t16\tMT192765.1\t17453\t42\t150M\t*\t0\t0\tACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGA\tAAAA Date: Tue, 19 Mar 2024 18:34:46 +0100 Subject: [PATCH 183/491] Add missing version capture for ciriquant_yml --- subworkflows/local/circrna_discovery.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 907cc2c7..4e081a4a 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -118,9 +118,9 @@ workflow CIRCRNA_DISCOVERY { // FIND_CIRC WORKFLOW: // - FIND_CIRC_ALIGN( reads, bowtie2_index, false, true ) - SAMTOOLS_INDEX( FIND_CIRC_ALIGN.out.aligned ) - SAMTOOLS_VIEW( FIND_CIRC_ALIGN.out.aligned.join( SAMTOOLS_INDEX.out.bai ), ch_fasta, [] ) + FIND_CIRC_ALIGN( reads, bowtie2_index, ch_fasta, false, true ) + SAMTOOLS_INDEX( FIND_CIRC_ALIGN.out.bam ) + SAMTOOLS_VIEW( FIND_CIRC_ALIGN.out.bam.join( SAMTOOLS_INDEX.out.bai ), ch_fasta, [] ) FIND_CIRC_ANCHORS( SAMTOOLS_VIEW.out.bam ) FIND_CIRC( FIND_CIRC_ANCHORS.out.anchors, bowtie2_index, fasta ) find_circ_filter = FIND_CIRC.out.bed.map{ meta, bed -> [ meta + [tool: "find_circ"], bed ] } From 5732485d563198fc545c426b9c37b7252a51144c Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 19:13:25 +0100 Subject: [PATCH 184/491] Fix some version capture problems --- modules/local/ciriquant/ciriquant/main.nf | 2 +- modules/local/psirc/index/main.nf | 9 ++++++++- modules/local/psirc/quant/main.nf | 6 ++++++ subworkflows/local/quantification.nf | 2 +- 4 files changed, 16 insertions(+), 3 deletions(-) diff --git a/modules/local/ciriquant/ciriquant/main.nf b/modules/local/ciriquant/ciriquant/main.nf index acf435a6..fab482ba 100644 --- a/modules/local/ciriquant/ciriquant/main.nf +++ b/modules/local/ciriquant/ciriquant/main.nf @@ -52,7 +52,7 @@ process CIRIQUANT { cat <<-END_VERSIONS > versions.yml "${task.process}": bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//') - ciriquant : \$(echo \$(CIRIquant --version 2>&1) | sed 's/CIRIquant //g' ) + ciriquant: \$(echo \$(CIRIquant --version 2>&1) | sed 's/CIRIquant //g' ) samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') stringtie: \$(stringtie --version 2>&1) hisat2: $VERSION diff --git a/modules/local/psirc/index/main.nf b/modules/local/psirc/index/main.nf index daca0402..7c10a533 100644 --- a/modules/local/psirc/index/main.nf +++ b/modules/local/psirc/index/main.nf @@ -8,10 +8,17 @@ process PSIRC_INDEX { tuple val(meta), path(fasta) output: - tuple val(meta), path("psirc.index") + tuple val(meta), path("psirc.index"), emit: index + path "versions.yml", emit: versions script: + def VERSION = '1.0' """ psirc-quant index -i psirc.index --make-unique $fasta + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + psirc-quant: $VERSION + END_VERSIONS """ } diff --git a/modules/local/psirc/quant/main.nf b/modules/local/psirc/quant/main.nf index aa949e3e..b23895e6 100644 --- a/modules/local/psirc/quant/main.nf +++ b/modules/local/psirc/quant/main.nf @@ -10,10 +10,16 @@ process PSIRC_QUANT { output: tuple val(meta), path("${meta.id}"), emit: directory + path "versions.yml" , emit: versions script: def single_end = meta.single_end ? "--single -l 76 -s 20" : "" """ psirc-quant quant -t $task.cpus -i $index -o $meta.id $single_end $reads + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + psirc-quant: $VERSION + END_VERSIONS """ } diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index e5db420d..af720ce0 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -49,7 +49,7 @@ workflow QUANTIFICATION { ) PSIRC_INDEX(MARK_CIRCULAR.out.output) - PSIRC_QUANT(reads, PSIRC_INDEX.out.collect()) + PSIRC_QUANT(reads, PSIRC_INDEX.out.index.collect()) CUSTOM_TX2GENE( ch_gtf, From d1adb3e4f013a5de29f73b732af7c06d69ae24f4 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 19:23:19 +0100 Subject: [PATCH 185/491] Fix missing version variable in psirc-quant --- modules/local/psirc/quant/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/local/psirc/quant/main.nf b/modules/local/psirc/quant/main.nf index b23895e6..9afe8150 100644 --- a/modules/local/psirc/quant/main.nf +++ b/modules/local/psirc/quant/main.nf @@ -14,6 +14,7 @@ process PSIRC_QUANT { script: def single_end = meta.single_end ? "--single -l 76 -s 20" : "" + def VERSION = '1.0' """ psirc-quant quant -t $task.cpus -i $index -o $meta.id $single_end $reads From 48f0dcae9431f9d854273bfb877fdf0d24eb36e7 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 19:24:38 +0100 Subject: [PATCH 186/491] Revert "Fix unchanged file" This reverts commit 18673fcef44b2fd0115fcd67655bac7379825ead. --- docs/images/nf-core-circrna_logo_dark.png | Bin 25216 -> 25192 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/docs/images/nf-core-circrna_logo_dark.png b/docs/images/nf-core-circrna_logo_dark.png index 869f35cbe9b6efda9efc5db2f2eb063f17c534cc..b48e7b08c6faa330c043d93a106076880d4157c8 100644 GIT binary patch delta 24534 zcmXVYbzD?k_wUdxjC2VM-3*PSFo2XucL+#_O6MVUXhFKWhY*I4mM)R*Qb~a!r0ep$ zzx(I;oHKi`wO8#G-wEzR+v!ECtwaOLRA4W3eXtE--;o_FrWUp2yix+3{zUyYHPkA1h zv3lC-xbfYFk@hx*=}Z)xSuhMvB0nfMFQ?uc&KXtKtdXdv025GUA^k+kspjTwFb2{{AgV=Nhe z52glOFL?)f+I6nAmfs$CbCRh{j6@z&L4YfZj=S~;RtMxFQ@SF@BMa(+25l$FQ~sW9 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zz{XY#I120=p>TEVn$YiL(#7fV_$r!rd;BR-9q0%-zw@d}f(4F@%uqQTar@uLeWY18 z_=X&Edtb+ZQRu`C{?Bhi#Kr@um_6j`(S&g}=Wc+v z^Sp0}1LlM}sA2xymglf(GV{<>2_=#P6=Sp6Gi8$C}#F6cfQ?tR5*OwrRaK){hY#u6!90+GE%HkG`7|eiaHw42HBIe?UVASWG zd*(NN5LK^*rhG-!H+)n-$`HX92>I}}`quoWEl7a@@Vsv31<3WHAJG>)g8uyh(SytG ze4b2V3%R~#+F!B)`e^h%NR>))_=oeDj90$t84f$pu)*~$E62cQi|4F^-4O7DK6xHh JZR2zMe*kpKTde>9 From b6f612dc5db3d530e701db1228b717da0b7af959 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 19 Mar 2024 19:27:18 +0100 Subject: [PATCH 187/491] Fix editorconfig checks --- bin/combine_quantification.py | 6 +++--- bin/counts_combined.py | 2 +- bin/merge_tools.py | 2 +- modules/local/quantification/transcriptome/main.nf | 2 +- subworkflows/local/circrna_discovery.nf | 2 +- 5 files changed, 7 insertions(+), 7 deletions(-) diff --git a/bin/combine_quantification.py b/bin/combine_quantification.py index d26ade6c..88601ebc 100755 --- a/bin/combine_quantification.py +++ b/bin/combine_quantification.py @@ -14,8 +14,8 @@ args = parser.parse_args() -df_annotation = pd.read_csv(args.circ_annotation, - sep='\t', header=None, +df_annotation = pd.read_csv(args.circ_annotation, + sep='\t', header=None, names=['chr', 'start', 'end', 'name', 'score', 'strand', 'type', 'gene', 'transcript'], index_col=['name']) @@ -48,4 +48,4 @@ df_combined = pd.concat([df_linear, df_circular], axis=0, sort=True) -df_combined.to_csv(args.out_combined, sep='\t') \ No newline at end of file +df_combined.to_csv(args.out_combined, sep='\t') diff --git a/bin/counts_combined.py b/bin/counts_combined.py index 7ae67065..99a9304e 100755 --- a/bin/counts_combined.py +++ b/bin/counts_combined.py @@ -28,4 +28,4 @@ df.index = df.index.map(lambda x: f'{x[0]}:{x[1]}-{x[2]}:{x[3]}') df.index.name = 'ID' -df.to_csv(args.out_tsv, sep='\t') \ No newline at end of file +df.to_csv(args.out_tsv, sep='\t') diff --git a/bin/merge_tools.py b/bin/merge_tools.py index 4246d0fd..fe81353d 100755 --- a/bin/merge_tools.py +++ b/bin/merge_tools.py @@ -17,7 +17,7 @@ df['tool_count'] = 1 -df = df.groupby(['chr', 'start', 'end', 'strand']).agg({'count': args.duplicates_fun, +df = df.groupby(['chr', 'start', 'end', 'strand']).agg({'count': args.duplicates_fun, 'tool_count': 'sum'}).reset_index() df = df[df['tool_count'] >= args.tool_filter] diff --git a/modules/local/quantification/transcriptome/main.nf b/modules/local/quantification/transcriptome/main.nf index 4d4d3028..747942c0 100644 --- a/modules/local/quantification/transcriptome/main.nf +++ b/modules/local/quantification/transcriptome/main.nf @@ -35,4 +35,4 @@ process TRANSCRIPTOME { gffread: \$(gffread --version 2>&1) END_VERSIONS """ -} \ No newline at end of file +} diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 4e081a4a..cf3d751b 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -245,7 +245,7 @@ workflow CIRCRNA_DISCOVERY { tools_selected = params.tool.split(',').collect{it.trim().toLowerCase()} - MERGE_TOOLS( ch_matrix.map{ meta, bed -> [ [id: meta.id], bed ] }.groupTuple(), + MERGE_TOOLS( ch_matrix.map{ meta, bed -> [ [id: meta.id], bed ] }.groupTuple(), tools_selected.size() > 1 ? tool_filter : 1, duplicates_fun ) COUNTS_COMBINED( MERGE_TOOLS.out.merged.map{ meta, bed -> bed }.collect() ) From f658463a4f47a11495ae43b28a896cfa980423ea Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Wed, 20 Mar 2024 09:39:49 +0100 Subject: [PATCH 188/491] Use gene names for annotation instead of ids --- bin/annotation.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/bin/annotation.py b/bin/annotation.py index ab9dc01d..a4d801f5 100755 --- a/bin/annotation.py +++ b/bin/annotation.py @@ -24,7 +24,7 @@ 14: 'attributes' } -attributes = ['gene_id', 'transcript_id'] +attributes = ['gene_name', 'transcript_id'] exon_boundary = args.exon_boundary @@ -36,7 +36,7 @@ df_intergenic = df[mask] df = df[~mask] df_intergenic['type'] = 'intergenic-circRNA' -df_intergenic['gene_id'] = 'NaN' +df_intergenic['gene_name'] = 'NaN' df_intergenic['transcript_id'] = 'NaN' # Convert attributes to a dictionary @@ -55,7 +55,7 @@ df = df.groupby(['chr', 'start', 'end', 'strand']).aggregate({ 'name': lambda x: x.iloc[0], 'score': lambda x: x.iloc[0], - 'gene_id': lambda x: list(x), + 'gene_name': lambda x: list(x), 'transcript_id': lambda x: list(x), 'perfect': lambda x: list(x) }) @@ -78,14 +78,14 @@ def determine_type(row): df['no_transcript'] = df['transcript_id'].apply(lambda x: all([type(value) != str and np.isnan(value) for value in x])) df['type'] = df.apply(lambda row: determine_type(row), axis=1) -df['gene_id'] = df.apply(lambda row: filter_perfect(row, 'gene_id'), axis=1) +df['gene_name'] = df.apply(lambda row: filter_perfect(row, 'gene_name'), axis=1) df['transcript_id'] = df.apply(lambda row: filter_perfect(row, 'transcript_id'), axis=1) # Drop perfect df = df.drop(['perfect'], axis=1) df = df.reset_index() df_intergenic = df_intergenic.reset_index() -bed_order = ['chr', 'start', 'end', 'name', 'score', 'strand', 'type', 'gene_id', 'transcript_id'] +bed_order = ['chr', 'start', 'end', 'name', 'score', 'strand', 'type', 'gene_name', 'transcript_id'] df = df[bed_order] df_intergenic = df_intergenic[bed_order] From 6d863a45bc7b78e24934a7c9e444e8c69fe78d5b Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 22 Mar 2024 08:29:41 +0100 Subject: [PATCH 189/491] Add GTF creation to annotation --- bin/annotation.py | 27 ++++++++++++++----- .../local/annotation/full_annotation/main.nf | 9 ++++--- 2 files changed, 26 insertions(+), 10 deletions(-) diff --git a/bin/annotation.py b/bin/annotation.py index a4d801f5..b1ca1383 100755 --- a/bin/annotation.py +++ b/bin/annotation.py @@ -3,11 +3,13 @@ import pandas as pd import numpy as np import argparse +import csv parser = argparse.ArgumentParser(description='Annotate circRNAs') parser.add_argument('--input', type=str, help='Path to the input file') parser.add_argument('--exon_boundary', type=int, help='Exon boundary') -parser.add_argument('--output', type=str, help='Path to the output file') +parser.add_argument('--output_bed', type=str, help='Path to the output bed file') +parser.add_argument('--output_gtf', type=str, help='Path to the output gtf') args = parser.parse_args() @@ -24,7 +26,7 @@ 14: 'attributes' } -attributes = ['gene_name', 'transcript_id'] +attributes = ['gene_id', 'gene_name', 'transcript_id'] exon_boundary = args.exon_boundary @@ -36,8 +38,9 @@ df_intergenic = df[mask] df = df[~mask] df_intergenic['type'] = 'intergenic-circRNA' -df_intergenic['gene_name'] = 'NaN' -df_intergenic['transcript_id'] = 'NaN' +df_intergenic['gene_id'] = 'integenic' + df_intergenic['name'] +df_intergenic['gene_name'] = 'integenic' + df_intergenic['name'] +df_intergenic['transcript_id'] = 'integenic' + df_intergenic['name'] # Convert attributes to a dictionary df['attributes'] = df['attributes'].apply(lambda row: dict([[value.strip(r'"') for value in entry.strip().split(' ')] for entry in row.split(';') if entry])) @@ -55,6 +58,7 @@ df = df.groupby(['chr', 'start', 'end', 'strand']).aggregate({ 'name': lambda x: x.iloc[0], 'score': lambda x: x.iloc[0], + 'gene_id': lambda x: list(x), 'gene_name': lambda x: list(x), 'transcript_id': lambda x: list(x), 'perfect': lambda x: list(x) @@ -78,6 +82,7 @@ def determine_type(row): df['no_transcript'] = df['transcript_id'].apply(lambda x: all([type(value) != str and np.isnan(value) for value in x])) df['type'] = df.apply(lambda row: determine_type(row), axis=1) +df['gene_id'] = df.apply(lambda row: filter_perfect(row, 'gene_id'), axis=1) df['gene_name'] = df.apply(lambda row: filter_perfect(row, 'gene_name'), axis=1) df['transcript_id'] = df.apply(lambda row: filter_perfect(row, 'transcript_id'), axis=1) # Drop perfect @@ -85,7 +90,7 @@ def determine_type(row): df = df.reset_index() df_intergenic = df_intergenic.reset_index() -bed_order = ['chr', 'start', 'end', 'name', 'score', 'strand', 'type', 'gene_name', 'transcript_id'] +bed_order = ['chr', 'start', 'end', 'name', 'score', 'strand', 'type', 'gene_id', 'gene_name', 'transcript_id'] df = df[bed_order] df_intergenic = df_intergenic[bed_order] @@ -94,4 +99,14 @@ def determine_type(row): # Sort by chr, start, end df = df.sort_values(['chr', 'start', 'end']) -df.to_csv(args.output, sep='\t', index=False, header=False) +df.to_csv(args.output_bed, sep='\t', index=False, header=False) + +# Convert to GTF +df['source'] = 'circRNA' +df['frame'] = '.' +df['attributes'] = 'gene_id "' + df['gene_id'] + '"; gene_name "' + df['gene_name'] + '"; transcript_id "' + df['name'] + '";' + +gtf_order = ['chr', 'source', 'type', 'start', 'end', 'score', 'strand', 'frame', 'attributes'] +df = df[gtf_order] + +df.to_csv(args.output_gtf, sep='\t', index=False, header=False, quoting=csv.QUOTE_NONE) diff --git a/modules/local/annotation/full_annotation/main.nf b/modules/local/annotation/full_annotation/main.nf index bf17b2cc..43030ca4 100644 --- a/modules/local/annotation/full_annotation/main.nf +++ b/modules/local/annotation/full_annotation/main.nf @@ -12,15 +12,16 @@ process ANNOTATION { val(exon_boundary) output: - tuple val(meta), path("${outfile}"), emit: bed + tuple val(meta), path("${out_bed}"), emit: bed + tuple val(meta), path("${out_gtf}"), emit: gtf path "versions.yml", emit: versions script: prefix = task.ext.prefix ?: "${meta.id}.annotation" - suffix = task.ext.suffix ?: "bed" - outfile = "${prefix}.${suffix}" + out_bed = "${prefix}.bed" + out_gtf = "${prefix}.gtf" """ - annotation.py --input ${intersection} --exon_boundary ${exon_boundary} --output ${outfile} + annotation.py --input ${intersection} --exon_boundary ${exon_boundary} --output_bed ${out_bed} --output_gtf ${out_gtf} cat <<-END_VERSIONS > versions.yml "${task.process}": From db88a4500b4d031a9774df0db452efaaddc586f2 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 22 Mar 2024 09:26:58 +0100 Subject: [PATCH 190/491] Switch to processing circRNAs more like standard transcripts --- bin/annotation.py | 8 +- bin/combine_quantification.py | 41 +--------- conf/modules.config | 16 +++- .../combine_quantification/main.nf | 10 +-- subworkflows/local/circrna_discovery.nf | 14 ++-- subworkflows/local/quantification.nf | 80 ++++++++----------- workflows/circrna/main.nf | 3 +- 7 files changed, 65 insertions(+), 107 deletions(-) diff --git a/bin/annotation.py b/bin/annotation.py index b1ca1383..17001e36 100755 --- a/bin/annotation.py +++ b/bin/annotation.py @@ -38,9 +38,9 @@ df_intergenic = df[mask] df = df[~mask] df_intergenic['type'] = 'intergenic-circRNA' -df_intergenic['gene_id'] = 'integenic' + df_intergenic['name'] -df_intergenic['gene_name'] = 'integenic' + df_intergenic['name'] -df_intergenic['transcript_id'] = 'integenic' + df_intergenic['name'] +df_intergenic['gene_id'] = 'intergenic_' + df_intergenic['name'] +df_intergenic['gene_name'] = 'intergenic_' + df_intergenic['name'] +df_intergenic['transcript_id'] = 'intergenic_' + df_intergenic['name'] # Convert attributes to a dictionary df['attributes'] = df['attributes'].apply(lambda row: dict([[value.strip(r'"') for value in entry.strip().split(' ')] for entry in row.split(';') if entry])) @@ -104,7 +104,7 @@ def determine_type(row): # Convert to GTF df['source'] = 'circRNA' df['frame'] = '.' -df['attributes'] = 'gene_id "' + df['gene_id'] + '"; gene_name "' + df['gene_name'] + '"; transcript_id "' + df['name'] + '";' +df['attributes'] = 'gene_id "' + df['gene_id'] + '"; gene_name "' + df['gene_name'] + '"; transcript_id "circ_' + df['name'] + '";' gtf_order = ['chr', 'source', 'type', 'start', 'end', 'score', 'strand', 'frame', 'attributes'] df = df[gtf_order] diff --git a/bin/combine_quantification.py b/bin/combine_quantification.py index 88601ebc..dd0b1307 100755 --- a/bin/combine_quantification.py +++ b/bin/combine_quantification.py @@ -6,46 +6,11 @@ parser = argparse.ArgumentParser(description='Merge quantification files into a single file') parser.add_argument('--inputs', type=str, nargs='+', help='List input files to merge') -parser.add_argument('--tx2gene', type=str, help='Path to tx2gene file') -parser.add_argument('--circ_annotation', type=str, help='Path to circRNA annotation file') -parser.add_argument('--out_linear', type=str, help='Path to output linear RNA quantification file') -parser.add_argument('--out_circular', type=str, help='Path to output circRNA quantification file') -parser.add_argument('--out_combined', type=str, help='Path to output combined quantification file') +parser.add_argument('--output', type=str, help='Path to output combined quantification file') args = parser.parse_args() -df_annotation = pd.read_csv(args.circ_annotation, - sep='\t', header=None, - names=['chr', 'start', 'end', 'name', 'score', 'strand', 'type', 'gene', 'transcript'], - index_col=['name']) - -df_tx2gene = pd.read_csv(args.tx2gene, sep='\t') - -dfs = [pd.read_csv(f, sep='\t', index_col=["gene_id", "gene_name"]) for f in args.inputs] +dfs = [pd.read_csv(f, sep='\t', index_col=[0, 1]) for f in args.inputs] df_combined = pd.concat(dfs, axis=1, sort=True) -# Split linear and circular -linear_mask = df_combined.index.get_level_values(0) \ - .isin(df_tx2gene["gene_id"]) -df_linear = df_combined[linear_mask].copy() -df_circular = df_combined[~linear_mask].copy() - -df_linear.to_csv(args.out_linear, sep='\t') - -# Perform annotation -df_annotation["annotation"] = df_annotation.apply(lambda row: 'intergenic' if row['type'] == 'intergenic-circRNA' else row['gene'], axis=1) -annotation_dict = df_annotation["annotation"].to_dict() - -df_circular.reset_index(inplace=True) -df_circular["gene_name"] = df_circular['gene_id'].map(annotation_dict) -df_circular.set_index(["gene_id", "gene_name"], inplace=True) - -df_circular.to_csv(args.out_circular, sep='\t') - -# Save combined -df_linear["type"] = "gene" -df_circular["type"] = "circRNA" - -df_combined = pd.concat([df_linear, df_circular], axis=0, sort=True) - -df_combined.to_csv(args.out_combined, sep='\t') +df_combined.to_csv(args.output, sep='\t') diff --git a/conf/modules.config b/conf/modules.config index fc6a6ba9..5ac28733 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -638,13 +638,18 @@ if (!params.skip_trimming) { ext.suffix = "intersect.bed" } - withName: COMBINE_ANNOTATIONS { + withName: COMBINE_ANNOTATION_BEDS { ext.args = "-k 1,1 -k2,2n -k3,3n -u" ext.suffix = "combined.bed" } + withName: COMBINE_ANNOTATION_GTFS { + ext.args = "-k 1,1 -k3,3n -k4,4n -u" + ext.suffix = "combined.gtf" + } + withName: REMOVE_SCORE_STRAND { - ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3, \".\", \".\", \$7, \$8, \$9 }'" + ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3, \".\", \".\", \$7, \$8, \$9, \$10 }'" ext.suffix = "tidy.bed" } @@ -672,6 +677,11 @@ if (!params.skip_trimming) { ext.suffix = "unique.bed" } + withName: COMBINE_TRANSCRIPTOME_GTFS { + ext.args = "-k 1,1 -k3,3n -k4,4n" + ext.suffix = "gtf" + } + withName: CIRCULAR_TRANSCRIPTOME { ext.args = "-nameOnly" } @@ -680,7 +690,7 @@ if (!params.skip_trimming) { // GAWK process that marks FASTA headers. // Leaves headers starting with "ENS" and non-header lines as is. // Adds "\tC" to the end of the header for all other headers - ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (!/^>/ || /^>ENS/) { print } else { print \$1 \"\\tC\" } }'" + ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (!/^>circ_/) { print } else { print \$1 \"\\tC\" } }'" ext.suffix = "marked.fasta" } diff --git a/modules/local/quantification/combine_quantification/main.nf b/modules/local/quantification/combine_quantification/main.nf index 975ae48f..41790d9b 100644 --- a/modules/local/quantification/combine_quantification/main.nf +++ b/modules/local/quantification/combine_quantification/main.nf @@ -8,23 +8,15 @@ process COMBINE_QUANTIFICATION { input: tuple val(meta), path(inputs) - tuple val(meta2), path(tx2gene) - tuple val(meta3), path(circ_annotation) output: - path("${meta.id}.linear.tsv") , emit: linear - path("${meta.id}.circular.tsv") , emit: circular path("${meta.id}.combined.tsv") , emit: combined path "versions.yml" , emit: versions script: """ combine_quantification.py --inputs ${inputs} \\ - --tx2gene ${tx2gene} \\ - --circ_annotation ${circ_annotation} \\ - --out_linear ${meta.id}.linear.tsv \\ - --out_circular ${meta.id}.circular.tsv \\ - --out_combined ${meta.id}.combined.tsv + --output ${meta.id}.combined.tsv cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index cf3d751b..9afb3c12 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -1,6 +1,7 @@ include { ANNOTATION } from '../../modules/local/annotation/full_annotation/main' -include { GNU_SORT as COMBINE_ANNOTATIONS } from '../../modules/nf-core/gnu/sort/main' +include { GNU_SORT as COMBINE_ANNOTATION_BEDS } from '../../modules/nf-core/gnu/sort/main' +include { GNU_SORT as COMBINE_ANNOTATION_GTFS } from '../../modules/nf-core/gnu/sort/main' include { GAWK as REMOVE_SCORE_STRAND } from '../../modules/nf-core/gawk/main' include { BEDTOOLS_INTERSECT as INTERSECT_ANNOTATION } from '../../modules/nf-core/bedtools/intersect/main' include { BOWTIE2_ALIGN as FIND_CIRC_ALIGN } from '../../modules/nf-core/bowtie2/align/main' @@ -216,13 +217,15 @@ workflow CIRCRNA_DISCOVERY { INTERSECT_ANNOTATION( circrna_filtered.combine(gtf), [[], []]) ANNOTATION( INTERSECT_ANNOTATION.out.intersect, exon_boundary ) - COMBINE_ANNOTATIONS(ANNOTATION.out.bed.map{ meta, bed -> bed}.collect().map{[[id: "annotation"], it]}) - REMOVE_SCORE_STRAND( COMBINE_ANNOTATIONS.out.sorted, []) + COMBINE_ANNOTATION_BEDS(ANNOTATION.out.bed.map{ meta, bed -> bed}.collect().map{[[id: "annotation"], it]}) + REMOVE_SCORE_STRAND( COMBINE_ANNOTATION_BEDS.out.sorted, []) + COMBINE_ANNOTATION_GTFS(ANNOTATION.out.gtf.map{ meta, gtf -> gtf}.collect().map{[[id: "annotation"], it]}) ch_versions = ch_versions.mix(INTERSECT_ANNOTATION.out.versions) ch_versions = ch_versions.mix(ANNOTATION.out.versions) - ch_versions = ch_versions.mix(COMBINE_ANNOTATIONS.out.versions) + ch_versions = ch_versions.mix(COMBINE_ANNOTATION_BEDS.out.versions) ch_versions = ch_versions.mix(REMOVE_SCORE_STRAND.out.versions) + ch_versions = ch_versions.mix(COMBINE_ANNOTATION_GTFS.out.versions) // // FASTA WORKFLOW: @@ -258,7 +261,8 @@ workflow CIRCRNA_DISCOVERY { emit: circrna_bed12 = ANNOTATION.out.bed fasta = FASTA.out.analysis_fasta - annotation = REMOVE_SCORE_STRAND.out.output + annotation_bed = REMOVE_SCORE_STRAND.out.output + annotation_gtf = COMBINE_ANNOTATION_GTFS.out.sorted counts_bed counts_tsv diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index af720ce0..6a64d35c 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -1,15 +1,14 @@ -include { TRANSCRIPTOME as LINEAR_TRANSCRIPTOME } from '../../modules/local/quantification/transcriptome/main' -include { BEDTOOLS_GETFASTA as CIRCULAR_TRANSCRIPTOME } from '../../modules/nf-core/bedtools/getfasta/main' -include { GAWK as COUNTS_TO_BED } from '../../modules/nf-core/gawk/main' -include { GNU_SORT as UNIQUE_REGIONS } from '../../modules/nf-core/gnu/sort/main' -include { CAT_CAT as CAT_TRANSCRIPTOME } from '../../modules/nf-core/cat/cat/main' +include { GNU_SORT as COMBINE_TRANSCRIPTOME_GTFS } from '../../modules/nf-core/gnu/sort/main' +include { TRANSCRIPTOME } from '../../modules/local/quantification/transcriptome/main' include { GAWK as MARK_CIRCULAR } from '../../modules/nf-core/gawk/main' include { PSIRC_INDEX } from '../../modules/local/psirc/index/main' include { PSIRC_QUANT } from '../../modules/local/psirc/quant/main' include { CUSTOM_TX2GENE } from '../../modules/nf-core/custom/tx2gene/main' include { TXIMETA_TXIMPORT } from '../../modules/nf-core/tximeta/tximport/main' -include { COMBINE_QUANTIFICATION as COMBINE_COUNTS } from '../../modules/local/quantification/combine_quantification/main' -include { COMBINE_QUANTIFICATION as COMBINE_TPM } from '../../modules/local/quantification/combine_quantification/main' +include { COMBINE_QUANTIFICATION as COMBINE_GENE_COUNTS } from '../../modules/local/quantification/combine_quantification/main' +include { COMBINE_QUANTIFICATION as COMBINE_GENE_TPM } from '../../modules/local/quantification/combine_quantification/main' +include { COMBINE_QUANTIFICATION as COMBINE_TX_COUNTS } from '../../modules/local/quantification/combine_quantification/main' +include { COMBINE_QUANTIFICATION as COMBINE_TX_TPM } from '../../modules/local/quantification/combine_quantification/main' workflow QUANTIFICATION { take: @@ -17,34 +16,22 @@ workflow QUANTIFICATION { ch_fasta counts reads - circ_annotation + circ_annotation_bed + circ_annotation_gtf main: ch_versions = Channel.empty() - LINEAR_TRANSCRIPTOME(ch_gtf, ch_fasta) - COUNTS_TO_BED(counts.map{counts -> [[id: "counts"], counts]}, []) - UNIQUE_REGIONS(COUNTS_TO_BED.out.output) - - CIRCULAR_TRANSCRIPTOME( - UNIQUE_REGIONS.out.sorted.map{meta, bed -> bed}, - ch_fasta.map{meta, fasta -> fasta} - ) - - CAT_TRANSCRIPTOME( - LINEAR_TRANSCRIPTOME.out.transcriptome.map{meta, fasta -> fasta}.mix( - CIRCULAR_TRANSCRIPTOME.out.fasta - ).collect().map(fastas -> [[id: "transcriptome"], fastas]) + COMBINE_TRANSCRIPTOME_GTFS( + ch_gtf.mix(circ_annotation_gtf).map{meta, gtf -> gtf}.collect().map{[[id: "transcriptome"], it]}, ) - MARK_CIRCULAR(CAT_TRANSCRIPTOME.out.file_out, []) + TRANSCRIPTOME(COMBINE_TRANSCRIPTOME_GTFS.out.sorted, ch_fasta) + MARK_CIRCULAR(TRANSCRIPTOME.out.transcriptome, []) ch_versions = ch_versions.mix( - LINEAR_TRANSCRIPTOME.out.versions, - COUNTS_TO_BED.out.versions, - UNIQUE_REGIONS.out.versions, - CIRCULAR_TRANSCRIPTOME.out.versions, - CAT_TRANSCRIPTOME.out.versions, + COMBINE_TRANSCRIPTOME_GTFS.out.versions, + TRANSCRIPTOME.out.versions, MARK_CIRCULAR.out.versions ) @@ -52,7 +39,7 @@ workflow QUANTIFICATION { PSIRC_QUANT(reads, PSIRC_INDEX.out.index.collect()) CUSTOM_TX2GENE( - ch_gtf, + COMBINE_TRANSCRIPTOME_GTFS.out.sorted, PSIRC_QUANT.out.directory.map{meta, quant -> quant}.collect().map{[[id: "quant"], it]}, "kallisto", "gene_id", @@ -72,34 +59,33 @@ workflow QUANTIFICATION { TXIMETA_TXIMPORT.out.versions ) - ch_counts = TXIMETA_TXIMPORT.out.counts_gene - ch_tpm = TXIMETA_TXIMPORT.out.tpm_gene + ch_gene_counts = TXIMETA_TXIMPORT.out.counts_gene + ch_gene_tpm = TXIMETA_TXIMPORT.out.tpm_gene - COMBINE_COUNTS( - ch_counts.map{meta, counts -> counts}.collect().map{[[id: "counts"], it]}, - CUSTOM_TX2GENE.out.tx2gene, - circ_annotation + COMBINE_GENE_COUNTS( + ch_gene_counts.map{meta, counts -> counts}.collect().map{[[id: "gene_counts"], it]} ) - COMBINE_TPM( - ch_tpm.map{meta, tpm -> tpm}.collect().map{[[id: "tpm"], it]}, - CUSTOM_TX2GENE.out.tx2gene, - circ_annotation + COMBINE_GENE_TPM( + ch_gene_tpm.map{meta, tpm -> tpm}.collect().map{[[id: "gene_tpm"], it]} + ) + + COMBINE_TX_COUNTS( + TXIMETA_TXIMPORT.out.counts_transcript.map{meta, counts -> counts}.collect().map{[[id: "tx_counts"], it]} + ) + + COMBINE_TX_TPM( + TXIMETA_TXIMPORT.out.tpm_transcript.map{meta, tpm -> tpm}.collect().map{[[id: "tx_tpm"], it]} ) ch_versions = ch_versions.mix( - COMBINE_COUNTS.out.versions, - COMBINE_TPM.out.versions + COMBINE_GENE_COUNTS.out.versions, + COMBINE_GENE_TPM.out.versions ) emit: - counts_linear = COMBINE_COUNTS.out.linear - counts_circular = COMBINE_COUNTS.out.circular - counts_combined = COMBINE_COUNTS.out.combined - - tpm_linear = COMBINE_TPM.out.linear - tpm_circular = COMBINE_TPM.out.circular - tpm_combined = COMBINE_TPM.out.combined + gene_counts = COMBINE_GENE_COUNTS.out.combined + gene_tpm = COMBINE_GENE_TPM.out.combined versions = ch_versions } diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 7c7d522f..cde056ff 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -162,7 +162,8 @@ workflow CIRCRNA { ch_fasta, CIRCRNA_DISCOVERY.out.counts_bed, FASTQC_TRIMGALORE.out.reads, - CIRCRNA_DISCOVERY.out.annotation + CIRCRNA_DISCOVERY.out.annotation_bed, + CIRCRNA_DISCOVERY.out.annotation_gtf ) ch_versions = ch_versions.mix(QUANTIFICATION.out.versions) From 8b7cf90b32dd5465a0359939a3bbcc45b7c3e02e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 22 Mar 2024 09:55:07 +0100 Subject: [PATCH 191/491] Switch to using CSVTK for joining quantifications --- conf/modules.config | 11 +--- modules.json | 5 ++ .../combine_quantification/main.nf | 28 ----------- modules/nf-core/csvtk/join/environment.yml | 7 +++ modules/nf-core/csvtk/join/main.nf | 50 +++++++++++++++++++ modules/nf-core/csvtk/join/meta.yml | 41 +++++++++++++++ subworkflows/local/quantification.nf | 40 ++++++++------- 7 files changed, 126 insertions(+), 56 deletions(-) delete mode 100644 modules/local/quantification/combine_quantification/main.nf create mode 100644 modules/nf-core/csvtk/join/environment.yml create mode 100644 modules/nf-core/csvtk/join/main.nf create mode 100644 modules/nf-core/csvtk/join/meta.yml diff --git a/conf/modules.config b/conf/modules.config index 5ac28733..9e9cde44 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -694,15 +694,8 @@ if (!params.skip_trimming) { ext.suffix = "marked.fasta" } - withName: COMBINE_COUNTS { - publishDir = [ - path: { "${params.outdir}/quantification/" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: COMBINE_TPM { + withName: ".*:JOIN_(GENE|TX)_(COUNTS|TPM)" { + ext.args = "-f 1,2 -t" publishDir = [ path: { "${params.outdir}/quantification/" }, mode: params.publish_dir_mode, diff --git a/modules.json b/modules.json index 751a3f5c..77b6ee5d 100644 --- a/modules.json +++ b/modules.json @@ -65,6 +65,11 @@ "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, + "csvtk/join": { + "branch": "master", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": ["modules"] + }, "csvtk/split": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", diff --git a/modules/local/quantification/combine_quantification/main.nf b/modules/local/quantification/combine_quantification/main.nf deleted file mode 100644 index 41790d9b..00000000 --- a/modules/local/quantification/combine_quantification/main.nf +++ /dev/null @@ -1,28 +0,0 @@ -process COMBINE_QUANTIFICATION { - label "process_single" - - conda "conda-forge::mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6==fccb0c41a243c639e11dd1be7b74f563e624fcca-0" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0': - 'biocontainers/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0' }" - - input: - tuple val(meta), path(inputs) - - output: - path("${meta.id}.combined.tsv") , emit: combined - path "versions.yml" , emit: versions - - script: - """ - combine_quantification.py --inputs ${inputs} \\ - --output ${meta.id}.combined.tsv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - python: \$(python --version | sed 's/Python //g') - pandas: \$(python -c "import pandas; print(pandas.__version__)") - numpy: \$(python -c "import numpy; print(numpy.__version__)") - END_VERSIONS - """ -} diff --git a/modules/nf-core/csvtk/join/environment.yml b/modules/nf-core/csvtk/join/environment.yml new file mode 100644 index 00000000..b488c861 --- /dev/null +++ b/modules/nf-core/csvtk/join/environment.yml @@ -0,0 +1,7 @@ +name: csvtk_join +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::csvtk=0.26.0 diff --git a/modules/nf-core/csvtk/join/main.nf b/modules/nf-core/csvtk/join/main.nf new file mode 100644 index 00000000..bf02e7f5 --- /dev/null +++ b/modules/nf-core/csvtk/join/main.nf @@ -0,0 +1,50 @@ +process CSVTK_JOIN { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/csvtk:0.26.0--h9ee0642_0': + 'biocontainers/csvtk:0.26.0--h9ee0642_0' }" + + input: + tuple val(meta), path(csv) + + output: + tuple val(meta), path("${prefix}.${out_extension}"), emit: csv + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + out_extension = args.contains('--out-delimiter "\t"') || args.contains('-D "\t"') || args.contains("-D \$'\t'") ? "tsv" : "csv" + """ + csvtk \\ + join \\ + $args \\ + --num-cpus $task.cpus \\ + --out-file ${prefix}.${out_extension} \\ + $csv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + csvtk: \$(echo \$( csvtk version | sed -e "s/csvtk v//g" )) + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + out_extension = args.contains('--out-delimiter "\t"') || args.contains('-D "\t"') || args.contains("-D \$'\t'") ? "tsv" : "csv" + """ + touch ${prefix}.${out_extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + csvtk: \$(echo \$( csvtk version | sed -e "s/csvtk v//g" )) + END_VERSIONS + """ +} diff --git a/modules/nf-core/csvtk/join/meta.yml b/modules/nf-core/csvtk/join/meta.yml new file mode 100644 index 00000000..a75ec40f --- /dev/null +++ b/modules/nf-core/csvtk/join/meta.yml @@ -0,0 +1,41 @@ +name: csvtk_join +description: Join two or more CSV (or TSV) tables by selected fields into a single table +keywords: + - join + - tsv + - csv +tools: + - csvtk: + description: A cross-platform, efficient, practical CSV/TSV toolkit + homepage: http://bioinf.shenwei.me/csvtk + documentation: http://bioinf.shenwei.me/csvtk + tool_dev_url: https://github.com/shenwei356/csvtk + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - csv: + type: file + description: CSV/TSV formatted files + pattern: "*.{csv,tsv}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "version.yml" + - csv: + type: file + description: Joined CSV/TSV file + pattern: "*.{csv,tsv}" +authors: + - "@anoronh4" +maintainers: + - "@anoronh4" diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index 6a64d35c..fccd30a1 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -1,14 +1,14 @@ -include { GNU_SORT as COMBINE_TRANSCRIPTOME_GTFS } from '../../modules/nf-core/gnu/sort/main' -include { TRANSCRIPTOME } from '../../modules/local/quantification/transcriptome/main' -include { GAWK as MARK_CIRCULAR } from '../../modules/nf-core/gawk/main' -include { PSIRC_INDEX } from '../../modules/local/psirc/index/main' -include { PSIRC_QUANT } from '../../modules/local/psirc/quant/main' -include { CUSTOM_TX2GENE } from '../../modules/nf-core/custom/tx2gene/main' -include { TXIMETA_TXIMPORT } from '../../modules/nf-core/tximeta/tximport/main' -include { COMBINE_QUANTIFICATION as COMBINE_GENE_COUNTS } from '../../modules/local/quantification/combine_quantification/main' -include { COMBINE_QUANTIFICATION as COMBINE_GENE_TPM } from '../../modules/local/quantification/combine_quantification/main' -include { COMBINE_QUANTIFICATION as COMBINE_TX_COUNTS } from '../../modules/local/quantification/combine_quantification/main' -include { COMBINE_QUANTIFICATION as COMBINE_TX_TPM } from '../../modules/local/quantification/combine_quantification/main' +include { GNU_SORT as COMBINE_TRANSCRIPTOME_GTFS } from '../../modules/nf-core/gnu/sort/main' +include { TRANSCRIPTOME } from '../../modules/local/quantification/transcriptome/main' +include { GAWK as MARK_CIRCULAR } from '../../modules/nf-core/gawk/main' +include { PSIRC_INDEX } from '../../modules/local/psirc/index/main' +include { PSIRC_QUANT } from '../../modules/local/psirc/quant/main' +include { CUSTOM_TX2GENE } from '../../modules/nf-core/custom/tx2gene/main' +include { TXIMETA_TXIMPORT } from '../../modules/nf-core/tximeta/tximport/main' +include { CSVTK_JOIN as JOIN_GENE_COUNTS } from '../../modules/nf-core/csvtk/join/main' +include { CSVTK_JOIN as JOIN_GENE_TPM } from '../../modules/nf-core/csvtk/join/main' +include { CSVTK_JOIN as JOIN_TX_COUNTS } from '../../modules/nf-core/csvtk/join/main' +include { CSVTK_JOIN as JOIN_TX_TPM } from '../../modules/nf-core/csvtk/join/main' workflow QUANTIFICATION { take: @@ -62,30 +62,32 @@ workflow QUANTIFICATION { ch_gene_counts = TXIMETA_TXIMPORT.out.counts_gene ch_gene_tpm = TXIMETA_TXIMPORT.out.tpm_gene - COMBINE_GENE_COUNTS( + JOIN_GENE_COUNTS( ch_gene_counts.map{meta, counts -> counts}.collect().map{[[id: "gene_counts"], it]} ) - COMBINE_GENE_TPM( + JOIN_GENE_TPM( ch_gene_tpm.map{meta, tpm -> tpm}.collect().map{[[id: "gene_tpm"], it]} ) - COMBINE_TX_COUNTS( + JOIN_TX_COUNTS( TXIMETA_TXIMPORT.out.counts_transcript.map{meta, counts -> counts}.collect().map{[[id: "tx_counts"], it]} ) - COMBINE_TX_TPM( + JOIN_TX_TPM( TXIMETA_TXIMPORT.out.tpm_transcript.map{meta, tpm -> tpm}.collect().map{[[id: "tx_tpm"], it]} ) ch_versions = ch_versions.mix( - COMBINE_GENE_COUNTS.out.versions, - COMBINE_GENE_TPM.out.versions + JOIN_GENE_COUNTS.out.versions, + JOIN_GENE_TPM.out.versions ) emit: - gene_counts = COMBINE_GENE_COUNTS.out.combined - gene_tpm = COMBINE_GENE_TPM.out.combined + gene_counts = JOIN_GENE_COUNTS.out.csv + gene_tpm = JOIN_GENE_TPM.out.csv + tx_counts = JOIN_TX_COUNTS.out.csv + tx_tpm = JOIN_TX_TPM.out.csv versions = ch_versions } From 2581c28a2b57a2cb50f183d1100dc4fa6ec4bbf7 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 22 Mar 2024 10:49:42 +0100 Subject: [PATCH 192/491] Implement splitting of circular and linear transcripts --- .../local/quantification/split_types/main.nf | 43 +++++++++++++++++++ subworkflows/local/quantification.nf | 26 ++++++++--- 2 files changed, 64 insertions(+), 5 deletions(-) create mode 100644 modules/local/quantification/split_types/main.nf diff --git a/modules/local/quantification/split_types/main.nf b/modules/local/quantification/split_types/main.nf new file mode 100644 index 00000000..a95b18af --- /dev/null +++ b/modules/local/quantification/split_types/main.nf @@ -0,0 +1,43 @@ +process SPLIT_TYPES { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gawk:5.1.0' : + 'biocontainers/gawk:5.1.0' }" + + input: + tuple val(meta), path(input) + + output: + tuple val(meta), path("linear.tsv") , emit: linear + tuple val(meta), path("circular.tsv"), emit: circular + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + """ + awk -F'\\t' \\ + 'NR==1 {print > "circular.tsv"; print > "linear.tsv"} \\ + NR>1 {if (\$1 ~ /^circ_/) print > "circular.tsv"; else print > "linear.tsv"}' ${input} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//') + END_VERSIONS + """ + + stub: + """ + touch linear.tsv + touch circular.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//') + END_VERSIONS + """ +} diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index fccd30a1..f2969a5f 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -9,6 +9,8 @@ include { CSVTK_JOIN as JOIN_GENE_COUNTS } from '../../modules/nf-core/c include { CSVTK_JOIN as JOIN_GENE_TPM } from '../../modules/nf-core/csvtk/join/main' include { CSVTK_JOIN as JOIN_TX_COUNTS } from '../../modules/nf-core/csvtk/join/main' include { CSVTK_JOIN as JOIN_TX_TPM } from '../../modules/nf-core/csvtk/join/main' +include { SPLIT_TYPES as SPLIT_TYPES_COUNTS } from '../../modules/local/quantification/split_types/main' +include { SPLIT_TYPES as SPLIT_TYPES_TPM } from '../../modules/local/quantification/split_types/main' workflow QUANTIFICATION { take: @@ -78,16 +80,30 @@ workflow QUANTIFICATION { TXIMETA_TXIMPORT.out.tpm_transcript.map{meta, tpm -> tpm}.collect().map{[[id: "tx_tpm"], it]} ) + SPLIT_TYPES_COUNTS( + JOIN_TX_COUNTS.out.csv + ) + + SPLIT_TYPES_TPM( + JOIN_TX_TPM.out.csv + ) + ch_versions = ch_versions.mix( JOIN_GENE_COUNTS.out.versions, - JOIN_GENE_TPM.out.versions + JOIN_GENE_TPM.out.versions, + JOIN_TX_COUNTS.out.versions, + JOIN_TX_TPM.out.versions ) emit: - gene_counts = JOIN_GENE_COUNTS.out.csv - gene_tpm = JOIN_GENE_TPM.out.csv - tx_counts = JOIN_TX_COUNTS.out.csv - tx_tpm = JOIN_TX_TPM.out.csv + gene_counts = JOIN_GENE_COUNTS.out.csv + gene_tpm = JOIN_GENE_TPM.out.csv + tx_counts = JOIN_TX_COUNTS.out.csv + tx_tpm = JOIN_TX_TPM.out.csv + linear_tx_counts = SPLIT_TYPES_COUNTS.out.linear + linear_tx_tpm = SPLIT_TYPES_TPM.out.linear + circular_tx_counts = SPLIT_TYPES_COUNTS.out.circular + circular_tx_tpm = SPLIT_TYPES_TPM.out.circular versions = ch_versions } From 12a1b380f9e840b58515e22ee17454a445d8ba71 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 22 Mar 2024 10:52:18 +0100 Subject: [PATCH 193/491] Simplify quantification script --- subworkflows/local/quantification.nf | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index f2969a5f..a17805cf 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -61,15 +61,12 @@ workflow QUANTIFICATION { TXIMETA_TXIMPORT.out.versions ) - ch_gene_counts = TXIMETA_TXIMPORT.out.counts_gene - ch_gene_tpm = TXIMETA_TXIMPORT.out.tpm_gene - JOIN_GENE_COUNTS( - ch_gene_counts.map{meta, counts -> counts}.collect().map{[[id: "gene_counts"], it]} + TXIMETA_TXIMPORT.out.counts_gene.map{meta, counts -> counts}.collect().map{[[id: "gene_counts"], it]} ) JOIN_GENE_TPM( - ch_gene_tpm.map{meta, tpm -> tpm}.collect().map{[[id: "gene_tpm"], it]} + TXIMETA_TXIMPORT.out.tpm_gene.map{meta, tpm -> tpm}.collect().map{[[id: "gene_tpm"], it]} ) JOIN_TX_COUNTS( @@ -92,7 +89,9 @@ workflow QUANTIFICATION { JOIN_GENE_COUNTS.out.versions, JOIN_GENE_TPM.out.versions, JOIN_TX_COUNTS.out.versions, - JOIN_TX_TPM.out.versions + JOIN_TX_TPM.out.versions, + SPLIT_TYPES_COUNTS.out.versions, + SPLIT_TYPES_TPM.out.versions ) emit: From 967fb00cb169a07fd05a7001ec14a966ca58eeab Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 22 Mar 2024 12:40:19 +0100 Subject: [PATCH 194/491] Add quantification type splitting to output --- conf/modules.config | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index 9e9cde44..fadfbf84 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -703,6 +703,14 @@ if (!params.skip_trimming) { ] } + withName: ".*:SPLIT_TYPES_(COUNTS|TPM)" { + publishDir = [ + path: { "${params.outdir}/quantification/" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + withName: TARGETSCAN_DATABASE { ext.when = { params.module.split(',').contains('mirna_prediction') } publishDir = [ From 6dd7a5a90b4d854d22bfe1935fe8cf6403fc6029 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 22 Mar 2024 15:04:45 +0100 Subject: [PATCH 195/491] Add filter for overlong circRNAs --- bin/annotation.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/bin/annotation.py b/bin/annotation.py index 17001e36..21bd9587 100755 --- a/bin/annotation.py +++ b/bin/annotation.py @@ -33,6 +33,9 @@ df = pd.read_csv(args.input, sep="\t", header=None, usecols=columns.keys()) df = df.rename(columns=columns) +# Remove overlong circRNAs +df = df[df['end'] - df['start'] <= 10_000] + # Extract circRNAs without match mask = df['tx_start'] == -1 df_intergenic = df[mask] From 9c62830dc059ed53dc5ea201239b4f7050a86168 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 19 Apr 2024 10:28:38 +0200 Subject: [PATCH 196/491] Remove ciriquant YML version capture --- subworkflows/local/circrna_discovery.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 9afb3c12..8ac26e69 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -143,7 +143,6 @@ workflow CIRCRNA_DISCOVERY { CIRIQUANT( reads, ch_gtf, ch_fasta, bwa_index, hisat2_index ) CIRIQUANT_FILTER( CIRIQUANT.out.gtf.map{ meta, gtf -> [ meta + [tool: "ciriquant"], gtf ] }, bsj_reads ) - ch_versions = ch_versions.mix(CIRIQUANT_YML.out.versions) ch_versions = ch_versions.mix(CIRIQUANT.out.versions) ch_versions = ch_versions.mix(CIRIQUANT_FILTER.out.versions) From 65f0f54825c86edd94bfb330bc90f6563e131a32 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 20 Apr 2024 09:51:29 +0200 Subject: [PATCH 197/491] Add draft tximeta support --- modules/local/psirc/quant/main.nf | 3 +- modules/local/tximeta/tximeta/main.nf | 47 ++++ .../local/tximeta/tximeta/templates/tximeta.r | 222 ++++++++++++++++++ nextflow.config | 2 + nextflow_schema.json | 5 + subworkflows/local/quantification.nf | 17 +- workflows/circrna/main.nf | 3 +- 7 files changed, 289 insertions(+), 10 deletions(-) create mode 100644 modules/local/tximeta/tximeta/main.nf create mode 100755 modules/local/tximeta/tximeta/templates/tximeta.r diff --git a/modules/local/psirc/quant/main.nf b/modules/local/psirc/quant/main.nf index 9afe8150..5761aaad 100644 --- a/modules/local/psirc/quant/main.nf +++ b/modules/local/psirc/quant/main.nf @@ -7,6 +7,7 @@ process PSIRC_QUANT { input: tuple val(meta), path(reads) tuple val(meta2), path(index) + val(bootstrap_samples) output: tuple val(meta), path("${meta.id}"), emit: directory @@ -16,7 +17,7 @@ process PSIRC_QUANT { def single_end = meta.single_end ? "--single -l 76 -s 20" : "" def VERSION = '1.0' """ - psirc-quant quant -t $task.cpus -i $index -o $meta.id $single_end $reads + psirc-quant quant -t $task.cpus -i $index -o $meta.id $single_end $reads -b $bootstrap_samples cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/tximeta/tximeta/main.nf b/modules/local/tximeta/tximeta/main.nf new file mode 100644 index 00000000..db263cf9 --- /dev/null +++ b/modules/local/tximeta/tximeta/main.nf @@ -0,0 +1,47 @@ +process TXIMETA_TXIMETA { + label "process_medium" + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bioconductor-tximeta%3A1.20.1--r43hdfd78af_1' : + 'biocontainers/bioconductor-tximeta:1.20.1--r43hdfd78af_1' }" + + input: + tuple val(meta), path("quants/*") + tuple val(meta2), path(tx2gene) + val quant_type + + output: + tuple val(meta), path("*gene_tpm.tsv") , emit: tpm_gene + tuple val(meta), path("*gene_counts.tsv") , emit: counts_gene + tuple val(meta), path("*gene_counts_length_scaled.tsv"), emit: counts_gene_length_scaled + tuple val(meta), path("*gene_counts_scaled.tsv") , emit: counts_gene_scaled + tuple val(meta), path("*gene_lengths.tsv") , emit: lengths_gene + tuple val(meta), path("*transcript_tpm.tsv") , emit: tpm_transcript + tuple val(meta), path("*transcript_counts.tsv") , emit: counts_transcript + tuple val(meta), path("*transcript_lengths.tsv") , emit: lengths_transcript + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + template 'tximeta.r' + + stub: + """ + touch ${meta.id}.gene_tpm.tsv + touch ${meta.id}.gene_counts.tsv + touch ${meta.id}.gene_counts_length_scaled.tsv + touch ${meta.id}.gene_counts_scaled.tsv + touch ${meta.id}.gene_lengths.tsv + touch ${meta.id}.transcript_tpm.tsv + touch ${meta.id}.transcript_counts.tsv + touch ${meta.id}.transcript_lengths.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bioconductor-tximeta: \$(Rscript -e "library(tximeta); cat(as.character(packageVersion('tximeta')))") + END_VERSIONS + """ +} diff --git a/modules/local/tximeta/tximeta/templates/tximeta.r b/modules/local/tximeta/tximeta/templates/tximeta.r new file mode 100755 index 00000000..56a24566 --- /dev/null +++ b/modules/local/tximeta/tximeta/templates/tximeta.r @@ -0,0 +1,222 @@ +#!/usr/bin/env Rscript --vanilla + +# Script for importing and processing transcript-level quantifications. +# Written by Lorena Pantano, later modified by Jonathan Manning, and released +# under the MIT license. + +# Loading required libraries +library(SummarizedExperiment) +library(tximport) + +################################################ +################################################ +## Functions ## +################################################ +################################################ + +#' Build a table from a SummarizedExperiment object +#' +#' This function takes a SummarizedExperiment object and a specific slot name to extract +#' assay data. It then combines the first two columns of the rowData with the specified +#' assay data slot into a new data table. +#' +#' @param se.obj A SummarizedExperiment object from which to build the table. +#' @param slot The name of the slot in the assays list from which to extract data. +#' +#' @return A data frame combining the first two columns of the rowData with the assay data from the specified slot. + +build_table <- function(se.obj, slot) { + cbind(rowData(se.obj)[,1:2], assays(se.obj)[[slot]]) +} + +#' Write a table to a file from a SummarizedExperiment object with given parameters +#' +#' This function generates a table from a SummarizedExperiment object using specified parameters +#' and writes the resulting table to a file. The file name is constructed using a prefix and a +#' suffix from the parameters, and the table is written with tab separation, without quoting text, +#' and without row names. +#' +#' @param params A list containing the parameters needed for file generation and table writing. +#' The list should include: +#' - `obj`: A SummarizedExperiment object from which to build the table. +#' - `slot`: The name of the slot in the assays list from which to extract data. +#' - `suffix`: Suffix to use for generating the file name. +#' +#' @return NULL The function is called for its side effect of writing a file and does not return anything. + +write_se_table <- function(params, prefix) { + file_name <- paste0(prefix, ".", params\$suffix) + write.table(build_table(params\$obj, params\$slot), file_name, + sep="\t", quote=FALSE, row.names = FALSE) +} + +#' Read Transcript Metadata from a Given Path +#' +#' This function reads transcript metadata from a specified file path. The file is expected to +#' be a tab-separated values file without headers, containing transcript information. The function +#' checks if the file is empty and stops execution with an error message if so. It reads the file +#' into a data frame, expecting columns for transcript IDs, gene IDs, and gene names. Additional +#' processing is done to ensure compatibility with a predefined data structure (e.g., `txi[[1]]`), +#' including adding missing entries and reordering based on the transcript IDs found in `txi[[1]]`. +#' +#' @param tinfo_path The file path to the transcript information file. +#' +#' @return A list containing three elements: +#' - `transcript`: A data frame with transcript IDs, gene IDs, and gene names, indexed by transcript IDs. +#' - `gene`: A data frame with unique gene IDs and gene names. +#' - `tx2gene`: A data frame mapping transcript IDs to gene IDs. + +read_transcript_info <- function(tinfo_path){ + info <- file.info(tinfo_path) + if (info\$size == 0) { + stop("tx2gene file is empty") + } + + transcript_info <- read.csv(tinfo_path, sep="\t", header = TRUE, + col.names = c("tx", "gene_id", "gene_name")) + + extra <- setdiff(rownames(txi[[1]]), as.character(transcript_info[["tx"]])) + transcript_info <- rbind(transcript_info, data.frame(tx=extra, gene_id=extra, gene_name=extra)) + transcript_info <- transcript_info[match(rownames(txi[[1]]), transcript_info[["tx"]]), ] + rownames(transcript_info) <- transcript_info[["tx"]] + + list(transcript = transcript_info, + gene = unique(transcript_info[,2:3]), + tx2gene = transcript_info[,1:2]) +} + +#' Create a SummarizedExperiment Object +#' +#' Constructs a SummarizedExperiment object using provided matrices for counts, abundance, and length, +#' along with metadata for columns and rows. This function facilitates the organization of experimental +#' data (e.g., RNA-seq or other high-throughput data) in a structured format that is convenient for +#' further analyses and visualization. +#' +#' @param counts A matrix or DataFrame containing counts data, with rows as features (e.g., genes) and +#' columns as samples. +#' @param abundance A matrix or DataFrame containing abundance data (e.g., TPM or FPKM) with the same +#' dimensions and row/column names as the counts data. +#' @param length A matrix or DataFrame containing feature lengths, matching the dimensions and row/column +#' names of the counts data. +#' @param col_data A DataFrame containing sample-level metadata, with rows corresponding to columns in the +#' counts, abundance, and length matrices. +#' @param row_data A DataFrame containing feature-level metadata, with rows corresponding to features in +#' the counts, abundance, and length matrices. +#' +#' @return A SummarizedExperiment object containing the supplied data and metadata. + +create_summarized_experiment <- function(counts, abundance, length, col_data, row_data) { + SummarizedExperiment(assays = list(counts = counts, abundance = abundance, length = length), + colData = col_data, + rowData = row_data) +} + +################################################ +################################################ +## Main script starts here ## +################################################ +################################################ + +# Define pattern for file names based on quantification type +pattern <- ifelse('$quant_type' == "kallisto", + ifelse(file.exists("quants/abundance.h5"), "abundance.h5", "abundance.tsv"), + "quant.sf") + +fns <- list.files('quants', pattern = pattern, recursive = T, full.names = T) +names <- basename(dirname(fns)) +names(fns) <- names + +# Import transcript-level quantifications +txi <- tximport(fns, type = '$quant_type', txOut = TRUE) + +# Read transcript and sample data +transcript_info <- read_transcript_info('$tx2gene') + +# Make coldata just to appease the summarizedexperiment +coldata <- data.frame(files = fns, names = names) +rownames(coldata) <- coldata[["names"]] + +# Create initial SummarizedExperiment object +se <- create_summarized_experiment(txi[["counts"]], txi[["abundance"]], txi[["length"]], + DataFrame(coldata), transcript_info\$transcript) + +# Setting parameters for writing tables +params <- list( + list(obj = se, slot = "abundance", suffix = "transcript_tpm.tsv"), + list(obj = se, slot = "counts", suffix = "transcript_counts.tsv"), + list(obj = se, slot = "length", suffix = "transcript_lengths.tsv") +) + +# Process gene-level data if tx2gene mapping is available +if ("tx2gene" %in% names(transcript_info) && !is.null(transcript_info\$tx2gene)) { + tx2gene <- transcript_info\$tx2gene + gi <- summarizeToGene(txi, tx2gene = tx2gene) + gi.ls <- summarizeToGene(txi, tx2gene = tx2gene, countsFromAbundance = "lengthScaledTPM") + gi.s <- summarizeToGene(txi, tx2gene = tx2gene, countsFromAbundance = "scaledTPM") + + gene_info <- transcript_info\$gene[match(rownames(gi[[1]]), transcript_info\$gene[["gene_id"]]),] + rownames(gene_info) <- gene_info[["tx"]] + + col_data_frame <- DataFrame(coldata) + + # Create gene-level SummarizedExperiment objects + gse <- create_summarized_experiment(gi[["counts"]], gi[["abundance"]], gi[["length"]], + col_data_frame, gene_info) + gse.ls <- create_summarized_experiment(gi.ls[["counts"]], gi.ls[["abundance"]], gi.ls[["length"]], + col_data_frame, gene_info) + gse.s <- create_summarized_experiment(gi.s[["counts"]], gi.s[["abundance"]], gi.s[["length"]], + col_data_frame, gene_info) + + params <- c(params, list( + list(obj = gse, slot = "length", suffix = "gene_lengths.tsv"), + list(obj = gse, slot = "abundance", suffix = "gene_tpm.tsv"), + list(obj = gse, slot = "counts", suffix = "gene_counts.tsv"), + list(obj = gse.ls, slot = "abundance", suffix = "gene_tpm_length_scaled.tsv"), + list(obj = gse.ls, slot = "counts", suffix = "gene_counts_length_scaled.tsv"), + list(obj = gse.s, slot = "abundance", suffix = "gene_tpm_scaled.tsv"), + list(obj = gse.s, slot = "counts", suffix = "gene_counts_scaled.tsv") + )) +} + +# Writing tables for each set of parameters + +prefix <- '' +if ('$task.ext.prefix' != 'null'){ + prefix = '$task.ext.prefix' +} else if ('$meta.id' != 'null'){ + prefix = '$meta.id' +} + +done <- lapply(params, write_se_table, prefix) + +################################################ +################################################ +## R SESSION INFO ## +################################################ +################################################ + +sink(paste(prefix, "R_sessionInfo.log", sep = '.')) +citation("tximeta") +print(sessionInfo()) +sink() + +################################################ +################################################ +## VERSIONS FILE ## +################################################ +################################################ + +r.version <- strsplit(version[['version.string']], ' ')[[1]][3] +tximeta.version <- as.character(packageVersion('tximeta')) + +writeLines( + c( + '"${task.process}":', + paste(' bioconductor-tximeta:', tximeta.version) + ), +'versions.yml') + +################################################ +################################################ +################################################ +################################################ diff --git a/nextflow.config b/nextflow.config index 257145b9..1c8eaf0b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -63,6 +63,8 @@ params { min_map_len = 40 min_fusion_distance = 200 + //> Quantification + bootstrap_samples = 30 //> MISC save_unaligned = false diff --git a/nextflow_schema.json b/nextflow_schema.json index 3cf5fd34..03fbbf3d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -165,6 +165,11 @@ "description": "Sequencing center information to be added to read group of BAM files.", "fa_icon": "fas fa-synagogue" }, + "bootstrap_samples":{ + "type": "integer", + "description": "Number of bootstrap samples to generate during quantification.", + "default": 30 + }, "save_unaligned": { "type": "boolean", "fa_icon": "fas fa-save", diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index a17805cf..01d20a9f 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -4,7 +4,7 @@ include { GAWK as MARK_CIRCULAR } from '../../modules/nf-core/g include { PSIRC_INDEX } from '../../modules/local/psirc/index/main' include { PSIRC_QUANT } from '../../modules/local/psirc/quant/main' include { CUSTOM_TX2GENE } from '../../modules/nf-core/custom/tx2gene/main' -include { TXIMETA_TXIMPORT } from '../../modules/nf-core/tximeta/tximport/main' +include { TXIMETA_TXIMETA } from '../../modules/local/tximeta/tximeta/main' include { CSVTK_JOIN as JOIN_GENE_COUNTS } from '../../modules/nf-core/csvtk/join/main' include { CSVTK_JOIN as JOIN_GENE_TPM } from '../../modules/nf-core/csvtk/join/main' include { CSVTK_JOIN as JOIN_TX_COUNTS } from '../../modules/nf-core/csvtk/join/main' @@ -20,6 +20,7 @@ workflow QUANTIFICATION { reads circ_annotation_bed circ_annotation_gtf + bootstrap_samples main: ch_versions = Channel.empty() @@ -38,7 +39,7 @@ workflow QUANTIFICATION { ) PSIRC_INDEX(MARK_CIRCULAR.out.output) - PSIRC_QUANT(reads, PSIRC_INDEX.out.index.collect()) + PSIRC_QUANT(reads, PSIRC_INDEX.out.index.collect(), bootstrap_samples) CUSTOM_TX2GENE( COMBINE_TRANSCRIPTOME_GTFS.out.sorted, @@ -48,7 +49,7 @@ workflow QUANTIFICATION { "gene_name" ) - TXIMETA_TXIMPORT( + TXIMETA_TXIMETA( PSIRC_QUANT.out.directory, CUSTOM_TX2GENE.out.tx2gene, "kallisto" @@ -58,23 +59,23 @@ workflow QUANTIFICATION { PSIRC_INDEX.out.versions, PSIRC_QUANT.out.versions, CUSTOM_TX2GENE.out.versions, - TXIMETA_TXIMPORT.out.versions + TXIMETA_TXIMETA.out.versions ) JOIN_GENE_COUNTS( - TXIMETA_TXIMPORT.out.counts_gene.map{meta, counts -> counts}.collect().map{[[id: "gene_counts"], it]} + TXIMETA_TXIMETA.out.counts_gene.map{meta, counts -> counts}.collect().map{[[id: "gene_counts"], it]} ) JOIN_GENE_TPM( - TXIMETA_TXIMPORT.out.tpm_gene.map{meta, tpm -> tpm}.collect().map{[[id: "gene_tpm"], it]} + TXIMETA_TXIMETA.out.tpm_gene.map{meta, tpm -> tpm}.collect().map{[[id: "gene_tpm"], it]} ) JOIN_TX_COUNTS( - TXIMETA_TXIMPORT.out.counts_transcript.map{meta, counts -> counts}.collect().map{[[id: "tx_counts"], it]} + TXIMETA_TXIMETA.out.counts_transcript.map{meta, counts -> counts}.collect().map{[[id: "tx_counts"], it]} ) JOIN_TX_TPM( - TXIMETA_TXIMPORT.out.tpm_transcript.map{meta, tpm -> tpm}.collect().map{[[id: "tx_tpm"], it]} + TXIMETA_TXIMETA.out.tpm_transcript.map{meta, tpm -> tpm}.collect().map{[[id: "tx_tpm"], it]} ) SPLIT_TYPES_COUNTS( diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index cde056ff..1c6c9872 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -163,7 +163,8 @@ workflow CIRCRNA { CIRCRNA_DISCOVERY.out.counts_bed, FASTQC_TRIMGALORE.out.reads, CIRCRNA_DISCOVERY.out.annotation_bed, - CIRCRNA_DISCOVERY.out.annotation_gtf + CIRCRNA_DISCOVERY.out.annotation_gtf, + params.bootstrap_samples ) ch_versions = ch_versions.mix(QUANTIFICATION.out.versions) From 74c08a3ef605ba2e63bbef725b74df76ed04867d Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 20 Apr 2024 10:01:32 +0200 Subject: [PATCH 198/491] Fix problem with erroneous abundance.h5 detection --- modules/local/tximeta/tximeta/templates/tximeta.r | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/modules/local/tximeta/tximeta/templates/tximeta.r b/modules/local/tximeta/tximeta/templates/tximeta.r index 56a24566..9a74585e 100755 --- a/modules/local/tximeta/tximeta/templates/tximeta.r +++ b/modules/local/tximeta/tximeta/templates/tximeta.r @@ -119,7 +119,9 @@ create_summarized_experiment <- function(counts, abundance, length, col_data, ro # Define pattern for file names based on quantification type pattern <- ifelse('$quant_type' == "kallisto", - ifelse(file.exists("quants/abundance.h5"), "abundance.h5", "abundance.tsv"), + ifelse(length(list.files('quants', pattern = "abundance.h5", recursive = T, full.names = T)) != 0, + "abundance.h5", + "abundance.tsv"), "quant.sf") fns <- list.files('quants', pattern = pattern, recursive = T, full.names = T) From 9bbcc2ec4866c072c676419184060bcd1d744fb1 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 20 Apr 2024 10:56:36 +0200 Subject: [PATCH 199/491] Update tximeta script --- .../local/tximeta/tximeta/templates/tximeta.r | 25 ++++++++----------- 1 file changed, 10 insertions(+), 15 deletions(-) diff --git a/modules/local/tximeta/tximeta/templates/tximeta.r b/modules/local/tximeta/tximeta/templates/tximeta.r index 9a74585e..c4ad9e2f 100755 --- a/modules/local/tximeta/tximeta/templates/tximeta.r +++ b/modules/local/tximeta/tximeta/templates/tximeta.r @@ -6,7 +6,7 @@ # Loading required libraries library(SummarizedExperiment) -library(tximport) +library(tximeta) ################################################ ################################################ @@ -75,9 +75,9 @@ read_transcript_info <- function(tinfo_path){ transcript_info <- read.csv(tinfo_path, sep="\t", header = TRUE, col.names = c("tx", "gene_id", "gene_name")) - extra <- setdiff(rownames(txi[[1]]), as.character(transcript_info[["tx"]])) + extra <- setdiff(rownames(se), as.character(transcript_info[["tx"]])) transcript_info <- rbind(transcript_info, data.frame(tx=extra, gene_id=extra, gene_name=extra)) - transcript_info <- transcript_info[match(rownames(txi[[1]]), transcript_info[["tx"]]), ] + transcript_info <- transcript_info[match(rownames(se), transcript_info[["tx"]]), ] rownames(transcript_info) <- transcript_info[["tx"]] list(transcript = transcript_info, @@ -128,20 +128,15 @@ fns <- list.files('quants', pattern = pattern, recursive = T, full.names = T) names <- basename(dirname(fns)) names(fns) <- names +coldata <- data.frame(files = fns, names = names) +rownames(coldata) <- coldata[["names"]] + # Import transcript-level quantifications -txi <- tximport(fns, type = '$quant_type', txOut = TRUE) +se <- tximeta(coldata, type = '$quant_type', txOut = TRUE) # Read transcript and sample data transcript_info <- read_transcript_info('$tx2gene') -# Make coldata just to appease the summarizedexperiment -coldata <- data.frame(files = fns, names = names) -rownames(coldata) <- coldata[["names"]] - -# Create initial SummarizedExperiment object -se <- create_summarized_experiment(txi[["counts"]], txi[["abundance"]], txi[["length"]], - DataFrame(coldata), transcript_info\$transcript) - # Setting parameters for writing tables params <- list( list(obj = se, slot = "abundance", suffix = "transcript_tpm.tsv"), @@ -152,9 +147,9 @@ params <- list( # Process gene-level data if tx2gene mapping is available if ("tx2gene" %in% names(transcript_info) && !is.null(transcript_info\$tx2gene)) { tx2gene <- transcript_info\$tx2gene - gi <- summarizeToGene(txi, tx2gene = tx2gene) - gi.ls <- summarizeToGene(txi, tx2gene = tx2gene, countsFromAbundance = "lengthScaledTPM") - gi.s <- summarizeToGene(txi, tx2gene = tx2gene, countsFromAbundance = "scaledTPM") + gi <- summarizeToGene(se, tx2gene = tx2gene) + gi.ls <- summarizeToGene(se, tx2gene = tx2gene, countsFromAbundance = "lengthScaledTPM") + gi.s <- summarizeToGene(se, tx2gene = tx2gene, countsFromAbundance = "scaledTPM") gene_info <- transcript_info\$gene[match(rownames(gi[[1]]), transcript_info\$gene[["gene_id"]]),] rownames(gene_info) <- gene_info[["tx"]] From a23b898bc1d6509400fca6c76393f9c1a794772a Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 20 Apr 2024 14:39:23 +0200 Subject: [PATCH 200/491] Switch to tximeta pure RDS approach --- modules/local/tximeta/tximeta/main.nf | 22 +-- .../local/tximeta/tximeta/templates/tximeta.r | 159 +----------------- subworkflows/local/quantification.nf | 19 ++- 3 files changed, 20 insertions(+), 180 deletions(-) diff --git a/modules/local/tximeta/tximeta/main.nf b/modules/local/tximeta/tximeta/main.nf index db263cf9..e1d2247b 100644 --- a/modules/local/tximeta/tximeta/main.nf +++ b/modules/local/tximeta/tximeta/main.nf @@ -8,36 +8,22 @@ process TXIMETA_TXIMETA { input: tuple val(meta), path("quants/*") - tuple val(meta2), path(tx2gene) val quant_type output: - tuple val(meta), path("*gene_tpm.tsv") , emit: tpm_gene - tuple val(meta), path("*gene_counts.tsv") , emit: counts_gene - tuple val(meta), path("*gene_counts_length_scaled.tsv"), emit: counts_gene_length_scaled - tuple val(meta), path("*gene_counts_scaled.tsv") , emit: counts_gene_scaled - tuple val(meta), path("*gene_lengths.tsv") , emit: lengths_gene - tuple val(meta), path("*transcript_tpm.tsv") , emit: tpm_transcript - tuple val(meta), path("*transcript_counts.tsv") , emit: counts_transcript - tuple val(meta), path("*transcript_lengths.tsv") , emit: lengths_transcript - path "versions.yml" , emit: versions + tuple val(meta), path("*.rds"), emit: se + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: + prefix = task.ext.prefix ?: meta.id template 'tximeta.r' stub: """ - touch ${meta.id}.gene_tpm.tsv - touch ${meta.id}.gene_counts.tsv - touch ${meta.id}.gene_counts_length_scaled.tsv - touch ${meta.id}.gene_counts_scaled.tsv - touch ${meta.id}.gene_lengths.tsv - touch ${meta.id}.transcript_tpm.tsv - touch ${meta.id}.transcript_counts.tsv - touch ${meta.id}.transcript_lengths.tsv + touch ${meta.id}_se.RDS cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/tximeta/tximeta/templates/tximeta.r b/modules/local/tximeta/tximeta/templates/tximeta.r index c4ad9e2f..878ada02 100755 --- a/modules/local/tximeta/tximeta/templates/tximeta.r +++ b/modules/local/tximeta/tximeta/templates/tximeta.r @@ -5,112 +5,8 @@ # under the MIT license. # Loading required libraries -library(SummarizedExperiment) library(tximeta) -################################################ -################################################ -## Functions ## -################################################ -################################################ - -#' Build a table from a SummarizedExperiment object -#' -#' This function takes a SummarizedExperiment object and a specific slot name to extract -#' assay data. It then combines the first two columns of the rowData with the specified -#' assay data slot into a new data table. -#' -#' @param se.obj A SummarizedExperiment object from which to build the table. -#' @param slot The name of the slot in the assays list from which to extract data. -#' -#' @return A data frame combining the first two columns of the rowData with the assay data from the specified slot. - -build_table <- function(se.obj, slot) { - cbind(rowData(se.obj)[,1:2], assays(se.obj)[[slot]]) -} - -#' Write a table to a file from a SummarizedExperiment object with given parameters -#' -#' This function generates a table from a SummarizedExperiment object using specified parameters -#' and writes the resulting table to a file. The file name is constructed using a prefix and a -#' suffix from the parameters, and the table is written with tab separation, without quoting text, -#' and without row names. -#' -#' @param params A list containing the parameters needed for file generation and table writing. -#' The list should include: -#' - `obj`: A SummarizedExperiment object from which to build the table. -#' - `slot`: The name of the slot in the assays list from which to extract data. -#' - `suffix`: Suffix to use for generating the file name. -#' -#' @return NULL The function is called for its side effect of writing a file and does not return anything. - -write_se_table <- function(params, prefix) { - file_name <- paste0(prefix, ".", params\$suffix) - write.table(build_table(params\$obj, params\$slot), file_name, - sep="\t", quote=FALSE, row.names = FALSE) -} - -#' Read Transcript Metadata from a Given Path -#' -#' This function reads transcript metadata from a specified file path. The file is expected to -#' be a tab-separated values file without headers, containing transcript information. The function -#' checks if the file is empty and stops execution with an error message if so. It reads the file -#' into a data frame, expecting columns for transcript IDs, gene IDs, and gene names. Additional -#' processing is done to ensure compatibility with a predefined data structure (e.g., `txi[[1]]`), -#' including adding missing entries and reordering based on the transcript IDs found in `txi[[1]]`. -#' -#' @param tinfo_path The file path to the transcript information file. -#' -#' @return A list containing three elements: -#' - `transcript`: A data frame with transcript IDs, gene IDs, and gene names, indexed by transcript IDs. -#' - `gene`: A data frame with unique gene IDs and gene names. -#' - `tx2gene`: A data frame mapping transcript IDs to gene IDs. - -read_transcript_info <- function(tinfo_path){ - info <- file.info(tinfo_path) - if (info\$size == 0) { - stop("tx2gene file is empty") - } - - transcript_info <- read.csv(tinfo_path, sep="\t", header = TRUE, - col.names = c("tx", "gene_id", "gene_name")) - - extra <- setdiff(rownames(se), as.character(transcript_info[["tx"]])) - transcript_info <- rbind(transcript_info, data.frame(tx=extra, gene_id=extra, gene_name=extra)) - transcript_info <- transcript_info[match(rownames(se), transcript_info[["tx"]]), ] - rownames(transcript_info) <- transcript_info[["tx"]] - - list(transcript = transcript_info, - gene = unique(transcript_info[,2:3]), - tx2gene = transcript_info[,1:2]) -} - -#' Create a SummarizedExperiment Object -#' -#' Constructs a SummarizedExperiment object using provided matrices for counts, abundance, and length, -#' along with metadata for columns and rows. This function facilitates the organization of experimental -#' data (e.g., RNA-seq or other high-throughput data) in a structured format that is convenient for -#' further analyses and visualization. -#' -#' @param counts A matrix or DataFrame containing counts data, with rows as features (e.g., genes) and -#' columns as samples. -#' @param abundance A matrix or DataFrame containing abundance data (e.g., TPM or FPKM) with the same -#' dimensions and row/column names as the counts data. -#' @param length A matrix or DataFrame containing feature lengths, matching the dimensions and row/column -#' names of the counts data. -#' @param col_data A DataFrame containing sample-level metadata, with rows corresponding to columns in the -#' counts, abundance, and length matrices. -#' @param row_data A DataFrame containing feature-level metadata, with rows corresponding to features in -#' the counts, abundance, and length matrices. -#' -#' @return A SummarizedExperiment object containing the supplied data and metadata. - -create_summarized_experiment <- function(counts, abundance, length, col_data, row_data) { - SummarizedExperiment(assays = list(counts = counts, abundance = abundance, length = length), - colData = col_data, - rowData = row_data) -} - ################################################ ################################################ ## Main script starts here ## @@ -134,57 +30,8 @@ rownames(coldata) <- coldata[["names"]] # Import transcript-level quantifications se <- tximeta(coldata, type = '$quant_type', txOut = TRUE) -# Read transcript and sample data -transcript_info <- read_transcript_info('$tx2gene') - -# Setting parameters for writing tables -params <- list( - list(obj = se, slot = "abundance", suffix = "transcript_tpm.tsv"), - list(obj = se, slot = "counts", suffix = "transcript_counts.tsv"), - list(obj = se, slot = "length", suffix = "transcript_lengths.tsv") -) - -# Process gene-level data if tx2gene mapping is available -if ("tx2gene" %in% names(transcript_info) && !is.null(transcript_info\$tx2gene)) { - tx2gene <- transcript_info\$tx2gene - gi <- summarizeToGene(se, tx2gene = tx2gene) - gi.ls <- summarizeToGene(se, tx2gene = tx2gene, countsFromAbundance = "lengthScaledTPM") - gi.s <- summarizeToGene(se, tx2gene = tx2gene, countsFromAbundance = "scaledTPM") - - gene_info <- transcript_info\$gene[match(rownames(gi[[1]]), transcript_info\$gene[["gene_id"]]),] - rownames(gene_info) <- gene_info[["tx"]] - - col_data_frame <- DataFrame(coldata) - - # Create gene-level SummarizedExperiment objects - gse <- create_summarized_experiment(gi[["counts"]], gi[["abundance"]], gi[["length"]], - col_data_frame, gene_info) - gse.ls <- create_summarized_experiment(gi.ls[["counts"]], gi.ls[["abundance"]], gi.ls[["length"]], - col_data_frame, gene_info) - gse.s <- create_summarized_experiment(gi.s[["counts"]], gi.s[["abundance"]], gi.s[["length"]], - col_data_frame, gene_info) - - params <- c(params, list( - list(obj = gse, slot = "length", suffix = "gene_lengths.tsv"), - list(obj = gse, slot = "abundance", suffix = "gene_tpm.tsv"), - list(obj = gse, slot = "counts", suffix = "gene_counts.tsv"), - list(obj = gse.ls, slot = "abundance", suffix = "gene_tpm_length_scaled.tsv"), - list(obj = gse.ls, slot = "counts", suffix = "gene_counts_length_scaled.tsv"), - list(obj = gse.s, slot = "abundance", suffix = "gene_tpm_scaled.tsv"), - list(obj = gse.s, slot = "counts", suffix = "gene_counts_scaled.tsv") - )) -} - -# Writing tables for each set of parameters - -prefix <- '' -if ('$task.ext.prefix' != 'null'){ - prefix = '$task.ext.prefix' -} else if ('$meta.id' != 'null'){ - prefix = '$meta.id' -} - -done <- lapply(params, write_se_table, prefix) +# Save summarized experiment to file +saveRDS(se, file = paste0('$prefix', '.rds')) ################################################ ################################################ @@ -192,7 +39,7 @@ done <- lapply(params, write_se_table, prefix) ################################################ ################################################ -sink(paste(prefix, "R_sessionInfo.log", sep = '.')) +sink(paste("R_sessionInfo.log", sep = '.')) citation("tximeta") print(sessionInfo()) sink() diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index 01d20a9f..92141240 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -4,7 +4,8 @@ include { GAWK as MARK_CIRCULAR } from '../../modules/nf-core/g include { PSIRC_INDEX } from '../../modules/local/psirc/index/main' include { PSIRC_QUANT } from '../../modules/local/psirc/quant/main' include { CUSTOM_TX2GENE } from '../../modules/nf-core/custom/tx2gene/main' -include { TXIMETA_TXIMETA } from '../../modules/local/tximeta/tximeta/main' +include { TXIMETA_TXIMPORT } from '../../modules/nf-core/tximeta/tximport/main' +include { TXIMETA_TXIMETA } from '../../modules/local/tximeta/tximeta/main' include { CSVTK_JOIN as JOIN_GENE_COUNTS } from '../../modules/nf-core/csvtk/join/main' include { CSVTK_JOIN as JOIN_GENE_TPM } from '../../modules/nf-core/csvtk/join/main' include { CSVTK_JOIN as JOIN_TX_COUNTS } from '../../modules/nf-core/csvtk/join/main' @@ -50,6 +51,11 @@ workflow QUANTIFICATION { ) TXIMETA_TXIMETA( + PSIRC_QUANT.out.directory, + "kallisto" + ) + + TXIMETA_TXIMPORT( PSIRC_QUANT.out.directory, CUSTOM_TX2GENE.out.tx2gene, "kallisto" @@ -59,23 +65,24 @@ workflow QUANTIFICATION { PSIRC_INDEX.out.versions, PSIRC_QUANT.out.versions, CUSTOM_TX2GENE.out.versions, - TXIMETA_TXIMETA.out.versions + TXIMETA_TXIMETA.out.versions, + TXIMETA_TXIMPORT.out.versions ) JOIN_GENE_COUNTS( - TXIMETA_TXIMETA.out.counts_gene.map{meta, counts -> counts}.collect().map{[[id: "gene_counts"], it]} + TXIMETA_TXIMPORT.out.counts_gene.map{meta, counts -> counts}.collect().map{[[id: "gene_counts"], it]} ) JOIN_GENE_TPM( - TXIMETA_TXIMETA.out.tpm_gene.map{meta, tpm -> tpm}.collect().map{[[id: "gene_tpm"], it]} + TXIMETA_TXIMPORT.out.tpm_gene.map{meta, tpm -> tpm}.collect().map{[[id: "gene_tpm"], it]} ) JOIN_TX_COUNTS( - TXIMETA_TXIMETA.out.counts_transcript.map{meta, counts -> counts}.collect().map{[[id: "tx_counts"], it]} + TXIMETA_TXIMPORT.out.counts_transcript.map{meta, counts -> counts}.collect().map{[[id: "tx_counts"], it]} ) JOIN_TX_TPM( - TXIMETA_TXIMETA.out.tpm_transcript.map{meta, tpm -> tpm}.collect().map{[[id: "tx_tpm"], it]} + TXIMETA_TXIMPORT.out.tpm_transcript.map{meta, tpm -> tpm}.collect().map{[[id: "tx_tpm"], it]} ) SPLIT_TYPES_COUNTS( From 6b261424a9f77e777a3e6aee29b833bb229234b1 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 20 Apr 2024 18:08:13 +0200 Subject: [PATCH 201/491] Implement basic swish functionality --- modules/local/fishpond/swish/environment.yml | 9 ++++ modules/local/fishpond/swish/main.nf | 30 ++++++++++++ .../local/fishpond/swish/templates/swish.r | 46 +++++++++++++++++++ modules/local/tximeta/tximeta/main.nf | 5 +- subworkflows/local/quantification.nf | 10 +++- workflows/circrna/main.nf | 3 +- 6 files changed, 99 insertions(+), 4 deletions(-) create mode 100644 modules/local/fishpond/swish/environment.yml create mode 100644 modules/local/fishpond/swish/main.nf create mode 100644 modules/local/fishpond/swish/templates/swish.r diff --git a/modules/local/fishpond/swish/environment.yml b/modules/local/fishpond/swish/environment.yml new file mode 100644 index 00000000..9af93313 --- /dev/null +++ b/modules/local/fishpond/swish/environment.yml @@ -0,0 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +name: "fishpond_swish" +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - "bioconda::bioconductor-fishpond=2.8.0-0" diff --git a/modules/local/fishpond/swish/main.nf b/modules/local/fishpond/swish/main.nf new file mode 100644 index 00000000..040c8443 --- /dev/null +++ b/modules/local/fishpond/swish/main.nf @@ -0,0 +1,30 @@ +process FISHPOND_SWISH { + tag "$meta.id" + label "process_medium" + + conda "${moduleDir}/environment.yaml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bioconductor-fishpond:2.8.0--r43hdfd78af_0' : + 'biocontainers/bioconductor-fishpond:2.8.0--r43hdfd78af_0' }" + + input: + tuple val(meta), path(experiments) + tuple val(meta2), path(phenotype) + + output: + tuple val(meta), path("${meta.id}.rds"), emit: swish + path "versions.yml" , emit: versions + + script: + template "swish.r" + + stub: + """ + touch ${meta.id}.RDS + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bioconductor-fishpond: \$(Rscript -e "library(fishpond); cat(as.character(packageVersion('fishpond')))") + END_VERSIONS + """ +} \ No newline at end of file diff --git a/modules/local/fishpond/swish/templates/swish.r b/modules/local/fishpond/swish/templates/swish.r new file mode 100644 index 00000000..c632508f --- /dev/null +++ b/modules/local/fishpond/swish/templates/swish.r @@ -0,0 +1,46 @@ +#!/usr/bin/env Rscript --vanilla + +library(fishpond) +library(SummarizedExperiment) + +paths <- c('${experiments.join("\', \'")}') +experiments <- lapply(paths, readRDS) + +phenotype <- read.csv('${phenotype}', stringsAsFactors = FALSE) + +se_assays <- list() + +for (se in experiments) { + assays <- assays(se) + # Iterate over named list of assays + for (assay_name in names(assays)) { + assay <- assays[[assay_name]] + + # Add assay to se_assays for its name + if (is.null(se_assays[[assay_name]])) { + se_assays[[assay_name]] <- assay + } else { + se_assays[[assay_name]] <- cbind(se_assays[[assay_name]], assay) + } + } +} + +se_cbind <- do.call(SummarizedExperiment::cbind, experiments) +se <- SummarizedExperiment(assays = se_assays, colData = colData(se_cbind), rowData = rowData(se_cbind)) + +# Join phenotype data +colData(se) <- merge(colData(se), phenotype, by.x="names", by.y="Sample_ID") +colData(se)\$condition <- as.factor(colData(se)\$condition) + +se <- scaleInfReps(se) +se <- labelKeep(se) +se <- swish(se, x="condition") + +saveRDS(se, '${meta.id}.rds') + +writeLines( + c( + '"${task.process}":', + paste(' bioconductor-fishpond:', packageVersion('fishpond')) + ), +'versions.yml') \ No newline at end of file diff --git a/modules/local/tximeta/tximeta/main.nf b/modules/local/tximeta/tximeta/main.nf index e1d2247b..c1be1d37 100644 --- a/modules/local/tximeta/tximeta/main.nf +++ b/modules/local/tximeta/tximeta/main.nf @@ -1,4 +1,5 @@ process TXIMETA_TXIMETA { + tag "$meta.id" label "process_medium" conda "${moduleDir}/environment.yml" @@ -12,7 +13,7 @@ process TXIMETA_TXIMETA { output: tuple val(meta), path("*.rds"), emit: se - path "versions.yml" , emit: versions + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -23,7 +24,7 @@ process TXIMETA_TXIMETA { stub: """ - touch ${meta.id}_se.RDS + touch ${meta.id}.rds cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index 92141240..715cc461 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -6,6 +6,7 @@ include { PSIRC_QUANT } from '../../modules/local/psi include { CUSTOM_TX2GENE } from '../../modules/nf-core/custom/tx2gene/main' include { TXIMETA_TXIMPORT } from '../../modules/nf-core/tximeta/tximport/main' include { TXIMETA_TXIMETA } from '../../modules/local/tximeta/tximeta/main' +include { FISHPOND_SWISH } from '../../modules/local/fishpond/swish/main' include { CSVTK_JOIN as JOIN_GENE_COUNTS } from '../../modules/nf-core/csvtk/join/main' include { CSVTK_JOIN as JOIN_GENE_TPM } from '../../modules/nf-core/csvtk/join/main' include { CSVTK_JOIN as JOIN_TX_COUNTS } from '../../modules/nf-core/csvtk/join/main' @@ -22,6 +23,7 @@ workflow QUANTIFICATION { circ_annotation_bed circ_annotation_gtf bootstrap_samples + ch_phenotype main: ch_versions = Channel.empty() @@ -55,6 +57,11 @@ workflow QUANTIFICATION { "kallisto" ) + FISHPOND_SWISH( + TXIMETA_TXIMETA.out.se.map{meta, se -> se}.collect().map{[[id: "experiments"], it]}, + ch_phenotype + ) + TXIMETA_TXIMPORT( PSIRC_QUANT.out.directory, CUSTOM_TX2GENE.out.tx2gene, @@ -66,7 +73,8 @@ workflow QUANTIFICATION { PSIRC_QUANT.out.versions, CUSTOM_TX2GENE.out.versions, TXIMETA_TXIMETA.out.versions, - TXIMETA_TXIMPORT.out.versions + TXIMETA_TXIMPORT.out.versions, + FISHPOND_SWISH.out.versions ) JOIN_GENE_COUNTS( diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 1c6c9872..5f1e27fb 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -164,7 +164,8 @@ workflow CIRCRNA { FASTQC_TRIMGALORE.out.reads, CIRCRNA_DISCOVERY.out.annotation_bed, CIRCRNA_DISCOVERY.out.annotation_gtf, - params.bootstrap_samples + params.bootstrap_samples, + ch_phenotype ) ch_versions = ch_versions.mix(QUANTIFICATION.out.versions) From 6c254a731441dc29d5dd8ce4953297e99b612b6c Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 20 Apr 2024 18:32:39 +0200 Subject: [PATCH 202/491] Fix linting --- modules/local/fishpond/swish/main.nf | 2 +- .../local/fishpond/swish/templates/swish.r | 24 +++++++++---------- subworkflows/local/quantification.nf | 2 +- 3 files changed, 14 insertions(+), 14 deletions(-) diff --git a/modules/local/fishpond/swish/main.nf b/modules/local/fishpond/swish/main.nf index 040c8443..ff1184ec 100644 --- a/modules/local/fishpond/swish/main.nf +++ b/modules/local/fishpond/swish/main.nf @@ -27,4 +27,4 @@ process FISHPOND_SWISH { bioconductor-fishpond: \$(Rscript -e "library(fishpond); cat(as.character(packageVersion('fishpond')))") END_VERSIONS """ -} \ No newline at end of file +} diff --git a/modules/local/fishpond/swish/templates/swish.r b/modules/local/fishpond/swish/templates/swish.r index c632508f..6ead02e7 100644 --- a/modules/local/fishpond/swish/templates/swish.r +++ b/modules/local/fishpond/swish/templates/swish.r @@ -11,18 +11,18 @@ phenotype <- read.csv('${phenotype}', stringsAsFactors = FALSE) se_assays <- list() for (se in experiments) { - assays <- assays(se) - # Iterate over named list of assays - for (assay_name in names(assays)) { - assay <- assays[[assay_name]] - - # Add assay to se_assays for its name - if (is.null(se_assays[[assay_name]])) { - se_assays[[assay_name]] <- assay - } else { - se_assays[[assay_name]] <- cbind(se_assays[[assay_name]], assay) + assays <- assays(se) + # Iterate over named list of assays + for (assay_name in names(assays)) { + assay <- assays[[assay_name]] + + # Add assay to se_assays for its name + if (is.null(se_assays[[assay_name]])) { + se_assays[[assay_name]] <- assay + } else { + se_assays[[assay_name]] <- cbind(se_assays[[assay_name]], assay) + } } - } } se_cbind <- do.call(SummarizedExperiment::cbind, experiments) @@ -43,4 +43,4 @@ writeLines( '"${task.process}":', paste(' bioconductor-fishpond:', packageVersion('fishpond')) ), -'versions.yml') \ No newline at end of file +'versions.yml') diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index 715cc461..c219fcb4 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -120,5 +120,5 @@ workflow QUANTIFICATION { circular_tx_counts = SPLIT_TYPES_COUNTS.out.circular circular_tx_tpm = SPLIT_TYPES_TPM.out.circular - versions = ch_versions + versions = ch_versions } From 48fc366228682d23e4210ae493d05e9cead2b8c2 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 20 Apr 2024 18:42:22 +0200 Subject: [PATCH 203/491] Prettier --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 03fbbf3d..2aaea8bb 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -165,7 +165,7 @@ "description": "Sequencing center information to be added to read group of BAM files.", "fa_icon": "fas fa-synagogue" }, - "bootstrap_samples":{ + "bootstrap_samples": { "type": "integer", "description": "Number of bootstrap samples to generate during quantification.", "default": 30 From 6ca97933552dcfa8584361a04737f4caea616695 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sun, 21 Apr 2024 14:19:51 +0200 Subject: [PATCH 204/491] Increase resource usage of quantification joining --- conf/modules.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/modules.config b/conf/modules.config index fadfbf84..f928106d 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -696,6 +696,7 @@ if (!params.skip_trimming) { withName: ".*:JOIN_(GENE|TX)_(COUNTS|TPM)" { ext.args = "-f 1,2 -t" + label = "process_medium" publishDir = [ path: { "${params.outdir}/quantification/" }, mode: params.publish_dir_mode, From c88bbf53f31c4d84505a83f2ac903a904bb243e2 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sun, 21 Apr 2024 17:09:35 +0200 Subject: [PATCH 205/491] Implement separate process for merging summarizedexperiment objects --- conf/modules.config | 1 + main.nf | 2 +- modules/local/fishpond/swish/main.nf | 6 +-- .../local/fishpond/swish/templates/swish.r | 32 +------------ .../merge_experiments/environment.yml | 9 ++++ .../quantification/merge_experiments/main.nf | 30 ++++++++++++ .../templates/merge_experiments.r | 47 +++++++++++++++++++ subworkflows/local/quantification.nf | 35 +++++++------- 8 files changed, 111 insertions(+), 51 deletions(-) create mode 100644 modules/local/quantification/merge_experiments/environment.yml create mode 100644 modules/local/quantification/merge_experiments/main.nf create mode 100644 modules/local/quantification/merge_experiments/templates/merge_experiments.r diff --git a/conf/modules.config b/conf/modules.config index f928106d..2e0a6320 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -697,6 +697,7 @@ if (!params.skip_trimming) { withName: ".*:JOIN_(GENE|TX)_(COUNTS|TPM)" { ext.args = "-f 1,2 -t" label = "process_medium" + maxRetries = 3 publishDir = [ path: { "${params.outdir}/quantification/" }, mode: params.publish_dir_mode, diff --git a/main.nf b/main.nf index a360b046..cf0a707b 100644 --- a/main.nf +++ b/main.nf @@ -59,7 +59,7 @@ workflow NFCORE_CIRCRNA { ch_fasta = Channel.value([[id: "fasta"], file(params.fasta, checkIfExists:true)]) ch_gtf = Channel.value([[id: "gtf"], file(params.gtf, checkIfExists:true)]) ch_mature = params.module.split(',').contains('mirna_prediction') ? Channel.value([[id: "mature"], file(params.mature, checkIfExists:true)]) : Channel.empty() - ch_phenotype = params.module.split(',').contains('differential_expression') ? Channel.value([[id: "phenotype"], file(params.phenotype, checkIfExists:true)]) : Channel.empty() + ch_phenotype = Channel.value([[id: "phenotype"], file(params.phenotype, checkIfExists:true)]) ch_species = params.module.split(',').contains('differential_expression') ? Channel.value(params.species_id) : Channel.empty() CIRCRNA ( diff --git a/modules/local/fishpond/swish/main.nf b/modules/local/fishpond/swish/main.nf index ff1184ec..5ac73202 100644 --- a/modules/local/fishpond/swish/main.nf +++ b/modules/local/fishpond/swish/main.nf @@ -8,11 +8,11 @@ process FISHPOND_SWISH { 'biocontainers/bioconductor-fishpond:2.8.0--r43hdfd78af_0' }" input: - tuple val(meta), path(experiments) - tuple val(meta2), path(phenotype) + tuple val(meta), path(experiment) + val(column) output: - tuple val(meta), path("${meta.id}.rds"), emit: swish + tuple val(meta), path("${meta.id}.swish.rds"), emit: swish path "versions.yml" , emit: versions script: diff --git a/modules/local/fishpond/swish/templates/swish.r b/modules/local/fishpond/swish/templates/swish.r index 6ead02e7..2b95a61a 100644 --- a/modules/local/fishpond/swish/templates/swish.r +++ b/modules/local/fishpond/swish/templates/swish.r @@ -1,40 +1,12 @@ #!/usr/bin/env Rscript --vanilla library(fishpond) -library(SummarizedExperiment) -paths <- c('${experiments.join("\', \'")}') -experiments <- lapply(paths, readRDS) - -phenotype <- read.csv('${phenotype}', stringsAsFactors = FALSE) - -se_assays <- list() - -for (se in experiments) { - assays <- assays(se) - # Iterate over named list of assays - for (assay_name in names(assays)) { - assay <- assays[[assay_name]] - - # Add assay to se_assays for its name - if (is.null(se_assays[[assay_name]])) { - se_assays[[assay_name]] <- assay - } else { - se_assays[[assay_name]] <- cbind(se_assays[[assay_name]], assay) - } - } -} - -se_cbind <- do.call(SummarizedExperiment::cbind, experiments) -se <- SummarizedExperiment(assays = se_assays, colData = colData(se_cbind), rowData = rowData(se_cbind)) - -# Join phenotype data -colData(se) <- merge(colData(se), phenotype, by.x="names", by.y="Sample_ID") -colData(se)\$condition <- as.factor(colData(se)\$condition) +se <- readRDS('$experiment') se <- scaleInfReps(se) se <- labelKeep(se) -se <- swish(se, x="condition") +se <- swish(se, x="$column") saveRDS(se, '${meta.id}.rds') diff --git a/modules/local/quantification/merge_experiments/environment.yml b/modules/local/quantification/merge_experiments/environment.yml new file mode 100644 index 00000000..381dba4d --- /dev/null +++ b/modules/local/quantification/merge_experiments/environment.yml @@ -0,0 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +name: "fishpond_swish" +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - "bioconda::bioconductor-summarizedexperiment=1.32.0" diff --git a/modules/local/quantification/merge_experiments/main.nf b/modules/local/quantification/merge_experiments/main.nf new file mode 100644 index 00000000..367a3082 --- /dev/null +++ b/modules/local/quantification/merge_experiments/main.nf @@ -0,0 +1,30 @@ +process MERGE_EXPERIMENTS { + tag "$meta.id" + label "process_medium" + + conda "${moduleDir}/environment.yaml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bioconductor-summarizedexperiment:1.32.0--r43hdfd78af_0' : + 'biocontainers/bioconductor-summarizedexperiment:1.32.0--r43hdfd78af_0' }" + + input: + tuple val(meta), path(experiments) + tuple val(meta2), path(phenotype) + + output: + tuple val(meta), path("${meta.id}.merged.rds"), emit: merged + path "versions.yml" , emit: versions + + script: + template "merge_experiments.r" + + stub: + """ + touch ${meta.id}.merged.rds + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bioconductor-summarizedexperiment: \$(Rscript -e "library(SummarizedExperiment); cat(as.character(packageVersion('SummarizedExperiment')))") + END_VERSIONS + """ +} diff --git a/modules/local/quantification/merge_experiments/templates/merge_experiments.r b/modules/local/quantification/merge_experiments/templates/merge_experiments.r new file mode 100644 index 00000000..51b5b666 --- /dev/null +++ b/modules/local/quantification/merge_experiments/templates/merge_experiments.r @@ -0,0 +1,47 @@ +#!/usr/bin/env Rscript --vanilla + +library(SummarizedExperiment) + +paths <- c('${experiments.join("\', \'")}') +experiments <- lapply(paths, readRDS) + +phenotype <- read.csv('${phenotype}', stringsAsFactors = FALSE) + +se_assays <- list() + +for (se in experiments) { + assays <- assays(se) + # Iterate over named list of assays + for (assay_name in names(assays)) { + assay <- assays[[assay_name]] + + # Add assay to se_assays for its name + if (is.null(se_assays[[assay_name]])) { + se_assays[[assay_name]] <- assay + } else { + se_assays[[assay_name]] <- cbind(se_assays[[assay_name]], assay) + } + } +} + +se_cbind <- do.call(SummarizedExperiment::cbind, experiments) +se <- SummarizedExperiment(assays = se_assays, colData = colData(se_cbind), rowData = rowData(se_cbind)) + +# Join phenotype data +colData(se) <- merge(colData(se), phenotype, by.x="names", by.y=colnames(phenotype)[1]) + +# Convert string columns to factors +for (col in colnames(colData(se))) { + if (is.character(colData(se)[[col]]) && !(col == "names")) { + colData(se)[[col]] <- as.factor(colData(se)[[col]]) + } +} + +saveRDS(se, '${meta.id}.merged.rds') + +writeLines( + c( + '"${task.process}":', + paste(' bioconductor-summarizedexperiment:', packageVersion('SummarizedExperiment')) + ), +'versions.yml') diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index c219fcb4..fbf030a5 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -1,18 +1,19 @@ -include { GNU_SORT as COMBINE_TRANSCRIPTOME_GTFS } from '../../modules/nf-core/gnu/sort/main' -include { TRANSCRIPTOME } from '../../modules/local/quantification/transcriptome/main' -include { GAWK as MARK_CIRCULAR } from '../../modules/nf-core/gawk/main' -include { PSIRC_INDEX } from '../../modules/local/psirc/index/main' -include { PSIRC_QUANT } from '../../modules/local/psirc/quant/main' -include { CUSTOM_TX2GENE } from '../../modules/nf-core/custom/tx2gene/main' -include { TXIMETA_TXIMPORT } from '../../modules/nf-core/tximeta/tximport/main' -include { TXIMETA_TXIMETA } from '../../modules/local/tximeta/tximeta/main' -include { FISHPOND_SWISH } from '../../modules/local/fishpond/swish/main' -include { CSVTK_JOIN as JOIN_GENE_COUNTS } from '../../modules/nf-core/csvtk/join/main' -include { CSVTK_JOIN as JOIN_GENE_TPM } from '../../modules/nf-core/csvtk/join/main' -include { CSVTK_JOIN as JOIN_TX_COUNTS } from '../../modules/nf-core/csvtk/join/main' -include { CSVTK_JOIN as JOIN_TX_TPM } from '../../modules/nf-core/csvtk/join/main' -include { SPLIT_TYPES as SPLIT_TYPES_COUNTS } from '../../modules/local/quantification/split_types/main' -include { SPLIT_TYPES as SPLIT_TYPES_TPM } from '../../modules/local/quantification/split_types/main' +include { GNU_SORT as COMBINE_TRANSCRIPTOME_GTFS } from '../../modules/nf-core/gnu/sort' +include { TRANSCRIPTOME } from '../../modules/local/quantification/transcriptome' +include { GAWK as MARK_CIRCULAR } from '../../modules/nf-core/gawk' +include { PSIRC_INDEX } from '../../modules/local/psirc/index' +include { PSIRC_QUANT } from '../../modules/local/psirc/quant' +include { CUSTOM_TX2GENE } from '../../modules/nf-core/custom/tx2gene' +include { TXIMETA_TXIMPORT } from '../../modules/nf-core/tximeta/tximport' +include { TXIMETA_TXIMETA } from '../../modules/local/tximeta/tximeta' +include { MERGE_EXPERIMENTS } from '../../modules/local/quantification/merge_experiments' +include { FISHPOND_SWISH } from '../../modules/local/fishpond/swish' +include { CSVTK_JOIN as JOIN_GENE_COUNTS } from '../../modules/nf-core/csvtk/join' +include { CSVTK_JOIN as JOIN_GENE_TPM } from '../../modules/nf-core/csvtk/join' +include { CSVTK_JOIN as JOIN_TX_COUNTS } from '../../modules/nf-core/csvtk/join' +include { CSVTK_JOIN as JOIN_TX_TPM } from '../../modules/nf-core/csvtk/join' +include { SPLIT_TYPES as SPLIT_TYPES_COUNTS } from '../../modules/local/quantification/split_types' +include { SPLIT_TYPES as SPLIT_TYPES_TPM } from '../../modules/local/quantification/split_types' workflow QUANTIFICATION { take: @@ -57,7 +58,7 @@ workflow QUANTIFICATION { "kallisto" ) - FISHPOND_SWISH( + MERGE_EXPERIMENTS( TXIMETA_TXIMETA.out.se.map{meta, se -> se}.collect().map{[[id: "experiments"], it]}, ch_phenotype ) @@ -74,7 +75,7 @@ workflow QUANTIFICATION { CUSTOM_TX2GENE.out.versions, TXIMETA_TXIMETA.out.versions, TXIMETA_TXIMPORT.out.versions, - FISHPOND_SWISH.out.versions + MERGE_EXPERIMENTS.out.versions ) JOIN_GENE_COUNTS( From 257d4da042c1bd1d9d816f49866fdf22cb2bf823 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Wed, 24 Apr 2024 07:12:21 +0200 Subject: [PATCH 206/491] Fix problematic stub in FISHPOND_SWISH --- modules/local/fishpond/swish/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/fishpond/swish/main.nf b/modules/local/fishpond/swish/main.nf index 5ac73202..cb011ec8 100644 --- a/modules/local/fishpond/swish/main.nf +++ b/modules/local/fishpond/swish/main.nf @@ -20,7 +20,7 @@ process FISHPOND_SWISH { stub: """ - touch ${meta.id}.RDS + touch ${meta.id}.swish.rds cat <<-END_VERSIONS > versions.yml "${task.process}": From aa266a5f7536903d14b94ba90864af2a5f7a4aec Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Wed, 24 Apr 2024 07:29:00 +0200 Subject: [PATCH 207/491] Add bam file output to psirc-quant --- modules.json | 5 + modules/local/psirc/quant/main.nf | 6 +- .../nf-core/samtools/faidx/environment.yml | 10 + modules/nf-core/samtools/faidx/main.nf | 50 ++++ modules/nf-core/samtools/faidx/meta.yml | 65 +++++ .../nf-core/samtools/faidx/tests/main.nf.test | 122 +++++++++ .../samtools/faidx/tests/main.nf.test.snap | 249 ++++++++++++++++++ .../samtools/faidx/tests/nextflow.config | 7 + .../samtools/faidx/tests/nextflow2.config | 6 + modules/nf-core/samtools/faidx/tests/tags.yml | 2 + subworkflows/local/prepare_genome.nf | 22 +- subworkflows/local/quantification.nf | 3 +- workflows/circrna/main.nf | 3 +- 13 files changed, 538 insertions(+), 12 deletions(-) create mode 100644 modules/nf-core/samtools/faidx/environment.yml create mode 100644 modules/nf-core/samtools/faidx/main.nf create mode 100644 modules/nf-core/samtools/faidx/meta.yml create mode 100644 modules/nf-core/samtools/faidx/tests/main.nf.test create mode 100644 modules/nf-core/samtools/faidx/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/faidx/tests/nextflow.config create mode 100644 modules/nf-core/samtools/faidx/tests/nextflow2.config create mode 100644 modules/nf-core/samtools/faidx/tests/tags.yml diff --git a/modules.json b/modules.json index 77b6ee5d..3cd8115e 100644 --- a/modules.json +++ b/modules.json @@ -125,6 +125,11 @@ "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", "installed_by": ["modules"] }, + "samtools/faidx": { + "branch": "master", + "git_sha": "f153f1f10e1083c49935565844cccb7453021682", + "installed_by": ["modules"] + }, "samtools/flagstat": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", diff --git a/modules/local/psirc/quant/main.nf b/modules/local/psirc/quant/main.nf index 5761aaad..edecc8f9 100644 --- a/modules/local/psirc/quant/main.nf +++ b/modules/local/psirc/quant/main.nf @@ -7,6 +7,8 @@ process PSIRC_QUANT { input: tuple val(meta), path(reads) tuple val(meta2), path(index) + tuple val(meta3), path(gtf) + tuple val(meta4), path(chrom_sizes) val(bootstrap_samples) output: @@ -15,9 +17,11 @@ process PSIRC_QUANT { script: def single_end = meta.single_end ? "--single -l 76 -s 20" : "" + def genomebam = gtf ? "--genomebam -g $gtf" : "" + def chromosomes = chrom_sizes ? "-c $chrom_sizes" : "" def VERSION = '1.0' """ - psirc-quant quant -t $task.cpus -i $index -o $meta.id $single_end $reads -b $bootstrap_samples + psirc-quant quant -t $task.cpus -i $index -o $meta.id $single_end $reads -b $bootstrap_samples $genomebam $chromosomes cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml new file mode 100644 index 00000000..9c24eb0a --- /dev/null +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -0,0 +1,10 @@ +name: samtools_faidx + +channels: + - conda-forge + - bioconda + - defaults + +dependencies: + - bioconda::htslib=1.19.1 + - bioconda::samtools=1.19.2 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf new file mode 100644 index 00000000..cfe7ad95 --- /dev/null +++ b/modules/nf-core/samtools/faidx/main.nf @@ -0,0 +1,50 @@ +process SAMTOOLS_FAIDX { + tag "$fasta" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : + 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + + input: + tuple val(meta), path(fasta) + tuple val(meta2), path(fai) + + output: + tuple val(meta), path ("*.{fa,fasta}") , emit: fa , optional: true + tuple val(meta), path ("*.fai") , emit: fai, optional: true + tuple val(meta), path ("*.gzi") , emit: gzi, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + """ + samtools \\ + faidx \\ + $fasta \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ + + stub: + def match = (task.ext.args =~ /-o(?:utput)?\s(.*)\s?/).findAll() + def fastacmd = match[0] ? "touch ${match[0][1]}" : '' + """ + ${fastacmd} + touch ${fasta}.fai + + cat <<-END_VERSIONS > versions.yml + + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml new file mode 100644 index 00000000..f3c25de2 --- /dev/null +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -0,0 +1,65 @@ +name: samtools_faidx +description: Index FASTA file +keywords: + - index + - fasta + - faidx +tools: + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: http://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fa: + type: file + description: FASTA file + pattern: "*.{fa}" + - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" + - gzi: + type: file + description: Optional gzip index file for compressed inputs + pattern: "*.gzi" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@drpatelh" + - "@ewels" + - "@phue" +maintainers: + - "@drpatelh" + - "@ewels" + - "@phue" diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test b/modules/nf-core/samtools/faidx/tests/main.nf.test new file mode 100644 index 00000000..17244ef2 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test @@ -0,0 +1,122 @@ +nextflow_process { + + name "Test Process SAMTOOLS_FAIDX" + script "../main.nf" + process "SAMTOOLS_FAIDX" + + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/faidx" + + test("test_samtools_faidx") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_bgzip") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)] + + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_fasta") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_stub_fasta") { + + config "./nextflow2.config" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_stub_fai") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap new file mode 100644 index 00000000..3e651ef6 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap @@ -0,0 +1,249 @@ +{ + "test_samtools_faidx": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T16:22:39.412601" + }, + "test_samtools_faidx_bgzip": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" + ] + ], + "3": [ + "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" + ] + ], + "versions": [ + "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T16:23:22.427966" + }, + "test_samtools_faidx_fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + ], + "fa": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36" + ] + ], + "fai": [ + + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T16:24:04.107537" + }, + "test_samtools_faidx_stub_fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + ], + "fa": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "fai": [ + + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T16:24:45.868463" + }, + "test_samtools_faidx_stub_fai": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T16:25:27.550554" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/tests/nextflow.config b/modules/nf-core/samtools/faidx/tests/nextflow.config new file mode 100644 index 00000000..f76a3ba0 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: SAMTOOLS_FAIDX { + ext.args = 'MT192765.1 -o extract.fa' + } + +} diff --git a/modules/nf-core/samtools/faidx/tests/nextflow2.config b/modules/nf-core/samtools/faidx/tests/nextflow2.config new file mode 100644 index 00000000..33ebbd5d --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/nextflow2.config @@ -0,0 +1,6 @@ +process { + + withName: SAMTOOLS_FAIDX { + ext.args = '-o extract.fa' + } +} diff --git a/modules/nf-core/samtools/faidx/tests/tags.yml b/modules/nf-core/samtools/faidx/tests/tags.yml new file mode 100644 index 00000000..e4a83948 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/faidx: + - modules/nf-core/samtools/faidx/** diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 5d3b0755..6c2c0b4b 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -1,12 +1,13 @@ -include { SEQKIT_SPLIT } from '../../modules/local/seqkit/split/main' -include { BOWTIE_BUILD } from '../../modules/nf-core/bowtie/build/main' -include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build/main' -include { BWA_INDEX } from '../../modules/nf-core/bwa/index/main' -include { HISAT2_EXTRACTSPLICESITES } from '../../modules/nf-core/hisat2/extractsplicesites/main' -include { HISAT2_BUILD } from '../../modules/nf-core/hisat2/build/main' -include { STAR_GENOMEGENERATE } from '../../modules/nf-core/star/genomegenerate/main' -include { SEGEMEHL_INDEX } from '../../modules/nf-core/segemehl/index/main' -include { GAWK as CLEAN_FASTA } from '../../modules/nf-core/gawk/main' +include { SEQKIT_SPLIT } from '../../modules/local/seqkit/split' +include { BOWTIE_BUILD } from '../../modules/nf-core/bowtie/build' +include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build' +include { BWA_INDEX } from '../../modules/nf-core/bwa/index' +include { HISAT2_EXTRACTSPLICESITES } from '../../modules/nf-core/hisat2/extractsplicesites' +include { HISAT2_BUILD } from '../../modules/nf-core/hisat2/build' +include { STAR_GENOMEGENERATE } from '../../modules/nf-core/star/genomegenerate' +include { SEGEMEHL_INDEX } from '../../modules/nf-core/segemehl/index' +include { GAWK as CLEAN_FASTA } from '../../modules/nf-core/gawk' +include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx' workflow PREPARE_GENOME { @@ -42,6 +43,8 @@ workflow PREPARE_GENOME { SEGEMEHL_INDEX(ch_fasta.map{ meta, fasta -> fasta}) // TODO: Add support for meta + SAMTOOLS_FAIDX(ch_fasta, [[], []]) + // Collect versions ch_versions = ch_versions.mix(SEQKIT_SPLIT.out.versions, BOWTIE_BUILD.out.versions, @@ -53,6 +56,7 @@ workflow PREPARE_GENOME { STAR_GENOMEGENERATE.out.versions) emit: + faidx = SAMTOOLS_FAIDX.out.fai bowtie = params.bowtie ?: BOWTIE_BUILD.out.index segemehl = params.segemehl ?: SEGEMEHL_INDEX.out.index bowtie2 = params.bowtie2 ? Channel.value([[id: "bowtie2"], file(params.bowtie2, checkIfExists: true)]) : BOWTIE2_BUILD.out.index.collect() diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index fbf030a5..9420fd2f 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -25,6 +25,7 @@ workflow QUANTIFICATION { circ_annotation_gtf bootstrap_samples ch_phenotype + ch_faidx main: ch_versions = Channel.empty() @@ -43,7 +44,7 @@ workflow QUANTIFICATION { ) PSIRC_INDEX(MARK_CIRCULAR.out.output) - PSIRC_QUANT(reads, PSIRC_INDEX.out.index.collect(), bootstrap_samples) + PSIRC_QUANT(reads, PSIRC_INDEX.out.index.collect(), MARK_CIRCULAR.out.output, ch_faidx, bootstrap_samples) CUSTOM_TX2GENE( COMBINE_TRANSCRIPTOME_GTFS.out.sorted, diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 5f1e27fb..b8bfa62d 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -165,7 +165,8 @@ workflow CIRCRNA { CIRCRNA_DISCOVERY.out.annotation_bed, CIRCRNA_DISCOVERY.out.annotation_gtf, params.bootstrap_samples, - ch_phenotype + ch_phenotype, + PREPARE_GENOME.out.faidx ) ch_versions = ch_versions.mix(QUANTIFICATION.out.versions) From 86996528ec322f9e03b1ea912b32913d0f886747 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Wed, 24 Apr 2024 16:33:29 +0200 Subject: [PATCH 208/491] Remove swish traces --- modules/local/fishpond/swish/environment.yml | 9 ------ modules/local/fishpond/swish/main.nf | 30 ------------------- .../local/fishpond/swish/templates/swish.r | 18 ----------- subworkflows/local/quantification.nf | 1 - 4 files changed, 58 deletions(-) delete mode 100644 modules/local/fishpond/swish/environment.yml delete mode 100644 modules/local/fishpond/swish/main.nf delete mode 100644 modules/local/fishpond/swish/templates/swish.r diff --git a/modules/local/fishpond/swish/environment.yml b/modules/local/fishpond/swish/environment.yml deleted file mode 100644 index 9af93313..00000000 --- a/modules/local/fishpond/swish/environment.yml +++ /dev/null @@ -1,9 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "fishpond_swish" -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - "bioconda::bioconductor-fishpond=2.8.0-0" diff --git a/modules/local/fishpond/swish/main.nf b/modules/local/fishpond/swish/main.nf deleted file mode 100644 index cb011ec8..00000000 --- a/modules/local/fishpond/swish/main.nf +++ /dev/null @@ -1,30 +0,0 @@ -process FISHPOND_SWISH { - tag "$meta.id" - label "process_medium" - - conda "${moduleDir}/environment.yaml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-fishpond:2.8.0--r43hdfd78af_0' : - 'biocontainers/bioconductor-fishpond:2.8.0--r43hdfd78af_0' }" - - input: - tuple val(meta), path(experiment) - val(column) - - output: - tuple val(meta), path("${meta.id}.swish.rds"), emit: swish - path "versions.yml" , emit: versions - - script: - template "swish.r" - - stub: - """ - touch ${meta.id}.swish.rds - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bioconductor-fishpond: \$(Rscript -e "library(fishpond); cat(as.character(packageVersion('fishpond')))") - END_VERSIONS - """ -} diff --git a/modules/local/fishpond/swish/templates/swish.r b/modules/local/fishpond/swish/templates/swish.r deleted file mode 100644 index 2b95a61a..00000000 --- a/modules/local/fishpond/swish/templates/swish.r +++ /dev/null @@ -1,18 +0,0 @@ -#!/usr/bin/env Rscript --vanilla - -library(fishpond) - -se <- readRDS('$experiment') - -se <- scaleInfReps(se) -se <- labelKeep(se) -se <- swish(se, x="$column") - -saveRDS(se, '${meta.id}.rds') - -writeLines( - c( - '"${task.process}":', - paste(' bioconductor-fishpond:', packageVersion('fishpond')) - ), -'versions.yml') diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index 9420fd2f..86cee630 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -7,7 +7,6 @@ include { CUSTOM_TX2GENE } from '../../modules/nf-core/c include { TXIMETA_TXIMPORT } from '../../modules/nf-core/tximeta/tximport' include { TXIMETA_TXIMETA } from '../../modules/local/tximeta/tximeta' include { MERGE_EXPERIMENTS } from '../../modules/local/quantification/merge_experiments' -include { FISHPOND_SWISH } from '../../modules/local/fishpond/swish' include { CSVTK_JOIN as JOIN_GENE_COUNTS } from '../../modules/nf-core/csvtk/join' include { CSVTK_JOIN as JOIN_GENE_TPM } from '../../modules/nf-core/csvtk/join' include { CSVTK_JOIN as JOIN_TX_COUNTS } from '../../modules/nf-core/csvtk/join' From 282ac3293de4efbb4504827fa5fcb56ba52c824a Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Wed, 24 Apr 2024 18:32:16 +0200 Subject: [PATCH 209/491] Remove check for overlong circRNAs --- bin/annotation.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/bin/annotation.py b/bin/annotation.py index 21bd9587..17001e36 100755 --- a/bin/annotation.py +++ b/bin/annotation.py @@ -33,9 +33,6 @@ df = pd.read_csv(args.input, sep="\t", header=None, usecols=columns.keys()) df = df.rename(columns=columns) -# Remove overlong circRNAs -df = df[df['end'] - df['start'] <= 10_000] - # Extract circRNAs without match mask = df['tx_start'] == -1 df_intergenic = df[mask] From 7e367ade97e128af997522ba1d21f02c28ca6cea Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 25 Apr 2024 08:02:26 +0200 Subject: [PATCH 210/491] Fix environment int COUNTS_COMBINED --- modules/local/count_matrix/combined/main.nf | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/modules/local/count_matrix/combined/main.nf b/modules/local/count_matrix/combined/main.nf index 5b3bc28a..7d1e1269 100644 --- a/modules/local/count_matrix/combined/main.nf +++ b/modules/local/count_matrix/combined/main.nf @@ -1,10 +1,10 @@ process COUNTS_COMBINED { label "process_single" - conda "conda-forge::mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6==fccb0c41a243c639e11dd1be7b74f563e624fcca-0" + conda "bioconda::pandas=1.5.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0': - 'biocontainers/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0' }" + 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : + 'biocontainers/pandas:1.5.2' }" input: path(beds) @@ -22,7 +22,6 @@ process COUNTS_COMBINED { "${task.process}": python: \$(python --version | sed 's/Python //g') pandas: \$(python -c "import pandas; print(pandas.__version__)") - numpy: \$(python -c "import numpy; print(numpy.__version__)") END_VERSIONS """ } From 2ae28facc94748a690fd4828daf1a3687e1d842e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 25 Apr 2024 09:28:53 +0200 Subject: [PATCH 211/491] Remove quay.io prefixes --- modules/local/annotation/parent_gene/main.nf | 2 +- modules/local/circexplorer2/reference/main.nf | 2 +- modules/local/circrna_finder/filter/main.nf | 2 +- modules/local/circtest/prepare/main.nf | 2 +- modules/local/circtest/test/main.nf | 2 +- modules/local/ciriquant/ciriquant/main.nf | 2 +- modules/local/dcc/dcc/main.nf | 2 +- modules/local/deseq2/differential_expression/main.nf | 2 +- modules/local/fasta/main.nf | 2 +- modules/local/find_circ/anchors/main.nf | 2 +- modules/local/find_circ/filter/main.nf | 2 +- modules/local/find_circ/find_circ/main.nf | 2 +- modules/local/mapsplice/align/main.nf | 2 +- modules/local/mirna_targets/main.nf | 2 +- modules/local/stringtie/prepde/main.nf | 2 +- modules/local/targetscan/predict/main.nf | 2 +- 16 files changed, 16 insertions(+), 16 deletions(-) diff --git a/modules/local/annotation/parent_gene/main.nf b/modules/local/annotation/parent_gene/main.nf index 9566f015..21f0b892 100644 --- a/modules/local/annotation/parent_gene/main.nf +++ b/modules/local/annotation/parent_gene/main.nf @@ -4,7 +4,7 @@ process PARENT_GENE { conda "bioconda::ucsc-gtftogenepred=377 bioconda::ucsc-genepredtobed=377 bioconda::bedtools=2.27.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-d7ee3552d06d8acebbc660507b48487c7369e221:07daadbfe8182aa3c974c7b78924d5c8730b922d-0' : - 'quay.io/biocontainers/mulled-v2-d7ee3552d06d8acebbc660507b48487c7369e221:07daadbfe8182aa3c974c7b78924d5c8730b922d-0' }" + 'biocontainers/mulled-v2-d7ee3552d06d8acebbc660507b48487c7369e221:07daadbfe8182aa3c974c7b78924d5c8730b922d-0' }" input: path circrna_matrix diff --git a/modules/local/circexplorer2/reference/main.nf b/modules/local/circexplorer2/reference/main.nf index 07571e4a..f16fa9c0 100644 --- a/modules/local/circexplorer2/reference/main.nf +++ b/modules/local/circexplorer2/reference/main.nf @@ -5,7 +5,7 @@ process CIRCEXPLORER2_REFERENCE { conda "bioconda::ucsc-gtftogenepred=377 bioconda::ucsc-genepredtobed=377 bioconda::bedtools=2.27.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-d7ee3552d06d8acebbc660507b48487c7369e221:07daadbfe8182aa3c974c7b78924d5c8730b922d-0' : - 'quay.io/biocontainers/mulled-v2-d7ee3552d06d8acebbc660507b48487c7369e221:07daadbfe8182aa3c974c7b78924d5c8730b922d-0' }" + 'biocontainers/mulled-v2-d7ee3552d06d8acebbc660507b48487c7369e221:07daadbfe8182aa3c974c7b78924d5c8730b922d-0' }" input: path gtf diff --git a/modules/local/circrna_finder/filter/main.nf b/modules/local/circrna_finder/filter/main.nf index 1182442f..1f781a32 100644 --- a/modules/local/circrna_finder/filter/main.nf +++ b/modules/local/circrna_finder/filter/main.nf @@ -5,7 +5,7 @@ process CIRCRNA_FINDER_FILTER { conda "bioconda::circrna_finder=1.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/circrna_finder%3A1.2--pl5321hdfd78af_1' : - 'quay.io/biocontainers/circrna_finder:1.2--pl5321hdfd78af_1' }" + 'biocontainers/circrna_finder:1.2--pl5321hdfd78af_1' }" input: tuple val(meta), path(sam), path(junction), path(tab) diff --git a/modules/local/circtest/prepare/main.nf b/modules/local/circtest/prepare/main.nf index 2fecd7b0..834c6063 100644 --- a/modules/local/circtest/prepare/main.nf +++ b/modules/local/circtest/prepare/main.nf @@ -4,7 +4,7 @@ process PREPARE_CLR_TEST { conda "conda-forge::r-base=4.2.2 conda-forge::r-aod=1.3.2 conda-forge::r-ggplot2=3.4.0 conda-forge::r-plyr=1.8.8" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c79b00aa4647c739dbe7e8480789d3ba67988f2e:0' : - 'quay.io/biocontainers/mulled-v2-c79b00aa4647c739dbe7e8480789d3ba67988f2e:0' }" + 'biocontainers/mulled-v2-c79b00aa4647c739dbe7e8480789d3ba67988f2e:0' }" input: path(gene_matrix) diff --git a/modules/local/circtest/test/main.nf b/modules/local/circtest/test/main.nf index 643f2c56..c7add5e6 100644 --- a/modules/local/circtest/test/main.nf +++ b/modules/local/circtest/test/main.nf @@ -4,7 +4,7 @@ process CIRCTEST { conda "conda-forge::r-base=4.2.2 conda-forge::r-aod=1.3.2 conda-forge::r-ggplot2=3.4.0 conda-forge::r-plyr=1.8.8" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c79b00aa4647c739dbe7e8480789d3ba67988f2e:0' : - 'quay.io/biocontainers/mulled-v2-c79b00aa4647c739dbe7e8480789d3ba67988f2e:0' }" + 'biocontainers/mulled-v2-c79b00aa4647c739dbe7e8480789d3ba67988f2e:0' }" input: path(circ_csv) diff --git a/modules/local/ciriquant/ciriquant/main.nf b/modules/local/ciriquant/ciriquant/main.nf index fab482ba..5c96fe14 100644 --- a/modules/local/ciriquant/ciriquant/main.nf +++ b/modules/local/ciriquant/ciriquant/main.nf @@ -5,7 +5,7 @@ process CIRIQUANT { conda "bioconda::ciriquant=1.1.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ciriquant:1.1.2--pyhdfd78af_2' : - 'quay.io/biocontainers/ciriquant:1.1.2--pyhdfd78af_2' }" + 'biocontainers/ciriquant:1.1.2--pyhdfd78af_2' }" input: tuple val(meta), path(reads) diff --git a/modules/local/dcc/dcc/main.nf b/modules/local/dcc/dcc/main.nf index 77dc2c55..9baad3ff 100644 --- a/modules/local/dcc/dcc/main.nf +++ b/modules/local/dcc/dcc/main.nf @@ -5,7 +5,7 @@ process DCC { conda "bioconda::circtools=1.2.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/circtools:1.2.1--pyh7cba7a3_0' : - 'quay.io/biocontainers/circtools:1.2.1--pyh7cba7a3_0' }" + 'biocontainers/circtools:1.2.1--pyh7cba7a3_0' }" input: tuple val(meta), path(pairs), path(mate1), path(mate2) diff --git a/modules/local/deseq2/differential_expression/main.nf b/modules/local/deseq2/differential_expression/main.nf index 86ee474c..560df2fc 100644 --- a/modules/local/deseq2/differential_expression/main.nf +++ b/modules/local/deseq2/differential_expression/main.nf @@ -4,7 +4,7 @@ process DESEQ2_DIFFERENTIAL_EXPRESSION { conda "r-base=3.6.3 conda-forge::r-argparser=0.6 conda-forge::r-dplyr=1.0.5 conda-forge::r-ggplot2=3.3.3 r-ggpubr=0.4.0 conda-forge::r-gplots=3.1.1 conda-forge::r-pheatmap=1.0.12 r-plyr=1.8.6 r-pvclust=2.2_0 r-rcolorbrewer=1.1_2 conda-forge::r-circlize=0.4.12 bioconductor-biomart=2.42.0 bioconductor-complexheatmap=2.2.0 bioconductor-deseq2=1.26.0 bioconductor-enhancedvolcano=1.4.0 bioconductor-ihw=1.14.0 bioconductor-org.hs.eg.db=3.10.0 bioconductor-pcatools=1.2.0 bioconductor-tximport=1.14.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-04b2ef814c9c6ab8c196c3e372521b88160dc260:e0cb4046baee3fd35fdbf883ba8af34e3e8af2e8-0' : - 'quay.io/biocontainers/mulled-v2-04b2ef814c9c6ab8c196c3e372521b88160dc260:e0cb4046baee3fd35fdbf883ba8af34e3e8af2e8-0' }" + 'biocontainers/mulled-v2-04b2ef814c9c6ab8c196c3e372521b88160dc260:e0cb4046baee3fd35fdbf883ba8af34e3e8af2e8-0' }" input: path(gene_matrix) diff --git a/modules/local/fasta/main.nf b/modules/local/fasta/main.nf index 63381c1b..d17b17d7 100644 --- a/modules/local/fasta/main.nf +++ b/modules/local/fasta/main.nf @@ -5,7 +5,7 @@ process FASTA { conda "bioconda::bedtools=2.30.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h7d7f7ad_2': - 'quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_2' }" + 'biocontainers/bedtools:2.30.0--h7d7f7ad_2' }" input: tuple val(meta), path(bed) diff --git a/modules/local/find_circ/anchors/main.nf b/modules/local/find_circ/anchors/main.nf index 5359497d..9bccb403 100644 --- a/modules/local/find_circ/anchors/main.nf +++ b/modules/local/find_circ/anchors/main.nf @@ -5,7 +5,7 @@ process FIND_CIRC_ANCHORS { conda "bioconda::find_circ=1.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/find_circ%3A1.2--hdfd78af_0' : - 'quay.io/biocontainers/find_circ:1.2--hdfd78af_0' }" + 'biocontainers/find_circ:1.2--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/local/find_circ/filter/main.nf b/modules/local/find_circ/filter/main.nf index c8e4f3a7..c4313b20 100644 --- a/modules/local/find_circ/filter/main.nf +++ b/modules/local/find_circ/filter/main.nf @@ -5,7 +5,7 @@ process FIND_CIRC_FILTER { conda "bioconda::find_circ=1.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/find_circ%3A1.2--hdfd78af_0' : - 'quay.io/biocontainers/find_circ:1.2--hdfd78af_0' }" + 'biocontainers/find_circ:1.2--hdfd78af_0' }" input: tuple val(meta), path(bed) diff --git a/modules/local/find_circ/find_circ/main.nf b/modules/local/find_circ/find_circ/main.nf index 242e195f..bd1bced2 100644 --- a/modules/local/find_circ/find_circ/main.nf +++ b/modules/local/find_circ/find_circ/main.nf @@ -5,7 +5,7 @@ process FIND_CIRC { conda "bioconda::find_circ=1.2 bioconda::bowtie2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-c27e472038a09e49d9147bc52903e12836302c12:60ffb3b15a2c40c669f8d38382b1e6e4b065f5e4-0' : - 'quay.io/biocontainers/mulled-v2-c27e472038a09e49d9147bc52903e12836302c12:60ffb3b15a2c40c669f8d38382b1e6e4b065f5e4-0' }" + 'biocontainers/mulled-v2-c27e472038a09e49d9147bc52903e12836302c12:60ffb3b15a2c40c669f8d38382b1e6e4b065f5e4-0' }" input: tuple val(meta), path(anchors) diff --git a/modules/local/mapsplice/align/main.nf b/modules/local/mapsplice/align/main.nf index 7dcbbbd3..a90930d6 100644 --- a/modules/local/mapsplice/align/main.nf +++ b/modules/local/mapsplice/align/main.nf @@ -5,7 +5,7 @@ process MAPSPLICE_ALIGN { conda "bioconda::mapsplice=2.2.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mapsplice:2.2.1--py27h07887db_0': - 'quay.io/biocontainers/mapsplice:2.2.1--py27h07887db_0' }" + 'biocontainers/mapsplice:2.2.1--py27h07887db_0' }" input: tuple val(meta), path(reads) diff --git a/modules/local/mirna_targets/main.nf b/modules/local/mirna_targets/main.nf index fdfee556..94b31eeb 100644 --- a/modules/local/mirna_targets/main.nf +++ b/modules/local/mirna_targets/main.nf @@ -5,7 +5,7 @@ process MIRNA_TARGETS { conda "bioconda::bedtools=2.30.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h7d7f7ad_2': - 'quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_2' }" + 'biocontainers/bedtools:2.30.0--h7d7f7ad_2' }" input: tuple val(meta), path(targetscan), path(miranda), path(bed12) diff --git a/modules/local/stringtie/prepde/main.nf b/modules/local/stringtie/prepde/main.nf index eb72483b..38f27434 100644 --- a/modules/local/stringtie/prepde/main.nf +++ b/modules/local/stringtie/prepde/main.nf @@ -4,7 +4,7 @@ process STRINGTIE_PREPDE { conda "bioconda::stringtie=2.2.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : - 'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }" + 'biocontainers/stringtie:2.2.1--hecb563c_2' }" input: path gtf diff --git a/modules/local/targetscan/predict/main.nf b/modules/local/targetscan/predict/main.nf index 12d3511e..450611c2 100644 --- a/modules/local/targetscan/predict/main.nf +++ b/modules/local/targetscan/predict/main.nf @@ -5,7 +5,7 @@ process TARGETSCAN { conda "bioconda::targetscan=7.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/targetscan:7.0--pl5321hdfd78af_0' : - 'quay.io/biocontainers/targetscan:7.0--pl5321hdfd78af_0' }" + 'biocontainers/targetscan:7.0--pl5321hdfd78af_0' }" input: tuple val(meta), path(fasta) From eceacd7e61d9f58f6a71064e0af7c97ea2b2f172 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 25 Apr 2024 09:33:37 +0200 Subject: [PATCH 212/491] Fix environment definition of MERGE_TOOLS --- modules/local/count_matrix/merge_tools/main.nf | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/modules/local/count_matrix/merge_tools/main.nf b/modules/local/count_matrix/merge_tools/main.nf index 55bdcde0..17f8556f 100644 --- a/modules/local/count_matrix/merge_tools/main.nf +++ b/modules/local/count_matrix/merge_tools/main.nf @@ -2,10 +2,10 @@ process MERGE_TOOLS { tag "$meta.id" label "process_single" - conda "conda-forge::mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6==fccb0c41a243c639e11dd1be7b74f563e624fcca-0" + conda "bioconda::pandas=1.5.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0': - 'biocontainers/mulled-v2-2076f4a3fb468a04063c9e6b7747a630abb457f6:fccb0c41a243c639e11dd1be7b74f563e624fcca-0' }" + 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : + 'biocontainers/pandas:1.5.2' }" input: tuple val(meta), path(beds) @@ -25,7 +25,6 @@ process MERGE_TOOLS { "${task.process}": python: \$(python --version | sed 's/Python //g') pandas: \$(python -c "import pandas; print(pandas.__version__)") - numpy: \$(python -c "import numpy; print(numpy.__version__)") END_VERSIONS """ } From 4cded24939feca3915e0f174e9de49da2cfe450f Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 8 May 2024 13:58:09 +0000 Subject: [PATCH 213/491] Template update for nf-core/tools version 2.14.0 --- .editorconfig | 6 +- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/awsfulltest.yml | 10 +- .github/workflows/awstest.yml | 12 +- .github/workflows/ci.yml | 4 +- .github/workflows/download_pipeline.yml | 22 ++- .github/workflows/fix-linting.yml | 6 +- .github/workflows/linting.yml | 18 +- .github/workflows/linting_comment.yml | 2 +- .github/workflows/release-announcements.yml | 6 +- .nf-core.yml | 1 + .pre-commit-config.yaml | 3 + README.md | 2 +- conf/base.config | 3 - conf/modules.config | 8 - conf/test.config | 2 +- conf/test_full.config | 2 +- docs/usage.md | 2 + modules.json | 4 +- modules/nf-core/fastqc/main.nf | 6 + nextflow.config | 176 +++++++++--------- nextflow_schema.json | 7 + pyproject.toml | 15 -- .../utils_nfcore_circrna_pipeline/main.nf | 16 +- .../nf-core/utils_nfcore_pipeline/main.nf | 8 +- workflows/circrna.nf | 46 +++-- 26 files changed, 220 insertions(+), 169 deletions(-) delete mode 100644 pyproject.toml diff --git a/.editorconfig b/.editorconfig index dd9ffa53..72dda289 100644 --- a/.editorconfig +++ b/.editorconfig @@ -28,10 +28,6 @@ indent_style = unset [/assets/email*] indent_size = unset -# ignore Readme -[README.md] -indent_style = unset - -# ignore python +# ignore python and markdown [*.{py,md}] indent_style = unset diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 364dd9b5..9d44ed38 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/circ - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/circrna/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/circrna _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). -- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`). +- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 7b6bd16d..8f7ea0eb 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -8,12 +8,12 @@ on: types: [published] workflow_dispatch: jobs: - run-tower: + run-platform: name: Run AWS full tests if: github.repository == 'nf-core/circrna' runs-on: ubuntu-latest steps: - - name: Launch workflow via tower + - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) @@ -33,7 +33,7 @@ jobs: - uses: actions/upload-artifact@v4 with: - name: Tower debug log file + name: Seqera Platform debug log file path: | - tower_action_*.log - tower_action_*.json + seqera_platform_action_*.log + seqera_platform_action_*.json diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 9590dcae..cbea731e 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -5,13 +5,13 @@ name: nf-core AWS test on: workflow_dispatch: jobs: - run-tower: + run-platform: name: Run AWS tests if: github.repository == 'nf-core/circrna' runs-on: ubuntu-latest steps: - # Launch workflow using Tower CLI tool action - - name: Launch workflow via tower + # Launch workflow using Seqera Platform CLI tool action + - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} @@ -27,7 +27,7 @@ jobs: - uses: actions/upload-artifact@v4 with: - name: Tower debug log file + name: Seqera Platform debug log file path: | - tower_action_*.log - tower_action_*.json + seqera_platform_action_*.log + seqera_platform_action_*.json diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 916fd86a..8bfcd749 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -28,10 +28,10 @@ jobs: - "latest-everything" steps: - name: Check out pipeline code - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@v2 with: version: "${{ matrix.NXF_VER }}" diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 08622fd5..2d20d644 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -14,6 +14,8 @@ on: pull_request: types: - opened + - edited + - synchronize branches: - master pull_request_target: @@ -28,11 +30,14 @@ jobs: runs-on: ubuntu-latest steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - name: Disk space cleanup + uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: - python-version: "3.11" + python-version: "3.12" architecture: "x64" - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 with: @@ -65,8 +70,17 @@ jobs: - name: Inspect download run: tree ./${{ env.REPOTITLE_LOWERCASE }} - - name: Run the downloaded pipeline + - name: Run the downloaded pipeline (stub) + id: stub_run_pipeline + continue-on-error: true env: NXF_SINGULARITY_CACHEDIR: ./ NXF_SINGULARITY_HOME_MOUNT: true run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + - name: Run the downloaded pipeline (stub run not supported) + id: run_pipeline + if: ${{ job.steps.stub_run_pipeline.status == failure() }} + env: + NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_HOME_MOUNT: true + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 505d843c..765c84e8 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -32,9 +32,9 @@ jobs: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} # Install and run pre-commit - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: - python-version: 3.11 + python-version: "3.12" - name: Install pre-commit run: pip install pre-commit diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 073e1876..a3fb2541 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,12 +14,12 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - - name: Set up Python 3.11 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - name: Set up Python 3.12 + uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: - python-version: 3.11 + python-version: "3.12" cache: "pip" - name: Install pre-commit @@ -32,14 +32,14 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: - python-version: "3.11" + python-version: "3.12" architecture: "x64" - name: Install dependencies @@ -60,7 +60,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index b706875f..40acc23f 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3 + uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index d468aeaa..03ecfcf7 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -12,7 +12,7 @@ jobs: - name: get topics and convert to hashtags id: get_topics run: | - curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT + echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: @@ -25,13 +25,13 @@ jobs: Please see the changelog: ${{ github.event.release.html_url }} - ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics + ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics send-tweet: runs-on: ubuntu-latest steps: - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: python-version: "3.10" - name: Install dependencies diff --git a/.nf-core.yml b/.nf-core.yml index 3805dc81..d6daa403 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1 +1,2 @@ repository_type: pipeline +nf_core_version: "2.14.0" diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index af57081f..4dc0f1dc 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -3,6 +3,9 @@ repos: rev: "v3.1.0" hooks: - id: prettier + additional_dependencies: + - prettier@3.2.5 + - repo: https://github.com/editorconfig-checker/editorconfig-checker.python rev: "2.7.3" hooks: diff --git a/README.md b/README.md index ab055f20..558557f1 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) -[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/circrna) +[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/circrna) [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23circrna-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/circrna)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) diff --git a/conf/base.config b/conf/base.config index 307e9381..cdf46e83 100644 --- a/conf/base.config +++ b/conf/base.config @@ -59,7 +59,4 @@ process { errorStrategy = 'retry' maxRetries = 2 } - withName:CUSTOM_DUMPSOFTWAREVERSIONS { - cache = false - } } diff --git a/conf/modules.config b/conf/modules.config index e3ea8fa6..d203d2b6 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -22,14 +22,6 @@ process { ext.args = '--quiet' } - withName: CUSTOM_DUMPSOFTWAREVERSIONS { - publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - pattern: '*_versions.yml' - ] - } - withName: 'MULTIQC' { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ diff --git a/conf/test.config b/conf/test.config index e1f2acda..a7c2516f 100644 --- a/conf/test.config +++ b/conf/test.config @@ -22,7 +22,7 @@ params { // Input data // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' + input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' // Genome references genome = 'R64-1-1' diff --git a/conf/test_full.config b/conf/test_full.config index a3b229ad..448193d7 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -17,7 +17,7 @@ params { // Input data for full size test // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA) // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' + input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' // Genome references genome = 'R64-1-1' diff --git a/docs/usage.md b/docs/usage.md index 8960ea47..98e72a06 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -156,6 +156,8 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) - `apptainer` - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) +- `wave` + - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later). - `conda` - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. diff --git a/modules.json b/modules.json index c0226feb..3b1e37ee 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "fastqc": { "branch": "master", - "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c", + "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", "installed_by": ["modules"] }, "multiqc": { @@ -26,7 +26,7 @@ }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 9e19a74c..d79f1c86 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -25,6 +25,11 @@ process FASTQC { def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } def rename_to = old_new_pairs*.join(' ').join(' ') def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') + + def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') + // FastQC memory value allowed range (100 - 10000) + def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) + """ printf "%s %s\\n" $rename_to | while read old_name new_name; do [ -f "\${new_name}" ] || ln -s \$old_name \$new_name @@ -33,6 +38,7 @@ process FASTQC { fastqc \\ $args \\ --threads $task.cpus \\ + --memory $fastqc_memory \\ $renamed_files cat <<-END_VERSIONS > versions.yml diff --git a/nextflow.config b/nextflow.config index 564acf64..13ad97ff 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,7 +16,8 @@ params { genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false - fasta = null// MultiQC options + + // MultiQC options multiqc_config = null multiqc_title = null multiqc_logo = null @@ -24,15 +25,16 @@ params { multiqc_methods_description = null // Boilerplate options - outdir = null - publish_dir_mode = 'copy' - email = null - email_on_fail = null - plaintext_email = false - monochrome_logs = false - hook_url = null - help = false - version = false + outdir = null + publish_dir_mode = 'copy' + email = null + email_on_fail = null + plaintext_email = false + monochrome_logs = false + hook_url = null + help = false + version = false + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' // Config options config_profile_name = null @@ -68,103 +70,109 @@ try { } // Load nf-core/circrna custom profiles from different institutions. -// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs! -// try { -// includeConfig "${params.custom_config_base}/pipeline/circrna.config" -// } catch (Exception e) { -// System.err.println("WARNING: Could not load nf-core/config/circrna profiles: ${params.custom_config_base}/pipeline/circrna.config") -// } +try { + includeConfig "${params.custom_config_base}/pipeline/circrna.config" +} catch (Exception e) { + System.err.println("WARNING: Could not load nf-core/config/circrna profiles: ${params.custom_config_base}/pipeline/circrna.config") +} profiles { debug { - dumpHashes = true - process.beforeScript = 'echo $HOSTNAME' - cleanup = false + dumpHashes = true + process.beforeScript = 'echo $HOSTNAME' + cleanup = false nextflow.enable.configProcessNamesValidation = true } conda { - conda.enabled = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - channels = ['conda-forge', 'bioconda', 'defaults'] - apptainer.enabled = false + conda.enabled = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + conda.channels = ['conda-forge', 'bioconda', 'defaults'] + apptainer.enabled = false } mamba { - conda.enabled = true - conda.useMamba = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + conda.enabled = true + conda.useMamba = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } docker { - docker.enabled = true - conda.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false - docker.runOptions = '-u $(id -u):$(id -g)' + docker.enabled = true + conda.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false + docker.runOptions = '-u $(id -u):$(id -g)' } arm { - docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { - singularity.enabled = true - singularity.autoMounts = true - conda.enabled = false - docker.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + singularity.enabled = true + singularity.autoMounts = true + conda.enabled = false + docker.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } podman { - podman.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + podman.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } shifter { - shifter.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + shifter.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } charliecloud { - charliecloud.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - apptainer.enabled = false + charliecloud.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + apptainer.enabled = false } apptainer { - apptainer.enabled = true - apptainer.autoMounts = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false + apptainer.enabled = true + apptainer.autoMounts = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } + wave { + apptainer.ociAutoPull = true + singularity.ociAutoPull = true + wave.enabled = true + wave.freeze = true + wave.strategy = 'conda,container' } gitpod { - executor.name = 'local' - executor.cpus = 4 - executor.memory = 8.GB + executor.name = 'local' + executor.cpus = 4 + executor.memory = 8.GB } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 01ffcd21..82858e99 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -265,6 +265,13 @@ "description": "Validation of parameters in lenient more.", "hidden": true, "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." + }, + "pipelines_testdata_base_path": { + "type": "string", + "fa_icon": "far fa-check-circle", + "description": "Base URL or local path to location of pipeline test dataset files", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/", + "hidden": true } } } diff --git a/pyproject.toml b/pyproject.toml deleted file mode 100644 index 56110621..00000000 --- a/pyproject.toml +++ /dev/null @@ -1,15 +0,0 @@ -# Config file for Python. Mostly used to configure linting of bin/*.py with Ruff. -# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation. -[tool.ruff] -line-length = 120 -target-version = "py38" -cache-dir = "~/.cache/ruff" - -[tool.ruff.lint] -select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"] - -[tool.ruff.lint.isort] -known-first-party = ["nf_core"] - -[tool.ruff.lint.per-file-ignores] -"__init__.py" = ["E402", "F401"] diff --git a/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf b/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf index 69918616..5ee14910 100644 --- a/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf @@ -140,6 +140,10 @@ workflow PIPELINE_COMPLETION { imNotification(summary_params, hook_url) } } + + workflow.onError { + log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting" + } } /* @@ -230,8 +234,16 @@ def methodsDescriptionText(mqc_methods_yaml) { meta["manifest_map"] = workflow.manifest.toMap() // Pipeline DOI - meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" - meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + if (meta.manifest_map.doi) { + // Using a loop to handle multiple DOIs + // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers + // Removing ` ` since the manifest.doi is a string and not a proper list + def temp_doi_ref = "" + String[] manifest_doi = meta.manifest_map.doi.tokenize(",") + for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2) + } else meta["doi_text"] = "" + meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " // Tool references meta["tool_citations"] = "" diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index a8b55d6f..14558c39 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -65,9 +65,15 @@ def checkProfileProvided(nextflow_cli_args) { // Citation string for pipeline // def workflowCitation() { + def temp_doi_ref = "" + String[] manifest_doi = workflow.manifest.doi.tokenize(",") + // Using a loop to handle multiple DOIs + // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers + // Removing ` ` since the manifest.doi is a string and not a proper list + for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + - " ${workflow.manifest.doi}\n\n" + + temp_doi_ref + "\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + diff --git a/workflows/circrna.nf b/workflows/circrna.nf index 5e577f9b..da558a8e 100644 --- a/workflows/circrna.nf +++ b/workflows/circrna.nf @@ -40,22 +40,44 @@ workflow CIRCRNA { // Collate and save software versions // softwareVersionsToYAML(ch_versions) - .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true) - .set { ch_collated_versions } + .collectFile( + storeDir: "${params.outdir}/pipeline_info", + name: 'nf_core_pipeline_software_mqc_versions.yml', + sort: true, + newLine: true + ).set { ch_collated_versions } // // MODULE: MultiQC // - ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) - ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() - ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") - ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) - ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) - ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false)) + ch_multiqc_config = Channel.fromPath( + "$projectDir/assets/multiqc_config.yml", checkIfExists: true) + ch_multiqc_custom_config = params.multiqc_config ? + Channel.fromPath(params.multiqc_config, checkIfExists: true) : + Channel.empty() + ch_multiqc_logo = params.multiqc_logo ? + Channel.fromPath(params.multiqc_logo, checkIfExists: true) : + Channel.empty() + + summary_params = paramsSummaryMap( + workflow, parameters_schema: "nextflow_schema.json") + ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) + + ch_multiqc_custom_methods_description = params.multiqc_methods_description ? + file(params.multiqc_methods_description, checkIfExists: true) : + file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) + ch_methods_description = Channel.value( + methodsDescriptionText(ch_multiqc_custom_methods_description)) + + ch_multiqc_files = ch_multiqc_files.mix( + ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) + ch_multiqc_files = ch_multiqc_files.mix( + ch_methods_description.collectFile( + name: 'methods_description_mqc.yaml', + sort: true + ) + ) MULTIQC ( ch_multiqc_files.collect(), From 80712a4951f6bc40a2e3de182d651ffc52d67f1d Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 9 May 2024 11:39:08 +0000 Subject: [PATCH 214/491] Template update for nf-core/tools version 2.14.1 --- .github/workflows/linting.yml | 1 - .nf-core.yml | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index a3fb2541..1fcafe88 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -20,7 +20,6 @@ jobs: uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: python-version: "3.12" - cache: "pip" - name: Install pre-commit run: pip install pre-commit diff --git a/.nf-core.yml b/.nf-core.yml index d6daa403..e0b85a77 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,2 +1,2 @@ repository_type: pipeline -nf_core_version: "2.14.0" +nf_core_version: "2.14.1" From 3f8d5d8eb3194667aa33b70005f42f2dfd06766e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 9 May 2024 21:09:45 +0200 Subject: [PATCH 215/491] Remove unnecessary module configs --- conf/modules.config | 85 --------------------------------------------- 1 file changed, 85 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 2e0a6320..1d82c383 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -18,14 +18,6 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - withName: SAMPLESHEET_CHECK { - publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - withName: CUSTOM_DUMPSOFTWAREVERSIONS { publishDir = [ path: { "${params.outdir}/pipeline_info" }, @@ -357,16 +349,6 @@ if (!params.skip_trimming) { ] } - withName: CIRIQUANT_YML { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('ciriquant') } - publishDir = [ - path: { "${params.outdir}/references/ciriquant" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_reference - ] - } - withName: CIRIQUANT { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('ciriquant') } publishDir = [ @@ -388,59 +370,6 @@ if (!params.skip_trimming) { ] } - withName: DCC_1ST_PASS { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('dcc') } - ext.args = [ "", - "--chimOutType Junctions WithinBAM", - "--outSAMunmapped Within", - "--outFilterType BySJout", - "--outReadsUnmapped None", - "--readFilesCommand zcat", - "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}", - "--limitSjdbInsertNsj ${params.limitSjdbInsertNsj}", - "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}", - "--chimSegmentMin ${params.chimSegmentMin}" - ].join(' ').trim() - publishDir = [ - path: { "${params.outdir}/circrna_discovery/dcc/intermediates/align/1st_pass" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates - ] - } - - withName: DCC_SJDB { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('dcc') } - publishDir = [ - path: { "${params.outdir}/circrna_discovery/dcc/intermediates/align/sjdb" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates - ] - } - - withName: DCC_2ND_PASS { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('dcc') } - ext.args = [ "", - "--chimOutType Junctions WithinBAM", - "--outSAMunmapped Within", - "--outFilterType BySJout", - "--outReadsUnmapped None", - "--readFilesCommand zcat", - "--sjdbFileChrStartEnd dataset.SJ.out.tab", - "--alignSJDBoverhangMin ${params.alignSJDBoverhangMin}", - "--limitSjdbInsertNsj ${params.limitSjdbInsertNsj}", - "--chimJunctionOverhangMin ${params.chimJunctionOverhangMin}", - "--chimSegmentMin ${params.chimSegmentMin}" - ].join(' ').trim() - publishDir = [ - path: { "${params.outdir}/circrna_discovery/dcc/intermediates/align/2nd_pass" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates - ] - } - withName: DCC_MATE1_1ST_PASS { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('dcc') } ext.prefix = { "${meta.id}_mate1" } @@ -667,25 +596,11 @@ if (!params.skip_trimming) { ext.when = { params.module.split(',').contains('circrna_discovery') } } - withName: COUNTS_TO_BED { - ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3, \".\", \".\" }'" - ext.suffix = "bed" - } - - withName: UNIQUE_REGIONS { - ext.args = "-k 1,1 -k2,2n -k3,3n -u" - ext.suffix = "unique.bed" - } - withName: COMBINE_TRANSCRIPTOME_GTFS { ext.args = "-k 1,1 -k3,3n -k4,4n" ext.suffix = "gtf" } - withName: CIRCULAR_TRANSCRIPTOME { - ext.args = "-nameOnly" - } - withName: MARK_CIRCULAR { // GAWK process that marks FASTA headers. // Leaves headers starting with "ENS" and non-header lines as is. From 70b3a5f96fb08e89b1904ff2221c8f651360b517 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 9 May 2024 21:10:50 +0200 Subject: [PATCH 216/491] Update modules --- modules.json | 4 +- modules/nf-core/bedtools/getfasta/main.nf | 23 ++++-- modules/nf-core/bedtools/getfasta/meta.yml | 12 +++- .../bedtools/getfasta/tests/main.nf.test | 62 ++++++++++++++++ .../bedtools/getfasta/tests/main.nf.test.snap | 72 +++++++++++++++++++ .../nf-core/bedtools/getfasta/tests/tags.yml | 2 + modules/nf-core/gawk/environment.yml | 7 ++ modules/nf-core/gawk/main.nf | 5 +- modules/nf-core/gawk/tests/main.nf.test | 56 +++++++++++++++ modules/nf-core/gawk/tests/main.nf.test.snap | 68 ++++++++++++++++++ modules/nf-core/gawk/tests/nextflow.config | 6 ++ .../tests/nextflow_with_program_file.config | 5 ++ modules/nf-core/gawk/tests/tags.yml | 2 + 13 files changed, 314 insertions(+), 10 deletions(-) create mode 100644 modules/nf-core/bedtools/getfasta/tests/main.nf.test create mode 100644 modules/nf-core/bedtools/getfasta/tests/main.nf.test.snap create mode 100644 modules/nf-core/bedtools/getfasta/tests/tags.yml create mode 100644 modules/nf-core/gawk/environment.yml create mode 100644 modules/nf-core/gawk/tests/main.nf.test create mode 100644 modules/nf-core/gawk/tests/main.nf.test.snap create mode 100644 modules/nf-core/gawk/tests/nextflow.config create mode 100644 modules/nf-core/gawk/tests/nextflow_with_program_file.config create mode 100644 modules/nf-core/gawk/tests/tags.yml diff --git a/modules.json b/modules.json index ef0f06e4..acc410f5 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "bedtools/getfasta": { "branch": "master", - "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", + "git_sha": "cdcdd5e3d806f0ff3983c40c69e0b07bb44ec299", "installed_by": ["modules"] }, "bedtools/intersect": { @@ -92,7 +92,7 @@ }, "gawk": { "branch": "master", - "git_sha": "dc3527855e7358c6d8400828754c0caa5f11698f", + "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5", "installed_by": ["modules"] }, "gnu/sort": { diff --git a/modules/nf-core/bedtools/getfasta/main.nf b/modules/nf-core/bedtools/getfasta/main.nf index 50549c7d..b316117d 100644 --- a/modules/nf-core/bedtools/getfasta/main.nf +++ b/modules/nf-core/bedtools/getfasta/main.nf @@ -1,5 +1,5 @@ process BEDTOOLS_GETFASTA { - tag "$bed" + tag "$meta.id" label 'process_single' conda "${moduleDir}/environment.yml" @@ -8,19 +8,20 @@ process BEDTOOLS_GETFASTA { 'biocontainers/bedtools:2.31.1--hf5e1c6e_0' }" input: - path bed + tuple val(meta), path(bed) path fasta output: - path "*.fa" , emit: fasta - path "versions.yml" , emit: versions + tuple val(meta), path("*.fa"), emit: fasta + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${bed.baseName}" + def prefix = task.ext.prefix ?: "${meta.id}" + if ("$fasta" == "${prefix}.fa") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ bedtools \\ getfasta \\ @@ -34,4 +35,16 @@ process BEDTOOLS_GETFASTA { bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + if ("$fasta" == "${prefix}.fa") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + touch ${prefix}.fa + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ } diff --git a/modules/nf-core/bedtools/getfasta/meta.yml b/modules/nf-core/bedtools/getfasta/meta.yml index 25fb19a1..41917fe3 100644 --- a/modules/nf-core/bedtools/getfasta/meta.yml +++ b/modules/nf-core/bedtools/getfasta/meta.yml @@ -8,9 +8,14 @@ tools: - bedtools: description: | A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. - documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html + documentation: https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html licence: ["MIT"] input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - bed: type: file description: Bed feature file @@ -20,6 +25,11 @@ input: description: Input fasta file pattern: "*.{fa,fasta}" output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - fasta: type: file description: Output fasta file with extracted sequences diff --git a/modules/nf-core/bedtools/getfasta/tests/main.nf.test b/modules/nf-core/bedtools/getfasta/tests/main.nf.test new file mode 100644 index 00000000..4da7552c --- /dev/null +++ b/modules/nf-core/bedtools/getfasta/tests/main.nf.test @@ -0,0 +1,62 @@ +nextflow_process { + + name "Test Process BEDTOOLS_GETFASTA" + script "../main.nf" + process "BEDTOOLS_GETFASTA" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/getfasta" + + test("sarscov2 - bed - fasta") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false], + file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true), + ] + + input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - bed - fasta - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false], + file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true), + ] + + input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/bedtools/getfasta/tests/main.nf.test.snap b/modules/nf-core/bedtools/getfasta/tests/main.nf.test.snap new file mode 100644 index 00000000..69bf33f7 --- /dev/null +++ b/modules/nf-core/bedtools/getfasta/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "sarscov2 - bed - fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fa:md5,41c3a45a57a16c04f828d8f8bb52df70" + ] + ], + "1": [ + "versions.yml:md5,427b4f64b2f05f28f0beef96c9f0d310" + ], + "fasta": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fa:md5,41c3a45a57a16c04f828d8f8bb52df70" + ] + ], + "versions": [ + "versions.yml:md5,427b4f64b2f05f28f0beef96c9f0d310" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-03T14:16:19.383758985" + }, + "sarscov2 - bed - fasta - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,427b4f64b2f05f28f0beef96c9f0d310" + ], + "fasta": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,427b4f64b2f05f28f0beef96c9f0d310" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-03T14:16:47.47010536" + } +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/getfasta/tests/tags.yml b/modules/nf-core/bedtools/getfasta/tests/tags.yml new file mode 100644 index 00000000..42ec3026 --- /dev/null +++ b/modules/nf-core/bedtools/getfasta/tests/tags.yml @@ -0,0 +1,2 @@ +bedtools/getfasta: + - "modules/nf-core/bedtools/getfasta/**" diff --git a/modules/nf-core/gawk/environment.yml b/modules/nf-core/gawk/environment.yml new file mode 100644 index 00000000..34513c7f --- /dev/null +++ b/modules/nf-core/gawk/environment.yml @@ -0,0 +1,7 @@ +name: gawk +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - anaconda::gawk=5.1.0 diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf index f856a1f8..578b448c 100644 --- a/modules/nf-core/gawk/main.nf +++ b/modules/nf-core/gawk/main.nf @@ -41,10 +41,11 @@ process GAWK { stub: prefix = task.ext.prefix ?: "${meta.id}" - suffix = task.ext.suffix ?: "${input.getExtension}" + suffix = task.ext.suffix ?: "${input.getExtension()}" + def create_cmd = suffix.endsWith("gz") ? "echo '' | gzip >" : "touch" """ - touch ${prefix}.${suffix} + ${create_cmd} ${prefix}.${suffix} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/gawk/tests/main.nf.test b/modules/nf-core/gawk/tests/main.nf.test new file mode 100644 index 00000000..fce82ca9 --- /dev/null +++ b/modules/nf-core/gawk/tests/main.nf.test @@ -0,0 +1,56 @@ +nextflow_process { + + name "Test Process GAWK" + script "../main.nf" + process "GAWK" + + tag "modules" + tag "modules_nfcore" + tag "gawk" + + test("convert fasta to bed") { + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("convert fasta to bed with program file") { + config "./nextflow_with_program_file.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[1] = Channel.of('BEGIN {FS="\t"}; {print \$1 FS "0" FS \$2}').collectFile(name:"program.txt") + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/gawk/tests/main.nf.test.snap b/modules/nf-core/gawk/tests/main.nf.test.snap new file mode 100644 index 00000000..ce207478 --- /dev/null +++ b/modules/nf-core/gawk/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "convert fasta to bed with program file": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "1": [ + "versions.yml:md5,4c320d8c98ca80690afd7651da1ba520" + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "versions": [ + "versions.yml:md5,4c320d8c98ca80690afd7651da1ba520" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.02.0" + }, + "timestamp": "2024-04-05T11:00:28.097563" + }, + "convert fasta to bed": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "1": [ + "versions.yml:md5,4c320d8c98ca80690afd7651da1ba520" + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "versions": [ + "versions.yml:md5,4c320d8c98ca80690afd7651da1ba520" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.02.0" + }, + "timestamp": "2024-04-05T10:28:15.625869" + } +} \ No newline at end of file diff --git a/modules/nf-core/gawk/tests/nextflow.config b/modules/nf-core/gawk/tests/nextflow.config new file mode 100644 index 00000000..6e5d43a3 --- /dev/null +++ b/modules/nf-core/gawk/tests/nextflow.config @@ -0,0 +1,6 @@ +process { + withName: GAWK { + ext.suffix = "bed" + ext.args2 = '\'BEGIN {FS="\t"}; {print \$1 FS "0" FS \$2}\'' + } +} diff --git a/modules/nf-core/gawk/tests/nextflow_with_program_file.config b/modules/nf-core/gawk/tests/nextflow_with_program_file.config new file mode 100644 index 00000000..693ad419 --- /dev/null +++ b/modules/nf-core/gawk/tests/nextflow_with_program_file.config @@ -0,0 +1,5 @@ +process { + withName: GAWK { + ext.suffix = "bed" + } +} diff --git a/modules/nf-core/gawk/tests/tags.yml b/modules/nf-core/gawk/tests/tags.yml new file mode 100644 index 00000000..72e4531d --- /dev/null +++ b/modules/nf-core/gawk/tests/tags.yml @@ -0,0 +1,2 @@ +gawk: + - "modules/nf-core/gawk/**" From 6dde17b13924604e1e6d4b2bdd1cbd71e2f46533 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 9 May 2024 21:11:43 +0200 Subject: [PATCH 217/491] Add samtools faidx version capture --- subworkflows/local/prepare_genome.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 6c2c0b4b..9d382295 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -53,7 +53,8 @@ workflow PREPARE_GENOME { HISAT2_EXTRACTSPLICESITES.out.versions, HISAT2_BUILD.out.versions, SEGEMEHL_INDEX.out.versions, - STAR_GENOMEGENERATE.out.versions) + STAR_GENOMEGENERATE.out.versions, + SAMTOOLS_FAIDX.out.versions) emit: faidx = SAMTOOLS_FAIDX.out.fai From eeb35ed90332747606bc111097a8db40d13f556d Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 9 May 2024 21:35:21 +0200 Subject: [PATCH 218/491] Remove unnecessary nextflow schema entry --- nextflow_schema.json | 7 ------- 1 file changed, 7 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 558c619c..2aaea8bb 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -544,13 +544,6 @@ "description": "Validation of parameters in lenient more.", "hidden": true, "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." - }, - "pipelines_testdata_base_path": { - "type": "string", - "fa_icon": "far fa-check-circle", - "description": "Base URL or local path to location of pipeline test dataset files", - "default": "https://raw.githubusercontent.com/nf-core/test-datasets/", - "hidden": true } } } From b3256a6965f97368a0217ad759fb6e3b8cd8a51c Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 29 Apr 2024 17:38:53 +0200 Subject: [PATCH 219/491] Implement process for removing overlong transcripts --- conf/modules.config | 5 +++++ subworkflows/local/quantification.nf | 10 ++++++++-- 2 files changed, 13 insertions(+), 2 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 1d82c383..cfb38ae1 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -601,6 +601,11 @@ if (!params.skip_trimming) { ext.suffix = "gtf" } + withName: EXCLUDE_OVERLONG_TRANSCRIPTS { + ext.args = "-v FS='\\t' -v OFS='\\t' '\$5-\$4 <= 10000 { print }'" + ext.suffix = "filtered.gtf" + } + withName: MARK_CIRCULAR { // GAWK process that marks FASTA headers. // Leaves headers starting with "ENS" and non-header lines as is. diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index 86cee630..b1c0d576 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -1,4 +1,5 @@ include { GNU_SORT as COMBINE_TRANSCRIPTOME_GTFS } from '../../modules/nf-core/gnu/sort' +include { GAWK as EXCLUDE_OVERLONG_TRANSCRIPTS } from '../../modules/nf-core/gawk' include { TRANSCRIPTOME } from '../../modules/local/quantification/transcriptome' include { GAWK as MARK_CIRCULAR } from '../../modules/nf-core/gawk' include { PSIRC_INDEX } from '../../modules/local/psirc/index' @@ -33,13 +34,18 @@ workflow QUANTIFICATION { ch_gtf.mix(circ_annotation_gtf).map{meta, gtf -> gtf}.collect().map{[[id: "transcriptome"], it]}, ) - TRANSCRIPTOME(COMBINE_TRANSCRIPTOME_GTFS.out.sorted, ch_fasta) + EXCLUDE_OVERLONG_TRANSCRIPTS( + COMBINE_TRANSCRIPTOME_GTFS.out.sorted, [] + ) + + TRANSCRIPTOME(EXCLUDE_OVERLONG_TRANSCRIPTS.out.output, ch_fasta) MARK_CIRCULAR(TRANSCRIPTOME.out.transcriptome, []) ch_versions = ch_versions.mix( COMBINE_TRANSCRIPTOME_GTFS.out.versions, TRANSCRIPTOME.out.versions, - MARK_CIRCULAR.out.versions + MARK_CIRCULAR.out.versions, + EXCLUDE_OVERLONG_TRANSCRIPTS.out.versions ) PSIRC_INDEX(MARK_CIRCULAR.out.output) From 1eea22c3ad3500be4e5f2a76c5b7b3e50708dcfb Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Wed, 1 May 2024 22:48:45 +0200 Subject: [PATCH 220/491] Use only merged circRNAs in further analyses --- bin/counts_combined.py | 12 ++-- bin/merge_tools.py | 5 ++ .../local/annotation/full_annotation/main.nf | 2 +- subworkflows/local/circrna_discovery.nf | 62 ++++++++++--------- 4 files changed, 42 insertions(+), 39 deletions(-) diff --git a/bin/counts_combined.py b/bin/counts_combined.py index 99a9304e..5c326451 100755 --- a/bin/counts_combined.py +++ b/bin/counts_combined.py @@ -11,21 +11,17 @@ args = parser.parse_args() -columns = ['chr', 'start', 'end', 'strand', 'count', 'tools'] +columns = ['chr', 'start', 'end', 'name', 'count', 'strand'] dfs = {os.path.basename(bed).split('.')[0]: pd.read_csv(bed, sep='\t', header=None, - names=columns, - index_col=[0, 1, 2, 3]) - .drop('tools', axis=1) for bed in args.beds} + names=columns) for bed in args.beds} dfs = [df.rename(columns={'count': sample}) for sample, df in dfs.items()] - df = pd.concat(dfs, axis=1) -df = df.fillna(0).astype(int) - df.to_csv(args.out_bed, sep='\t') -df.index = df.index.map(lambda x: f'{x[0]}:{x[1]}-{x[2]}:{x[3]}') +df.index = df['name'] df.index.name = 'ID' +df.drop('name', axis=1, inplace=True) df.to_csv(args.out_tsv, sep='\t') diff --git a/bin/merge_tools.py b/bin/merge_tools.py index fe81353d..32bacab1 100755 --- a/bin/merge_tools.py +++ b/bin/merge_tools.py @@ -21,4 +21,9 @@ 'tool_count': 'sum'}).reset_index() df = df[df['tool_count'] >= args.tool_filter] +df.drop('tool_count', axis=1, inplace=True) +df["name"] = df["chr"] + ":" + df["start"].astype(str) + "-" + df["end"].astype(str) + ":" + df["strand"] + +df = df[['chr', 'start', 'end', 'name', 'count', 'strand']] + df.to_csv(args.output, sep='\t', index=False, header=False) diff --git a/modules/local/annotation/full_annotation/main.nf b/modules/local/annotation/full_annotation/main.nf index 43030ca4..207cd463 100644 --- a/modules/local/annotation/full_annotation/main.nf +++ b/modules/local/annotation/full_annotation/main.nf @@ -1,5 +1,5 @@ process ANNOTATION { - tag "$meta.id" + tag "$meta.id:$meta.tool" label 'process_single' conda "bioconda::pandas=1.5.2" diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 8ac26e69..7eb06ef7 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -201,6 +201,26 @@ workflow CIRCRNA_DISCOVERY { ch_versions = ch_versions.mix(MAPSPLICE_ANNOTATE.out.versions) ch_versions = ch_versions.mix(MAPSPLICE_FILTER.out.versions) + // + // COUNT MATRIX WORKFLOW: + // + + ch_matrix = CIRCEXPLORER2_FLT.out.matrix.mix(SEGEMEHL_FILTER.out.matrix, + CIRCRNA_FINDER_FILTER.out.matrix, + FIND_CIRC_FILTER.out.matrix, + CIRIQUANT_FILTER.out.matrix, + DCC_FILTER.out.matrix, + MAPSPLICE_FILTER.out.matrix) + + tools_selected = params.tool.split(',').collect{it.trim().toLowerCase()} + + MERGE_TOOLS( ch_matrix.map{ meta, bed -> [ [id: meta.id], bed ] }.groupTuple(), + tools_selected.size() > 1 ? tool_filter : 1, duplicates_fun ) + COUNTS_COMBINED( MERGE_TOOLS.out.merged.map{ meta, bed -> bed }.collect() ) + + ch_versions = ch_versions.mix(MERGE_TOOLS.out.versions) + ch_versions = ch_versions.mix(COUNTS_COMBINED.out.versions) + // // ANNOTATION WORKFLOW: // @@ -212,13 +232,18 @@ workflow CIRCRNA_DISCOVERY { FIND_CIRC_FILTER.out.results, CIRIQUANT_FILTER.out.results, DCC_FILTER.out.results, - MAPSPLICE_FILTER.out.results) + MAPSPLICE_FILTER.out.results, + MERGE_TOOLS.out.merged.map{ meta, bed -> [meta + [tool: "merged"], bed] }) INTERSECT_ANNOTATION( circrna_filtered.combine(gtf), [[], []]) ANNOTATION( INTERSECT_ANNOTATION.out.intersect, exon_boundary ) - COMBINE_ANNOTATION_BEDS(ANNOTATION.out.bed.map{ meta, bed -> bed}.collect().map{[[id: "annotation"], it]}) + + ch_annotation_bed_merged = ANNOTATION.out.bed.filter{ meta, bed -> meta.tool == "merged" } + ch_annotation_gtf_merged = ANNOTATION.out.gtf.filter{ meta, gtf -> meta.tool == "merged" } + + COMBINE_ANNOTATION_BEDS(ch_annotation_bed_merged.map{ meta, bed -> bed}.collect().map{[[id: "annotation"], it]}) REMOVE_SCORE_STRAND( COMBINE_ANNOTATION_BEDS.out.sorted, []) - COMBINE_ANNOTATION_GTFS(ANNOTATION.out.gtf.map{ meta, gtf -> gtf}.collect().map{[[id: "annotation"], it]}) + COMBINE_ANNOTATION_GTFS(ch_annotation_gtf_merged.map{ meta, gtf -> gtf}.collect().map{[[id: "annotation"], it]}) ch_versions = ch_versions.mix(INTERSECT_ANNOTATION.out.versions) ch_versions = ch_versions.mix(ANNOTATION.out.versions) @@ -230,40 +255,17 @@ workflow CIRCRNA_DISCOVERY { // FASTA WORKFLOW: // - FASTA( ANNOTATION.out.bed, fasta ) + FASTA( ch_annotation_bed_merged, fasta ) ch_versions = ch_versions.mix(FASTA.out.versions) - // - // COUNT MATRIX WORKFLOW: - // - - ch_matrix = CIRCEXPLORER2_FLT.out.matrix.mix(SEGEMEHL_FILTER.out.matrix, - CIRCRNA_FINDER_FILTER.out.matrix, - FIND_CIRC_FILTER.out.matrix, - CIRIQUANT_FILTER.out.matrix, - DCC_FILTER.out.matrix, - MAPSPLICE_FILTER.out.matrix) - - tools_selected = params.tool.split(',').collect{it.trim().toLowerCase()} - - MERGE_TOOLS( ch_matrix.map{ meta, bed -> [ [id: meta.id], bed ] }.groupTuple(), - tools_selected.size() > 1 ? tool_filter : 1, duplicates_fun ) - - COUNTS_COMBINED( MERGE_TOOLS.out.merged.map{ meta, bed -> bed }.collect() ) - - counts_bed = COUNTS_COMBINED.out.counts_bed - counts_tsv = COUNTS_COMBINED.out.counts_tsv - ch_versions = ch_versions.mix(MERGE_TOOLS.out.versions) - ch_versions = ch_versions.mix(COUNTS_COMBINED.out.versions) - emit: - circrna_bed12 = ANNOTATION.out.bed + circrna_bed12 = ch_annotation_bed_merged fasta = FASTA.out.analysis_fasta annotation_bed = REMOVE_SCORE_STRAND.out.output annotation_gtf = COMBINE_ANNOTATION_GTFS.out.sorted - counts_bed - counts_tsv + counts_bed = COUNTS_COMBINED.out.counts_bed + counts_tsv = COUNTS_COMBINED.out.counts_tsv versions = ch_versions } From 5ebf6b8d55fda41662ca9578952493eda593cc43 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 2 May 2024 18:56:53 +0200 Subject: [PATCH 221/491] Implement upset plots --- modules/local/upset/main.nf | 17 +++++ modules/local/upset/templates/upset.py | 60 +++++++++++++++ subworkflows/local/circrna_discovery.nf | 99 ++++++++++++++----------- 3 files changed, 132 insertions(+), 44 deletions(-) create mode 100644 modules/local/upset/main.nf create mode 100644 modules/local/upset/templates/upset.py diff --git a/modules/local/upset/main.nf b/modules/local/upset/main.nf new file mode 100644 index 00000000..0381e74b --- /dev/null +++ b/modules/local/upset/main.nf @@ -0,0 +1,17 @@ +process UPSET { + tag "$meta.id" + label 'process_single' + + conda "conda-forge::python=3.8.3 conda-forge::numpy=1.20.* conda-forge::pandas=1.2.* conda-forge::upsetplot=0.4.4" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-f42a44964bca5225c7860882e231a7b5488b5485:47ef981087c59f79fdbcab4d9d7316e9ac2e688d-0' : + 'biocontainers/mulled-v2-f42a44964bca5225c7860882e231a7b5488b5485:47ef981087c59f79fdbcab4d9d7316e9ac2e688d-0' }" + input: + tuple val(meta), val(tools), path(beds) + + output: + path "versions.yml", emit: versions + + script: + template "upset.py" +} diff --git a/modules/local/upset/templates/upset.py b/modules/local/upset/templates/upset.py new file mode 100644 index 00000000..778f57aa --- /dev/null +++ b/modules/local/upset/templates/upset.py @@ -0,0 +1,60 @@ +#!/usr/bin/env python3 + +import pandas as pd +import platform +import upsetplot +import matplotlib +import matplotlib.pyplot as plt +import distutils.version + + +def format_yaml_like(data: dict, indent: int = 0) -> str: + """Formats a dictionary to a YAML-like string. + + Args: + data (dict): The dictionary to format. + indent (int): The current indentation level. + + Returns: + str: A string formatted as YAML. + """ + yaml_str = "" + for key, value in data.items(): + spaces = " " * indent + if isinstance(value, dict): + yaml_str += f"{spaces}{key}:\\n{format_yaml_like(value, indent + 1)}" + else: + yaml_str += f"{spaces}{key}: {value}\\n" + return yaml_str + +df_tools = pd.DataFrame( + { + "tool": "${tools.join(' ')}".split(" "), + "file": "${beds.join(' ')}".split(" ") + } +) + +tool_files = df_tools.groupby("tool")["file"].apply(lambda x: set(x)).to_dict() +tool_ids = {} + +for tool, files in tool_files.items(): + df_tool = pd.concat([pd.read_csv(f, sep="\\t", header=None) for f in files]) + tool_ids[tool] = set(df_tool[3].unique()) + +dataset = upsetplot.from_contents(tool_ids) + +upsetplot.plot(dataset, orientation='horizontal') +plt.savefig("${meta.id}.png") + +# Create version file +versions = { + "${task.process}" : { + "python": platform.python_version(), + "pandas": pd.__version__, + "upsetplot": upsetplot.__version__, + "matplotlib": matplotlib.__version__ + } +} + +with open("versions.yml", "w") as f: + f.write(format_yaml_like(versions)) \ No newline at end of file diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 7eb06ef7..8a37b33d 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -1,43 +1,45 @@ -include { ANNOTATION } from '../../modules/local/annotation/full_annotation/main' -include { GNU_SORT as COMBINE_ANNOTATION_BEDS } from '../../modules/nf-core/gnu/sort/main' -include { GNU_SORT as COMBINE_ANNOTATION_GTFS } from '../../modules/nf-core/gnu/sort/main' -include { GAWK as REMOVE_SCORE_STRAND } from '../../modules/nf-core/gawk/main' -include { BEDTOOLS_INTERSECT as INTERSECT_ANNOTATION } from '../../modules/nf-core/bedtools/intersect/main' -include { BOWTIE2_ALIGN as FIND_CIRC_ALIGN } from '../../modules/nf-core/bowtie2/align/main' -include { SAMTOOLS_VIEW } from '../../modules/nf-core/samtools/view/main' -include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main' -include { FIND_CIRC_ANCHORS } from '../../modules/local/find_circ/anchors/main' -include { FIND_CIRC } from '../../modules/local/find_circ/find_circ/main' -include { FIND_CIRC_FILTER } from '../../modules/local/find_circ/filter/main' -include { CIRIQUANT } from '../../modules/local/ciriquant/ciriquant/main' -include { CIRIQUANT_FILTER } from '../../modules/local/ciriquant/filter/main' -include { CIRCRNA_FINDER_FILTER } from '../../modules/local/circrna_finder/filter/main' -include { SEGEMEHL_ALIGN } from '../../modules/nf-core/segemehl/align/main' -include { SEGEMEHL_FILTER } from '../../modules/local/segemehl/filter/main' -include { STAR_ALIGN as STAR_1ST_PASS } from '../../modules/nf-core/star/align/main' -include { STAR_ALIGN as STAR_2ND_PASS } from '../../modules/nf-core/star/align/main' -include { SJDB as STAR_SJDB } from '../../modules/local/star/sjdb/main' -include { STAR_ALIGN as DCC_MATE1_1ST_PASS } from '../../modules/nf-core/star/align/main' -include { STAR_ALIGN as DCC_MATE1_2ND_PASS } from '../../modules/nf-core/star/align/main' -include { SJDB as DCC_MATE1_SJDB } from '../../modules/local/star/sjdb/main' -include { STAR_ALIGN as DCC_MATE2_1ST_PASS } from '../../modules/nf-core/star/align/main' -include { STAR_ALIGN as DCC_MATE2_2ND_PASS } from '../../modules/nf-core/star/align/main' -include { SJDB as DCC_MATE2_SJDB } from '../../modules/local/star/sjdb/main' -include { DCC } from '../../modules/local/dcc/dcc/main' -include { DCC_FILTER } from '../../modules/local/dcc/filter/main' -include { MAPSPLICE_ALIGN } from '../../modules/local/mapsplice/align/main' -include { FASTA } from '../../modules/local/fasta/main' -include { MERGE_TOOLS } from '../../modules/local/count_matrix/merge_tools/main' -include { COUNTS_COMBINED } from '../../modules/local/count_matrix/combined/main' -include { CIRCEXPLORER2_REFERENCE as CIRCEXPLORER2_REF } from '../../modules/local/circexplorer2/reference/main' -include { CIRCEXPLORER2_PARSE as CIRCEXPLORER2_PAR } from '../../modules/nf-core/circexplorer2/parse/main' -include { CIRCEXPLORER2_ANNOTATE as CIRCEXPLORER2_ANN } from '../../modules/nf-core/circexplorer2/annotate/main' -include { CIRCEXPLORER2_FILTER as CIRCEXPLORER2_FLT } from '../../modules/local/circexplorer2/filter/main' -include { CIRCEXPLORER2_REFERENCE as MAPSPLICE_REFERENCE } from '../../modules/local/circexplorer2/reference/main' -include { CIRCEXPLORER2_PARSE as MAPSPLICE_PARSE } from '../../modules/nf-core/circexplorer2/parse/main' -include { CIRCEXPLORER2_ANNOTATE as MAPSPLICE_ANNOTATE } from '../../modules/nf-core/circexplorer2/annotate/main' -include { CIRCEXPLORER2_FILTER as MAPSPLICE_FILTER } from '../../modules/local/circexplorer2/filter/main' +include { ANNOTATION } from '../../modules/local/annotation/full_annotation' +include { GNU_SORT as COMBINE_ANNOTATION_BEDS } from '../../modules/nf-core/gnu/sort' +include { GNU_SORT as COMBINE_ANNOTATION_GTFS } from '../../modules/nf-core/gnu/sort' +include { GAWK as REMOVE_SCORE_STRAND } from '../../modules/nf-core/gawk' +include { BEDTOOLS_INTERSECT as INTERSECT_ANNOTATION } from '../../modules/nf-core/bedtools/intersect' +include { BOWTIE2_ALIGN as FIND_CIRC_ALIGN } from '../../modules/nf-core/bowtie2/align' +include { SAMTOOLS_VIEW } from '../../modules/nf-core/samtools/view' +include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index' +include { FIND_CIRC_ANCHORS } from '../../modules/local/find_circ/anchors' +include { FIND_CIRC } from '../../modules/local/find_circ/find_circ' +include { FIND_CIRC_FILTER } from '../../modules/local/find_circ/filter' +include { CIRIQUANT } from '../../modules/local/ciriquant/ciriquant' +include { CIRIQUANT_FILTER } from '../../modules/local/ciriquant/filter' +include { CIRCRNA_FINDER_FILTER } from '../../modules/local/circrna_finder/filter' +include { SEGEMEHL_ALIGN } from '../../modules/nf-core/segemehl/align' +include { SEGEMEHL_FILTER } from '../../modules/local/segemehl/filter' +include { STAR_ALIGN as STAR_1ST_PASS } from '../../modules/nf-core/star/align' +include { STAR_ALIGN as STAR_2ND_PASS } from '../../modules/nf-core/star/align' +include { SJDB as STAR_SJDB } from '../../modules/local/star/sjdb' +include { STAR_ALIGN as DCC_MATE1_1ST_PASS } from '../../modules/nf-core/star/align' +include { STAR_ALIGN as DCC_MATE1_2ND_PASS } from '../../modules/nf-core/star/align' +include { SJDB as DCC_MATE1_SJDB } from '../../modules/local/star/sjdb' +include { STAR_ALIGN as DCC_MATE2_1ST_PASS } from '../../modules/nf-core/star/align' +include { STAR_ALIGN as DCC_MATE2_2ND_PASS } from '../../modules/nf-core/star/align' +include { SJDB as DCC_MATE2_SJDB } from '../../modules/local/star/sjdb' +include { DCC } from '../../modules/local/dcc/dcc' +include { DCC_FILTER } from '../../modules/local/dcc/filter' +include { MAPSPLICE_ALIGN } from '../../modules/local/mapsplice/align' +include { FASTA } from '../../modules/local/fasta' +include { MERGE_TOOLS } from '../../modules/local/count_matrix/merge_tools' +include { COUNTS_COMBINED } from '../../modules/local/count_matrix/combined' +include { CIRCEXPLORER2_REFERENCE as CIRCEXPLORER2_REF } from '../../modules/local/circexplorer2/reference' +include { CIRCEXPLORER2_PARSE as CIRCEXPLORER2_PAR } from '../../modules/nf-core/circexplorer2/parse' +include { CIRCEXPLORER2_ANNOTATE as CIRCEXPLORER2_ANN } from '../../modules/nf-core/circexplorer2/annotate' +include { CIRCEXPLORER2_FILTER as CIRCEXPLORER2_FLT } from '../../modules/local/circexplorer2/filter' +include { CIRCEXPLORER2_REFERENCE as MAPSPLICE_REFERENCE } from '../../modules/local/circexplorer2/reference' +include { CIRCEXPLORER2_PARSE as MAPSPLICE_PARSE } from '../../modules/nf-core/circexplorer2/parse' +include { CIRCEXPLORER2_ANNOTATE as MAPSPLICE_ANNOTATE } from '../../modules/nf-core/circexplorer2/annotate' +include { CIRCEXPLORER2_FILTER as MAPSPLICE_FILTER } from '../../modules/local/circexplorer2/filter' +include { UPSET as UPSET_SAMPLES } from '../../modules/local/upset' +include { UPSET as UPSET_ALL } from '../../modules/local/upset' workflow CIRCRNA_DISCOVERY { @@ -227,15 +229,24 @@ workflow CIRCRNA_DISCOVERY { ch_biotypes = Channel.fromPath("${projectDir}/bin/unwanted_biotypes.txt") - circrna_filtered = CIRCEXPLORER2_FLT.out.results.mix(SEGEMEHL_FILTER.out.results, + circrna_tools = CIRCEXPLORER2_FLT.out.results.mix(SEGEMEHL_FILTER.out.results, CIRCRNA_FINDER_FILTER.out.results, FIND_CIRC_FILTER.out.results, CIRIQUANT_FILTER.out.results, DCC_FILTER.out.results, - MAPSPLICE_FILTER.out.results, - MERGE_TOOLS.out.merged.map{ meta, bed -> [meta + [tool: "merged"], bed] }) - - INTERSECT_ANNOTATION( circrna_filtered.combine(gtf), [[], []]) + MAPSPLICE_FILTER.out.results) + + UPSET_SAMPLES( circrna_tools.map{ meta, bed -> [meta.id, meta.tool, bed]} + .groupTuple() + .map{ sample, tools, beds -> [[id: sample], tools, beds]} ) + UPSET_ALL( circrna_tools.map{ meta, bed -> ["all", meta.tool, bed] } + .groupTuple() + .map{ sample, tools, beds -> [[id: sample], tools, beds]} ) + + circrna_incl_merged = circrna_tools.mix( + MERGE_TOOLS.out.merged.map{ meta, bed -> [meta + [tool: "merged"], bed] }) + + INTERSECT_ANNOTATION( circrna_incl_merged.combine(gtf), [[], []]) ANNOTATION( INTERSECT_ANNOTATION.out.intersect, exon_boundary ) ch_annotation_bed_merged = ANNOTATION.out.bed.filter{ meta, bed -> meta.tool == "merged" } From a9bd254bc673562070283c8d4bfa2478752c9281 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 2 May 2024 19:01:47 +0200 Subject: [PATCH 222/491] Refine upset functionality --- modules/local/upset/main.nf | 3 ++- modules/local/upset/templates/upset.py | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/modules/local/upset/main.nf b/modules/local/upset/main.nf index 0381e74b..75fed9ad 100644 --- a/modules/local/upset/main.nf +++ b/modules/local/upset/main.nf @@ -10,7 +10,8 @@ process UPSET { tuple val(meta), val(tools), path(beds) output: - path "versions.yml", emit: versions + tuple val(meta), path("*.png"), emit: plot + path "versions.yml" , emit: versions script: template "upset.py" diff --git a/modules/local/upset/templates/upset.py b/modules/local/upset/templates/upset.py index 778f57aa..050900d1 100644 --- a/modules/local/upset/templates/upset.py +++ b/modules/local/upset/templates/upset.py @@ -43,7 +43,7 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: dataset = upsetplot.from_contents(tool_ids) -upsetplot.plot(dataset, orientation='horizontal') +upsetplot.plot(dataset, orientation='horizontal', show_counts=True) plt.savefig("${meta.id}.png") # Create version file From d5f511ce2f20cc87480ba1cf7bd82015146d822f Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 2 May 2024 21:06:39 +0200 Subject: [PATCH 223/491] Add upset plots to multiqc --- modules/local/upset/main.nf | 1 + modules/local/upset/templates/upset.py | 23 +++++++++++++++++++++-- subworkflows/local/circrna_discovery.nf | 5 +++++ workflows/circrna/main.nf | 1 + 4 files changed, 28 insertions(+), 2 deletions(-) diff --git a/modules/local/upset/main.nf b/modules/local/upset/main.nf index 75fed9ad..e8ab89d1 100644 --- a/modules/local/upset/main.nf +++ b/modules/local/upset/main.nf @@ -11,6 +11,7 @@ process UPSET { output: tuple val(meta), path("*.png"), emit: plot + path "*.upset_mqc.json" , emit: multiqc path "versions.yml" , emit: versions script: diff --git a/modules/local/upset/templates/upset.py b/modules/local/upset/templates/upset.py index 050900d1..ff4a78da 100644 --- a/modules/local/upset/templates/upset.py +++ b/modules/local/upset/templates/upset.py @@ -6,7 +6,8 @@ import matplotlib import matplotlib.pyplot as plt import distutils.version - +import base64 +import json def format_yaml_like(data: dict, indent: int = 0) -> str: """Formats a dictionary to a YAML-like string. @@ -44,7 +45,25 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: dataset = upsetplot.from_contents(tool_ids) upsetplot.plot(dataset, orientation='horizontal', show_counts=True) -plt.savefig("${meta.id}.png") +plot_file = "${meta.id}.upset.png" +plt.savefig(plot_file) + +image_string = base64.b64encode(open(plot_file, "rb").read()).decode("utf-8") +image_html = f'
    ' + +multiqc = { + 'id': "${meta.id}_upset", + 'parent_id': "upset_plots", + 'parent_name': 'UpSet Plots', + 'parent_description': 'UpSet plots showing the overlap between tools for each sample', + 'section_name': 'UpSet: ${meta.id}', + 'description': 'UpSet plot showing the overlap between tools for sample ${meta.id}', + 'plot_type': 'image', + 'data': image_html +} + +with open("${meta.id}.upset_mqc.json", "w") as f: + f.write(json.dumps(multiqc, indent=4)) # Create version file versions = { diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 8a37b33d..f706161f 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -61,6 +61,7 @@ workflow CIRCRNA_DISCOVERY { main: ch_versions = Channel.empty() + ch_multiqc_files = Channel.empty() fasta = ch_fasta.map{meta, fasta -> fasta} gtf = ch_gtf.map{meta, gtf -> gtf} @@ -242,6 +243,9 @@ workflow CIRCRNA_DISCOVERY { UPSET_ALL( circrna_tools.map{ meta, bed -> ["all", meta.tool, bed] } .groupTuple() .map{ sample, tools, beds -> [[id: sample], tools, beds]} ) + + ch_multiqc_files = ch_multiqc_files.mix(UPSET_SAMPLES.out.multiqc) + ch_multiqc_files = ch_multiqc_files.mix(UPSET_ALL.out.multiqc) circrna_incl_merged = circrna_tools.mix( MERGE_TOOLS.out.merged.map{ meta, bed -> [meta + [tool: "merged"], bed] }) @@ -278,5 +282,6 @@ workflow CIRCRNA_DISCOVERY { counts_bed = COUNTS_COMBINED.out.counts_bed counts_tsv = COUNTS_COMBINED.out.counts_tsv + multiqc_files = ch_multiqc_files versions = ch_versions } diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index b8bfa62d..1b0f89cd 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -151,6 +151,7 @@ workflow CIRCRNA { params.exon_boundary ) + ch_multiqc_files = ch_multiqc_files.mix(CIRCRNA_DISCOVERY.out.multiqc_files) ch_versions = ch_versions.mix(CIRCRNA_DISCOVERY.out.versions) // From 8095b809542fe4e91b2900ca4276e88be9ffa6b1 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 2 May 2024 21:18:46 +0200 Subject: [PATCH 224/491] Fix linting --- modules/local/upset/templates/upset.py | 2 +- subworkflows/local/circrna_discovery.nf | 6 ++++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/modules/local/upset/templates/upset.py b/modules/local/upset/templates/upset.py index ff4a78da..ed70890b 100644 --- a/modules/local/upset/templates/upset.py +++ b/modules/local/upset/templates/upset.py @@ -76,4 +76,4 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: } with open("versions.yml", "w") as f: - f.write(format_yaml_like(versions)) \ No newline at end of file + f.write(format_yaml_like(versions)) diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index f706161f..35e2fe72 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -236,7 +236,7 @@ workflow CIRCRNA_DISCOVERY { CIRIQUANT_FILTER.out.results, DCC_FILTER.out.results, MAPSPLICE_FILTER.out.results) - + UPSET_SAMPLES( circrna_tools.map{ meta, bed -> [meta.id, meta.tool, bed]} .groupTuple() .map{ sample, tools, beds -> [[id: sample], tools, beds]} ) @@ -246,7 +246,9 @@ workflow CIRCRNA_DISCOVERY { ch_multiqc_files = ch_multiqc_files.mix(UPSET_SAMPLES.out.multiqc) ch_multiqc_files = ch_multiqc_files.mix(UPSET_ALL.out.multiqc) - + ch_versions = ch_versions.mix(UPSET_SAMPLES.out.versions) + ch_versions = ch_versions.mix(UPSET_ALL.out.versions) + circrna_incl_merged = circrna_tools.mix( MERGE_TOOLS.out.merged.map{ meta, bed -> [meta + [tool: "merged"], bed] }) From 020c8eaa1f06e41db05ea43bbb91c3c4b67cff79 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 2 May 2024 22:11:32 +0200 Subject: [PATCH 225/491] Fix pandas bug --- modules/local/upset/templates/upset.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/upset/templates/upset.py b/modules/local/upset/templates/upset.py index ed70890b..f0378bf8 100644 --- a/modules/local/upset/templates/upset.py +++ b/modules/local/upset/templates/upset.py @@ -35,7 +35,7 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: } ) -tool_files = df_tools.groupby("tool")["file"].apply(lambda x: set(x)).to_dict() +tool_files = df_tools.groupby("tool").agg(lambda x: x.tolist())["file"].to_dict() tool_ids = {} for tool, files in tool_files.items(): From d99821cffa322096998f3d549e71e0937183a037 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 2 May 2024 22:33:35 +0200 Subject: [PATCH 226/491] Disable upset plots if only one tool is enabled --- conf/modules.config | 8 ++++++++ modules/local/upset/main.nf | 3 +++ 2 files changed, 11 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index cfb38ae1..68535f27 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -562,6 +562,14 @@ if (!params.skip_trimming) { ] } + withName: UPSET_SAMPLES { + ext.when = { params.tool.split(',').length > 1 } + } + + withName: UPSET_ALL { + ext.when = { params.tool.split(',').length > 1 } + } + withName: INTERSECT_ANNOTATION { ext.args = "-loj" ext.suffix = "intersect.bed" diff --git a/modules/local/upset/main.nf b/modules/local/upset/main.nf index e8ab89d1..1ff4bf6f 100644 --- a/modules/local/upset/main.nf +++ b/modules/local/upset/main.nf @@ -9,6 +9,9 @@ process UPSET { input: tuple val(meta), val(tools), path(beds) + when: + task.ext.when == null || task.ext.when + output: tuple val(meta), path("*.png"), emit: plot path "*.upset_mqc.json" , emit: multiqc From bf06573eeeccd8302ac7c3ce9404fea3f45f472c Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 6 May 2024 12:17:32 +0200 Subject: [PATCH 227/491] Add annotation as rowdata to summarizedExperiment --- .../local/quantification/merge_experiments/environment.yml | 2 +- modules/local/quantification/merge_experiments/main.nf | 5 +++-- .../merge_experiments/templates/merge_experiments.r | 5 +++++ modules/local/upset/main.nf | 2 +- subworkflows/local/quantification.nf | 3 ++- 5 files changed, 12 insertions(+), 5 deletions(-) diff --git a/modules/local/quantification/merge_experiments/environment.yml b/modules/local/quantification/merge_experiments/environment.yml index 381dba4d..cfc21aba 100644 --- a/modules/local/quantification/merge_experiments/environment.yml +++ b/modules/local/quantification/merge_experiments/environment.yml @@ -6,4 +6,4 @@ channels: - bioconda - defaults dependencies: - - "bioconda::bioconductor-summarizedexperiment=1.32.0" + - "bioconda::bioconductor-rtracklayer==1.62.0--r43ha9d7317_0" diff --git a/modules/local/quantification/merge_experiments/main.nf b/modules/local/quantification/merge_experiments/main.nf index 367a3082..3b422b75 100644 --- a/modules/local/quantification/merge_experiments/main.nf +++ b/modules/local/quantification/merge_experiments/main.nf @@ -4,12 +4,13 @@ process MERGE_EXPERIMENTS { conda "${moduleDir}/environment.yaml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-summarizedexperiment:1.32.0--r43hdfd78af_0' : - 'biocontainers/bioconductor-summarizedexperiment:1.32.0--r43hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-rtracklayer:1.62.0--r43ha9d7317_0' : + 'biocontainers/bioconductor-rtracklayer:1.62.0--r43ha9d7317_0' }" input: tuple val(meta), path(experiments) tuple val(meta2), path(phenotype) + tuple val(meta3), path(gtf) output: tuple val(meta), path("${meta.id}.merged.rds"), emit: merged diff --git a/modules/local/quantification/merge_experiments/templates/merge_experiments.r b/modules/local/quantification/merge_experiments/templates/merge_experiments.r index 51b5b666..5dd2bfb2 100644 --- a/modules/local/quantification/merge_experiments/templates/merge_experiments.r +++ b/modules/local/quantification/merge_experiments/templates/merge_experiments.r @@ -6,6 +6,7 @@ paths <- c('${experiments.join("\', \'")}') experiments <- lapply(paths, readRDS) phenotype <- read.csv('${phenotype}', stringsAsFactors = FALSE) +annotation <- rtracklayer::import('${gtf}') se_assays <- list() @@ -37,6 +38,10 @@ for (col in colnames(colData(se))) { } } +# Add transcript annotation +annotation <- annotation[match(rownames(se), annotation\$transcript_id),] +rowData(se) <- annotation + saveRDS(se, '${meta.id}.merged.rds') writeLines( diff --git a/modules/local/upset/main.nf b/modules/local/upset/main.nf index 1ff4bf6f..08babf76 100644 --- a/modules/local/upset/main.nf +++ b/modules/local/upset/main.nf @@ -14,7 +14,7 @@ process UPSET { output: tuple val(meta), path("*.png"), emit: plot - path "*.upset_mqc.json" , emit: multiqc + path "*.upset_mqc.json" , emit: multiqc path "versions.yml" , emit: versions script: diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index b1c0d576..403140ce 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -66,7 +66,8 @@ workflow QUANTIFICATION { MERGE_EXPERIMENTS( TXIMETA_TXIMETA.out.se.map{meta, se -> se}.collect().map{[[id: "experiments"], it]}, - ch_phenotype + ch_phenotype, + EXCLUDE_OVERLONG_TRANSCRIPTS.out.output ) TXIMETA_TXIMPORT( From 15bd62c5ea248972782a7f5995a153f838f7ec0d Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 10 May 2024 14:18:50 +0200 Subject: [PATCH 228/491] Prepare for TPM addition --- subworkflows/local/quantification.nf | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index 403140ce..df65579a 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -64,12 +64,6 @@ workflow QUANTIFICATION { "kallisto" ) - MERGE_EXPERIMENTS( - TXIMETA_TXIMETA.out.se.map{meta, se -> se}.collect().map{[[id: "experiments"], it]}, - ch_phenotype, - EXCLUDE_OVERLONG_TRANSCRIPTS.out.output - ) - TXIMETA_TXIMPORT( PSIRC_QUANT.out.directory, CUSTOM_TX2GENE.out.tx2gene, @@ -81,8 +75,7 @@ workflow QUANTIFICATION { PSIRC_QUANT.out.versions, CUSTOM_TX2GENE.out.versions, TXIMETA_TXIMETA.out.versions, - TXIMETA_TXIMPORT.out.versions, - MERGE_EXPERIMENTS.out.versions + TXIMETA_TXIMPORT.out.versions ) JOIN_GENE_COUNTS( @@ -109,13 +102,21 @@ workflow QUANTIFICATION { JOIN_TX_TPM.out.csv ) + + MERGE_EXPERIMENTS( + TXIMETA_TXIMETA.out.se.map{meta, se -> se}.collect().map{[[id: "experiments"], it]}, + ch_phenotype, + EXCLUDE_OVERLONG_TRANSCRIPTS.out.output + ) + ch_versions = ch_versions.mix( JOIN_GENE_COUNTS.out.versions, JOIN_GENE_TPM.out.versions, JOIN_TX_COUNTS.out.versions, JOIN_TX_TPM.out.versions, SPLIT_TYPES_COUNTS.out.versions, - SPLIT_TYPES_TPM.out.versions + SPLIT_TYPES_TPM.out.versions, + MERGE_EXPERIMENTS.out.versions ) emit: From dbc4042750510c4394d17162c9aa57e4a669e053 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 10 May 2024 17:46:10 +0200 Subject: [PATCH 229/491] Fix DeSeq compatibility problems --- bin/DEA.R | 2 +- bin/counts_combined.py | 8 +++++--- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/bin/DEA.R b/bin/DEA.R index b40dbfa7..ea5960b7 100755 --- a/bin/DEA.R +++ b/bin/DEA.R @@ -283,7 +283,7 @@ DESeq2 <- function(inputdata, data_type){ rm(tmp) dds <- DESeqDataSetFromMatrix( - countData=inputdata$circ, + countData=round(inputdata$circ), colData=inputdata$pheno, design = inputdata$design) diff --git a/bin/counts_combined.py b/bin/counts_combined.py index 5c326451..f50fe3db 100755 --- a/bin/counts_combined.py +++ b/bin/counts_combined.py @@ -15,13 +15,15 @@ dfs = {os.path.basename(bed).split('.')[0]: pd.read_csv(bed, sep='\t', header=None, + index_col=["chr", "start", "end", "strand"], + usecols=["chr", "start", "end", "strand", "count"], names=columns) for bed in args.beds} dfs = [df.rename(columns={'count': sample}) for sample, df in dfs.items()] df = pd.concat(dfs, axis=1) -df.to_csv(args.out_bed, sep='\t') +df = df.fillna(0) +df.to_csv(args.out_bed, sep='\t', header=True, index=True) -df.index = df['name'] +df.index = df.index.map(lambda x: f'{x[0]}:{x[1]}-{x[2]}:{x[3]}') df.index.name = 'ID' -df.drop('name', axis=1, inplace=True) df.to_csv(args.out_tsv, sep='\t') From 86af7b2abe18e63d6efbac38c88b1d87e76c1428 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 10 May 2024 18:45:25 +0200 Subject: [PATCH 230/491] Add TPM the quantification RDS --- modules/local/quantification/merge_experiments/main.nf | 3 ++- .../merge_experiments/templates/merge_experiments.r | 4 ++++ subworkflows/local/quantification.nf | 3 ++- 3 files changed, 8 insertions(+), 2 deletions(-) diff --git a/modules/local/quantification/merge_experiments/main.nf b/modules/local/quantification/merge_experiments/main.nf index 3b422b75..9e14df7e 100644 --- a/modules/local/quantification/merge_experiments/main.nf +++ b/modules/local/quantification/merge_experiments/main.nf @@ -8,9 +8,10 @@ process MERGE_EXPERIMENTS { 'biocontainers/bioconductor-rtracklayer:1.62.0--r43ha9d7317_0' }" input: - tuple val(meta), path(experiments) + tuple val(meta), path(experiments) tuple val(meta2), path(phenotype) tuple val(meta3), path(gtf) + tuple val(meta4), path(tpm) output: tuple val(meta), path("${meta.id}.merged.rds"), emit: merged diff --git a/modules/local/quantification/merge_experiments/templates/merge_experiments.r b/modules/local/quantification/merge_experiments/templates/merge_experiments.r index 5dd2bfb2..a166190b 100644 --- a/modules/local/quantification/merge_experiments/templates/merge_experiments.r +++ b/modules/local/quantification/merge_experiments/templates/merge_experiments.r @@ -7,6 +7,7 @@ experiments <- lapply(paths, readRDS) phenotype <- read.csv('${phenotype}', stringsAsFactors = FALSE) annotation <- rtracklayer::import('${gtf}') +tpm <- read.table('${tpm}', header=TRUE, row.names=1)[, -1] se_assays <- list() @@ -42,6 +43,9 @@ for (col in colnames(colData(se))) { annotation <- annotation[match(rownames(se), annotation\$transcript_id),] rowData(se) <- annotation +# Add TPM +assay(se, "tpm", withDimnames = FALSE) <- tpm[rownames(se), colData(se)\$names] + saveRDS(se, '${meta.id}.merged.rds') writeLines( diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index df65579a..ee9ad8be 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -106,7 +106,8 @@ workflow QUANTIFICATION { MERGE_EXPERIMENTS( TXIMETA_TXIMETA.out.se.map{meta, se -> se}.collect().map{[[id: "experiments"], it]}, ch_phenotype, - EXCLUDE_OVERLONG_TRANSCRIPTS.out.output + EXCLUDE_OVERLONG_TRANSCRIPTS.out.output, + JOIN_TX_TPM.out.csv ) ch_versions = ch_versions.mix( From 6cdc67feb88413349d85e77bcaf52be2b9a09c88 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Wed, 22 May 2024 07:35:05 +0200 Subject: [PATCH 231/491] Fix GTF attribute splitting --- bin/annotation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/annotation.py b/bin/annotation.py index 17001e36..877ed877 100755 --- a/bin/annotation.py +++ b/bin/annotation.py @@ -43,7 +43,7 @@ df_intergenic['transcript_id'] = 'intergenic_' + df_intergenic['name'] # Convert attributes to a dictionary -df['attributes'] = df['attributes'].apply(lambda row: dict([[value.strip(r'"') for value in entry.strip().split(' ')] for entry in row.split(';') if entry])) +df['attributes'] = df['attributes'].apply(lambda row: dict([[value.strip(r'"') for value in entry.strip().split(' ', 1)] for entry in row.split(';') if entry])) # Keep only the attributes we want df['attributes'] = df['attributes'].apply(lambda row: {key: row[key] for key in attributes if key in row}) # Convert attributes to columns From e273f70e30a6654ec46058b13efabf40e7438d14 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Wed, 22 May 2024 09:15:38 +0200 Subject: [PATCH 232/491] Simplify FASTA extraction --- bin/backsplice_gen.sh | 37 --------------------- conf/modules.config | 7 ++-- modules/local/fasta/main.nf | 44 ------------------------- subworkflows/local/circrna_discovery.nf | 11 ++++--- 4 files changed, 11 insertions(+), 88 deletions(-) delete mode 100755 bin/backsplice_gen.sh delete mode 100644 modules/local/fasta/main.nf diff --git a/bin/backsplice_gen.sh b/bin/backsplice_gen.sh deleted file mode 100755 index 3134046b..00000000 --- a/bin/backsplice_gen.sh +++ /dev/null @@ -1,37 +0,0 @@ -#!/usr/bin/env bash - -## Shell script to generate backsplice sequence from circRNA sequence. -## Author: Barry Digby -## License: MIT - -## .fa = backsplice .fasta = canonical to publish - -file_prefix=$(basename $1 .fa) - -# Split multi-fasta file into single records -mkdir canonical_seqs && mv $1 canonical_seqs/ -ls -d canonical_seqs/*.fa | while read -r line; do -cat $line | awk '{if (substr($0, 1, 1)==">") {filename=(substr($0,2) ".fa")} print $0 > filename}' -done - -# add backsplice site to individual fasta files -for file in *.fa; do - fn=$(basename $file .fa) - cat $file | grep ">" > header.txt - cat $file | grep -v ">" | cut -c1-20 > 20bp.txt - cat $file | grep -v ">" > seqs.txt - paste seqs.txt 20bp.txt | sed -e 's/\t//' > seqs_20bp.txt - paste header.txt seqs_20bp.txt | sed -e 's/\t/\n/' > ${fn}.fasta - rm header.txt 20bp.txt seqs.txt seqs_20bp.txt -done - -# rm single fasta entries from while read line -rm *.fa -# merge backsplice fastas into one for miRNA pred -cat *.fasta > ${file_prefix}.fa -# remove intermediate for loop fasta file -rm *.fasta -# move canonical seqs back to publish to outdir -ls -d canonical_seqs/*.fa | while read -r line; do -mv $line ${file_prefix}.fasta -done diff --git a/conf/modules.config b/conf/modules.config index 68535f27..7cf1f74c 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -590,13 +590,14 @@ if (!params.skip_trimming) { ext.suffix = "tidy.bed" } - withName: FASTA { - ext.when = { params.module.split(',').contains('circrna_discovery') } + withName: ADD_BACKSPLICE { + ext.args = "'{ if (/^>/) { print \$0 } else { start = substr(\$0, 1, 25); print \$0 start } }'" + ext.suffix = "backspliced.fa" publishDir = [ path: { "${params.outdir}/circrna_discovery/${meta.tool}/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - pattern: "*.fasta" + pattern: "*.backspliced.fa" ] } diff --git a/modules/local/fasta/main.nf b/modules/local/fasta/main.nf deleted file mode 100644 index d17b17d7..00000000 --- a/modules/local/fasta/main.nf +++ /dev/null @@ -1,44 +0,0 @@ -process FASTA { - tag "${meta.id}:${meta.tool}" - label 'process_single' - - conda "bioconda::bedtools=2.30.0" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h7d7f7ad_2': - 'biocontainers/bedtools:2.30.0--h7d7f7ad_2' }" - - input: - tuple val(meta), path(bed) - path(fasta, stageAs: 'fasta.input') // TODO: Remove input renaming, currently necessary to prevent problems with the backsplice_gen.sh script - - output: - tuple val(meta), path("${prefix}.fa"), emit: analysis_fasta - path("${prefix}.fasta") , emit: publish_fasta - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" - """ - ## FASTA sequences (bedtools does not like the extra annotation info - split will not work properly) - cut -d\$'\\t' -f1-12 $bed > bed12.tmp - bedtools getfasta -fi $fasta -bed bed12.tmp -s -split -name > circ_seq.tmp - - ## clean fasta header - grep -A 1 '>' circ_seq.tmp | cut -d: -f1,2,3 > ${prefix}.fa && rm circ_seq.tmp - - ## add backsplice sequence for miRanda Targetscan, publish canonical FASTA to results. - backsplice_gen.sh ${prefix}.fa - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") - cut: \$(cut --version | head -n 1 | cut -d' ' -f4) - END_VERSIONS - """ -} - - diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 35e2fe72..c162f8f8 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -27,7 +27,6 @@ include { SJDB as DCC_MATE2_SJDB } from '../../modules/l include { DCC } from '../../modules/local/dcc/dcc' include { DCC_FILTER } from '../../modules/local/dcc/filter' include { MAPSPLICE_ALIGN } from '../../modules/local/mapsplice/align' -include { FASTA } from '../../modules/local/fasta' include { MERGE_TOOLS } from '../../modules/local/count_matrix/merge_tools' include { COUNTS_COMBINED } from '../../modules/local/count_matrix/combined' include { CIRCEXPLORER2_REFERENCE as CIRCEXPLORER2_REF } from '../../modules/local/circexplorer2/reference' @@ -40,6 +39,8 @@ include { CIRCEXPLORER2_ANNOTATE as MAPSPLICE_ANNOTATE } from '../../modules/n include { CIRCEXPLORER2_FILTER as MAPSPLICE_FILTER } from '../../modules/local/circexplorer2/filter' include { UPSET as UPSET_SAMPLES } from '../../modules/local/upset' include { UPSET as UPSET_ALL } from '../../modules/local/upset' +include { BEDTOOLS_GETFASTA } from '../../modules/nf-core/bedtools/getfasta' +include { GAWK as ADD_BACKSPLICE } from '../../modules/nf-core/gawk' workflow CIRCRNA_DISCOVERY { @@ -272,13 +273,15 @@ workflow CIRCRNA_DISCOVERY { // FASTA WORKFLOW: // - FASTA( ch_annotation_bed_merged, fasta ) + BEDTOOLS_GETFASTA( ch_annotation_bed_merged, fasta ) + ADD_BACKSPLICE( BEDTOOLS_GETFASTA.out.fasta, []) - ch_versions = ch_versions.mix(FASTA.out.versions) + ch_versions = ch_versions.mix(BEDTOOLS_GETFASTA.out.versions) + ch_versions = ch_versions.mix(ADD_BACKSPLICE.out.versions) emit: circrna_bed12 = ch_annotation_bed_merged - fasta = FASTA.out.analysis_fasta + fasta = ADD_BACKSPLICE.out.output annotation_bed = REMOVE_SCORE_STRAND.out.output annotation_gtf = COMBINE_ANNOTATION_GTFS.out.sorted counts_bed = COUNTS_COMBINED.out.counts_bed From 1bb983b2b80d80779ad5aad61a7d4cb57e60c95b Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 08:21:50 +0200 Subject: [PATCH 233/491] Simplify STAR and SEGEMEHL discovery --- conf/modules.config | 15 +++---- subworkflows/local/circrna_discovery.nf | 55 +++++++++-------------- subworkflows/local/discovery/segemehl.nf | 29 ++++++++++++ subworkflows/local/discovery/star2pass.nf | 34 ++++++++++++++ subworkflows/local/prepare_genome.nf | 5 --- workflows/circrna/main.nf | 2 - 6 files changed, 89 insertions(+), 51 deletions(-) create mode 100644 subworkflows/local/discovery/segemehl.nf create mode 100644 subworkflows/local/discovery/star2pass.nf diff --git a/conf/modules.config b/conf/modules.config index 7cf1f74c..b13926e9 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -143,7 +143,7 @@ if (!params.skip_trimming) { ] } - withName: SEGEMEHL_INDEX { + withName: '.*:SEGEMEHL:INDEX' { ext.when = { !params.segemehl && params.tool.split(',').contains('segemehl') && params.module.split(',').contains('circrna_discovery') } publishDir = [ path: { "${params.outdir}/references/index/segemehl" }, @@ -155,7 +155,7 @@ if (!params.skip_trimming) { // circRNA - withName: SEGEMEHL_ALIGN { + withName: '.*:SEGEMEHL:ALIGN' { ext.when = { params.tool.split(',').contains('segemehl') && params.module.split(',').contains('circrna_discovery') } ext.args = [ "", "-b", @@ -169,8 +169,7 @@ if (!params.skip_trimming) { ] } - withName: SEGEMEHL_FILTER { - ext.when = { params.tool.split(',').contains('segemehl') && params.module.split(',').contains('circrna_discovery') } + withName: '.*:SEGEMEHL:FILTER' { publishDir = [ path: { "${params.outdir}/circrna_discovery/segemehl/intermediates/${meta.id}" }, mode: params.publish_dir_mode, @@ -180,7 +179,7 @@ if (!params.skip_trimming) { ] } - withName: STAR_1ST_PASS { + withName: '.*:STAR2PASS:PASS_1' { ext.when = { params.module.split(',').contains('circrna_discovery') && ( params.tool.split(',').contains('circexplorer2') || params.tool.split(',').contains('circrna_finder') ) } ext.args = [ "", "--chimOutType Junctions WithinBAM", @@ -201,8 +200,7 @@ if (!params.skip_trimming) { ] } - withName: STAR_SJDB { - ext.when = { params.module.split(',').contains('circrna_discovery') && ( params.tool.split(',').contains('circexplorer2') || params.tool.split(',').contains('circrna_finder') ) } + withName: '.*:STAR2PASS:SJDB' { publishDir = [ path: { "${params.outdir}/circrna_discovery/star/sjdb" }, mode: params.publish_dir_mode, @@ -211,8 +209,7 @@ if (!params.skip_trimming) { ] } - withName: STAR_2ND_PASS { - ext.when = { params.module.split(',').contains('circrna_discovery') && ( params.tool.split(',').contains('circexplorer2') || params.tool.split(',').contains('circrna_finder') ) } + withName: '.*:STAR2PASS:PASS_2' { ext.args = [ "", params.tool.split(',').contains('circrna_finder') ? "--chimOutType Junctions SeparateSAMold" : "--chimOutType Junctions WithinBAM", "--outSAMunmapped Within", diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index c162f8f8..f0688cc0 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -1,4 +1,4 @@ - +// MODULES include { ANNOTATION } from '../../modules/local/annotation/full_annotation' include { GNU_SORT as COMBINE_ANNOTATION_BEDS } from '../../modules/nf-core/gnu/sort' include { GNU_SORT as COMBINE_ANNOTATION_GTFS } from '../../modules/nf-core/gnu/sort' @@ -13,11 +13,6 @@ include { FIND_CIRC_FILTER } from '../../modules/l include { CIRIQUANT } from '../../modules/local/ciriquant/ciriquant' include { CIRIQUANT_FILTER } from '../../modules/local/ciriquant/filter' include { CIRCRNA_FINDER_FILTER } from '../../modules/local/circrna_finder/filter' -include { SEGEMEHL_ALIGN } from '../../modules/nf-core/segemehl/align' -include { SEGEMEHL_FILTER } from '../../modules/local/segemehl/filter' -include { STAR_ALIGN as STAR_1ST_PASS } from '../../modules/nf-core/star/align' -include { STAR_ALIGN as STAR_2ND_PASS } from '../../modules/nf-core/star/align' -include { SJDB as STAR_SJDB } from '../../modules/local/star/sjdb' include { STAR_ALIGN as DCC_MATE1_1ST_PASS } from '../../modules/nf-core/star/align' include { STAR_ALIGN as DCC_MATE1_2ND_PASS } from '../../modules/nf-core/star/align' include { SJDB as DCC_MATE1_SJDB } from '../../modules/local/star/sjdb' @@ -42,6 +37,10 @@ include { UPSET as UPSET_ALL } from '../../modules/l include { BEDTOOLS_GETFASTA } from '../../modules/nf-core/bedtools/getfasta' include { GAWK as ADD_BACKSPLICE } from '../../modules/nf-core/gawk' +// SUBWORKFLOWS +include { SEGEMEHL } from './discovery/segemehl' +include { STAR2PASS } from './discovery/star2pass' + workflow CIRCRNA_DISCOVERY { take: @@ -53,7 +52,6 @@ workflow CIRCRNA_DISCOVERY { bwa_index chromosomes hisat2_index - segemehl_index star_index bsj_reads tool_filter @@ -66,40 +64,27 @@ workflow CIRCRNA_DISCOVERY { fasta = ch_fasta.map{meta, fasta -> fasta} gtf = ch_gtf.map{meta, gtf -> gtf} - // - // SEGEMEHL WORKFLOW: - // - SEGEMEHL_ALIGN( reads, fasta, segemehl_index ) - segemehl_filter = SEGEMEHL_ALIGN.out.results.map{ meta, results -> [ meta + [tool: "segemehl"], results ] } - SEGEMEHL_FILTER( segemehl_filter, bsj_reads ) - - ch_versions = ch_versions.mix(SEGEMEHL_ALIGN.out.versions) - ch_versions = ch_versions.mix(SEGEMEHL_FILTER.out.versions) + // STAR CONSTANT PARAMETERS + star_ignore_sjdbgtf = true + seq_center = params.seq_center ?: '' + seq_platform = '' // - // STAR WORFKLOW: + // DISCOVERY TOOLS: // + tools = params.tool.split(',').collect{it.trim().toLowerCase()} + SEGEMEHL( reads, fasta, params.segemehl, bsj_reads ) + STAR2PASS( reads, star_index, ch_gtf, bsj_reads, star_ignore_sjdbgtf, seq_center, seq_platform ) - // Define variables here, star_ignore_sjdbgtf not supposed to be toggled by user. - star_ignore_sjdbgtf = true - seq_center = params.seq_center ?: '' - seq_platform = '' - - STAR_1ST_PASS( reads, star_index, ch_gtf, star_ignore_sjdbgtf, seq_platform, seq_center) - sjdb = STAR_1ST_PASS.out.tab.map{ meta, tab -> return tab }.collect().map{[[id: "star_sjdb"], it]} - STAR_SJDB( sjdb, bsj_reads ) - STAR_2ND_PASS( reads, star_index, STAR_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) - - ch_versions = ch_versions.mix(STAR_1ST_PASS.out.versions) - ch_versions = ch_versions.mix(STAR_SJDB.out.versions) - ch_versions = ch_versions.mix(STAR_2ND_PASS.out.versions) + ch_versions = ch_versions.mix(SEGEMEHL.out.versions) + ch_versions = ch_versions.mix(STAR2PASS.out.versions) // // CIRCEXPLORER2 WORKFLOW: // CIRCEXPLORER2_REF( gtf ) - CIRCEXPLORER2_PAR( STAR_2ND_PASS.out.junction ) + CIRCEXPLORER2_PAR( STAR2PASS.out.junction ) CIRCEXPLORER2_ANN( CIRCEXPLORER2_PAR.out.junction, fasta, CIRCEXPLORER2_REF.out.txt ) circexplorer2_filter = CIRCEXPLORER2_ANN.out.txt.map{ meta, txt -> [ meta + [tool: "circexplorer2"], txt ] } CIRCEXPLORER2_FLT( circexplorer2_filter, bsj_reads ) @@ -113,7 +98,7 @@ workflow CIRCRNA_DISCOVERY { // CIRCRNA_FINDER WORKFLOW: // - circrna_finder_stage = STAR_2ND_PASS.out.sam.join( STAR_2ND_PASS.out.junction).join(STAR_2ND_PASS.out.tab) + circrna_finder_stage = STAR2PASS.out.sam.join( STAR2PASS.out.junction).join(STAR2PASS.out.tab) circrna_finder_filter = circrna_finder_stage.map{ meta, sam, junction, tab -> [ meta + [tool: "circrna_finder"], sam, junction, tab ] } CIRCRNA_FINDER_FILTER( circrna_finder_filter, fasta, bsj_reads ) @@ -164,7 +149,7 @@ workflow CIRCRNA_DISCOVERY { DCC_MATE2_SJDB( DCC_MATE2_1ST_PASS.out.tab.map{ meta, tab -> return tab }.collect().map{[[id: "mate2_sjdb"], it]}, bsj_reads ) DCC_MATE2_2ND_PASS( mate2, star_index, DCC_MATE2_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) - dcc_stage = STAR_2ND_PASS.out.junction.map{ meta, junction -> return [ meta.id, meta, junction]} + dcc_stage = STAR2PASS.out.junction.map{ meta, junction -> return [ meta.id, meta, junction]} .join( DCC_MATE1_2ND_PASS.out.junction.map{ meta, junction -> return [ meta.id, junction] }, remainder: true @@ -209,7 +194,7 @@ workflow CIRCRNA_DISCOVERY { // COUNT MATRIX WORKFLOW: // - ch_matrix = CIRCEXPLORER2_FLT.out.matrix.mix(SEGEMEHL_FILTER.out.matrix, + ch_matrix = CIRCEXPLORER2_FLT.out.matrix.mix(SEGEMEHL.out.matrix, CIRCRNA_FINDER_FILTER.out.matrix, FIND_CIRC_FILTER.out.matrix, CIRIQUANT_FILTER.out.matrix, @@ -231,7 +216,7 @@ workflow CIRCRNA_DISCOVERY { ch_biotypes = Channel.fromPath("${projectDir}/bin/unwanted_biotypes.txt") - circrna_tools = CIRCEXPLORER2_FLT.out.results.mix(SEGEMEHL_FILTER.out.results, + circrna_tools = CIRCEXPLORER2_FLT.out.results.mix(SEGEMEHL.out.results, CIRCRNA_FINDER_FILTER.out.results, FIND_CIRC_FILTER.out.results, CIRIQUANT_FILTER.out.results, diff --git a/subworkflows/local/discovery/segemehl.nf b/subworkflows/local/discovery/segemehl.nf new file mode 100644 index 00000000..1d380fd1 --- /dev/null +++ b/subworkflows/local/discovery/segemehl.nf @@ -0,0 +1,29 @@ +include { SEGEMEHL_INDEX as INDEX } from '../../../modules/nf-core/segemehl/index' +include { SEGEMEHL_ALIGN as ALIGN } from '../../../modules/nf-core/segemehl/align' +include { SEGEMEHL_FILTER as FILTER } from '../../../modules/local/segemehl/filter' + + +workflow SEGEMEHL { + take: + reads + fasta + index + bsj_reads + + main: + ch_versions = Channel.empty() + + index = index ?: INDEX( fasta ).index + ALIGN( reads, fasta, index ) + FILTER( ALIGN.out.results + .map{ meta, results -> [ meta + [tool: "segemehl"], results ] }, bsj_reads ) + + ch_versions = ch_versions.mix(ALIGN.out.versions) + ch_versions = ch_versions.mix(FILTER.out.versions) + + emit: + matrix = FILTER.out.matrix + results = FILTER.out.results + + versions = ch_versions +} \ No newline at end of file diff --git a/subworkflows/local/discovery/star2pass.nf b/subworkflows/local/discovery/star2pass.nf new file mode 100644 index 00000000..65ce3e34 --- /dev/null +++ b/subworkflows/local/discovery/star2pass.nf @@ -0,0 +1,34 @@ +include { STAR_ALIGN as PASS_1 } from '../../../modules/nf-core/star/align' +include { STAR_ALIGN as PASS_2 } from '../../../modules/nf-core/star/align' +include { SJDB } from '../../../modules/local/star/sjdb' + + +workflow STAR2PASS { + take: + reads + star_index + ch_gtf + bsj_reads + ignore_sjdbgtf + seq_center + seq_platform + + main: + ch_versions = Channel.empty() + + PASS_1( reads, star_index, ch_gtf, ignore_sjdbgtf, seq_platform, seq_center) + sjdb = PASS_1.out.tab.map{ meta, tab -> return tab }.collect().map{[[id: "star_sjdb"], it]} + SJDB( sjdb, bsj_reads ) + PASS_2( reads, star_index, SJDB.out.sjtab, ignore_sjdbgtf, seq_platform, seq_center ) + + ch_versions = ch_versions.mix(PASS_1.out.versions) + ch_versions = ch_versions.mix(SJDB.out.versions) + ch_versions = ch_versions.mix(PASS_2.out.versions) + + emit: + junction = PASS_2.out.junction + sam = PASS_2.out.sam + tab = PASS_2.out.tab + + versions = ch_versions +} \ No newline at end of file diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 9d382295..140ba463 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -5,7 +5,6 @@ include { BWA_INDEX } from '../../modules/nf-core/bwa/index' include { HISAT2_EXTRACTSPLICESITES } from '../../modules/nf-core/hisat2/extractsplicesites' include { HISAT2_BUILD } from '../../modules/nf-core/hisat2/build' include { STAR_GENOMEGENERATE } from '../../modules/nf-core/star/genomegenerate' -include { SEGEMEHL_INDEX } from '../../modules/nf-core/segemehl/index' include { GAWK as CLEAN_FASTA } from '../../modules/nf-core/gawk' include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx' @@ -41,8 +40,6 @@ workflow PREPARE_GENOME { STAR_GENOMEGENERATE(ch_fasta, ch_gtf) - SEGEMEHL_INDEX(ch_fasta.map{ meta, fasta -> fasta}) // TODO: Add support for meta - SAMTOOLS_FAIDX(ch_fasta, [[], []]) // Collect versions @@ -52,14 +49,12 @@ workflow PREPARE_GENOME { BWA_INDEX.out.versions, HISAT2_EXTRACTSPLICESITES.out.versions, HISAT2_BUILD.out.versions, - SEGEMEHL_INDEX.out.versions, STAR_GENOMEGENERATE.out.versions, SAMTOOLS_FAIDX.out.versions) emit: faidx = SAMTOOLS_FAIDX.out.fai bowtie = params.bowtie ?: BOWTIE_BUILD.out.index - segemehl = params.segemehl ?: SEGEMEHL_INDEX.out.index bowtie2 = params.bowtie2 ? Channel.value([[id: "bowtie2"], file(params.bowtie2, checkIfExists: true)]) : BOWTIE2_BUILD.out.index.collect() bwa = params.bwa ? Channel.value([[id: "bwa"], file(params.bwa, checkIfExists: true)]) : BWA_INDEX.out.index.collect() hisat2 = params.hisat2 ? Channel.value([[id: "hisat2"], file(params.hisat2, checkIfExists: true)]) : HISAT2_BUILD.out.index.collect() diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 1b0f89cd..4da9fe94 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -117,7 +117,6 @@ workflow CIRCRNA { chromosomes = PREPARE_GENOME.out.chromosomes hisat2_index = PREPARE_GENOME.out.hisat2 star_index = PREPARE_GENOME.out.star - segemehl_index = PREPARE_GENOME.out.segemehl ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) // MODULE: Run FastQC, trimgalore! @@ -143,7 +142,6 @@ workflow CIRCRNA { bwa_index, chromosomes, hisat2_index, - segemehl_index, star_index, params.bsj_reads, params.tool_filter, From aa4597e03c593af17cdcd1b7c92a64ac78a19758 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 08:33:13 +0200 Subject: [PATCH 234/491] Simplify CIRCEXPLORER2 workflow --- conf/modules.config | 8 ++--- subworkflows/local/circrna_discovery.nf | 30 ++++------------- subworkflows/local/discovery/circexplorer2.nf | 32 +++++++++++++++++++ 3 files changed, 43 insertions(+), 27 deletions(-) create mode 100644 subworkflows/local/discovery/circexplorer2.nf diff --git a/conf/modules.config b/conf/modules.config index b13926e9..fcd3213c 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -230,7 +230,7 @@ if (!params.skip_trimming) { ] } - withName: CIRCEXPLORER2_REF { + withName: '.*:CIRCEXPLORER2:REFERENCE' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('circexplorer2') } ext.args = [ "", "-genePredExt", @@ -244,7 +244,7 @@ if (!params.skip_trimming) { ] } - withName: CIRCEXPLORER2_PAR { + withName: '.*:CIRCEXPLORER2:PARSE' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('circexplorer2') } publishDir = [ path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates/${meta.id}" }, @@ -254,7 +254,7 @@ if (!params.skip_trimming) { ] } - withName: CIRCEXPLORER2_ANN { + withName: '.*:CIRCEXPLORER2:ANNOTATE' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('circexplorer2') } publishDir = [ path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates/${meta.id}" }, @@ -264,7 +264,7 @@ if (!params.skip_trimming) { ] } - withName: CIRCEXPLORER2_FLT { + withName: '.*:CIRCEXPLORER2:FILTER' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('circexplorer2') } publishDir = [ path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates/${meta.id}" }, diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index f0688cc0..91a7e2c7 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -24,10 +24,6 @@ include { DCC_FILTER } from '../../modules/l include { MAPSPLICE_ALIGN } from '../../modules/local/mapsplice/align' include { MERGE_TOOLS } from '../../modules/local/count_matrix/merge_tools' include { COUNTS_COMBINED } from '../../modules/local/count_matrix/combined' -include { CIRCEXPLORER2_REFERENCE as CIRCEXPLORER2_REF } from '../../modules/local/circexplorer2/reference' -include { CIRCEXPLORER2_PARSE as CIRCEXPLORER2_PAR } from '../../modules/nf-core/circexplorer2/parse' -include { CIRCEXPLORER2_ANNOTATE as CIRCEXPLORER2_ANN } from '../../modules/nf-core/circexplorer2/annotate' -include { CIRCEXPLORER2_FILTER as CIRCEXPLORER2_FLT } from '../../modules/local/circexplorer2/filter' include { CIRCEXPLORER2_REFERENCE as MAPSPLICE_REFERENCE } from '../../modules/local/circexplorer2/reference' include { CIRCEXPLORER2_PARSE as MAPSPLICE_PARSE } from '../../modules/nf-core/circexplorer2/parse' include { CIRCEXPLORER2_ANNOTATE as MAPSPLICE_ANNOTATE } from '../../modules/nf-core/circexplorer2/annotate' @@ -38,8 +34,9 @@ include { BEDTOOLS_GETFASTA } from '../../modules/n include { GAWK as ADD_BACKSPLICE } from '../../modules/nf-core/gawk' // SUBWORKFLOWS -include { SEGEMEHL } from './discovery/segemehl' -include { STAR2PASS } from './discovery/star2pass' +include { SEGEMEHL } from './discovery/segemehl' +include { STAR2PASS } from './discovery/star2pass' +include { CIRCEXPLORER2 } from './discovery/circexplorer2' workflow CIRCRNA_DISCOVERY { @@ -75,24 +72,11 @@ workflow CIRCRNA_DISCOVERY { tools = params.tool.split(',').collect{it.trim().toLowerCase()} SEGEMEHL( reads, fasta, params.segemehl, bsj_reads ) STAR2PASS( reads, star_index, ch_gtf, bsj_reads, star_ignore_sjdbgtf, seq_center, seq_platform ) + CIRCEXPLORER2( gtf, fasta, STAR2PASS.out.junction, bsj_reads ) ch_versions = ch_versions.mix(SEGEMEHL.out.versions) ch_versions = ch_versions.mix(STAR2PASS.out.versions) - - // - // CIRCEXPLORER2 WORKFLOW: - // - - CIRCEXPLORER2_REF( gtf ) - CIRCEXPLORER2_PAR( STAR2PASS.out.junction ) - CIRCEXPLORER2_ANN( CIRCEXPLORER2_PAR.out.junction, fasta, CIRCEXPLORER2_REF.out.txt ) - circexplorer2_filter = CIRCEXPLORER2_ANN.out.txt.map{ meta, txt -> [ meta + [tool: "circexplorer2"], txt ] } - CIRCEXPLORER2_FLT( circexplorer2_filter, bsj_reads ) - - ch_versions = ch_versions.mix(CIRCEXPLORER2_REF.out.versions) - ch_versions = ch_versions.mix(CIRCEXPLORER2_PAR.out.versions) - ch_versions = ch_versions.mix(CIRCEXPLORER2_ANN.out.versions) - ch_versions = ch_versions.mix(CIRCEXPLORER2_FLT.out.versions) + ch_versions = ch_versions.mix(CIRCEXPLORER2.out.versions) // // CIRCRNA_FINDER WORKFLOW: @@ -194,7 +178,7 @@ workflow CIRCRNA_DISCOVERY { // COUNT MATRIX WORKFLOW: // - ch_matrix = CIRCEXPLORER2_FLT.out.matrix.mix(SEGEMEHL.out.matrix, + ch_matrix = CIRCEXPLORER2.out.matrix.mix(SEGEMEHL.out.matrix, CIRCRNA_FINDER_FILTER.out.matrix, FIND_CIRC_FILTER.out.matrix, CIRIQUANT_FILTER.out.matrix, @@ -216,7 +200,7 @@ workflow CIRCRNA_DISCOVERY { ch_biotypes = Channel.fromPath("${projectDir}/bin/unwanted_biotypes.txt") - circrna_tools = CIRCEXPLORER2_FLT.out.results.mix(SEGEMEHL.out.results, + circrna_tools = CIRCEXPLORER2.out.results.mix(SEGEMEHL.out.results, CIRCRNA_FINDER_FILTER.out.results, FIND_CIRC_FILTER.out.results, CIRIQUANT_FILTER.out.results, diff --git a/subworkflows/local/discovery/circexplorer2.nf b/subworkflows/local/discovery/circexplorer2.nf new file mode 100644 index 00000000..ce39f039 --- /dev/null +++ b/subworkflows/local/discovery/circexplorer2.nf @@ -0,0 +1,32 @@ +include { CIRCEXPLORER2_REFERENCE as REFERENCE } from '../../../modules/local/circexplorer2/reference' +include { CIRCEXPLORER2_PARSE as PARSE } from '../../../modules/nf-core/circexplorer2/parse' +include { CIRCEXPLORER2_ANNOTATE as ANNOTATE } from '../../../modules/nf-core/circexplorer2/annotate' +include { CIRCEXPLORER2_FILTER as FILTER } from '../../../modules/local/circexplorer2/filter' + +workflow CIRCEXPLORER2 { + take: + gtf + fasta + star_junctions + bsj_reads + + main: + ch_versions = Channel.empty() + + REFERENCE( gtf ) + PARSE( star_junctions ) + ANNOTATE( PARSE.out.junction, fasta, REFERENCE.out.txt ) + FILTER( ANNOTATE.out.txt + .map{ meta, txt -> [ meta + [tool: "circexplorer2"], txt ] }, bsj_reads ) + + ch_versions = ch_versions.mix(REFERENCE.out.versions) + ch_versions = ch_versions.mix(PARSE.out.versions) + ch_versions = ch_versions.mix(ANNOTATE.out.versions) + ch_versions = ch_versions.mix(FILTER.out.versions) + + emit: + matrix = FILTER.out.matrix + results = FILTER.out.results + + versions = ch_versions +} \ No newline at end of file From 14b0f122e0136f2736f5e9e87aa1b5652043ed81 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 08:41:18 +0200 Subject: [PATCH 235/491] Simplify CIRCRNA_FINDER --- conf/modules.config | 2 +- subworkflows/local/circrna_discovery.nf | 23 ++++++---------- .../local/discovery/circrna_finder.nf | 27 +++++++++++++++++++ 3 files changed, 36 insertions(+), 16 deletions(-) create mode 100644 subworkflows/local/discovery/circrna_finder.nf diff --git a/conf/modules.config b/conf/modules.config index fcd3213c..e45acb8e 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -275,7 +275,7 @@ if (!params.skip_trimming) { ] } - withName: CIRCRNA_FINDER_FILTER { + withName: '.*:CIRCRNA_FINDER:FILTER' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('circrna_finder') } publishDir = [ path: { "${params.outdir}/circrna_discovery/circrna_finder/intermediates/${meta.id}" }, diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 91a7e2c7..7ae57095 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -12,7 +12,6 @@ include { FIND_CIRC } from '../../modules/l include { FIND_CIRC_FILTER } from '../../modules/local/find_circ/filter' include { CIRIQUANT } from '../../modules/local/ciriquant/ciriquant' include { CIRIQUANT_FILTER } from '../../modules/local/ciriquant/filter' -include { CIRCRNA_FINDER_FILTER } from '../../modules/local/circrna_finder/filter' include { STAR_ALIGN as DCC_MATE1_1ST_PASS } from '../../modules/nf-core/star/align' include { STAR_ALIGN as DCC_MATE1_2ND_PASS } from '../../modules/nf-core/star/align' include { SJDB as DCC_MATE1_SJDB } from '../../modules/local/star/sjdb' @@ -34,9 +33,10 @@ include { BEDTOOLS_GETFASTA } from '../../modules/n include { GAWK as ADD_BACKSPLICE } from '../../modules/nf-core/gawk' // SUBWORKFLOWS -include { SEGEMEHL } from './discovery/segemehl' -include { STAR2PASS } from './discovery/star2pass' -include { CIRCEXPLORER2 } from './discovery/circexplorer2' +include { SEGEMEHL } from './discovery/segemehl' +include { STAR2PASS } from './discovery/star2pass' +include { CIRCEXPLORER2 } from './discovery/circexplorer2' +include { CIRCRNA_FINDER } from './discovery/circrna_finder' workflow CIRCRNA_DISCOVERY { @@ -73,20 +73,13 @@ workflow CIRCRNA_DISCOVERY { SEGEMEHL( reads, fasta, params.segemehl, bsj_reads ) STAR2PASS( reads, star_index, ch_gtf, bsj_reads, star_ignore_sjdbgtf, seq_center, seq_platform ) CIRCEXPLORER2( gtf, fasta, STAR2PASS.out.junction, bsj_reads ) + CIRCRNA_FINDER( fasta, STAR2PASS.out.sam, STAR2PASS.out.junction, STAR2PASS.out.tab, bsj_reads ) ch_versions = ch_versions.mix(SEGEMEHL.out.versions) ch_versions = ch_versions.mix(STAR2PASS.out.versions) ch_versions = ch_versions.mix(CIRCEXPLORER2.out.versions) + ch_versions = ch_versions.mix(CIRCRNA_FINDER.out.versions) - // - // CIRCRNA_FINDER WORKFLOW: - // - - circrna_finder_stage = STAR2PASS.out.sam.join( STAR2PASS.out.junction).join(STAR2PASS.out.tab) - circrna_finder_filter = circrna_finder_stage.map{ meta, sam, junction, tab -> [ meta + [tool: "circrna_finder"], sam, junction, tab ] } - CIRCRNA_FINDER_FILTER( circrna_finder_filter, fasta, bsj_reads ) - - ch_versions = ch_versions.mix(CIRCRNA_FINDER_FILTER.out.versions) // // FIND_CIRC WORKFLOW: @@ -179,7 +172,7 @@ workflow CIRCRNA_DISCOVERY { // ch_matrix = CIRCEXPLORER2.out.matrix.mix(SEGEMEHL.out.matrix, - CIRCRNA_FINDER_FILTER.out.matrix, + CIRCRNA_FINDER.out.matrix, FIND_CIRC_FILTER.out.matrix, CIRIQUANT_FILTER.out.matrix, DCC_FILTER.out.matrix, @@ -201,7 +194,7 @@ workflow CIRCRNA_DISCOVERY { ch_biotypes = Channel.fromPath("${projectDir}/bin/unwanted_biotypes.txt") circrna_tools = CIRCEXPLORER2.out.results.mix(SEGEMEHL.out.results, - CIRCRNA_FINDER_FILTER.out.results, + CIRCRNA_FINDER.out.results, FIND_CIRC_FILTER.out.results, CIRIQUANT_FILTER.out.results, DCC_FILTER.out.results, diff --git a/subworkflows/local/discovery/circrna_finder.nf b/subworkflows/local/discovery/circrna_finder.nf new file mode 100644 index 00000000..b4564b7b --- /dev/null +++ b/subworkflows/local/discovery/circrna_finder.nf @@ -0,0 +1,27 @@ +include { CIRCRNA_FINDER_FILTER as FILTER } from '../../../modules/local/circrna_finder/filter' + +workflow CIRCRNA_FINDER { + take: + fasta + star_sam + star_junctions + star_tab + bsj_reads + + main: + ch_versions = Channel.empty() + + ch_joined = star_sam.join(star_junctions).join(star_tab) + .map{ meta, sam, junction, tab -> + [ meta + [tool: "circrna_finder"], sam, junction, tab ] } + + FILTER( ch_joined, fasta, bsj_reads ) + + ch_versions = ch_versions.mix(FILTER.out.versions) + + emit: + matrix = FILTER.out.matrix + results = FILTER.out.results + + versions = ch_versions +} \ No newline at end of file From 5032443a80f86bbcfd1225ad6ad6df641a8c6ffb Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 08:55:58 +0200 Subject: [PATCH 236/491] Simplify FIND_CIRC --- conf/modules.config | 10 +++--- subworkflows/local/circrna_discovery.nf | 31 +++--------------- subworkflows/local/discovery/find_circ.nf | 39 +++++++++++++++++++++++ 3 files changed, 48 insertions(+), 32 deletions(-) create mode 100644 subworkflows/local/discovery/find_circ.nf diff --git a/conf/modules.config b/conf/modules.config index e45acb8e..f405c3c6 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -286,7 +286,7 @@ if (!params.skip_trimming) { ] } - withName: FIND_CIRC_ALIGN { + withName: '.*:FIND_CIRC:ALIGN' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('find_circ') } ext.args = [ "", "--very-sensitive", @@ -303,7 +303,7 @@ if (!params.skip_trimming) { ] } - withName: SAMTOOLS_VIEW { + withName: '.*:FIND_CIRC:SAMTOOLS_VIEW' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('find_circ') } ext.prefix = { "${meta.id}_unmapped" } ext.args = "-hf 4" @@ -315,7 +315,7 @@ if (!params.skip_trimming) { ] } - withName: FIND_CIRC_ANCHORS { + withName: '.*:FIND_CIRC:ANCHORS' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('find_circ') } publishDir = [ path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, @@ -325,7 +325,7 @@ if (!params.skip_trimming) { ] } - withName: FIND_CIRC { + withName: '.*:FIND_CIRC:RUN' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('find_circ') } publishDir = [ path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, @@ -335,7 +335,7 @@ if (!params.skip_trimming) { ] } - withName: FIND_CIRC_FILTER { + withName: '.*:FIND_CIRC:FILTER' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('find_circ') } publishDir = [ path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 7ae57095..9249319a 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -4,12 +4,6 @@ include { GNU_SORT as COMBINE_ANNOTATION_BEDS } from '../../modules/n include { GNU_SORT as COMBINE_ANNOTATION_GTFS } from '../../modules/nf-core/gnu/sort' include { GAWK as REMOVE_SCORE_STRAND } from '../../modules/nf-core/gawk' include { BEDTOOLS_INTERSECT as INTERSECT_ANNOTATION } from '../../modules/nf-core/bedtools/intersect' -include { BOWTIE2_ALIGN as FIND_CIRC_ALIGN } from '../../modules/nf-core/bowtie2/align' -include { SAMTOOLS_VIEW } from '../../modules/nf-core/samtools/view' -include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index' -include { FIND_CIRC_ANCHORS } from '../../modules/local/find_circ/anchors' -include { FIND_CIRC } from '../../modules/local/find_circ/find_circ' -include { FIND_CIRC_FILTER } from '../../modules/local/find_circ/filter' include { CIRIQUANT } from '../../modules/local/ciriquant/ciriquant' include { CIRIQUANT_FILTER } from '../../modules/local/ciriquant/filter' include { STAR_ALIGN as DCC_MATE1_1ST_PASS } from '../../modules/nf-core/star/align' @@ -37,6 +31,7 @@ include { SEGEMEHL } from './discovery/segemehl' include { STAR2PASS } from './discovery/star2pass' include { CIRCEXPLORER2 } from './discovery/circexplorer2' include { CIRCRNA_FINDER } from './discovery/circrna_finder' +include { FIND_CIRC } from './discovery/find_circ' workflow CIRCRNA_DISCOVERY { @@ -74,31 +69,13 @@ workflow CIRCRNA_DISCOVERY { STAR2PASS( reads, star_index, ch_gtf, bsj_reads, star_ignore_sjdbgtf, seq_center, seq_platform ) CIRCEXPLORER2( gtf, fasta, STAR2PASS.out.junction, bsj_reads ) CIRCRNA_FINDER( fasta, STAR2PASS.out.sam, STAR2PASS.out.junction, STAR2PASS.out.tab, bsj_reads ) + FIND_CIRC( reads, bowtie2_index, ch_fasta, bsj_reads ) ch_versions = ch_versions.mix(SEGEMEHL.out.versions) ch_versions = ch_versions.mix(STAR2PASS.out.versions) ch_versions = ch_versions.mix(CIRCEXPLORER2.out.versions) ch_versions = ch_versions.mix(CIRCRNA_FINDER.out.versions) - - - // - // FIND_CIRC WORKFLOW: - // - - FIND_CIRC_ALIGN( reads, bowtie2_index, ch_fasta, false, true ) - SAMTOOLS_INDEX( FIND_CIRC_ALIGN.out.bam ) - SAMTOOLS_VIEW( FIND_CIRC_ALIGN.out.bam.join( SAMTOOLS_INDEX.out.bai ), ch_fasta, [] ) - FIND_CIRC_ANCHORS( SAMTOOLS_VIEW.out.bam ) - FIND_CIRC( FIND_CIRC_ANCHORS.out.anchors, bowtie2_index, fasta ) - find_circ_filter = FIND_CIRC.out.bed.map{ meta, bed -> [ meta + [tool: "find_circ"], bed ] } - FIND_CIRC_FILTER( find_circ_filter, bsj_reads ) - - ch_versions = ch_versions.mix(FIND_CIRC_ALIGN.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions) - ch_versions = ch_versions.mix(FIND_CIRC_ANCHORS.out.versions) ch_versions = ch_versions.mix(FIND_CIRC.out.versions) - ch_versions = ch_versions.mix(FIND_CIRC_FILTER.out.versions) // // CIRIQUANT WORKFLOW: @@ -173,7 +150,7 @@ workflow CIRCRNA_DISCOVERY { ch_matrix = CIRCEXPLORER2.out.matrix.mix(SEGEMEHL.out.matrix, CIRCRNA_FINDER.out.matrix, - FIND_CIRC_FILTER.out.matrix, + FIND_CIRC.out.matrix, CIRIQUANT_FILTER.out.matrix, DCC_FILTER.out.matrix, MAPSPLICE_FILTER.out.matrix) @@ -195,7 +172,7 @@ workflow CIRCRNA_DISCOVERY { circrna_tools = CIRCEXPLORER2.out.results.mix(SEGEMEHL.out.results, CIRCRNA_FINDER.out.results, - FIND_CIRC_FILTER.out.results, + FIND_CIRC.out.results, CIRIQUANT_FILTER.out.results, DCC_FILTER.out.results, MAPSPLICE_FILTER.out.results) diff --git a/subworkflows/local/discovery/find_circ.nf b/subworkflows/local/discovery/find_circ.nf new file mode 100644 index 00000000..d8d0a14c --- /dev/null +++ b/subworkflows/local/discovery/find_circ.nf @@ -0,0 +1,39 @@ +include { BOWTIE2_ALIGN as ALIGN } from '../../../modules/nf-core/bowtie2/align' +include { SAMTOOLS_VIEW } from '../../../modules/nf-core/samtools/view' +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index' +include { FIND_CIRC_ANCHORS as ANCHORS } from '../../../modules/local/find_circ/anchors' +include { FIND_CIRC as RUN } from '../../../modules/local/find_circ/find_circ' +include { FIND_CIRC_FILTER as FILTER } from '../../../modules/local/find_circ/filter' + + +workflow FIND_CIRC { + take: + reads + bowtie2_index + ch_fasta + bsj_reads + + main: + ch_versions = Channel.empty() + + ALIGN( reads, bowtie2_index, ch_fasta, false, true ) + SAMTOOLS_INDEX( ALIGN.out.bam ) + SAMTOOLS_VIEW( ALIGN.out.bam.join( SAMTOOLS_INDEX.out.bai ), ch_fasta, [] ) + ANCHORS( SAMTOOLS_VIEW.out.bam ) + RUN( ANCHORS.out.anchors, bowtie2_index, ch_fasta.map{ meta, fasta -> fasta } ) + FILTER( RUN.out.bed.map{ meta, bed -> + [ meta + [tool: "find_circ"], bed ] }, bsj_reads ) + + ch_versions = ch_versions.mix(ALIGN.out.versions) + ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions) + ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions) + ch_versions = ch_versions.mix(ANCHORS.out.versions) + ch_versions = ch_versions.mix(RUN.out.versions) + ch_versions = ch_versions.mix(FILTER.out.versions) + + emit: + matrix = FILTER.out.matrix + results = FILTER.out.results + + versions = ch_versions +} \ No newline at end of file From bb73664bb526f1dea2d4b0d60720724e47fc4b47 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 09:03:42 +0200 Subject: [PATCH 237/491] Simplify CIRIQUANT --- conf/modules.config | 4 ++-- subworkflows/local/circrna_discovery.nf | 19 ++++----------- subworkflows/local/discovery/ciriquant.nf | 28 +++++++++++++++++++++++ 3 files changed, 34 insertions(+), 17 deletions(-) create mode 100644 subworkflows/local/discovery/ciriquant.nf diff --git a/conf/modules.config b/conf/modules.config index f405c3c6..496763cb 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -346,7 +346,7 @@ if (!params.skip_trimming) { ] } - withName: CIRIQUANT { + withName: '.*:CIRIQUANT:RUN' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('ciriquant') } publishDir = [ path: { "${params.outdir}/circrna_discovery/ciriquant/intermediates/${meta.id}" }, @@ -356,7 +356,7 @@ if (!params.skip_trimming) { ] } - withName: CIRIQUANT_FILTER { + withName: '.*:CIRIQUANT:FILTER' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('ciriquant') } publishDir = [ path: { "${params.outdir}/circrna_discovery/ciriquant/intermediates/${meta.id}" }, diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 9249319a..5216240a 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -4,8 +4,6 @@ include { GNU_SORT as COMBINE_ANNOTATION_BEDS } from '../../modules/n include { GNU_SORT as COMBINE_ANNOTATION_GTFS } from '../../modules/nf-core/gnu/sort' include { GAWK as REMOVE_SCORE_STRAND } from '../../modules/nf-core/gawk' include { BEDTOOLS_INTERSECT as INTERSECT_ANNOTATION } from '../../modules/nf-core/bedtools/intersect' -include { CIRIQUANT } from '../../modules/local/ciriquant/ciriquant' -include { CIRIQUANT_FILTER } from '../../modules/local/ciriquant/filter' include { STAR_ALIGN as DCC_MATE1_1ST_PASS } from '../../modules/nf-core/star/align' include { STAR_ALIGN as DCC_MATE1_2ND_PASS } from '../../modules/nf-core/star/align' include { SJDB as DCC_MATE1_SJDB } from '../../modules/local/star/sjdb' @@ -32,6 +30,7 @@ include { STAR2PASS } from './discovery/star2pass' include { CIRCEXPLORER2 } from './discovery/circexplorer2' include { CIRCRNA_FINDER } from './discovery/circrna_finder' include { FIND_CIRC } from './discovery/find_circ' +include { CIRIQUANT } from './discovery/ciriquant' workflow CIRCRNA_DISCOVERY { @@ -70,24 +69,14 @@ workflow CIRCRNA_DISCOVERY { CIRCEXPLORER2( gtf, fasta, STAR2PASS.out.junction, bsj_reads ) CIRCRNA_FINDER( fasta, STAR2PASS.out.sam, STAR2PASS.out.junction, STAR2PASS.out.tab, bsj_reads ) FIND_CIRC( reads, bowtie2_index, ch_fasta, bsj_reads ) + CIRIQUANT( reads, ch_gtf, ch_fasta, bwa_index, hisat2_index, bsj_reads ) ch_versions = ch_versions.mix(SEGEMEHL.out.versions) ch_versions = ch_versions.mix(STAR2PASS.out.versions) ch_versions = ch_versions.mix(CIRCEXPLORER2.out.versions) ch_versions = ch_versions.mix(CIRCRNA_FINDER.out.versions) ch_versions = ch_versions.mix(FIND_CIRC.out.versions) - - // - // CIRIQUANT WORKFLOW: - // - - // only need path to bwa, only need path to hisat2. - // do not want to upset the collect declr for all indices just for this. - CIRIQUANT( reads, ch_gtf, ch_fasta, bwa_index, hisat2_index ) - CIRIQUANT_FILTER( CIRIQUANT.out.gtf.map{ meta, gtf -> [ meta + [tool: "ciriquant"], gtf ] }, bsj_reads ) - ch_versions = ch_versions.mix(CIRIQUANT.out.versions) - ch_versions = ch_versions.mix(CIRIQUANT_FILTER.out.versions) // // DCC WORKFLOW @@ -151,7 +140,7 @@ workflow CIRCRNA_DISCOVERY { ch_matrix = CIRCEXPLORER2.out.matrix.mix(SEGEMEHL.out.matrix, CIRCRNA_FINDER.out.matrix, FIND_CIRC.out.matrix, - CIRIQUANT_FILTER.out.matrix, + CIRIQUANT.out.matrix, DCC_FILTER.out.matrix, MAPSPLICE_FILTER.out.matrix) @@ -173,7 +162,7 @@ workflow CIRCRNA_DISCOVERY { circrna_tools = CIRCEXPLORER2.out.results.mix(SEGEMEHL.out.results, CIRCRNA_FINDER.out.results, FIND_CIRC.out.results, - CIRIQUANT_FILTER.out.results, + CIRIQUANT.out.results, DCC_FILTER.out.results, MAPSPLICE_FILTER.out.results) diff --git a/subworkflows/local/discovery/ciriquant.nf b/subworkflows/local/discovery/ciriquant.nf new file mode 100644 index 00000000..b4e4c381 --- /dev/null +++ b/subworkflows/local/discovery/ciriquant.nf @@ -0,0 +1,28 @@ +include { CIRIQUANT as RUN } from '../../../modules/local/ciriquant/ciriquant' +include { CIRIQUANT_FILTER as FILTER } from '../../../modules/local/ciriquant/filter' + +workflow CIRIQUANT { + take: + reads + ch_gtf + ch_fasta + bwa_index + hisat2_index + bsj_reads + + main: + ch_versions = Channel.empty() + + RUN( reads, ch_gtf, ch_fasta, bwa_index, hisat2_index ) + FILTER( RUN.out.gtf.map{ meta, gtf -> + [ meta + [tool: "ciriquant"], gtf ] }, bsj_reads ) + + ch_versions = ch_versions.mix(RUN.out.versions) + ch_versions = ch_versions.mix(FILTER.out.versions) + + emit: + matrix = FILTER.out.matrix + results = FILTER.out.results + + versions = ch_versions +} \ No newline at end of file From 3491bed6acdda18c1b2bb1c1f64ceaefc5c444f3 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 09:17:42 +0200 Subject: [PATCH 238/491] Simplify DCC --- conf/modules.config | 14 ++--- subworkflows/local/circrna_discovery.nf | 52 ++----------------- subworkflows/local/discovery/dcc.nf | 68 +++++++++++++++++++++++++ 3 files changed, 80 insertions(+), 54 deletions(-) create mode 100644 subworkflows/local/discovery/dcc.nf diff --git a/conf/modules.config b/conf/modules.config index 496763cb..2848a9d1 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -367,7 +367,7 @@ if (!params.skip_trimming) { ] } - withName: DCC_MATE1_1ST_PASS { + withName: '.*:DCC:MATE1_1ST_PASS' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('dcc') } ext.prefix = { "${meta.id}_mate1" } ext.args = [ "", @@ -389,7 +389,7 @@ if (!params.skip_trimming) { ] } - withName: DCC_MATE1_SJDB { + withName: '.*:DCC:MATE1_SJDB' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('dcc') } publishDir = [ path: { "${params.outdir}/circrna_discovery/dcc/intermediates/mate1/sjdb" }, @@ -399,7 +399,7 @@ if (!params.skip_trimming) { ] } - withName: DCC_MATE1_2ND_PASS { + withName: '.*:DCC:MATE1_2ND_PASS' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('dcc') } ext.prefix = { "${meta.id}_mate1" } ext.args = [ "", @@ -422,7 +422,7 @@ if (!params.skip_trimming) { ] } - withName: DCC_MATE2_1ST_PASS { + withName: '.*:DCC:MATE2_1ST_PASS' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('dcc') } ext.prefix = { "${meta.id}_mate2" } ext.args = [ "", @@ -444,7 +444,7 @@ if (!params.skip_trimming) { ] } - withName: DCC_MATE2_SJDB { + withName: '.*:DCC:MATE2_SJDB' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('dcc') } publishDir = [ path: { "${params.outdir}/circrna_discovery/dcc/intermediates/mate2/sjdb" }, @@ -454,7 +454,7 @@ if (!params.skip_trimming) { ] } - withName: DCC_MATE2_2ND_PASS { + withName: '.*:DCC:MATE2_2ND_PASS' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('dcc') } ext.prefix = { "${meta.id}_mate2" } ext.args = [ "", @@ -477,7 +477,7 @@ if (!params.skip_trimming) { ] } - withName: DCC { + withName: '.*:DCC:RUN' { ext.when = { params.tool.split(',').contains('dcc') && params.module.split(',').contains('circrna_discovery') } publishDir = [ path: { "${params.outdir}/circrna_discovery/dcc/intermediates/${meta.id}" }, diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 5216240a..eaa03e61 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -4,14 +4,6 @@ include { GNU_SORT as COMBINE_ANNOTATION_BEDS } from '../../modules/n include { GNU_SORT as COMBINE_ANNOTATION_GTFS } from '../../modules/nf-core/gnu/sort' include { GAWK as REMOVE_SCORE_STRAND } from '../../modules/nf-core/gawk' include { BEDTOOLS_INTERSECT as INTERSECT_ANNOTATION } from '../../modules/nf-core/bedtools/intersect' -include { STAR_ALIGN as DCC_MATE1_1ST_PASS } from '../../modules/nf-core/star/align' -include { STAR_ALIGN as DCC_MATE1_2ND_PASS } from '../../modules/nf-core/star/align' -include { SJDB as DCC_MATE1_SJDB } from '../../modules/local/star/sjdb' -include { STAR_ALIGN as DCC_MATE2_1ST_PASS } from '../../modules/nf-core/star/align' -include { STAR_ALIGN as DCC_MATE2_2ND_PASS } from '../../modules/nf-core/star/align' -include { SJDB as DCC_MATE2_SJDB } from '../../modules/local/star/sjdb' -include { DCC } from '../../modules/local/dcc/dcc' -include { DCC_FILTER } from '../../modules/local/dcc/filter' include { MAPSPLICE_ALIGN } from '../../modules/local/mapsplice/align' include { MERGE_TOOLS } from '../../modules/local/count_matrix/merge_tools' include { COUNTS_COMBINED } from '../../modules/local/count_matrix/combined' @@ -31,6 +23,7 @@ include { CIRCEXPLORER2 } from './discovery/circexplorer2' include { CIRCRNA_FINDER } from './discovery/circrna_finder' include { FIND_CIRC } from './discovery/find_circ' include { CIRIQUANT } from './discovery/ciriquant' +include { DCC } from './discovery/dcc' workflow CIRCRNA_DISCOVERY { @@ -70,6 +63,7 @@ workflow CIRCRNA_DISCOVERY { CIRCRNA_FINDER( fasta, STAR2PASS.out.sam, STAR2PASS.out.junction, STAR2PASS.out.tab, bsj_reads ) FIND_CIRC( reads, bowtie2_index, ch_fasta, bsj_reads ) CIRIQUANT( reads, ch_gtf, ch_fasta, bwa_index, hisat2_index, bsj_reads ) + DCC( reads, ch_fasta, ch_gtf, star_index, STAR2PASS.out.junction, star_ignore_sjdbgtf, seq_platform, seq_center, bsj_reads ) ch_versions = ch_versions.mix(SEGEMEHL.out.versions) ch_versions = ch_versions.mix(STAR2PASS.out.versions) @@ -77,44 +71,8 @@ workflow CIRCRNA_DISCOVERY { ch_versions = ch_versions.mix(CIRCRNA_FINDER.out.versions) ch_versions = ch_versions.mix(FIND_CIRC.out.versions) ch_versions = ch_versions.mix(CIRIQUANT.out.versions) - - // - // DCC WORKFLOW - // - - mate1 = reads.filter{ meta, reads -> !meta.single_end }.map{ meta, reads -> return [ [id: meta.id, single_end: true], reads[0] ] } - DCC_MATE1_1ST_PASS( mate1, star_index, ch_gtf, star_ignore_sjdbgtf, seq_platform, seq_center ) - DCC_MATE1_SJDB( DCC_MATE1_1ST_PASS.out.tab.map{ meta, tab -> return tab }.collect().map{[[id: "mate1_sjdb"], it]}, bsj_reads ) - DCC_MATE1_2ND_PASS( mate1, star_index, DCC_MATE1_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) - - mate2 = reads.filter{ meta, reads -> !meta.single_end }.map{ meta, reads -> return [ [id: meta.id, single_end: true], reads[1] ] } - DCC_MATE2_1ST_PASS( mate2, star_index, ch_gtf, star_ignore_sjdbgtf, seq_platform, seq_center ) - DCC_MATE2_SJDB( DCC_MATE2_1ST_PASS.out.tab.map{ meta, tab -> return tab }.collect().map{[[id: "mate2_sjdb"], it]}, bsj_reads ) - DCC_MATE2_2ND_PASS( mate2, star_index, DCC_MATE2_SJDB.out.sjtab, star_ignore_sjdbgtf, seq_platform, seq_center ) - - dcc_stage = STAR2PASS.out.junction.map{ meta, junction -> return [ meta.id, meta, junction]} - .join( - DCC_MATE1_2ND_PASS.out.junction.map{ meta, junction -> return [ meta.id, junction] }, - remainder: true - ) - .join( - DCC_MATE2_2ND_PASS.out.junction.map{ meta, junction -> return [ meta.id, junction] }, - remainder: true - ) - .map{ id, meta, junction, mate1, mate2 -> return [ meta, junction, mate1, mate2 ]} - - dcc = dcc_stage.map{ it -> [ it[0], it[1], it[2] ?: [], it[3] ?: [] ] } - DCC( dcc, fasta, gtf ) - DCC_FILTER( DCC.out.txt.map{ meta, txt -> [ meta + [tool: "dcc"], txt ] }, bsj_reads ) - - ch_versions = ch_versions.mix(DCC_MATE1_1ST_PASS.out.versions) - ch_versions = ch_versions.mix(DCC_MATE1_SJDB.out.versions) - ch_versions = ch_versions.mix(DCC_MATE1_2ND_PASS.out.versions) - ch_versions = ch_versions.mix(DCC_MATE2_1ST_PASS.out.versions) - ch_versions = ch_versions.mix(DCC_MATE2_SJDB.out.versions) - ch_versions = ch_versions.mix(DCC_MATE2_2ND_PASS.out.versions) ch_versions = ch_versions.mix(DCC.out.versions) - ch_versions = ch_versions.mix(DCC_FILTER.out.versions) + // // MAPSPLICE WORKFLOW: @@ -141,7 +99,7 @@ workflow CIRCRNA_DISCOVERY { CIRCRNA_FINDER.out.matrix, FIND_CIRC.out.matrix, CIRIQUANT.out.matrix, - DCC_FILTER.out.matrix, + DCC.out.matrix, MAPSPLICE_FILTER.out.matrix) tools_selected = params.tool.split(',').collect{it.trim().toLowerCase()} @@ -163,7 +121,7 @@ workflow CIRCRNA_DISCOVERY { CIRCRNA_FINDER.out.results, FIND_CIRC.out.results, CIRIQUANT.out.results, - DCC_FILTER.out.results, + DCC.out.results, MAPSPLICE_FILTER.out.results) UPSET_SAMPLES( circrna_tools.map{ meta, bed -> [meta.id, meta.tool, bed]} diff --git a/subworkflows/local/discovery/dcc.nf b/subworkflows/local/discovery/dcc.nf new file mode 100644 index 00000000..96ccca6b --- /dev/null +++ b/subworkflows/local/discovery/dcc.nf @@ -0,0 +1,68 @@ +include { STAR_ALIGN as MATE1_1ST_PASS } from '../../../modules/nf-core/star/align' +include { STAR_ALIGN as MATE1_2ND_PASS } from '../../../modules/nf-core/star/align' +include { SJDB as MATE1_SJDB } from '../../../modules/local/star/sjdb' +include { STAR_ALIGN as MATE2_1ST_PASS } from '../../../modules/nf-core/star/align' +include { STAR_ALIGN as MATE2_2ND_PASS } from '../../../modules/nf-core/star/align' +include { SJDB as MATE2_SJDB } from '../../../modules/local/star/sjdb' +include { DCC as RUN } from '../../../modules/local/dcc/dcc' +include { DCC_FILTER as FILTER } from '../../../modules/local/dcc/filter' + +workflow DCC { + take: + reads + ch_fasta + ch_gtf + star_index + star_junction + ignore_sjdbgtf + seq_platform + seq_center + bsj_reads + + main: + ch_versions = Channel.empty() + + mate1 = reads.filter{ meta, reads -> !meta.single_end } + .map{ meta, reads -> return [ [id: meta.id, single_end: true], reads[0] ] } + MATE1_1ST_PASS( mate1, star_index, ch_gtf, ignore_sjdbgtf, seq_platform, seq_center ) + MATE1_SJDB( MATE1_1ST_PASS.out.tab + .map{ meta, tab -> return tab }.collect().map{[[id: "mate1_sjdb"], it]}, bsj_reads ) + MATE1_2ND_PASS( mate1, star_index, MATE1_SJDB.out.sjtab, ignore_sjdbgtf, seq_platform, seq_center ) + + mate2 = reads.filter{ meta, reads -> !meta.single_end } + .map{ meta, reads -> return [ [id: meta.id, single_end: true], reads[1] ] } + MATE2_1ST_PASS( mate2, star_index, ch_gtf, ignore_sjdbgtf, seq_platform, seq_center ) + MATE2_SJDB( MATE2_1ST_PASS.out.tab + .map{ meta, tab -> return tab }.collect().map{[[id: "mate2_sjdb"], it]}, bsj_reads ) + MATE2_2ND_PASS( mate2, star_index, MATE2_SJDB.out.sjtab, ignore_sjdbgtf, seq_platform, seq_center ) + + dcc_stage = star_junction.map{ meta, junction -> return [ meta.id, meta, junction]} + .join( + MATE1_2ND_PASS.out.junction.map{ meta, junction -> return [ meta.id, junction] }, + remainder: true + ) + .join( + MATE2_2ND_PASS.out.junction.map{ meta, junction -> return [ meta.id, junction] }, + remainder: true + ) + .map{ id, meta, junction, mate1, mate2 -> return [ meta, junction, mate1, mate2 ]} + + dcc = dcc_stage.map{ it -> [ it[0], it[1], it[2] ?: [], it[3] ?: [] ] } + RUN( dcc, ch_fasta.map{ meta, fasta -> fasta }, ch_gtf.map{ meta, gtf -> gtf } ) + FILTER( RUN.out.txt.map{ meta, txt -> [ meta + [tool: "dcc"], txt ] }, bsj_reads ) + + ch_versions = ch_versions.mix(MATE1_1ST_PASS.out.versions) + ch_versions = ch_versions.mix(MATE1_SJDB.out.versions) + ch_versions = ch_versions.mix(MATE1_2ND_PASS.out.versions) + ch_versions = ch_versions.mix(MATE2_1ST_PASS.out.versions) + ch_versions = ch_versions.mix(MATE2_SJDB.out.versions) + ch_versions = ch_versions.mix(MATE2_2ND_PASS.out.versions) + ch_versions = ch_versions.mix(RUN.out.versions) + ch_versions = ch_versions.mix(FILTER.out.versions) + + emit: + matrix = FILTER.out.matrix + results = FILTER.out.results + + versions = ch_versions +} \ No newline at end of file From 6c9eefc2654bbaab8819a07a90c19f4ce002942c Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 09:36:41 +0200 Subject: [PATCH 239/491] Simplify MAPSPLICE --- conf/modules.config | 10 +++--- subworkflows/local/circrna_discovery.nf | 31 +++--------------- subworkflows/local/discovery/mapsplice.nf | 39 +++++++++++++++++++++++ 3 files changed, 49 insertions(+), 31 deletions(-) create mode 100644 subworkflows/local/discovery/mapsplice.nf diff --git a/conf/modules.config b/conf/modules.config index 2848a9d1..fba00b41 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -487,7 +487,7 @@ if (!params.skip_trimming) { ] } - withName: MAPSPLICE_REFERENCE { + withName: '.*:MAPSPLICE:REFERENCE' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('mapsplice') } ext.args = [ "", "-genePredExt", @@ -501,7 +501,7 @@ if (!params.skip_trimming) { ] } - withName: MAPSPLICE_ALIGN { + withName: '.*:MAPSPLICE:ALIGN' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('mapsplice') } ext.args = [ "", "--seglen ${params.seglen}", @@ -519,7 +519,7 @@ if (!params.skip_trimming) { ] } - withName: MAPSPLICE_PARSE { + withName: '.*:MAPSPLICE:PARSE' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('mapsplice') } publishDir = [ path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates/${meta.id}" }, @@ -529,7 +529,7 @@ if (!params.skip_trimming) { ] } - withName: MAPSPLICE_ANNOTATE { + withName: '.*:MAPSPLICE:ANNOTATE' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('mapsplice') } publishDir = [ path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates/${meta.id}" }, @@ -539,7 +539,7 @@ if (!params.skip_trimming) { ] } - withName: MAPSPLICE_FILTER { + withName: '.*:MAPSPLICE:FILTER' { ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('mapsplice') } publishDir = [ path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates/${meta.id}" }, diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index eaa03e61..09978746 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -4,13 +4,8 @@ include { GNU_SORT as COMBINE_ANNOTATION_BEDS } from '../../modules/n include { GNU_SORT as COMBINE_ANNOTATION_GTFS } from '../../modules/nf-core/gnu/sort' include { GAWK as REMOVE_SCORE_STRAND } from '../../modules/nf-core/gawk' include { BEDTOOLS_INTERSECT as INTERSECT_ANNOTATION } from '../../modules/nf-core/bedtools/intersect' -include { MAPSPLICE_ALIGN } from '../../modules/local/mapsplice/align' include { MERGE_TOOLS } from '../../modules/local/count_matrix/merge_tools' include { COUNTS_COMBINED } from '../../modules/local/count_matrix/combined' -include { CIRCEXPLORER2_REFERENCE as MAPSPLICE_REFERENCE } from '../../modules/local/circexplorer2/reference' -include { CIRCEXPLORER2_PARSE as MAPSPLICE_PARSE } from '../../modules/nf-core/circexplorer2/parse' -include { CIRCEXPLORER2_ANNOTATE as MAPSPLICE_ANNOTATE } from '../../modules/nf-core/circexplorer2/annotate' -include { CIRCEXPLORER2_FILTER as MAPSPLICE_FILTER } from '../../modules/local/circexplorer2/filter' include { UPSET as UPSET_SAMPLES } from '../../modules/local/upset' include { UPSET as UPSET_ALL } from '../../modules/local/upset' include { BEDTOOLS_GETFASTA } from '../../modules/nf-core/bedtools/getfasta' @@ -24,6 +19,7 @@ include { CIRCRNA_FINDER } from './discovery/circrna_finder' include { FIND_CIRC } from './discovery/find_circ' include { CIRIQUANT } from './discovery/ciriquant' include { DCC } from './discovery/dcc' +include { MAPSPLICE } from './discovery/mapsplice' workflow CIRCRNA_DISCOVERY { @@ -56,7 +52,6 @@ workflow CIRCRNA_DISCOVERY { // // DISCOVERY TOOLS: // - tools = params.tool.split(',').collect{it.trim().toLowerCase()} SEGEMEHL( reads, fasta, params.segemehl, bsj_reads ) STAR2PASS( reads, star_index, ch_gtf, bsj_reads, star_ignore_sjdbgtf, seq_center, seq_platform ) CIRCEXPLORER2( gtf, fasta, STAR2PASS.out.junction, bsj_reads ) @@ -64,6 +59,7 @@ workflow CIRCRNA_DISCOVERY { FIND_CIRC( reads, bowtie2_index, ch_fasta, bsj_reads ) CIRIQUANT( reads, ch_gtf, ch_fasta, bwa_index, hisat2_index, bsj_reads ) DCC( reads, ch_fasta, ch_gtf, star_index, STAR2PASS.out.junction, star_ignore_sjdbgtf, seq_platform, seq_center, bsj_reads ) + MAPSPLICE( reads, gtf, fasta, bowtie_index, chromosomes, STAR2PASS.out.junction, bsj_reads ) ch_versions = ch_versions.mix(SEGEMEHL.out.versions) ch_versions = ch_versions.mix(STAR2PASS.out.versions) @@ -72,24 +68,7 @@ workflow CIRCRNA_DISCOVERY { ch_versions = ch_versions.mix(FIND_CIRC.out.versions) ch_versions = ch_versions.mix(CIRIQUANT.out.versions) ch_versions = ch_versions.mix(DCC.out.versions) - - - // - // MAPSPLICE WORKFLOW: - // - - MAPSPLICE_REFERENCE( gtf ) - MAPSPLICE_ALIGN( reads, bowtie_index, chromosomes, gtf ) - MAPSPLICE_PARSE( MAPSPLICE_ALIGN.out.raw_fusions ) - MAPSPLICE_ANNOTATE( MAPSPLICE_PARSE.out.junction, fasta, MAPSPLICE_REFERENCE.out.txt ) - mapsplice_filter = MAPSPLICE_ANNOTATE.out.txt.map{ meta, txt -> [ meta + [tool: "mapsplice"], txt ] } - MAPSPLICE_FILTER( mapsplice_filter, bsj_reads ) - - ch_versions = ch_versions.mix(MAPSPLICE_REFERENCE.out.versions) - ch_versions = ch_versions.mix(MAPSPLICE_ALIGN.out.versions) - ch_versions = ch_versions.mix(MAPSPLICE_PARSE.out.versions) - ch_versions = ch_versions.mix(MAPSPLICE_ANNOTATE.out.versions) - ch_versions = ch_versions.mix(MAPSPLICE_FILTER.out.versions) + ch_versions = ch_versions.mix(MAPSPLICE.out.versions) // // COUNT MATRIX WORKFLOW: @@ -100,7 +79,7 @@ workflow CIRCRNA_DISCOVERY { FIND_CIRC.out.matrix, CIRIQUANT.out.matrix, DCC.out.matrix, - MAPSPLICE_FILTER.out.matrix) + MAPSPLICE.out.matrix) tools_selected = params.tool.split(',').collect{it.trim().toLowerCase()} @@ -122,7 +101,7 @@ workflow CIRCRNA_DISCOVERY { FIND_CIRC.out.results, CIRIQUANT.out.results, DCC.out.results, - MAPSPLICE_FILTER.out.results) + MAPSPLICE.out.results) UPSET_SAMPLES( circrna_tools.map{ meta, bed -> [meta.id, meta.tool, bed]} .groupTuple() diff --git a/subworkflows/local/discovery/mapsplice.nf b/subworkflows/local/discovery/mapsplice.nf new file mode 100644 index 00000000..d4640047 --- /dev/null +++ b/subworkflows/local/discovery/mapsplice.nf @@ -0,0 +1,39 @@ +include { CIRCEXPLORER2_REFERENCE as REFERENCE } from '../../../modules/local/circexplorer2/reference' +include { MAPSPLICE_ALIGN as ALIGN } from '../../../modules/local/mapsplice/align' +include { CIRCEXPLORER2_PARSE as PARSE } from '../../../modules/nf-core/circexplorer2/parse' +include { CIRCEXPLORER2_ANNOTATE as ANNOTATE } from '../../../modules/nf-core/circexplorer2/annotate' +include { CIRCEXPLORER2_FILTER as FILTER } from '../../../modules/local/circexplorer2/filter' + + +workflow MAPSPLICE { + take: + reads + gtf + fasta + bowtie_index + chromosomes + star_junctions + bsj_reads + + main: + ch_versions = Channel.empty() + + REFERENCE( gtf ) + ALIGN( reads, bowtie_index, chromosomes, gtf ) + PARSE( ALIGN.out.raw_fusions ) + ANNOTATE( PARSE.out.junction, fasta, REFERENCE.out.txt ) + FILTER( ANNOTATE.out.txt.map{ meta, txt -> + [ meta + [tool: "mapsplice"], txt ] }, bsj_reads ) + + ch_versions = ch_versions.mix(REFERENCE.out.versions) + ch_versions = ch_versions.mix(ALIGN.out.versions) + ch_versions = ch_versions.mix(PARSE.out.versions) + ch_versions = ch_versions.mix(ANNOTATE.out.versions) + ch_versions = ch_versions.mix(FILTER.out.versions) + + emit: + matrix = FILTER.out.matrix + results = FILTER.out.results + + versions = ch_versions +} \ No newline at end of file From 291c14e3c4a9e391658f9156f10ec0f6038e473e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 09:50:24 +0200 Subject: [PATCH 240/491] Restructure discovery tool calls --- subworkflows/local/circrna_discovery.nf | 70 ++++++++++++++----------- 1 file changed, 40 insertions(+), 30 deletions(-) diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 09978746..53b99144 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -39,48 +39,65 @@ workflow CIRCRNA_DISCOVERY { exon_boundary main: - ch_versions = Channel.empty() + ch_versions = Channel.empty() + ch_matrix = Channel.empty() + ch_results = Channel.empty() ch_multiqc_files = Channel.empty() - fasta = ch_fasta.map{meta, fasta -> fasta} - gtf = ch_gtf.map{meta, gtf -> gtf} + fasta = ch_fasta.map{meta, fasta -> fasta} + gtf = ch_gtf.map{meta, gtf -> gtf} - // STAR CONSTANT PARAMETERS + // STAR 2-PASS-MODE star_ignore_sjdbgtf = true seq_center = params.seq_center ?: '' seq_platform = '' + STAR2PASS( reads, star_index, ch_gtf, bsj_reads, star_ignore_sjdbgtf, seq_center, seq_platform ) + ch_versions = ch_versions.mix(STAR2PASS.out.versions) // // DISCOVERY TOOLS: // SEGEMEHL( reads, fasta, params.segemehl, bsj_reads ) - STAR2PASS( reads, star_index, ch_gtf, bsj_reads, star_ignore_sjdbgtf, seq_center, seq_platform ) - CIRCEXPLORER2( gtf, fasta, STAR2PASS.out.junction, bsj_reads ) - CIRCRNA_FINDER( fasta, STAR2PASS.out.sam, STAR2PASS.out.junction, STAR2PASS.out.tab, bsj_reads ) - FIND_CIRC( reads, bowtie2_index, ch_fasta, bsj_reads ) - CIRIQUANT( reads, ch_gtf, ch_fasta, bwa_index, hisat2_index, bsj_reads ) - DCC( reads, ch_fasta, ch_gtf, star_index, STAR2PASS.out.junction, star_ignore_sjdbgtf, seq_platform, seq_center, bsj_reads ) - MAPSPLICE( reads, gtf, fasta, bowtie_index, chromosomes, STAR2PASS.out.junction, bsj_reads ) - ch_versions = ch_versions.mix(SEGEMEHL.out.versions) - ch_versions = ch_versions.mix(STAR2PASS.out.versions) + ch_matrix = ch_matrix .mix(SEGEMEHL.out.matrix) + ch_results = ch_results .mix(SEGEMEHL.out.results) + + CIRCEXPLORER2( gtf, fasta, STAR2PASS.out.junction, bsj_reads ) ch_versions = ch_versions.mix(CIRCEXPLORER2.out.versions) + ch_matrix = ch_matrix .mix(CIRCEXPLORER2.out.matrix) + ch_results = ch_results .mix(CIRCEXPLORER2.out.results) + + CIRCRNA_FINDER( fasta, STAR2PASS.out.sam, STAR2PASS.out.junction, + STAR2PASS.out.tab, bsj_reads ) ch_versions = ch_versions.mix(CIRCRNA_FINDER.out.versions) + ch_matrix = ch_matrix .mix(CIRCRNA_FINDER.out.matrix) + ch_results = ch_results .mix(CIRCRNA_FINDER.out.results) + + FIND_CIRC( reads, bowtie2_index, ch_fasta, bsj_reads ) ch_versions = ch_versions.mix(FIND_CIRC.out.versions) + ch_matrix = ch_matrix .mix(FIND_CIRC.out.matrix) + ch_results = ch_results .mix(FIND_CIRC.out.results) + + CIRIQUANT( reads, ch_gtf, ch_fasta, bwa_index, hisat2_index, bsj_reads ) ch_versions = ch_versions.mix(CIRIQUANT.out.versions) + ch_matrix = ch_matrix.mix(CIRIQUANT.out.matrix) + ch_results = ch_results.mix(CIRIQUANT.out.results) + + DCC( reads, ch_fasta, ch_gtf, star_index, STAR2PASS.out.junction, + star_ignore_sjdbgtf, seq_platform, seq_center, bsj_reads ) ch_versions = ch_versions.mix(DCC.out.versions) + ch_matrix = ch_matrix.mix(DCC.out.matrix) + ch_results = ch_results.mix(DCC.out.results) + + MAPSPLICE( reads, gtf, fasta, bowtie_index, chromosomes, + STAR2PASS.out.junction, bsj_reads ) ch_versions = ch_versions.mix(MAPSPLICE.out.versions) + ch_matrix = ch_matrix.mix(MAPSPLICE.out.matrix) + ch_results = ch_results.mix(MAPSPLICE.out.results) // // COUNT MATRIX WORKFLOW: // - ch_matrix = CIRCEXPLORER2.out.matrix.mix(SEGEMEHL.out.matrix, - CIRCRNA_FINDER.out.matrix, - FIND_CIRC.out.matrix, - CIRIQUANT.out.matrix, - DCC.out.matrix, - MAPSPLICE.out.matrix) - tools_selected = params.tool.split(',').collect{it.trim().toLowerCase()} MERGE_TOOLS( ch_matrix.map{ meta, bed -> [ [id: meta.id], bed ] }.groupTuple(), @@ -96,17 +113,10 @@ workflow CIRCRNA_DISCOVERY { ch_biotypes = Channel.fromPath("${projectDir}/bin/unwanted_biotypes.txt") - circrna_tools = CIRCEXPLORER2.out.results.mix(SEGEMEHL.out.results, - CIRCRNA_FINDER.out.results, - FIND_CIRC.out.results, - CIRIQUANT.out.results, - DCC.out.results, - MAPSPLICE.out.results) - - UPSET_SAMPLES( circrna_tools.map{ meta, bed -> [meta.id, meta.tool, bed]} + UPSET_SAMPLES( ch_results.map{ meta, bed -> [meta.id, meta.tool, bed]} .groupTuple() .map{ sample, tools, beds -> [[id: sample], tools, beds]} ) - UPSET_ALL( circrna_tools.map{ meta, bed -> ["all", meta.tool, bed] } + UPSET_ALL( ch_results.map{ meta, bed -> ["all", meta.tool, bed] } .groupTuple() .map{ sample, tools, beds -> [[id: sample], tools, beds]} ) @@ -115,7 +125,7 @@ workflow CIRCRNA_DISCOVERY { ch_versions = ch_versions.mix(UPSET_SAMPLES.out.versions) ch_versions = ch_versions.mix(UPSET_ALL.out.versions) - circrna_incl_merged = circrna_tools.mix( + circrna_incl_merged = ch_results.mix( MERGE_TOOLS.out.merged.map{ meta, bed -> [meta + [tool: "merged"], bed] }) INTERSECT_ANNOTATION( circrna_incl_merged.combine(gtf), [[], []]) From 5fa979b254e04bd2b1bfdb7273a792279d9e83f5 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 10:08:33 +0200 Subject: [PATCH 241/491] Restructure discovery downstream workflows --- subworkflows/local/circrna_discovery.nf | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 53b99144..324eb223 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -95,7 +95,7 @@ workflow CIRCRNA_DISCOVERY { ch_results = ch_results.mix(MAPSPLICE.out.results) // - // COUNT MATRIX WORKFLOW: + // CREATE COUNT MATRIX // tools_selected = params.tool.split(',').collect{it.trim().toLowerCase()} @@ -108,11 +108,9 @@ workflow CIRCRNA_DISCOVERY { ch_versions = ch_versions.mix(COUNTS_COMBINED.out.versions) // - // ANNOTATION WORKFLOW: + // UPSET PLOTS // - ch_biotypes = Channel.fromPath("${projectDir}/bin/unwanted_biotypes.txt") - UPSET_SAMPLES( ch_results.map{ meta, bed -> [meta.id, meta.tool, bed]} .groupTuple() .map{ sample, tools, beds -> [[id: sample], tools, beds]} ) @@ -125,6 +123,10 @@ workflow CIRCRNA_DISCOVERY { ch_versions = ch_versions.mix(UPSET_SAMPLES.out.versions) ch_versions = ch_versions.mix(UPSET_ALL.out.versions) + // + // ANNOTATION WORKFLOW: + // + circrna_incl_merged = ch_results.mix( MERGE_TOOLS.out.merged.map{ meta, bed -> [meta + [tool: "merged"], bed] }) From a7465489e0934293ae8993b3ad3711fbfdb19124 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 10:23:50 +0200 Subject: [PATCH 242/491] Simplify annotation workflow --- conf/modules.config | 8 ++-- subworkflows/local/circrna_discovery.nf | 47 +++++++--------------- subworkflows/local/discovery/annotation.nf | 38 +++++++++++++++++ 3 files changed, 57 insertions(+), 36 deletions(-) create mode 100644 subworkflows/local/discovery/annotation.nf diff --git a/conf/modules.config b/conf/modules.config index fba00b41..5cf8f43b 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -567,22 +567,22 @@ if (!params.skip_trimming) { ext.when = { params.tool.split(',').length > 1 } } - withName: INTERSECT_ANNOTATION { + withName: '.*:ANNOTATION:INTERSECT' { ext.args = "-loj" ext.suffix = "intersect.bed" } - withName: COMBINE_ANNOTATION_BEDS { + withName: '.*:ANNOTATION:COMBINE_BEDS' { ext.args = "-k 1,1 -k2,2n -k3,3n -u" ext.suffix = "combined.bed" } - withName: COMBINE_ANNOTATION_GTFS { + withName: '.*:ANNOTATION:COMBINE_GTFS' { ext.args = "-k 1,1 -k3,3n -k4,4n -u" ext.suffix = "combined.gtf" } - withName: REMOVE_SCORE_STRAND { + withName: '.*:ANNOTATION:REMOVE_SCORE_STRAND' { ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3, \".\", \".\", \$7, \$8, \$9, \$10 }'" ext.suffix = "tidy.bed" } diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 324eb223..740dc3a4 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -1,9 +1,4 @@ // MODULES -include { ANNOTATION } from '../../modules/local/annotation/full_annotation' -include { GNU_SORT as COMBINE_ANNOTATION_BEDS } from '../../modules/nf-core/gnu/sort' -include { GNU_SORT as COMBINE_ANNOTATION_GTFS } from '../../modules/nf-core/gnu/sort' -include { GAWK as REMOVE_SCORE_STRAND } from '../../modules/nf-core/gawk' -include { BEDTOOLS_INTERSECT as INTERSECT_ANNOTATION } from '../../modules/nf-core/bedtools/intersect' include { MERGE_TOOLS } from '../../modules/local/count_matrix/merge_tools' include { COUNTS_COMBINED } from '../../modules/local/count_matrix/combined' include { UPSET as UPSET_SAMPLES } from '../../modules/local/upset' @@ -20,6 +15,7 @@ include { FIND_CIRC } from './discovery/find_circ' include { CIRIQUANT } from './discovery/ciriquant' include { DCC } from './discovery/dcc' include { MAPSPLICE } from './discovery/mapsplice' +include { ANNOTATION } from './discovery/annotation' workflow CIRCRNA_DISCOVERY { @@ -104,6 +100,9 @@ workflow CIRCRNA_DISCOVERY { tools_selected.size() > 1 ? tool_filter : 1, duplicates_fun ) COUNTS_COMBINED( MERGE_TOOLS.out.merged.map{ meta, bed -> bed }.collect() ) + ch_results_incl_merged = ch_results.mix( + MERGE_TOOLS.out.merged.map{ meta, bed -> [meta + [tool: "merged"], bed] }) + ch_versions = ch_versions.mix(MERGE_TOOLS.out.versions) ch_versions = ch_versions.mix(COUNTS_COMBINED.out.versions) @@ -127,43 +126,27 @@ workflow CIRCRNA_DISCOVERY { // ANNOTATION WORKFLOW: // - circrna_incl_merged = ch_results.mix( - MERGE_TOOLS.out.merged.map{ meta, bed -> [meta + [tool: "merged"], bed] }) - - INTERSECT_ANNOTATION( circrna_incl_merged.combine(gtf), [[], []]) - ANNOTATION( INTERSECT_ANNOTATION.out.intersect, exon_boundary ) - - ch_annotation_bed_merged = ANNOTATION.out.bed.filter{ meta, bed -> meta.tool == "merged" } - ch_annotation_gtf_merged = ANNOTATION.out.gtf.filter{ meta, gtf -> meta.tool == "merged" } - - COMBINE_ANNOTATION_BEDS(ch_annotation_bed_merged.map{ meta, bed -> bed}.collect().map{[[id: "annotation"], it]}) - REMOVE_SCORE_STRAND( COMBINE_ANNOTATION_BEDS.out.sorted, []) - COMBINE_ANNOTATION_GTFS(ch_annotation_gtf_merged.map{ meta, gtf -> gtf}.collect().map{[[id: "annotation"], it]}) - - ch_versions = ch_versions.mix(INTERSECT_ANNOTATION.out.versions) + ANNOTATION( ch_results_incl_merged, gtf, exon_boundary ) ch_versions = ch_versions.mix(ANNOTATION.out.versions) - ch_versions = ch_versions.mix(COMBINE_ANNOTATION_BEDS.out.versions) - ch_versions = ch_versions.mix(REMOVE_SCORE_STRAND.out.versions) - ch_versions = ch_versions.mix(COMBINE_ANNOTATION_GTFS.out.versions) // // FASTA WORKFLOW: // - BEDTOOLS_GETFASTA( ch_annotation_bed_merged, fasta ) + BEDTOOLS_GETFASTA( ANNOTATION.out.merged_bed, fasta ) ADD_BACKSPLICE( BEDTOOLS_GETFASTA.out.fasta, []) ch_versions = ch_versions.mix(BEDTOOLS_GETFASTA.out.versions) ch_versions = ch_versions.mix(ADD_BACKSPLICE.out.versions) emit: - circrna_bed12 = ch_annotation_bed_merged - fasta = ADD_BACKSPLICE.out.output - annotation_bed = REMOVE_SCORE_STRAND.out.output - annotation_gtf = COMBINE_ANNOTATION_GTFS.out.sorted - counts_bed = COUNTS_COMBINED.out.counts_bed - counts_tsv = COUNTS_COMBINED.out.counts_tsv - - multiqc_files = ch_multiqc_files - versions = ch_versions + circrna_bed12 = ANNOTATION.out.merged_bed + fasta = ADD_BACKSPLICE.out.output + annotation_bed = ANNOTATION.out.bed + annotation_gtf = ANNOTATION.out.gtf + counts_bed = COUNTS_COMBINED.out.counts_bed + counts_tsv = COUNTS_COMBINED.out.counts_tsv + + multiqc_files = ch_multiqc_files + versions = ch_versions } diff --git a/subworkflows/local/discovery/annotation.nf b/subworkflows/local/discovery/annotation.nf new file mode 100644 index 00000000..feded6a5 --- /dev/null +++ b/subworkflows/local/discovery/annotation.nf @@ -0,0 +1,38 @@ +include { BEDTOOLS_INTERSECT as INTERSECT } from '../../../modules/nf-core/bedtools/intersect' +include { ANNOTATION as ANNOTATE } from '../../../modules/local/annotation/full_annotation' +include { GNU_SORT as COMBINE_BEDS } from '../../../modules/nf-core/gnu/sort' +include { GAWK as REMOVE_SCORE_STRAND } from '../../../modules/nf-core/gawk' +include { GNU_SORT as COMBINE_GTFS } from '../../../modules/nf-core/gnu/sort' + +workflow ANNOTATION { + take: + regions + gtf + exon_boundary + + main: + ch_versions = Channel.empty() + + INTERSECT( regions.combine(gtf), [[], []]) + ANNOTATE( INTERSECT.out.intersect, exon_boundary ) + + ch_bed_merged = ANNOTATE.out.bed.filter{ meta, bed -> meta.tool == "merged" } + ch_gtf_merged = ANNOTATE.out.gtf.filter{ meta, gtf -> meta.tool == "merged" } + + COMBINE_BEDS(ch_bed_merged.map{ meta, bed -> bed}.collect().map{[[id: "annotation"], it]}) + REMOVE_SCORE_STRAND( COMBINE_BEDS.out.sorted, []) + COMBINE_GTFS(ch_gtf_merged.map{ meta, gtf -> gtf}.collect().map{[[id: "annotation"], it]}) + + ch_versions = ch_versions.mix(INTERSECT.out.versions) + ch_versions = ch_versions.mix(ANNOTATE.out.versions) + ch_versions = ch_versions.mix(COMBINE_BEDS.out.versions) + ch_versions = ch_versions.mix(REMOVE_SCORE_STRAND.out.versions) + ch_versions = ch_versions.mix(COMBINE_GTFS.out.versions) + + emit: + merged_bed = ch_bed_merged + bed = REMOVE_SCORE_STRAND.out.output + gtf = COMBINE_GTFS.out.sorted + + versions = ch_versions +} \ No newline at end of file From ca5abfaedf5e81760f2bce211f4be0898647aade Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 10:48:01 +0200 Subject: [PATCH 243/491] Change the way discovery tools are disabled --- conf/modules.config | 26 ------- subworkflows/local/circrna_discovery.nf | 96 +++++++++++++++---------- 2 files changed, 57 insertions(+), 65 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 5cf8f43b..781bce3c 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -144,7 +144,6 @@ if (!params.skip_trimming) { } withName: '.*:SEGEMEHL:INDEX' { - ext.when = { !params.segemehl && params.tool.split(',').contains('segemehl') && params.module.split(',').contains('circrna_discovery') } publishDir = [ path: { "${params.outdir}/references/index/segemehl" }, mode: params.publish_dir_mode, @@ -156,7 +155,6 @@ if (!params.skip_trimming) { // circRNA withName: '.*:SEGEMEHL:ALIGN' { - ext.when = { params.tool.split(',').contains('segemehl') && params.module.split(',').contains('circrna_discovery') } ext.args = [ "", "-b", "-S" @@ -231,7 +229,6 @@ if (!params.skip_trimming) { } withName: '.*:CIRCEXPLORER2:REFERENCE' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('circexplorer2') } ext.args = [ "", "-genePredExt", "-geneNameAsName2" @@ -245,7 +242,6 @@ if (!params.skip_trimming) { } withName: '.*:CIRCEXPLORER2:PARSE' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('circexplorer2') } publishDir = [ path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates/${meta.id}" }, mode: params.publish_dir_mode, @@ -255,7 +251,6 @@ if (!params.skip_trimming) { } withName: '.*:CIRCEXPLORER2:ANNOTATE' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('circexplorer2') } publishDir = [ path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates/${meta.id}" }, mode: params.publish_dir_mode, @@ -265,7 +260,6 @@ if (!params.skip_trimming) { } withName: '.*:CIRCEXPLORER2:FILTER' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('circexplorer2') } publishDir = [ path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates/${meta.id}" }, mode: params.publish_dir_mode, @@ -276,7 +270,6 @@ if (!params.skip_trimming) { } withName: '.*:CIRCRNA_FINDER:FILTER' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('circrna_finder') } publishDir = [ path: { "${params.outdir}/circrna_discovery/circrna_finder/intermediates/${meta.id}" }, mode: params.publish_dir_mode, @@ -287,7 +280,6 @@ if (!params.skip_trimming) { } withName: '.*:FIND_CIRC:ALIGN' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('find_circ') } ext.args = [ "", "--very-sensitive", "--mm", @@ -304,7 +296,6 @@ if (!params.skip_trimming) { } withName: '.*:FIND_CIRC:SAMTOOLS_VIEW' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('find_circ') } ext.prefix = { "${meta.id}_unmapped" } ext.args = "-hf 4" publishDir = [ @@ -316,7 +307,6 @@ if (!params.skip_trimming) { } withName: '.*:FIND_CIRC:ANCHORS' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('find_circ') } publishDir = [ path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, @@ -326,7 +316,6 @@ if (!params.skip_trimming) { } withName: '.*:FIND_CIRC:RUN' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('find_circ') } publishDir = [ path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, @@ -336,7 +325,6 @@ if (!params.skip_trimming) { } withName: '.*:FIND_CIRC:FILTER' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('find_circ') } publishDir = [ path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, @@ -347,7 +335,6 @@ if (!params.skip_trimming) { } withName: '.*:CIRIQUANT:RUN' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('ciriquant') } publishDir = [ path: { "${params.outdir}/circrna_discovery/ciriquant/intermediates/${meta.id}" }, mode: params.publish_dir_mode, @@ -357,7 +344,6 @@ if (!params.skip_trimming) { } withName: '.*:CIRIQUANT:FILTER' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('ciriquant') } publishDir = [ path: { "${params.outdir}/circrna_discovery/ciriquant/intermediates/${meta.id}" }, mode: params.publish_dir_mode, @@ -368,7 +354,6 @@ if (!params.skip_trimming) { } withName: '.*:DCC:MATE1_1ST_PASS' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('dcc') } ext.prefix = { "${meta.id}_mate1" } ext.args = [ "", "--chimOutType Junctions WithinBAM", @@ -390,7 +375,6 @@ if (!params.skip_trimming) { } withName: '.*:DCC:MATE1_SJDB' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('dcc') } publishDir = [ path: { "${params.outdir}/circrna_discovery/dcc/intermediates/mate1/sjdb" }, mode: params.publish_dir_mode, @@ -400,7 +384,6 @@ if (!params.skip_trimming) { } withName: '.*:DCC:MATE1_2ND_PASS' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('dcc') } ext.prefix = { "${meta.id}_mate1" } ext.args = [ "", "--chimOutType Junctions WithinBAM", @@ -423,7 +406,6 @@ if (!params.skip_trimming) { } withName: '.*:DCC:MATE2_1ST_PASS' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('dcc') } ext.prefix = { "${meta.id}_mate2" } ext.args = [ "", "--chimOutType Junctions WithinBAM", @@ -445,7 +427,6 @@ if (!params.skip_trimming) { } withName: '.*:DCC:MATE2_SJDB' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('dcc') } publishDir = [ path: { "${params.outdir}/circrna_discovery/dcc/intermediates/mate2/sjdb" }, mode: params.publish_dir_mode, @@ -455,7 +436,6 @@ if (!params.skip_trimming) { } withName: '.*:DCC:MATE2_2ND_PASS' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('dcc') } ext.prefix = { "${meta.id}_mate2" } ext.args = [ "", "--chimOutType Junctions WithinBAM", @@ -478,7 +458,6 @@ if (!params.skip_trimming) { } withName: '.*:DCC:RUN' { - ext.when = { params.tool.split(',').contains('dcc') && params.module.split(',').contains('circrna_discovery') } publishDir = [ path: { "${params.outdir}/circrna_discovery/dcc/intermediates/${meta.id}" }, mode: params.publish_dir_mode, @@ -488,7 +467,6 @@ if (!params.skip_trimming) { } withName: '.*:MAPSPLICE:REFERENCE' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('mapsplice') } ext.args = [ "", "-genePredExt", "-geneNameAsName2" @@ -502,7 +480,6 @@ if (!params.skip_trimming) { } withName: '.*:MAPSPLICE:ALIGN' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('mapsplice') } ext.args = [ "", "--seglen ${params.seglen}", "--min-intron ${params.min_intron}", @@ -520,7 +497,6 @@ if (!params.skip_trimming) { } withName: '.*:MAPSPLICE:PARSE' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('mapsplice') } publishDir = [ path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates/${meta.id}" }, mode: params.publish_dir_mode, @@ -530,7 +506,6 @@ if (!params.skip_trimming) { } withName: '.*:MAPSPLICE:ANNOTATE' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('mapsplice') } publishDir = [ path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates/${meta.id}" }, mode: params.publish_dir_mode, @@ -540,7 +515,6 @@ if (!params.skip_trimming) { } withName: '.*:MAPSPLICE:FILTER' { - ext.when = { params.module.split(',').contains('circrna_discovery') && params.tool.split(',').contains('mapsplice') } publishDir = [ path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates/${meta.id}" }, mode: params.publish_dir_mode, diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 740dc3a4..2096ddb7 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -52,50 +52,68 @@ workflow CIRCRNA_DISCOVERY { // // DISCOVERY TOOLS: // - SEGEMEHL( reads, fasta, params.segemehl, bsj_reads ) - ch_versions = ch_versions.mix(SEGEMEHL.out.versions) - ch_matrix = ch_matrix .mix(SEGEMEHL.out.matrix) - ch_results = ch_results .mix(SEGEMEHL.out.results) - - CIRCEXPLORER2( gtf, fasta, STAR2PASS.out.junction, bsj_reads ) - ch_versions = ch_versions.mix(CIRCEXPLORER2.out.versions) - ch_matrix = ch_matrix .mix(CIRCEXPLORER2.out.matrix) - ch_results = ch_results .mix(CIRCEXPLORER2.out.results) - - CIRCRNA_FINDER( fasta, STAR2PASS.out.sam, STAR2PASS.out.junction, - STAR2PASS.out.tab, bsj_reads ) - ch_versions = ch_versions.mix(CIRCRNA_FINDER.out.versions) - ch_matrix = ch_matrix .mix(CIRCRNA_FINDER.out.matrix) - ch_results = ch_results .mix(CIRCRNA_FINDER.out.results) - - FIND_CIRC( reads, bowtie2_index, ch_fasta, bsj_reads ) - ch_versions = ch_versions.mix(FIND_CIRC.out.versions) - ch_matrix = ch_matrix .mix(FIND_CIRC.out.matrix) - ch_results = ch_results .mix(FIND_CIRC.out.results) - - CIRIQUANT( reads, ch_gtf, ch_fasta, bwa_index, hisat2_index, bsj_reads ) - ch_versions = ch_versions.mix(CIRIQUANT.out.versions) - ch_matrix = ch_matrix.mix(CIRIQUANT.out.matrix) - ch_results = ch_results.mix(CIRIQUANT.out.results) - - DCC( reads, ch_fasta, ch_gtf, star_index, STAR2PASS.out.junction, - star_ignore_sjdbgtf, seq_platform, seq_center, bsj_reads ) - ch_versions = ch_versions.mix(DCC.out.versions) - ch_matrix = ch_matrix.mix(DCC.out.matrix) - ch_results = ch_results.mix(DCC.out.results) - - MAPSPLICE( reads, gtf, fasta, bowtie_index, chromosomes, - STAR2PASS.out.junction, bsj_reads ) - ch_versions = ch_versions.mix(MAPSPLICE.out.versions) - ch_matrix = ch_matrix.mix(MAPSPLICE.out.matrix) - ch_results = ch_results.mix(MAPSPLICE.out.results) + tools_selected = params.tool.split(',').collect{it.trim().toLowerCase()} + + if (tools_selected.size() == 0) { + error 'No tools selected for circRNA discovery.' + } + + if (tools_selected.contains('segemehl')) { + SEGEMEHL( reads, fasta, params.segemehl, bsj_reads ) + ch_versions = ch_versions.mix(SEGEMEHL.out.versions) + ch_matrix = ch_matrix .mix(SEGEMEHL.out.matrix) + ch_results = ch_results .mix(SEGEMEHL.out.results) + } + + if (tools_selected.contains('circexplorer2')) { + CIRCEXPLORER2( gtf, fasta, STAR2PASS.out.junction, bsj_reads ) + ch_versions = ch_versions.mix(CIRCEXPLORER2.out.versions) + ch_matrix = ch_matrix .mix(CIRCEXPLORER2.out.matrix) + ch_results = ch_results .mix(CIRCEXPLORER2.out.results) + } + + if (tools_selected.contains('circrna_finder')) { + CIRCRNA_FINDER( fasta, STAR2PASS.out.sam, STAR2PASS.out.junction, + STAR2PASS.out.tab, bsj_reads ) + ch_versions = ch_versions.mix(CIRCRNA_FINDER.out.versions) + ch_matrix = ch_matrix .mix(CIRCRNA_FINDER.out.matrix) + ch_results = ch_results .mix(CIRCRNA_FINDER.out.results) + } + + if (tools_selected.contains('find_circ')) { + FIND_CIRC( reads, bowtie2_index, ch_fasta, bsj_reads ) + ch_versions = ch_versions.mix(FIND_CIRC.out.versions) + ch_matrix = ch_matrix .mix(FIND_CIRC.out.matrix) + ch_results = ch_results .mix(FIND_CIRC.out.results) + } + + if (tools_selected.contains('ciriquant')) { + CIRIQUANT( reads, ch_gtf, ch_fasta, bwa_index, hisat2_index, bsj_reads ) + ch_versions = ch_versions.mix(CIRIQUANT.out.versions) + ch_matrix = ch_matrix .mix(CIRIQUANT.out.matrix) + ch_results = ch_results .mix(CIRIQUANT.out.results) + } + + if (tools_selected.contains('dcc')) { + DCC( reads, ch_fasta, ch_gtf, star_index, STAR2PASS.out.junction, + star_ignore_sjdbgtf, seq_platform, seq_center, bsj_reads ) + ch_versions = ch_versions.mix(DCC.out.versions) + ch_matrix = ch_matrix.mix(DCC.out.matrix) + ch_results = ch_results.mix(DCC.out.results) + } + + if (tools_selected.contains('mapsplice')) { + MAPSPLICE( reads, gtf, fasta, bowtie_index, chromosomes, + STAR2PASS.out.junction, bsj_reads ) + ch_versions = ch_versions.mix(MAPSPLICE.out.versions) + ch_matrix = ch_matrix.mix(MAPSPLICE.out.matrix) + ch_results = ch_results.mix(MAPSPLICE.out.results) + } // // CREATE COUNT MATRIX // - tools_selected = params.tool.split(',').collect{it.trim().toLowerCase()} - MERGE_TOOLS( ch_matrix.map{ meta, bed -> [ [id: meta.id], bed ] }.groupTuple(), tools_selected.size() > 1 ? tool_filter : 1, duplicates_fun ) COUNTS_COMBINED( MERGE_TOOLS.out.merged.map{ meta, bed -> bed }.collect() ) From 27b5ab7b2972cedb10023c19cf8993b05e03bef1 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 11:13:12 +0200 Subject: [PATCH 244/491] Switch segemehl to bed output --- bin/merge_tools.py | 11 +++------- conf/modules.config | 10 ++++++--- subworkflows/local/circrna_discovery.nf | 28 ++++++++++-------------- subworkflows/local/discovery/segemehl.nf | 11 +++++----- 4 files changed, 26 insertions(+), 34 deletions(-) diff --git a/bin/merge_tools.py b/bin/merge_tools.py index 32bacab1..3d6a1396 100755 --- a/bin/merge_tools.py +++ b/bin/merge_tools.py @@ -11,19 +11,14 @@ args = parser.parse_args() -columns = ['chr', 'start', 'end', 'strand', 'count'] +columns = ['chr', 'start', 'end', 'name', 'count', 'strand'] dfs = [pd.read_csv(bed, sep='\t', header=None, names=columns) for bed in args.beds] df = pd.concat(dfs) df['tool_count'] = 1 - -df = df.groupby(['chr', 'start', 'end', 'strand']).agg({'count': args.duplicates_fun, +df = df.groupby(['chr', 'start', 'end', 'strand', 'name']).agg({'count': args.duplicates_fun, 'tool_count': 'sum'}).reset_index() df = df[df['tool_count'] >= args.tool_filter] -df.drop('tool_count', axis=1, inplace=True) -df["name"] = df["chr"] + ":" + df["start"].astype(str) + "-" + df["end"].astype(str) + ":" + df["strand"] - -df = df[['chr', 'start', 'end', 'name', 'count', 'strand']] - +df = df[columns] df.to_csv(args.output, sep='\t', index=False, header=False) diff --git a/conf/modules.config b/conf/modules.config index 781bce3c..c284c678 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -167,13 +167,17 @@ if (!params.skip_trimming) { ] } - withName: '.*:SEGEMEHL:FILTER' { + withName: '.*:SEGEMEHL:UNIFY' { + // Keep only rows with ";C;" in column 4 + // Print $1 $2 $3 $1:$2-$3 $5 $6 + ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (\$4 ~ /;C;/) { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$5, \$6 } }'" + ext.suffix = "segemehl.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/segemehl/intermediates/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/segemehl/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates, - pattern: "*circs.bed" + pattern: "*.segemehl.bed" ] } diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 2096ddb7..9cbbf4a0 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -36,8 +36,7 @@ workflow CIRCRNA_DISCOVERY { main: ch_versions = Channel.empty() - ch_matrix = Channel.empty() - ch_results = Channel.empty() + ch_bed = Channel.empty() ch_multiqc_files = Channel.empty() fasta = ch_fasta.map{meta, fasta -> fasta} gtf = ch_gtf.map{meta, gtf -> gtf} @@ -61,60 +60,55 @@ workflow CIRCRNA_DISCOVERY { if (tools_selected.contains('segemehl')) { SEGEMEHL( reads, fasta, params.segemehl, bsj_reads ) ch_versions = ch_versions.mix(SEGEMEHL.out.versions) - ch_matrix = ch_matrix .mix(SEGEMEHL.out.matrix) - ch_results = ch_results .mix(SEGEMEHL.out.results) + ch_bed = ch_bed .mix(SEGEMEHL.out.bed) } if (tools_selected.contains('circexplorer2')) { CIRCEXPLORER2( gtf, fasta, STAR2PASS.out.junction, bsj_reads ) ch_versions = ch_versions.mix(CIRCEXPLORER2.out.versions) - ch_matrix = ch_matrix .mix(CIRCEXPLORER2.out.matrix) - ch_results = ch_results .mix(CIRCEXPLORER2.out.results) + ch_bed = ch_bed .mix(CIRCEXPLORER2.out.bed) } if (tools_selected.contains('circrna_finder')) { CIRCRNA_FINDER( fasta, STAR2PASS.out.sam, STAR2PASS.out.junction, STAR2PASS.out.tab, bsj_reads ) ch_versions = ch_versions.mix(CIRCRNA_FINDER.out.versions) - ch_matrix = ch_matrix .mix(CIRCRNA_FINDER.out.matrix) - ch_results = ch_results .mix(CIRCRNA_FINDER.out.results) + ch_bed = ch_bed .mix(CIRCRNA_FINDER.out.bed) } if (tools_selected.contains('find_circ')) { FIND_CIRC( reads, bowtie2_index, ch_fasta, bsj_reads ) ch_versions = ch_versions.mix(FIND_CIRC.out.versions) - ch_matrix = ch_matrix .mix(FIND_CIRC.out.matrix) - ch_results = ch_results .mix(FIND_CIRC.out.results) + ch_bed = ch_bed .mix(FIND_CIRC.out.bed) } if (tools_selected.contains('ciriquant')) { CIRIQUANT( reads, ch_gtf, ch_fasta, bwa_index, hisat2_index, bsj_reads ) ch_versions = ch_versions.mix(CIRIQUANT.out.versions) - ch_matrix = ch_matrix .mix(CIRIQUANT.out.matrix) - ch_results = ch_results .mix(CIRIQUANT.out.results) + ch_bed = ch_bed .mix(CIRIQUANT.out.bed) } if (tools_selected.contains('dcc')) { DCC( reads, ch_fasta, ch_gtf, star_index, STAR2PASS.out.junction, star_ignore_sjdbgtf, seq_platform, seq_center, bsj_reads ) ch_versions = ch_versions.mix(DCC.out.versions) - ch_matrix = ch_matrix.mix(DCC.out.matrix) - ch_results = ch_results.mix(DCC.out.results) + ch_bed = ch_bed .mix(DCC.out.bed) } if (tools_selected.contains('mapsplice')) { MAPSPLICE( reads, gtf, fasta, bowtie_index, chromosomes, STAR2PASS.out.junction, bsj_reads ) ch_versions = ch_versions.mix(MAPSPLICE.out.versions) - ch_matrix = ch_matrix.mix(MAPSPLICE.out.matrix) - ch_results = ch_results.mix(MAPSPLICE.out.results) + ch_bed = ch_bed .mix(MAPSPLICE.out.bed) } // // CREATE COUNT MATRIX // - MERGE_TOOLS( ch_matrix.map{ meta, bed -> [ [id: meta.id], bed ] }.groupTuple(), + ch_results = Channel.empty() + + MERGE_TOOLS( ch_bed.map{ meta, bed -> [ [id: meta.id], bed ] }.groupTuple(), tools_selected.size() > 1 ? tool_filter : 1, duplicates_fun ) COUNTS_COMBINED( MERGE_TOOLS.out.merged.map{ meta, bed -> bed }.collect() ) diff --git a/subworkflows/local/discovery/segemehl.nf b/subworkflows/local/discovery/segemehl.nf index 1d380fd1..1d0aae2f 100644 --- a/subworkflows/local/discovery/segemehl.nf +++ b/subworkflows/local/discovery/segemehl.nf @@ -1,6 +1,6 @@ include { SEGEMEHL_INDEX as INDEX } from '../../../modules/nf-core/segemehl/index' include { SEGEMEHL_ALIGN as ALIGN } from '../../../modules/nf-core/segemehl/align' -include { SEGEMEHL_FILTER as FILTER } from '../../../modules/local/segemehl/filter' +include { GAWK as UNIFY } from '../../../modules/nf-core/gawk' workflow SEGEMEHL { @@ -15,15 +15,14 @@ workflow SEGEMEHL { index = index ?: INDEX( fasta ).index ALIGN( reads, fasta, index ) - FILTER( ALIGN.out.results - .map{ meta, results -> [ meta + [tool: "segemehl"], results ] }, bsj_reads ) + UNIFY( ALIGN.out.results + .map{ meta, results -> [ meta + [tool: "segemehl"], results ] }, [] ) ch_versions = ch_versions.mix(ALIGN.out.versions) - ch_versions = ch_versions.mix(FILTER.out.versions) + ch_versions = ch_versions.mix(UNIFY.out.versions) emit: - matrix = FILTER.out.matrix - results = FILTER.out.results + bed = UNIFY.out.output versions = ch_versions } \ No newline at end of file From d5d0f26c87ea7ae71e7d8674924e417a35c53690 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 11:22:42 +0200 Subject: [PATCH 245/491] Implement central BSJ filtering --- conf/modules.config | 6 ++++++ subworkflows/local/circrna_discovery.nf | 8 ++++++-- subworkflows/local/discovery/segemehl.nf | 1 - 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index c284c678..5bba4969 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -528,6 +528,12 @@ if (!params.skip_trimming) { ] } + withName: 'FILTER_BSJS' { + // Make sure score is higher or equal to the threshold + ext.args = { "-v FS='\\t' -v OFS='\\t' '{ if (\$5 >= ${params.bsj_reads}) { print } }'" } + ext.suffix = "filtered.bed" + } + withName: ANNOTATION { ext.prefix = { "${meta.id}.${meta.tool}.annotated" } publishDir = [ diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 9cbbf4a0..4f6bd514 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -1,4 +1,5 @@ // MODULES +include { GAWK as FILTER_BSJS } from '../../modules/nf-core/gawk' include { MERGE_TOOLS } from '../../modules/local/count_matrix/merge_tools' include { COUNTS_COMBINED } from '../../modules/local/count_matrix/combined' include { UPSET as UPSET_SAMPLES } from '../../modules/local/upset' @@ -58,7 +59,7 @@ workflow CIRCRNA_DISCOVERY { } if (tools_selected.contains('segemehl')) { - SEGEMEHL( reads, fasta, params.segemehl, bsj_reads ) + SEGEMEHL( reads, fasta, params.segemehl ) ch_versions = ch_versions.mix(SEGEMEHL.out.versions) ch_bed = ch_bed .mix(SEGEMEHL.out.bed) } @@ -102,13 +103,16 @@ workflow CIRCRNA_DISCOVERY { ch_bed = ch_bed .mix(MAPSPLICE.out.bed) } + FILTER_BSJS( ch_bed, [] ) + ch_versions = ch_versions.mix(FILTER_BSJS.out.versions) + // // CREATE COUNT MATRIX // ch_results = Channel.empty() - MERGE_TOOLS( ch_bed.map{ meta, bed -> [ [id: meta.id], bed ] }.groupTuple(), + MERGE_TOOLS( FILTER_BSJS.out.output.map{ meta, bed -> [ [id: meta.id], bed ] }.groupTuple(), tools_selected.size() > 1 ? tool_filter : 1, duplicates_fun ) COUNTS_COMBINED( MERGE_TOOLS.out.merged.map{ meta, bed -> bed }.collect() ) diff --git a/subworkflows/local/discovery/segemehl.nf b/subworkflows/local/discovery/segemehl.nf index 1d0aae2f..d50ed70a 100644 --- a/subworkflows/local/discovery/segemehl.nf +++ b/subworkflows/local/discovery/segemehl.nf @@ -8,7 +8,6 @@ workflow SEGEMEHL { reads fasta index - bsj_reads main: ch_versions = Channel.empty() From 749c4362a281dad4eff859f214c064fc5d3c192c Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 11:37:27 +0200 Subject: [PATCH 246/491] Implement circexplorer2 unification --- conf/modules.config | 10 ++++++---- subworkflows/local/circrna_discovery.nf | 2 +- subworkflows/local/discovery/circexplorer2.nf | 12 +++++------- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 5bba4969..694ea5bd 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -263,13 +263,15 @@ if (!params.skip_trimming) { ] } - withName: '.*:CIRCEXPLORER2:FILTER' { + withName: '.*:CIRCEXPLORER2:UNIFY' { + ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$10, \$6 }'" + ext.suffix = "circexplorer2.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/circexplorer2/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates, - pattern: "*circs.bed" + pattern: "*.circexplorer2.bed" ] } @@ -531,7 +533,7 @@ if (!params.skip_trimming) { withName: 'FILTER_BSJS' { // Make sure score is higher or equal to the threshold ext.args = { "-v FS='\\t' -v OFS='\\t' '{ if (\$5 >= ${params.bsj_reads}) { print } }'" } - ext.suffix = "filtered.bed" + ext.suffix = {"${meta.tool}.filtered.bed"} } withName: ANNOTATION { diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 4f6bd514..cc263643 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -65,7 +65,7 @@ workflow CIRCRNA_DISCOVERY { } if (tools_selected.contains('circexplorer2')) { - CIRCEXPLORER2( gtf, fasta, STAR2PASS.out.junction, bsj_reads ) + CIRCEXPLORER2( gtf, fasta, STAR2PASS.out.junction ) ch_versions = ch_versions.mix(CIRCEXPLORER2.out.versions) ch_bed = ch_bed .mix(CIRCEXPLORER2.out.bed) } diff --git a/subworkflows/local/discovery/circexplorer2.nf b/subworkflows/local/discovery/circexplorer2.nf index ce39f039..2a04386c 100644 --- a/subworkflows/local/discovery/circexplorer2.nf +++ b/subworkflows/local/discovery/circexplorer2.nf @@ -1,14 +1,13 @@ include { CIRCEXPLORER2_REFERENCE as REFERENCE } from '../../../modules/local/circexplorer2/reference' include { CIRCEXPLORER2_PARSE as PARSE } from '../../../modules/nf-core/circexplorer2/parse' include { CIRCEXPLORER2_ANNOTATE as ANNOTATE } from '../../../modules/nf-core/circexplorer2/annotate' -include { CIRCEXPLORER2_FILTER as FILTER } from '../../../modules/local/circexplorer2/filter' +include { GAWK as UNIFY } from '../../../modules/nf-core/gawk' workflow CIRCEXPLORER2 { take: gtf fasta star_junctions - bsj_reads main: ch_versions = Channel.empty() @@ -16,17 +15,16 @@ workflow CIRCEXPLORER2 { REFERENCE( gtf ) PARSE( star_junctions ) ANNOTATE( PARSE.out.junction, fasta, REFERENCE.out.txt ) - FILTER( ANNOTATE.out.txt - .map{ meta, txt -> [ meta + [tool: "circexplorer2"], txt ] }, bsj_reads ) + UNIFY( ANNOTATE.out.txt + .map{ meta, txt -> [ meta + [tool: "circexplorer2"], txt ] }, [] ) ch_versions = ch_versions.mix(REFERENCE.out.versions) ch_versions = ch_versions.mix(PARSE.out.versions) ch_versions = ch_versions.mix(ANNOTATE.out.versions) - ch_versions = ch_versions.mix(FILTER.out.versions) + ch_versions = ch_versions.mix(UNIFY.out.versions) emit: - matrix = FILTER.out.matrix - results = FILTER.out.results + bed = UNIFY.out.output versions = ch_versions } \ No newline at end of file From bc09e30aa576dcefbe50b0a1d19f7d4d6ef9e4a1 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 11:55:09 +0200 Subject: [PATCH 247/491] Unify find_circ --- conf/modules.config | 9 ++++++--- subworkflows/local/circrna_discovery.nf | 2 +- subworkflows/local/discovery/find_circ.nf | 13 +++++-------- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 694ea5bd..e4f6ae77 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -330,13 +330,16 @@ if (!params.skip_trimming) { ] } - withName: '.*:FIND_CIRC:FILTER' { + withName: '.*:FIND_CIRC:UNIFY' { + // Keep only rows with UNAMBIGUOUS_BP and ANCHOR_UNIQUE in $18 + ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (\$18 ~ /UNAMBIGUOUS_BP/ && \$18 ~ /ANCHOR_UNIQUE/) { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$5, \$6 } }'" + ext.suffix = "find_circ.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/find_circ/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates, - pattern: "*circs.bed" + pattern: "*.find_circ.bed" ] } diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index cc263643..804046fc 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -78,7 +78,7 @@ workflow CIRCRNA_DISCOVERY { } if (tools_selected.contains('find_circ')) { - FIND_CIRC( reads, bowtie2_index, ch_fasta, bsj_reads ) + FIND_CIRC( reads, bowtie2_index, ch_fasta ) ch_versions = ch_versions.mix(FIND_CIRC.out.versions) ch_bed = ch_bed .mix(FIND_CIRC.out.bed) } diff --git a/subworkflows/local/discovery/find_circ.nf b/subworkflows/local/discovery/find_circ.nf index d8d0a14c..de4cb143 100644 --- a/subworkflows/local/discovery/find_circ.nf +++ b/subworkflows/local/discovery/find_circ.nf @@ -3,15 +3,13 @@ include { SAMTOOLS_VIEW } from '../../../modules/nf-core/samtools include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index' include { FIND_CIRC_ANCHORS as ANCHORS } from '../../../modules/local/find_circ/anchors' include { FIND_CIRC as RUN } from '../../../modules/local/find_circ/find_circ' -include { FIND_CIRC_FILTER as FILTER } from '../../../modules/local/find_circ/filter' - +include { GAWK as UNIFY } from '../../../modules/nf-core/gawk' workflow FIND_CIRC { take: reads bowtie2_index ch_fasta - bsj_reads main: ch_versions = Channel.empty() @@ -21,19 +19,18 @@ workflow FIND_CIRC { SAMTOOLS_VIEW( ALIGN.out.bam.join( SAMTOOLS_INDEX.out.bai ), ch_fasta, [] ) ANCHORS( SAMTOOLS_VIEW.out.bam ) RUN( ANCHORS.out.anchors, bowtie2_index, ch_fasta.map{ meta, fasta -> fasta } ) - FILTER( RUN.out.bed.map{ meta, bed -> - [ meta + [tool: "find_circ"], bed ] }, bsj_reads ) + UNIFY( RUN.out.bed.map{ meta, bed -> + [ meta + [tool: "find_circ"], bed ] }, [] ) ch_versions = ch_versions.mix(ALIGN.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions) ch_versions = ch_versions.mix(ANCHORS.out.versions) ch_versions = ch_versions.mix(RUN.out.versions) - ch_versions = ch_versions.mix(FILTER.out.versions) + ch_versions = ch_versions.mix(UNIFY.out.versions) emit: - matrix = FILTER.out.matrix - results = FILTER.out.results + bed = UNIFY.out.output versions = ch_versions } \ No newline at end of file From e02cb54dc09fbe98e1c651f4540f39460e3afdad Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 12:13:22 +0200 Subject: [PATCH 248/491] Unify ciriquant --- conf/modules.config | 13 +++++++++---- subworkflows/local/circrna_discovery.nf | 2 +- subworkflows/local/discovery/ciriquant.nf | 14 ++++++-------- 3 files changed, 16 insertions(+), 13 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index e4f6ae77..ebe7ff50 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -352,13 +352,18 @@ if (!params.skip_trimming) { ] } - withName: '.*:CIRIQUANT:FILTER' { + withName: '.*:CIRIQUANT:UNIFY' { + // Drop all rows starting with # + // $count is $14 until the dot (never has decimals) + // Print $1 $4 $5 $1:$4-$5:$7 $count $7 + ext.args = "-v OFS='\\t' '{ count = substr(\$14, 1, index(\$14, \".\") - 1); print \$1, \$4, \$5, \$1 \":\" \$4 \"-\" \$5 \":\" \$7, count, \$7 }'" + ext.suffix = "ciriquant.bed" + publishDir = [ - path: { "${params.outdir}/circrna_discovery/ciriquant/intermediates/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/ciriquant/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates, - pattern: "*circs.bed" + pattern: "*.ciriquant.bed" ] } diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 804046fc..95650a4b 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -84,7 +84,7 @@ workflow CIRCRNA_DISCOVERY { } if (tools_selected.contains('ciriquant')) { - CIRIQUANT( reads, ch_gtf, ch_fasta, bwa_index, hisat2_index, bsj_reads ) + CIRIQUANT( reads, ch_gtf, ch_fasta, bwa_index, hisat2_index ) ch_versions = ch_versions.mix(CIRIQUANT.out.versions) ch_bed = ch_bed .mix(CIRIQUANT.out.bed) } diff --git a/subworkflows/local/discovery/ciriquant.nf b/subworkflows/local/discovery/ciriquant.nf index b4e4c381..eb85bbe1 100644 --- a/subworkflows/local/discovery/ciriquant.nf +++ b/subworkflows/local/discovery/ciriquant.nf @@ -1,5 +1,5 @@ -include { CIRIQUANT as RUN } from '../../../modules/local/ciriquant/ciriquant' -include { CIRIQUANT_FILTER as FILTER } from '../../../modules/local/ciriquant/filter' +include { CIRIQUANT as RUN } from '../../../modules/local/ciriquant/ciriquant' +include { GAWK as UNIFY } from '../../../modules/nf-core/gawk' workflow CIRIQUANT { take: @@ -8,21 +8,19 @@ workflow CIRIQUANT { ch_fasta bwa_index hisat2_index - bsj_reads main: ch_versions = Channel.empty() RUN( reads, ch_gtf, ch_fasta, bwa_index, hisat2_index ) - FILTER( RUN.out.gtf.map{ meta, gtf -> - [ meta + [tool: "ciriquant"], gtf ] }, bsj_reads ) + UNIFY( RUN.out.gtf.map{ meta, gtf -> + [ meta + [tool: "ciriquant"], gtf ] }, [] ) ch_versions = ch_versions.mix(RUN.out.versions) - ch_versions = ch_versions.mix(FILTER.out.versions) + ch_versions = ch_versions.mix(UNIFY.out.versions) emit: - matrix = FILTER.out.matrix - results = FILTER.out.results + bed = UNIFY.out.output versions = ch_versions } \ No newline at end of file From de9645cd44710b8985d821f01e940ad3bed6640b Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 12:19:36 +0200 Subject: [PATCH 249/491] Unify DCC --- conf/modules.config | 12 ++++++++++++ subworkflows/local/discovery/dcc.nf | 9 ++++----- 2 files changed, 16 insertions(+), 5 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index ebe7ff50..7004d0b4 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -480,6 +480,18 @@ if (!params.skip_trimming) { ] } + withName: '.*:DCC:UNIFY' { + ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$4, \$5, \$4 }'" + ext.suffix = "dcc.bed" + publishDir = [ + path: { "${params.outdir}/circrna_discovery/dcc/${meta.id}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + enabled: params.save_intermediates, + pattern: "*.dcc.bed" + ] + } + withName: '.*:MAPSPLICE:REFERENCE' { ext.args = [ "", "-genePredExt", diff --git a/subworkflows/local/discovery/dcc.nf b/subworkflows/local/discovery/dcc.nf index 96ccca6b..52772c93 100644 --- a/subworkflows/local/discovery/dcc.nf +++ b/subworkflows/local/discovery/dcc.nf @@ -5,7 +5,7 @@ include { STAR_ALIGN as MATE2_1ST_PASS } from '../../../modules/nf-core/star/ali include { STAR_ALIGN as MATE2_2ND_PASS } from '../../../modules/nf-core/star/align' include { SJDB as MATE2_SJDB } from '../../../modules/local/star/sjdb' include { DCC as RUN } from '../../../modules/local/dcc/dcc' -include { DCC_FILTER as FILTER } from '../../../modules/local/dcc/filter' +include { GAWK as UNIFY } from '../../../modules/nf-core/gawk' workflow DCC { take: @@ -49,7 +49,7 @@ workflow DCC { dcc = dcc_stage.map{ it -> [ it[0], it[1], it[2] ?: [], it[3] ?: [] ] } RUN( dcc, ch_fasta.map{ meta, fasta -> fasta }, ch_gtf.map{ meta, gtf -> gtf } ) - FILTER( RUN.out.txt.map{ meta, txt -> [ meta + [tool: "dcc"], txt ] }, bsj_reads ) + UNIFY( RUN.out.txt.map{ meta, txt -> [ meta + [tool: "dcc"], txt ] }, [] ) ch_versions = ch_versions.mix(MATE1_1ST_PASS.out.versions) ch_versions = ch_versions.mix(MATE1_SJDB.out.versions) @@ -58,11 +58,10 @@ workflow DCC { ch_versions = ch_versions.mix(MATE2_SJDB.out.versions) ch_versions = ch_versions.mix(MATE2_2ND_PASS.out.versions) ch_versions = ch_versions.mix(RUN.out.versions) - ch_versions = ch_versions.mix(FILTER.out.versions) + ch_versions = ch_versions.mix(UNIFY.out.versions) emit: - matrix = FILTER.out.matrix - results = FILTER.out.results + bed = UNIFY.out.output versions = ch_versions } \ No newline at end of file From 0dd9a4f7f73e0ef8621660ff6bbcf7c0d433662f Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 12:26:42 +0200 Subject: [PATCH 250/491] Unify mapsplice --- conf/modules.config | 13 +++++-------- subworkflows/local/circrna_discovery.nf | 2 +- subworkflows/local/discovery/mapsplice.nf | 13 +++++-------- 3 files changed, 11 insertions(+), 17 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 7004d0b4..2641f9ef 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -176,7 +176,6 @@ if (!params.skip_trimming) { path: { "${params.outdir}/circrna_discovery/segemehl/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates, pattern: "*.segemehl.bed" ] } @@ -270,7 +269,6 @@ if (!params.skip_trimming) { path: { "${params.outdir}/circrna_discovery/circexplorer2/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates, pattern: "*.circexplorer2.bed" ] } @@ -338,7 +336,6 @@ if (!params.skip_trimming) { path: { "${params.outdir}/circrna_discovery/find_circ/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates, pattern: "*.find_circ.bed" ] } @@ -487,7 +484,6 @@ if (!params.skip_trimming) { path: { "${params.outdir}/circrna_discovery/dcc/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates, pattern: "*.dcc.bed" ] } @@ -540,13 +536,14 @@ if (!params.skip_trimming) { ] } - withName: '.*:MAPSPLICE:FILTER' { + withName: '.*:MAPSPLICE:UNIFY' { + ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$10, \$6 }'" + ext.suffix = "mapsplice.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/mapsplice/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates, - pattern: "*circs.bed" + pattern: "*.mapsplice.bed" ] } diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 95650a4b..984546f0 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -98,7 +98,7 @@ workflow CIRCRNA_DISCOVERY { if (tools_selected.contains('mapsplice')) { MAPSPLICE( reads, gtf, fasta, bowtie_index, chromosomes, - STAR2PASS.out.junction, bsj_reads ) + STAR2PASS.out.junction ) ch_versions = ch_versions.mix(MAPSPLICE.out.versions) ch_bed = ch_bed .mix(MAPSPLICE.out.bed) } diff --git a/subworkflows/local/discovery/mapsplice.nf b/subworkflows/local/discovery/mapsplice.nf index d4640047..847515de 100644 --- a/subworkflows/local/discovery/mapsplice.nf +++ b/subworkflows/local/discovery/mapsplice.nf @@ -2,8 +2,7 @@ include { CIRCEXPLORER2_REFERENCE as REFERENCE } from '../../../modules/local/ci include { MAPSPLICE_ALIGN as ALIGN } from '../../../modules/local/mapsplice/align' include { CIRCEXPLORER2_PARSE as PARSE } from '../../../modules/nf-core/circexplorer2/parse' include { CIRCEXPLORER2_ANNOTATE as ANNOTATE } from '../../../modules/nf-core/circexplorer2/annotate' -include { CIRCEXPLORER2_FILTER as FILTER } from '../../../modules/local/circexplorer2/filter' - +include { GAWK as UNIFY } from '../../../modules/nf-core/gawk' workflow MAPSPLICE { take: @@ -13,7 +12,6 @@ workflow MAPSPLICE { bowtie_index chromosomes star_junctions - bsj_reads main: ch_versions = Channel.empty() @@ -22,18 +20,17 @@ workflow MAPSPLICE { ALIGN( reads, bowtie_index, chromosomes, gtf ) PARSE( ALIGN.out.raw_fusions ) ANNOTATE( PARSE.out.junction, fasta, REFERENCE.out.txt ) - FILTER( ANNOTATE.out.txt.map{ meta, txt -> - [ meta + [tool: "mapsplice"], txt ] }, bsj_reads ) + UNIFY( ANNOTATE.out.txt.map{ meta, txt -> + [ meta + [tool: "mapsplice"], txt ] }, [] ) ch_versions = ch_versions.mix(REFERENCE.out.versions) ch_versions = ch_versions.mix(ALIGN.out.versions) ch_versions = ch_versions.mix(PARSE.out.versions) ch_versions = ch_versions.mix(ANNOTATE.out.versions) - ch_versions = ch_versions.mix(FILTER.out.versions) + ch_versions = ch_versions.mix(UNIFY.out.versions) emit: - matrix = FILTER.out.matrix - results = FILTER.out.results + bed = UNIFY.out.output versions = ch_versions } \ No newline at end of file From 4fa56f31fd8a9328a5881911c26aaa45a73a8c95 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 15:33:39 +0200 Subject: [PATCH 251/491] Unify circrna_finder --- conf/modules.config | 15 ++++++- modules/local/circrna_finder/filter/main.nf | 43 ------------------- modules/local/circrna_finder/main.nf | 34 +++++++++++++++ subworkflows/local/circrna_discovery.nf | 2 +- .../local/discovery/circrna_finder.nf | 14 +++--- 5 files changed, 55 insertions(+), 53 deletions(-) delete mode 100644 modules/local/circrna_finder/filter/main.nf create mode 100644 modules/local/circrna_finder/main.nf diff --git a/conf/modules.config b/conf/modules.config index 2641f9ef..a2425657 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -273,13 +273,24 @@ if (!params.skip_trimming) { ] } - withName: '.*:CIRCRNA_FINDER:FILTER' { + withName: '.*:CIRCRNA_FINDER:MAIN' { publishDir = [ path: { "${params.outdir}/circrna_discovery/circrna_finder/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, enabled: params.save_intermediates, - pattern: "*circs.bed" + pattern: "*.bed" + ] + } + + withName: '.*:CIRCRNA_FINDER:UNIFY' { + ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$5, \$6 }'" + ext.suffix = "circrna_finder.bed" + publishDir = [ + path: { "${params.outdir}/circrna_discovery/circrna_finder/${meta.id}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + pattern: "*.circrna_finder.bed" ] } diff --git a/modules/local/circrna_finder/filter/main.nf b/modules/local/circrna_finder/filter/main.nf deleted file mode 100644 index 1f781a32..00000000 --- a/modules/local/circrna_finder/filter/main.nf +++ /dev/null @@ -1,43 +0,0 @@ -process CIRCRNA_FINDER_FILTER { - tag "$meta.id" - label 'process_low' - - conda "bioconda::circrna_finder=1.2" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/circrna_finder%3A1.2--pl5321hdfd78af_1' : - 'biocontainers/circrna_finder:1.2--pl5321hdfd78af_1' }" - - input: - tuple val(meta), path(sam), path(junction), path(tab) - path fasta - val bsj_reads - - output: - tuple val(meta), path("${prefix}_circrna_finder_circs.bed"), emit: results - tuple val(meta), path("${prefix}_circrna_finder.bed") , emit: matrix - tuple val(meta), path("*filteredJunctions*") , emit: intermediates - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = 'v1.2' - """ - mkdir -p star_dir && mv *.tab *.junction *.sam star_dir - postProcessStarAlignment.pl --starDir star_dir/ --outDir ./ - - awk '{if(\$5 >= ${bsj_reads}) print \$0}' ${prefix}.filteredJunctions.bed | awk -v OFS="\\t" -F"\\t" '{print \$1,\$2,\$3,\$6,\$5}' > ${prefix}_circrna_finder.bed - - awk -v OFS="\\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_circrna_finder.bed > ${prefix}_circrna_finder_circs.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - awk: \$(awk --version | head -n1 | cut -d' ' -f3 | sed 's/,//g' ) - cat: \$(cat --version | head -n 1 | sed -e 's/cat (GNU coreutils) //') - circRNA_finder: $VERSION - END_VERSIONS - """ -} diff --git a/modules/local/circrna_finder/main.nf b/modules/local/circrna_finder/main.nf new file mode 100644 index 00000000..e9a40720 --- /dev/null +++ b/modules/local/circrna_finder/main.nf @@ -0,0 +1,34 @@ +process CIRCRNA_FINDER { + tag "$meta.id" + label 'process_low' + + conda "bioconda::circrna_finder=1.2" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/circrna_finder%3A1.2--pl5321hdfd78af_1' : + 'biocontainers/circrna_finder:1.2--pl5321hdfd78af_1' }" + + input: + tuple val(meta), path(star_input, stageAs: 'input/') + + output: + tuple val(meta), path("${prefix}.filteredJunctions.bed"), emit: results + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = 'v1.2' + """ + postProcessStarAlignment.pl --starDir input/ --outDir ./ + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + awk: \$(awk --version | head -n1 | cut -d' ' -f3 | sed 's/,//g' ) + cat: \$(cat --version | head -n 1 | sed -e 's/cat (GNU coreutils) //') + circRNA_finder: $VERSION + END_VERSIONS + """ +} diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 984546f0..ccb2a332 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -72,7 +72,7 @@ workflow CIRCRNA_DISCOVERY { if (tools_selected.contains('circrna_finder')) { CIRCRNA_FINDER( fasta, STAR2PASS.out.sam, STAR2PASS.out.junction, - STAR2PASS.out.tab, bsj_reads ) + STAR2PASS.out.tab ) ch_versions = ch_versions.mix(CIRCRNA_FINDER.out.versions) ch_bed = ch_bed .mix(CIRCRNA_FINDER.out.bed) } diff --git a/subworkflows/local/discovery/circrna_finder.nf b/subworkflows/local/discovery/circrna_finder.nf index b4564b7b..4e9c7e4e 100644 --- a/subworkflows/local/discovery/circrna_finder.nf +++ b/subworkflows/local/discovery/circrna_finder.nf @@ -1,4 +1,5 @@ -include { CIRCRNA_FINDER_FILTER as FILTER } from '../../../modules/local/circrna_finder/filter' +include { CIRCRNA_FINDER as MAIN } from '../../../modules/local/circrna_finder' +include { GAWK as UNIFY } from '../../../modules/nf-core/gawk' workflow CIRCRNA_FINDER { take: @@ -6,22 +7,21 @@ workflow CIRCRNA_FINDER { star_sam star_junctions star_tab - bsj_reads main: ch_versions = Channel.empty() ch_joined = star_sam.join(star_junctions).join(star_tab) .map{ meta, sam, junction, tab -> - [ meta + [tool: "circrna_finder"], sam, junction, tab ] } + [ meta + [tool: "circrna_finder"], [sam, junction, tab] ] } - FILTER( ch_joined, fasta, bsj_reads ) + MAIN( ch_joined ) + UNIFY( MAIN.out.results, [] ) - ch_versions = ch_versions.mix(FILTER.out.versions) + ch_versions = ch_versions.mix(MAIN.out.versions) emit: - matrix = FILTER.out.matrix - results = FILTER.out.results + bed = UNIFY.out.output versions = ch_versions } \ No newline at end of file From 01b7899d89c78e2aa6c8187cd836203042dfe3e6 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 15:36:57 +0200 Subject: [PATCH 252/491] Rename RUN to MAIN in all occurrences --- conf/modules.config | 6 +++--- subworkflows/local/discovery/ciriquant.nf | 10 +++++----- subworkflows/local/discovery/dcc.nf | 8 ++++---- subworkflows/local/discovery/find_circ.nf | 8 ++++---- 4 files changed, 16 insertions(+), 16 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index a2425657..ef25fa26 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -330,7 +330,7 @@ if (!params.skip_trimming) { ] } - withName: '.*:FIND_CIRC:RUN' { + withName: '.*:FIND_CIRC:MAIN' { publishDir = [ path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, @@ -351,7 +351,7 @@ if (!params.skip_trimming) { ] } - withName: '.*:CIRIQUANT:RUN' { + withName: '.*:CIRIQUANT:MAIN' { publishDir = [ path: { "${params.outdir}/circrna_discovery/ciriquant/intermediates/${meta.id}" }, mode: params.publish_dir_mode, @@ -479,7 +479,7 @@ if (!params.skip_trimming) { ] } - withName: '.*:DCC:RUN' { + withName: '.*:DCC:MAIN' { publishDir = [ path: { "${params.outdir}/circrna_discovery/dcc/intermediates/${meta.id}" }, mode: params.publish_dir_mode, diff --git a/subworkflows/local/discovery/ciriquant.nf b/subworkflows/local/discovery/ciriquant.nf index eb85bbe1..63b0d26c 100644 --- a/subworkflows/local/discovery/ciriquant.nf +++ b/subworkflows/local/discovery/ciriquant.nf @@ -1,5 +1,5 @@ -include { CIRIQUANT as RUN } from '../../../modules/local/ciriquant/ciriquant' -include { GAWK as UNIFY } from '../../../modules/nf-core/gawk' +include { CIRIQUANT as MAIN } from '../../../modules/local/ciriquant/ciriquant' +include { GAWK as UNIFY } from '../../../modules/nf-core/gawk' workflow CIRIQUANT { take: @@ -12,11 +12,11 @@ workflow CIRIQUANT { main: ch_versions = Channel.empty() - RUN( reads, ch_gtf, ch_fasta, bwa_index, hisat2_index ) - UNIFY( RUN.out.gtf.map{ meta, gtf -> + MAIN( reads, ch_gtf, ch_fasta, bwa_index, hisat2_index ) + UNIFY( MAIN.out.gtf.map{ meta, gtf -> [ meta + [tool: "ciriquant"], gtf ] }, [] ) - ch_versions = ch_versions.mix(RUN.out.versions) + ch_versions = ch_versions.mix(MAIN.out.versions) ch_versions = ch_versions.mix(UNIFY.out.versions) emit: diff --git a/subworkflows/local/discovery/dcc.nf b/subworkflows/local/discovery/dcc.nf index 52772c93..6cb613ae 100644 --- a/subworkflows/local/discovery/dcc.nf +++ b/subworkflows/local/discovery/dcc.nf @@ -4,7 +4,7 @@ include { SJDB as MATE1_SJDB } from '../../../modules/local/star/sjdb' include { STAR_ALIGN as MATE2_1ST_PASS } from '../../../modules/nf-core/star/align' include { STAR_ALIGN as MATE2_2ND_PASS } from '../../../modules/nf-core/star/align' include { SJDB as MATE2_SJDB } from '../../../modules/local/star/sjdb' -include { DCC as RUN } from '../../../modules/local/dcc/dcc' +include { DCC as MAIN } from '../../../modules/local/dcc/dcc' include { GAWK as UNIFY } from '../../../modules/nf-core/gawk' workflow DCC { @@ -48,8 +48,8 @@ workflow DCC { .map{ id, meta, junction, mate1, mate2 -> return [ meta, junction, mate1, mate2 ]} dcc = dcc_stage.map{ it -> [ it[0], it[1], it[2] ?: [], it[3] ?: [] ] } - RUN( dcc, ch_fasta.map{ meta, fasta -> fasta }, ch_gtf.map{ meta, gtf -> gtf } ) - UNIFY( RUN.out.txt.map{ meta, txt -> [ meta + [tool: "dcc"], txt ] }, [] ) + MAIN( dcc, ch_fasta.map{ meta, fasta -> fasta }, ch_gtf.map{ meta, gtf -> gtf } ) + UNIFY( MAIN.out.txt.map{ meta, txt -> [ meta + [tool: "dcc"], txt ] }, [] ) ch_versions = ch_versions.mix(MATE1_1ST_PASS.out.versions) ch_versions = ch_versions.mix(MATE1_SJDB.out.versions) @@ -57,7 +57,7 @@ workflow DCC { ch_versions = ch_versions.mix(MATE2_1ST_PASS.out.versions) ch_versions = ch_versions.mix(MATE2_SJDB.out.versions) ch_versions = ch_versions.mix(MATE2_2ND_PASS.out.versions) - ch_versions = ch_versions.mix(RUN.out.versions) + ch_versions = ch_versions.mix(MAIN.out.versions) ch_versions = ch_versions.mix(UNIFY.out.versions) emit: diff --git a/subworkflows/local/discovery/find_circ.nf b/subworkflows/local/discovery/find_circ.nf index de4cb143..c1f3772d 100644 --- a/subworkflows/local/discovery/find_circ.nf +++ b/subworkflows/local/discovery/find_circ.nf @@ -2,7 +2,7 @@ include { BOWTIE2_ALIGN as ALIGN } from '../../../modules/nf-core/bowtie2/ include { SAMTOOLS_VIEW } from '../../../modules/nf-core/samtools/view' include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index' include { FIND_CIRC_ANCHORS as ANCHORS } from '../../../modules/local/find_circ/anchors' -include { FIND_CIRC as RUN } from '../../../modules/local/find_circ/find_circ' +include { FIND_CIRC as MAIN } from '../../../modules/local/find_circ/find_circ' include { GAWK as UNIFY } from '../../../modules/nf-core/gawk' workflow FIND_CIRC { @@ -18,15 +18,15 @@ workflow FIND_CIRC { SAMTOOLS_INDEX( ALIGN.out.bam ) SAMTOOLS_VIEW( ALIGN.out.bam.join( SAMTOOLS_INDEX.out.bai ), ch_fasta, [] ) ANCHORS( SAMTOOLS_VIEW.out.bam ) - RUN( ANCHORS.out.anchors, bowtie2_index, ch_fasta.map{ meta, fasta -> fasta } ) - UNIFY( RUN.out.bed.map{ meta, bed -> + MAIN( ANCHORS.out.anchors, bowtie2_index, ch_fasta.map{ meta, fasta -> fasta } ) + UNIFY( MAIN.out.bed.map{ meta, bed -> [ meta + [tool: "find_circ"], bed ] }, [] ) ch_versions = ch_versions.mix(ALIGN.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions) ch_versions = ch_versions.mix(ANCHORS.out.versions) - ch_versions = ch_versions.mix(RUN.out.versions) + ch_versions = ch_versions.mix(MAIN.out.versions) ch_versions = ch_versions.mix(UNIFY.out.versions) emit: From a6a82f3155b0e8a53bdd81c9fde60d60968435d9 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 15:39:38 +0200 Subject: [PATCH 253/491] Add circrna_finder unify version capture --- subworkflows/local/discovery/circrna_finder.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/subworkflows/local/discovery/circrna_finder.nf b/subworkflows/local/discovery/circrna_finder.nf index 4e9c7e4e..c57bbe94 100644 --- a/subworkflows/local/discovery/circrna_finder.nf +++ b/subworkflows/local/discovery/circrna_finder.nf @@ -19,6 +19,7 @@ workflow CIRCRNA_FINDER { UNIFY( MAIN.out.results, [] ) ch_versions = ch_versions.mix(MAIN.out.versions) + ch_versions = ch_versions.mix(UNIFY.out.versions) emit: bed = UNIFY.out.output From aca81ce88d857a9e32cc63ca3b0176f5dc3762af Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 15:47:45 +0200 Subject: [PATCH 254/491] Remove tool-specific filtering artifacts --- modules/local/circexplorer2/filter/main.nf | 36 ---------------- modules/local/ciriquant/filter/main.nf | 43 ------------------- .../local/ciriquant/{ciriquant => }/main.nf | 0 modules/local/dcc/filter/main.nf | 35 --------------- modules/local/dcc/{dcc => }/main.nf | 0 modules/local/find_circ/filter/main.nf | 42 ------------------ modules/local/segemehl/filter/main.nf | 39 ----------------- subworkflows/local/discovery/ciriquant.nf | 2 +- subworkflows/local/discovery/dcc.nf | 2 +- 9 files changed, 2 insertions(+), 197 deletions(-) delete mode 100644 modules/local/circexplorer2/filter/main.nf delete mode 100644 modules/local/ciriquant/filter/main.nf rename modules/local/ciriquant/{ciriquant => }/main.nf (100%) delete mode 100644 modules/local/dcc/filter/main.nf rename modules/local/dcc/{dcc => }/main.nf (100%) delete mode 100644 modules/local/find_circ/filter/main.nf delete mode 100644 modules/local/segemehl/filter/main.nf diff --git a/modules/local/circexplorer2/filter/main.nf b/modules/local/circexplorer2/filter/main.nf deleted file mode 100644 index 3b6cc9bf..00000000 --- a/modules/local/circexplorer2/filter/main.nf +++ /dev/null @@ -1,36 +0,0 @@ -process CIRCEXPLORER2_FILTER { - tag "$meta.id" - label 'process_single' - - conda "conda-forge::sed=4.7" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" - - input: - tuple val(meta), path(txt) - val(bsj_reads) - - output: - tuple val(meta), path("${prefix}_${meta.tool}_circs.bed"), emit: results - tuple val(meta), path("${prefix}_${meta.tool}.bed") , emit: matrix - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.3.4' - """ - awk '{if(\$13 >= ${bsj_reads}) print \$0}' ${prefix}.txt | awk -v OFS="\\t" '{print \$1,\$2,\$3,\$6,\$13}' > ${prefix}_${meta.tool}.bed - - awk -v OFS="\\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_${meta.tool}.bed > ${prefix}_${meta.tool}_circs.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - mawk: $VERSION - END_VERSIONS - """ -} diff --git a/modules/local/ciriquant/filter/main.nf b/modules/local/ciriquant/filter/main.nf deleted file mode 100644 index c36e4638..00000000 --- a/modules/local/ciriquant/filter/main.nf +++ /dev/null @@ -1,43 +0,0 @@ -process CIRIQUANT_FILTER { - tag "$meta.id" - label 'process_single' - - conda "conda-forge::sed=4.7" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" - - input: - tuple val(meta), path(gtf) - val bsj_reads - - output: - tuple val(meta), path("${prefix}_ciriquant_circs.bed"), emit: results - tuple val(meta), path("${prefix}_ciriquant.bed") , emit: matrix - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.3.4' - """ - grep -v "#" ${prefix}.gtf | awk '{print \$14}' | cut -d '.' -f1 > counts - grep -v "#" ${prefix}.gtf | awk -v OFS="\\t" '{print \$1,\$4,\$5,\$7}' > ${prefix}.tmp - paste ${prefix}.tmp counts > ${prefix}_unfilt.bed - - awk '{if(\$5 >= ${bsj_reads}) print \$0}' ${prefix}_unfilt.bed > ${prefix}_filt.bed - grep -v '^\$' ${prefix}_filt.bed > ${prefix}_ciriquant - - awk -v OFS="\\t" '{\$2-=1;print}' ${prefix}_ciriquant > ${prefix}_ciriquant.bed - rm ${prefix}.gtf - - awk -v OFS="\\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_ciriquant.bed > ${prefix}_ciriquant_circs.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - mawk: $VERSION - END_VERSIONS - """ -} diff --git a/modules/local/ciriquant/ciriquant/main.nf b/modules/local/ciriquant/main.nf similarity index 100% rename from modules/local/ciriquant/ciriquant/main.nf rename to modules/local/ciriquant/main.nf diff --git a/modules/local/dcc/filter/main.nf b/modules/local/dcc/filter/main.nf deleted file mode 100644 index 78d3e571..00000000 --- a/modules/local/dcc/filter/main.nf +++ /dev/null @@ -1,35 +0,0 @@ -process DCC_FILTER { - tag "$meta.id" - label 'process_single' - - conda "conda-forge::sed=4.7" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" - - input: - tuple val(meta), path(txt) - val bsj_reads - - output: - tuple val(meta), path("${prefix}_dcc_circs.bed"), emit: results - tuple val(meta), path("${prefix}_dcc.bed") , emit: matrix - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.3.4' - """ - awk '{if(\$5 >= ${bsj_reads}) print \$0}' ${prefix}.txt > ${prefix}_dcc.filtered - awk -v OFS="\\t" '{\$2-=1;print}' ${prefix}_dcc.filtered > ${prefix}_dcc.bed - awk -v OFS="\\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_dcc.bed > ${prefix}_dcc_circs.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - mawk: $VERSION - END_VERSIONS - """ -} diff --git a/modules/local/dcc/dcc/main.nf b/modules/local/dcc/main.nf similarity index 100% rename from modules/local/dcc/dcc/main.nf rename to modules/local/dcc/main.nf diff --git a/modules/local/find_circ/filter/main.nf b/modules/local/find_circ/filter/main.nf deleted file mode 100644 index c4313b20..00000000 --- a/modules/local/find_circ/filter/main.nf +++ /dev/null @@ -1,42 +0,0 @@ -process FIND_CIRC_FILTER { - tag "$meta.id" - label "process_low" - - conda "bioconda::find_circ=1.2" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/find_circ%3A1.2--hdfd78af_0' : - 'biocontainers/find_circ:1.2--hdfd78af_0' }" - - input: - tuple val(meta), path(bed) - val bsj_reads - - output: - tuple val(meta), path("${prefix}_find_circ_circs.bed"), emit: results - tuple val(meta), path("${prefix}_find_circ.bed") , emit: matrix - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.2' - """ - grep CIRCULAR $bed | \ - grep -v chrM | \ - awk '\$5>=${bsj_reads}' | \ - grep UNAMBIGUOUS_BP | grep ANCHOR_UNIQUE | \ - maxlength.py 100000 \ - > ${prefix}.txt - - tail -n +2 ${prefix}.txt | awk -v OFS="\\t" '{print \$1,\$2,\$3,\$6,\$5}' > ${prefix}_find_circ.bed - - awk -v OFS="\\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_find_circ.bed > ${prefix}_find_circ_circs.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - find_circ: $VERSION - END_VERSIONS - """ -} diff --git a/modules/local/segemehl/filter/main.nf b/modules/local/segemehl/filter/main.nf deleted file mode 100644 index a1cf9929..00000000 --- a/modules/local/segemehl/filter/main.nf +++ /dev/null @@ -1,39 +0,0 @@ -process SEGEMEHL_FILTER { - tag "$meta.id" - label 'process_single' - - conda "conda-forge::sed=4.7" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" - - input: - tuple val(meta), path(results) - val(bsj_reads) - - output: - tuple val(meta), path("${prefix}_segemehl_circs.bed"), emit: results - tuple val(meta), path("${prefix}_segemehl.bed") , emit: matrix - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '1.3.4' - """ - grep ';C;' ${prefix}.sngl.bed | awk -v OFS="\\t" '{print \$1,\$2,\$3,\$6}' | sort | uniq -c | awk -v OFS="\\t" '{print \$2,\$3,\$4,\$5,\$1}' > ${prefix}_collapsed.bed - - awk -v OFS="\\t" -v BSJ=${bsj_reads} '{if(\$5>=BSJ) print \$0}' ${prefix}_collapsed.bed > ${prefix}_segemehl.bed - - awk -v OFS="\\t" '{print \$1, \$2, \$3, \$1":"\$2"-"\$3":"\$4, \$5, \$4}' ${prefix}_segemehl.bed > ${prefix}_segemehl_circs.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - mawk: $VERSION - sort: \$(sort --version | head -n 1 | sed -e 's/sort (GNU coreutils) //g') - END_VERSIONS - """ -} diff --git a/subworkflows/local/discovery/ciriquant.nf b/subworkflows/local/discovery/ciriquant.nf index 63b0d26c..7bf8c617 100644 --- a/subworkflows/local/discovery/ciriquant.nf +++ b/subworkflows/local/discovery/ciriquant.nf @@ -1,4 +1,4 @@ -include { CIRIQUANT as MAIN } from '../../../modules/local/ciriquant/ciriquant' +include { CIRIQUANT as MAIN } from '../../../modules/local/ciriquant' include { GAWK as UNIFY } from '../../../modules/nf-core/gawk' workflow CIRIQUANT { diff --git a/subworkflows/local/discovery/dcc.nf b/subworkflows/local/discovery/dcc.nf index 6cb613ae..ecc88c2b 100644 --- a/subworkflows/local/discovery/dcc.nf +++ b/subworkflows/local/discovery/dcc.nf @@ -4,7 +4,7 @@ include { SJDB as MATE1_SJDB } from '../../../modules/local/star/sjdb' include { STAR_ALIGN as MATE2_1ST_PASS } from '../../../modules/nf-core/star/align' include { STAR_ALIGN as MATE2_2ND_PASS } from '../../../modules/nf-core/star/align' include { SJDB as MATE2_SJDB } from '../../../modules/local/star/sjdb' -include { DCC as MAIN } from '../../../modules/local/dcc/dcc' +include { DCC as MAIN } from '../../../modules/local/dcc' include { GAWK as UNIFY } from '../../../modules/nf-core/gawk' workflow DCC { From fca047500f674091ba5a04cc9499ccc76fa6b6af Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 16:04:27 +0200 Subject: [PATCH 255/491] Remove technical debt with former "results" channel --- bin/{counts_combined.py => merge_samples.py} | 0 conf/modules.config | 4 --- .../{combined => merge_samples}/main.nf | 4 +-- subworkflows/local/circrna_discovery.nf | 36 +++++++++---------- 4 files changed, 19 insertions(+), 25 deletions(-) rename bin/{counts_combined.py => merge_samples.py} (100%) rename modules/local/count_matrix/{combined => merge_samples}/main.nf (85%) diff --git a/bin/counts_combined.py b/bin/merge_samples.py similarity index 100% rename from bin/counts_combined.py rename to bin/merge_samples.py diff --git a/conf/modules.config b/conf/modules.config index ef25fa26..1636d137 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -612,10 +612,6 @@ if (!params.skip_trimming) { ] } - withName: COUNTS_COMBINED { - ext.when = { params.module.split(',').contains('circrna_discovery') } - } - withName: COMBINE_TRANSCRIPTOME_GTFS { ext.args = "-k 1,1 -k3,3n -k4,4n" ext.suffix = "gtf" diff --git a/modules/local/count_matrix/combined/main.nf b/modules/local/count_matrix/merge_samples/main.nf similarity index 85% rename from modules/local/count_matrix/combined/main.nf rename to modules/local/count_matrix/merge_samples/main.nf index 7d1e1269..b286c757 100644 --- a/modules/local/count_matrix/combined/main.nf +++ b/modules/local/count_matrix/merge_samples/main.nf @@ -1,4 +1,4 @@ -process COUNTS_COMBINED { +process MERGE_SAMPLES { label "process_single" conda "bioconda::pandas=1.5.2" @@ -16,7 +16,7 @@ process COUNTS_COMBINED { script: """ - counts_combined.py --beds ${beds} --out_bed merged_counts.bed --out_tsv merged_counts.tsv + merge_samples.py --beds ${beds} --out_bed merged_counts.bed --out_tsv merged_counts.tsv cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index ccb2a332..a8ae043a 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -1,11 +1,11 @@ // MODULES -include { GAWK as FILTER_BSJS } from '../../modules/nf-core/gawk' -include { MERGE_TOOLS } from '../../modules/local/count_matrix/merge_tools' -include { COUNTS_COMBINED } from '../../modules/local/count_matrix/combined' -include { UPSET as UPSET_SAMPLES } from '../../modules/local/upset' -include { UPSET as UPSET_ALL } from '../../modules/local/upset' -include { BEDTOOLS_GETFASTA } from '../../modules/nf-core/bedtools/getfasta' -include { GAWK as ADD_BACKSPLICE } from '../../modules/nf-core/gawk' +include { GAWK as FILTER_BSJS } from '../../modules/nf-core/gawk' +include { MERGE_TOOLS } from '../../modules/local/count_matrix/merge_tools' +include { MERGE_SAMPLES } from '../../modules/local/count_matrix/merge_samples' +include { UPSET as UPSET_SAMPLES } from '../../modules/local/upset' +include { UPSET as UPSET_ALL } from '../../modules/local/upset' +include { BEDTOOLS_GETFASTA } from '../../modules/nf-core/bedtools/getfasta' +include { GAWK as ADD_BACKSPLICE } from '../../modules/nf-core/gawk' // SUBWORKFLOWS include { SEGEMEHL } from './discovery/segemehl' @@ -103,33 +103,31 @@ workflow CIRCRNA_DISCOVERY { ch_bed = ch_bed .mix(MAPSPLICE.out.bed) } - FILTER_BSJS( ch_bed, [] ) + ch_bed = FILTER_BSJS( ch_bed, [] ).output ch_versions = ch_versions.mix(FILTER_BSJS.out.versions) // // CREATE COUNT MATRIX // - ch_results = Channel.empty() - - MERGE_TOOLS( FILTER_BSJS.out.output.map{ meta, bed -> [ [id: meta.id], bed ] }.groupTuple(), + MERGE_TOOLS( ch_bed.map{ meta, bed -> [ [id: meta.id], bed ] }.groupTuple(), tools_selected.size() > 1 ? tool_filter : 1, duplicates_fun ) - COUNTS_COMBINED( MERGE_TOOLS.out.merged.map{ meta, bed -> bed }.collect() ) + MERGE_SAMPLES( MERGE_TOOLS.out.merged.map{ meta, bed -> bed }.collect() ) - ch_results_incl_merged = ch_results.mix( + ch_bed_incl_merged = ch_bed.mix( MERGE_TOOLS.out.merged.map{ meta, bed -> [meta + [tool: "merged"], bed] }) ch_versions = ch_versions.mix(MERGE_TOOLS.out.versions) - ch_versions = ch_versions.mix(COUNTS_COMBINED.out.versions) + ch_versions = ch_versions.mix(MERGE_SAMPLES.out.versions) // // UPSET PLOTS // - UPSET_SAMPLES( ch_results.map{ meta, bed -> [meta.id, meta.tool, bed]} + UPSET_SAMPLES( ch_bed.map{ meta, bed -> [meta.id, meta.tool, bed]} .groupTuple() .map{ sample, tools, beds -> [[id: sample], tools, beds]} ) - UPSET_ALL( ch_results.map{ meta, bed -> ["all", meta.tool, bed] } + UPSET_ALL( ch_bed.map{ meta, bed -> ["all", meta.tool, bed] } .groupTuple() .map{ sample, tools, beds -> [[id: sample], tools, beds]} ) @@ -142,7 +140,7 @@ workflow CIRCRNA_DISCOVERY { // ANNOTATION WORKFLOW: // - ANNOTATION( ch_results_incl_merged, gtf, exon_boundary ) + ANNOTATION( ch_bed_incl_merged, gtf, exon_boundary ) ch_versions = ch_versions.mix(ANNOTATION.out.versions) // @@ -160,8 +158,8 @@ workflow CIRCRNA_DISCOVERY { fasta = ADD_BACKSPLICE.out.output annotation_bed = ANNOTATION.out.bed annotation_gtf = ANNOTATION.out.gtf - counts_bed = COUNTS_COMBINED.out.counts_bed - counts_tsv = COUNTS_COMBINED.out.counts_tsv + counts_bed = MERGE_SAMPLES.out.counts_bed + counts_tsv = MERGE_SAMPLES.out.counts_tsv multiqc_files = ch_multiqc_files versions = ch_versions From e6e31570ec418ab3d44752e40095954e80f8a5b1 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 24 May 2024 16:18:40 +0200 Subject: [PATCH 256/491] Remove unnecessary checks if circrna_discovery is enabled --- conf/modules.config | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 1636d137..a1cd75c2 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -81,7 +81,7 @@ if (!params.skip_trimming) { } withName: BOWTIE_BUILD { - ext.when = { !params.bowtie && params.tool.split(',').contains('mapsplice') && params.module.split(',').contains('circrna_discovery') } + ext.when = { !params.bowtie && params.tool.split(',').contains('mapsplice') } publishDir = [ path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, @@ -91,7 +91,7 @@ if (!params.skip_trimming) { } withName: BOWTIE2_BUILD { - ext.when = { !params.bowtie2 && params.tool.split(',').contains('find_circ') && params.module.split(',').contains('circrna_discovery') } + ext.when = { !params.bowtie2 && params.tool.split(',').contains('find_circ') } publishDir = [ path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, @@ -101,7 +101,7 @@ if (!params.skip_trimming) { } withName: BWA_INDEX { - ext.when = { !params.bwa && params.tool.split(',').contains('ciriquant') && params.module.split(',').contains('circrna_discovery') } + ext.when = { !params.bwa && params.tool.split(',').contains('ciriquant') } publishDir = [ path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, @@ -131,7 +131,7 @@ if (!params.skip_trimming) { } withName: STAR_GENOMEGENERATE { - ext.when = { !params.star && params.module.split(',').contains('circrna_discovery') && ( params.tool.split(',').contains('circexplorer2') || params.tool.split(',').contains('dcc') || params.tool.split(',').contains('circrna_finder') ) } + ext.when = { !params.star && ( params.tool.split(',').contains('circexplorer2') || params.tool.split(',').contains('dcc') || params.tool.split(',').contains('circrna_finder') ) } ext.args = [ "", params.sjdboverhang ? "--sjdbOverhang ${params.sjdboverhang}" : '', ].join(' ').trim() @@ -181,7 +181,7 @@ if (!params.skip_trimming) { } withName: '.*:STAR2PASS:PASS_1' { - ext.when = { params.module.split(',').contains('circrna_discovery') && ( params.tool.split(',').contains('circexplorer2') || params.tool.split(',').contains('circrna_finder') ) } + ext.when = { params.tool.split(',').contains('circexplorer2') || params.tool.split(',').contains('circrna_finder') } ext.args = [ "", "--chimOutType Junctions WithinBAM", "--outSAMunmapped Within", From f351b961d185f7173f3d7a4c2f73bf051930595f Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 27 May 2024 15:09:40 +0200 Subject: [PATCH 257/491] Fix code style problems --- subworkflows/local/discovery/annotation.nf | 4 ++-- subworkflows/local/discovery/circexplorer2.nf | 6 +++--- subworkflows/local/discovery/circrna_finder.nf | 10 +++++----- subworkflows/local/discovery/ciriquant.nf | 4 ++-- subworkflows/local/discovery/dcc.nf | 8 ++++---- subworkflows/local/discovery/find_circ.nf | 4 ++-- subworkflows/local/discovery/mapsplice.nf | 6 +++--- subworkflows/local/discovery/segemehl.nf | 2 +- subworkflows/local/discovery/star2pass.nf | 4 ++-- 9 files changed, 24 insertions(+), 24 deletions(-) diff --git a/subworkflows/local/discovery/annotation.nf b/subworkflows/local/discovery/annotation.nf index feded6a5..d865a5da 100644 --- a/subworkflows/local/discovery/annotation.nf +++ b/subworkflows/local/discovery/annotation.nf @@ -9,7 +9,7 @@ workflow ANNOTATION { regions gtf exon_boundary - + main: ch_versions = Channel.empty() @@ -35,4 +35,4 @@ workflow ANNOTATION { gtf = COMBINE_GTFS.out.sorted versions = ch_versions -} \ No newline at end of file +} diff --git a/subworkflows/local/discovery/circexplorer2.nf b/subworkflows/local/discovery/circexplorer2.nf index 2a04386c..b3908e91 100644 --- a/subworkflows/local/discovery/circexplorer2.nf +++ b/subworkflows/local/discovery/circexplorer2.nf @@ -8,10 +8,10 @@ workflow CIRCEXPLORER2 { gtf fasta star_junctions - + main: ch_versions = Channel.empty() - + REFERENCE( gtf ) PARSE( star_junctions ) ANNOTATE( PARSE.out.junction, fasta, REFERENCE.out.txt ) @@ -27,4 +27,4 @@ workflow CIRCEXPLORER2 { bed = UNIFY.out.output versions = ch_versions -} \ No newline at end of file +} diff --git a/subworkflows/local/discovery/circrna_finder.nf b/subworkflows/local/discovery/circrna_finder.nf index c57bbe94..a4545939 100644 --- a/subworkflows/local/discovery/circrna_finder.nf +++ b/subworkflows/local/discovery/circrna_finder.nf @@ -7,22 +7,22 @@ workflow CIRCRNA_FINDER { star_sam star_junctions star_tab - + main: ch_versions = Channel.empty() ch_joined = star_sam.join(star_junctions).join(star_tab) - .map{ meta, sam, junction, tab -> + .map{ meta, sam, junction, tab -> [ meta + [tool: "circrna_finder"], [sam, junction, tab] ] } - + MAIN( ch_joined ) UNIFY( MAIN.out.results, [] ) ch_versions = ch_versions.mix(MAIN.out.versions) ch_versions = ch_versions.mix(UNIFY.out.versions) - + emit: bed = UNIFY.out.output versions = ch_versions -} \ No newline at end of file +} diff --git a/subworkflows/local/discovery/ciriquant.nf b/subworkflows/local/discovery/ciriquant.nf index 7bf8c617..7340e6e1 100644 --- a/subworkflows/local/discovery/ciriquant.nf +++ b/subworkflows/local/discovery/ciriquant.nf @@ -8,7 +8,7 @@ workflow CIRIQUANT { ch_fasta bwa_index hisat2_index - + main: ch_versions = Channel.empty() @@ -23,4 +23,4 @@ workflow CIRIQUANT { bed = UNIFY.out.output versions = ch_versions -} \ No newline at end of file +} diff --git a/subworkflows/local/discovery/dcc.nf b/subworkflows/local/discovery/dcc.nf index ecc88c2b..4bb1103d 100644 --- a/subworkflows/local/discovery/dcc.nf +++ b/subworkflows/local/discovery/dcc.nf @@ -18,10 +18,10 @@ workflow DCC { seq_platform seq_center bsj_reads - + main: ch_versions = Channel.empty() - + mate1 = reads.filter{ meta, reads -> !meta.single_end } .map{ meta, reads -> return [ [id: meta.id, single_end: true], reads[0] ] } MATE1_1ST_PASS( mate1, star_index, ch_gtf, ignore_sjdbgtf, seq_platform, seq_center ) @@ -62,6 +62,6 @@ workflow DCC { emit: bed = UNIFY.out.output - + versions = ch_versions -} \ No newline at end of file +} diff --git a/subworkflows/local/discovery/find_circ.nf b/subworkflows/local/discovery/find_circ.nf index c1f3772d..ce0cc557 100644 --- a/subworkflows/local/discovery/find_circ.nf +++ b/subworkflows/local/discovery/find_circ.nf @@ -10,7 +10,7 @@ workflow FIND_CIRC { reads bowtie2_index ch_fasta - + main: ch_versions = Channel.empty() @@ -33,4 +33,4 @@ workflow FIND_CIRC { bed = UNIFY.out.output versions = ch_versions -} \ No newline at end of file +} diff --git a/subworkflows/local/discovery/mapsplice.nf b/subworkflows/local/discovery/mapsplice.nf index 847515de..f8112426 100644 --- a/subworkflows/local/discovery/mapsplice.nf +++ b/subworkflows/local/discovery/mapsplice.nf @@ -12,7 +12,7 @@ workflow MAPSPLICE { bowtie_index chromosomes star_junctions - + main: ch_versions = Channel.empty() @@ -28,9 +28,9 @@ workflow MAPSPLICE { ch_versions = ch_versions.mix(PARSE.out.versions) ch_versions = ch_versions.mix(ANNOTATE.out.versions) ch_versions = ch_versions.mix(UNIFY.out.versions) - + emit: bed = UNIFY.out.output versions = ch_versions -} \ No newline at end of file +} diff --git a/subworkflows/local/discovery/segemehl.nf b/subworkflows/local/discovery/segemehl.nf index d50ed70a..5aa4b342 100644 --- a/subworkflows/local/discovery/segemehl.nf +++ b/subworkflows/local/discovery/segemehl.nf @@ -24,4 +24,4 @@ workflow SEGEMEHL { bed = UNIFY.out.output versions = ch_versions -} \ No newline at end of file +} diff --git a/subworkflows/local/discovery/star2pass.nf b/subworkflows/local/discovery/star2pass.nf index 65ce3e34..4e216545 100644 --- a/subworkflows/local/discovery/star2pass.nf +++ b/subworkflows/local/discovery/star2pass.nf @@ -12,7 +12,7 @@ workflow STAR2PASS { ignore_sjdbgtf seq_center seq_platform - + main: ch_versions = Channel.empty() @@ -31,4 +31,4 @@ workflow STAR2PASS { tab = PASS_2.out.tab versions = ch_versions -} \ No newline at end of file +} From 43a1c4d7521101d34c073ebf04d780a76a4c7fd2 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 30 May 2024 13:48:16 +0200 Subject: [PATCH 258/491] Update nf-core modules --- modules.json | 16 +- modules/nf-core/bowtie2/align/main.nf | 2 +- modules/nf-core/bowtie2/align/meta.yml | 43 ++++-- modules/nf-core/bwa/index/environment.yml | 2 +- modules/nf-core/bwa/index/main.nf | 4 +- modules/nf-core/bwa/index/meta.yml | 1 + .../nf-core/bwa/index/tests/main.nf.test.snap | 10 +- modules/nf-core/cat/fastq/tests/main.nf.test | 2 + modules/nf-core/csvtk/join/environment.yml | 2 +- modules/nf-core/csvtk/join/main.nf | 5 +- modules/nf-core/csvtk/join/tests/main.nf.test | 64 ++++++++ .../csvtk/join/tests/main.nf.test.snap | 60 ++++++++ .../nf-core/csvtk/join/tests/nextflow.config | 5 + modules/nf-core/csvtk/join/tests/tags.yml | 2 + modules/nf-core/csvtk/split/environment.yml | 3 +- modules/nf-core/csvtk/split/main.nf | 17 ++- .../nf-core/csvtk/split/tests/main.nf.test | 62 ++++++++ .../csvtk/split/tests/main.nf.test.snap | 72 +++++++++ .../nf-core/csvtk/split/tests/nextflow.config | 5 + modules/nf-core/csvtk/split/tests/tags.yml | 2 + modules/nf-core/gawk/environment.yml | 2 +- modules/nf-core/gawk/main.nf | 4 +- modules/nf-core/gawk/tests/main.nf.test.snap | 16 +- modules/nf-core/segemehl/align/main.nf | 11 +- modules/nf-core/segemehl/align/meta.yml | 35 ++++- .../nf-core/segemehl/align/tests/main.nf.test | 140 ++++++++++++++++++ .../segemehl/align/tests/main.nf.test.snap | 50 +++++++ .../nf-core/segemehl/align/tests/split.config | 5 + modules/nf-core/segemehl/align/tests/tags.yml | 2 + .../tximeta/tximport/templates/tximport.r | 2 - .../tximeta/tximport/tests/main.nf.test.snap | 72 ++++----- 31 files changed, 626 insertions(+), 92 deletions(-) create mode 100644 modules/nf-core/csvtk/join/tests/main.nf.test create mode 100644 modules/nf-core/csvtk/join/tests/main.nf.test.snap create mode 100644 modules/nf-core/csvtk/join/tests/nextflow.config create mode 100644 modules/nf-core/csvtk/join/tests/tags.yml create mode 100644 modules/nf-core/csvtk/split/tests/main.nf.test create mode 100644 modules/nf-core/csvtk/split/tests/main.nf.test.snap create mode 100644 modules/nf-core/csvtk/split/tests/nextflow.config create mode 100644 modules/nf-core/csvtk/split/tests/tags.yml create mode 100644 modules/nf-core/segemehl/align/tests/main.nf.test create mode 100644 modules/nf-core/segemehl/align/tests/main.nf.test.snap create mode 100644 modules/nf-core/segemehl/align/tests/split.config create mode 100644 modules/nf-core/segemehl/align/tests/tags.yml diff --git a/modules.json b/modules.json index acc410f5..6e535782 100644 --- a/modules.json +++ b/modules.json @@ -32,7 +32,7 @@ }, "bowtie2/align": { "branch": "master", - "git_sha": "0fe30831abbc2ed115e46e92330edf38f56edc3d", + "git_sha": "e4bad511789f16d0df39ee306b2cd50418365048", "installed_by": ["modules"] }, "bowtie2/build": { @@ -42,7 +42,7 @@ }, "bwa/index": { "branch": "master", - "git_sha": "6278bf9afd4a4b2d00fa6052250e73da3d91546f", + "git_sha": "086fa66260595e123b0ea47a6512539b72a9afa3", "installed_by": ["modules"] }, "cat/cat": { @@ -52,7 +52,7 @@ }, "cat/fastq": { "branch": "master", - "git_sha": "0997b47c93c06b49aa7b3fefda87e728312cf2ca", + "git_sha": "4fc983ad0b30e6e32696fa7d980c76c7bfe1c03e", "installed_by": ["modules"] }, "circexplorer2/annotate": { @@ -67,12 +67,12 @@ }, "csvtk/join": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "614abbf126f287a3068dc86997b2e1b6a93abe20", "installed_by": ["modules"] }, "csvtk/split": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "614abbf126f287a3068dc86997b2e1b6a93abe20", "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { @@ -92,7 +92,7 @@ }, "gawk": { "branch": "master", - "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5", + "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08", "installed_by": ["modules"] }, "gnu/sort": { @@ -162,7 +162,7 @@ }, "segemehl/align": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "9a6b0745dbb5359286d36dee2183ffab240abba0", "installed_by": ["modules"] }, "segemehl/index": { @@ -192,7 +192,7 @@ }, "tximeta/tximport": { "branch": "master", - "git_sha": "c275c3baac6df8f0c7c500760a0cf014ce7b525d", + "git_sha": "5d095e8413da1f4c72b7d07ce87f75c09482486f", "installed_by": ["modules"] } } diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf index 96a7027d..809525ad 100644 --- a/modules/nf-core/bowtie2/align/main.nf +++ b/modules/nf-core/bowtie2/align/main.nf @@ -1,6 +1,6 @@ process BOWTIE2_ALIGN { tag "$meta.id" - label "process_high" + label 'process_high' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? diff --git a/modules/nf-core/bowtie2/align/meta.yml b/modules/nf-core/bowtie2/align/meta.yml index e66811d0..38610e0e 100644 --- a/modules/nf-core/bowtie2/align/meta.yml +++ b/modules/nf-core/bowtie2/align/meta.yml @@ -36,6 +36,15 @@ input: type: file description: Bowtie2 genome index files pattern: "*.ebwt" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Bowtie2 genome fasta file + pattern: "*.fasta" - save_unaligned: type: boolean description: | @@ -46,22 +55,38 @@ input: description: use samtools sort (true) or samtools view (false) pattern: "true or false" output: - - aligned: + - sam: type: file - description: Output BAM/SAM file containing read alignments - pattern: "*.{bam,sam}" - - versions: + description: Output SAM file containing read alignments + pattern: "*.sam" + - bam: type: file - description: File containing software versions - pattern: "versions.yml" - - fastq: + description: Output BAM file containing read alignments + pattern: "*.bam" + - cram: type: file - description: Unaligned FastQ files - pattern: "*.fastq.gz" + description: Output CRAM file containing read alignments + pattern: "*.cram" + - csi: + type: file + description: Output SAM/BAM index for large inputs + pattern: "*.csi" + - crai: + type: file + description: Output CRAM index + pattern: "*.crai" - log: type: file description: Aligment log pattern: "*.log" + - fastq: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bwa/index/environment.yml b/modules/nf-core/bwa/index/environment.yml index 5d3cb323..126e0034 100644 --- a/modules/nf-core/bwa/index/environment.yml +++ b/modules/nf-core/bwa/index/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::bwa=0.7.17 + - bioconda::bwa=0.7.18 diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf index 24b5a2ea..2e48b6ca 100644 --- a/modules/nf-core/bwa/index/main.nf +++ b/modules/nf-core/bwa/index/main.nf @@ -4,8 +4,8 @@ process BWA_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bwa:0.7.17--hed695b0_7' : - 'biocontainers/bwa:0.7.17--hed695b0_7' }" + 'https://depot.galaxyproject.org/singularity/bwa:0.7.18--he4a0461_0' : + 'biocontainers/bwa:0.7.18--he4a0461_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/bwa/index/meta.yml b/modules/nf-core/bwa/index/meta.yml index 730628d0..4c7d30f3 100644 --- a/modules/nf-core/bwa/index/meta.yml +++ b/modules/nf-core/bwa/index/meta.yml @@ -43,3 +43,4 @@ authors: maintainers: - "@drpatelh" - "@maxulysse" + - "@gallvp" diff --git a/modules/nf-core/bwa/index/tests/main.nf.test.snap b/modules/nf-core/bwa/index/tests/main.nf.test.snap index e51ad5bf..7c8f0465 100644 --- a/modules/nf-core/bwa/index/tests/main.nf.test.snap +++ b/modules/nf-core/bwa/index/tests/main.nf.test.snap @@ -17,7 +17,7 @@ ] ], "1": [ - "versions.yml:md5,0f20525da90e7489a7ebb02adca3265f" + "versions.yml:md5,a64462ac7dfb21f4ade9b02e7f65c5bb" ], "index": [ [ @@ -34,10 +34,14 @@ ] ], "versions": [ - "versions.yml:md5,0f20525da90e7489a7ebb02adca3265f" + "versions.yml:md5,a64462ac7dfb21f4ade9b02e7f65c5bb" ] } ], - "timestamp": "2023-10-17T17:20:20.180927714" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-16T11:40:09.925307" } } \ No newline at end of file diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test index dab2e14c..a71dcb8d 100644 --- a/modules/nf-core/cat/fastq/tests/main.nf.test +++ b/modules/nf-core/cat/fastq/tests/main.nf.test @@ -1,3 +1,5 @@ +// NOTE The version snaps may not be consistant +// https://github.com/nf-core/modules/pull/4087#issuecomment-1767948035 nextflow_process { name "Test Process CAT_FASTQ" diff --git a/modules/nf-core/csvtk/join/environment.yml b/modules/nf-core/csvtk/join/environment.yml index b488c861..5b6c6468 100644 --- a/modules/nf-core/csvtk/join/environment.yml +++ b/modules/nf-core/csvtk/join/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::csvtk=0.26.0 + - bioconda::csvtk=0.30.0 diff --git a/modules/nf-core/csvtk/join/main.nf b/modules/nf-core/csvtk/join/main.nf index bf02e7f5..5f3afeea 100644 --- a/modules/nf-core/csvtk/join/main.nf +++ b/modules/nf-core/csvtk/join/main.nf @@ -4,8 +4,8 @@ process CSVTK_JOIN { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/csvtk:0.26.0--h9ee0642_0': - 'biocontainers/csvtk:0.26.0--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/csvtk:0.30.0--h9ee0642_0': + 'biocontainers/csvtk:0.30.0--h9ee0642_0' }" input: tuple val(meta), path(csv) @@ -36,7 +36,6 @@ process CSVTK_JOIN { """ stub: - def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" out_extension = args.contains('--out-delimiter "\t"') || args.contains('-D "\t"') || args.contains("-D \$'\t'") ? "tsv" : "csv" """ diff --git a/modules/nf-core/csvtk/join/tests/main.nf.test b/modules/nf-core/csvtk/join/tests/main.nf.test new file mode 100644 index 00000000..3cf178c4 --- /dev/null +++ b/modules/nf-core/csvtk/join/tests/main.nf.test @@ -0,0 +1,64 @@ +nextflow_process { + + name "Test Process CSVTK_JOIN" + script "../main.nf" + process "CSVTK_JOIN" + + tag "modules" + tag "modules_nfcore" + tag "csvtk" + tag "csvtk/join" + + test("join - csv") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file("https://github.com/nf-core/test-datasets/raw/bacass/bacass_hybrid.csv", checkIfExists: true), + file("https://github.com/nf-core/test-datasets/raw/bacass/bacass_short.csv", checkIfExists: true), + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("join - csv - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file("https://github.com/nf-core/test-datasets/raw/bacass/bacass_hybrid.csv", checkIfExists: true), + file("https://github.com/nf-core/test-datasets/raw/bacass/bacass_short.csv", checkIfExists: true), + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/csvtk/join/tests/main.nf.test.snap b/modules/nf-core/csvtk/join/tests/main.nf.test.snap new file mode 100644 index 00000000..b124788b --- /dev/null +++ b/modules/nf-core/csvtk/join/tests/main.nf.test.snap @@ -0,0 +1,60 @@ +{ + "join - csv": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.csv:md5,d0ad82ca096c7e05eb9f9a04194c9e30" + ] + ], + "1": [ + "versions.yml:md5,e76147e4eca968d23543e7007522f1d3" + ], + "csv": [ + [ + { + "id": "test" + }, + "test.csv:md5,d0ad82ca096c7e05eb9f9a04194c9e30" + ] + ], + "versions": [ + "versions.yml:md5,e76147e4eca968d23543e7007522f1d3" + ] + } + ], + "timestamp": "2024-05-21T15:45:44.045434" + }, + "join - csv - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,e76147e4eca968d23543e7007522f1d3" + ], + "csv": [ + [ + { + "id": "test" + }, + "test.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e76147e4eca968d23543e7007522f1d3" + ] + } + ], + "timestamp": "2024-05-21T15:45:55.59201" + } +} \ No newline at end of file diff --git a/modules/nf-core/csvtk/join/tests/nextflow.config b/modules/nf-core/csvtk/join/tests/nextflow.config new file mode 100644 index 00000000..1b14393a --- /dev/null +++ b/modules/nf-core/csvtk/join/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: CSVTK_JOIN { + ext.args = "--fields 'ID;ID' -p -e -d \"\t\" -D \",\"" + } +} diff --git a/modules/nf-core/csvtk/join/tests/tags.yml b/modules/nf-core/csvtk/join/tests/tags.yml new file mode 100644 index 00000000..6c3a0fa6 --- /dev/null +++ b/modules/nf-core/csvtk/join/tests/tags.yml @@ -0,0 +1,2 @@ +csvtk/join: + - "modules/nf-core/csvtk/join/**" diff --git a/modules/nf-core/csvtk/split/environment.yml b/modules/nf-core/csvtk/split/environment.yml index 146d94db..ec08bb43 100644 --- a/modules/nf-core/csvtk/split/environment.yml +++ b/modules/nf-core/csvtk/split/environment.yml @@ -1,6 +1,7 @@ +name: csvtk_split channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::csvtk=0.23.0 + - bioconda::csvtk=0.30.0 diff --git a/modules/nf-core/csvtk/split/main.nf b/modules/nf-core/csvtk/split/main.nf index cf17556c..1b7d5dd1 100644 --- a/modules/nf-core/csvtk/split/main.nf +++ b/modules/nf-core/csvtk/split/main.nf @@ -4,8 +4,8 @@ process CSVTK_SPLIT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/csvtk:0.23.0--h9ee0642_0' : - 'biocontainers/csvtk:0.23.0--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/csvtk:0.30.0--h9ee0642_0' : + 'biocontainers/csvtk:0.30.0--h9ee0642_0' }" input: tuple val(meta), path(csv) @@ -40,4 +40,17 @@ process CSVTK_SPLIT { csvtk: \$(echo \$( csvtk version | sed -e 's/csvtk v//g' )) END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + out_extension = args.contains('--out-delimiter "\t"') || args.contains('-D "\t"') || args.contains("-D \$'\t'") ? "tsv" : "csv" + """ + touch ${prefix}.${out_extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + csvtk: \$(echo \$( csvtk version | sed -e "s/csvtk v//g" )) + END_VERSIONS + """ } diff --git a/modules/nf-core/csvtk/split/tests/main.nf.test b/modules/nf-core/csvtk/split/tests/main.nf.test new file mode 100644 index 00000000..f3c49926 --- /dev/null +++ b/modules/nf-core/csvtk/split/tests/main.nf.test @@ -0,0 +1,62 @@ +nextflow_process { + + name "Test Process CSVTK_SPLIT" + script "../main.nf" + process "CSVTK_SPLIT" + + tag "modules" + tag "modules_nfcore" + tag "csvtk" + tag "csvtk/split" + + test("split - csv") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true) ] + ] + input[1] = "tsv" + input[2] = "tsv" + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("split - csv - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true) ] + ] + input[1] = "tsv" + input[2] = "tsv" + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/csvtk/split/tests/main.nf.test.snap b/modules/nf-core/csvtk/split/tests/main.nf.test.snap new file mode 100644 index 00000000..f0ec9def --- /dev/null +++ b/modules/nf-core/csvtk/split/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "split - csv - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,b17a61b0c41b19f7df3740979d68a8a0" + ], + "split_csv": [ + [ + { + "id": "test" + }, + "test.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,b17a61b0c41b19f7df3740979d68a8a0" + ] + } + ], + "timestamp": "2024-05-22T10:02:46.053585" + }, + "split - csv": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "test-1.tsv:md5,2827284f1a6f41dd14ef82fb6a36ebad", + "test-11.tsv:md5,6c5555d689c4e685d35d6e394ad6e1e6", + "test-2.tsv:md5,589a2add7f0b8e998d4959e5d883e7d5", + "test-4.tsv:md5,e51cd0bfc35f5353d1fb75f723772ed0", + "test-NA.tsv:md5,20afd42832c6cf5821f9862d285c9350" + ] + ] + ], + "1": [ + "versions.yml:md5,b17a61b0c41b19f7df3740979d68a8a0" + ], + "split_csv": [ + [ + { + "id": "test" + }, + [ + "test-1.tsv:md5,2827284f1a6f41dd14ef82fb6a36ebad", + "test-11.tsv:md5,6c5555d689c4e685d35d6e394ad6e1e6", + "test-2.tsv:md5,589a2add7f0b8e998d4959e5d883e7d5", + "test-4.tsv:md5,e51cd0bfc35f5353d1fb75f723772ed0", + "test-NA.tsv:md5,20afd42832c6cf5821f9862d285c9350" + ] + ] + ], + "versions": [ + "versions.yml:md5,b17a61b0c41b19f7df3740979d68a8a0" + ] + } + ], + "timestamp": "2024-05-22T10:02:35.8578" + } +} \ No newline at end of file diff --git a/modules/nf-core/csvtk/split/tests/nextflow.config b/modules/nf-core/csvtk/split/tests/nextflow.config new file mode 100644 index 00000000..8f5a6f7e --- /dev/null +++ b/modules/nf-core/csvtk/split/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: CSVTK_SPLIT { + ext.args = "-C \'&\' --fields \'first_name\' " + } +} diff --git a/modules/nf-core/csvtk/split/tests/tags.yml b/modules/nf-core/csvtk/split/tests/tags.yml new file mode 100644 index 00000000..0d7dc029 --- /dev/null +++ b/modules/nf-core/csvtk/split/tests/tags.yml @@ -0,0 +1,2 @@ +csvtk/split: + - "modules/nf-core/csvtk/split/**" diff --git a/modules/nf-core/gawk/environment.yml b/modules/nf-core/gawk/environment.yml index 34513c7f..3d98a08b 100644 --- a/modules/nf-core/gawk/environment.yml +++ b/modules/nf-core/gawk/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - anaconda::gawk=5.1.0 + - conda-forge::gawk=5.3.0 diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf index 578b448c..ca468929 100644 --- a/modules/nf-core/gawk/main.nf +++ b/modules/nf-core/gawk/main.nf @@ -4,8 +4,8 @@ process GAWK { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gawk:5.1.0' : - 'biocontainers/gawk:5.1.0' }" + 'https://depot.galaxyproject.org/singularity/gawk:5.3.0' : + 'biocontainers/gawk:5.3.0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/gawk/tests/main.nf.test.snap b/modules/nf-core/gawk/tests/main.nf.test.snap index ce207478..4f3a759c 100644 --- a/modules/nf-core/gawk/tests/main.nf.test.snap +++ b/modules/nf-core/gawk/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,4c320d8c98ca80690afd7651da1ba520" + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" ], "output": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,4c320d8c98ca80690afd7651da1ba520" + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nextflow": "24.03.0" }, - "timestamp": "2024-04-05T11:00:28.097563" + "timestamp": "2024-05-17T15:20:02.495430346" }, "convert fasta to bed": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,4c320d8c98ca80690afd7651da1ba520" + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" ], "output": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,4c320d8c98ca80690afd7651da1ba520" + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.02.0" + "nextflow": "24.03.0" }, - "timestamp": "2024-04-05T10:28:15.625869" + "timestamp": "2024-05-17T15:19:53.291809648" } } \ No newline at end of file diff --git a/modules/nf-core/segemehl/align/main.nf b/modules/nf-core/segemehl/align/main.nf index 77f88820..fa829a73 100644 --- a/modules/nf-core/segemehl/align/main.nf +++ b/modules/nf-core/segemehl/align/main.nf @@ -13,8 +13,11 @@ process SEGEMEHL_ALIGN { path(index) output: - tuple val(meta), path("${prefix}/*"), emit: results - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}/${prefix}.${suffix}"), emit: alignment + tuple val(meta), path("${prefix}/${prefix}.trns.txt") , emit: trans_alignments, optional: true + tuple val(meta), path("${prefix}/${prefix}.mult.bed") , emit: multi_bed, optional: true + tuple val(meta), path("${prefix}/${prefix}.sngl.bed") , emit: single_bed, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -23,7 +26,7 @@ process SEGEMEHL_ALIGN { def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" def reads = meta.single_end ? "-q ${reads}" : "-q ${reads[0]} -p ${reads[1]}" - def suffix = ( args.contains("-b") || args.contains("--bamabafixoida") ) ? "bam" : "sam" + suffix = ( args.contains("-b") || args.contains("--bamabafixoida") ) ? "bam" : "sam" """ mkdir -p $prefix @@ -43,7 +46,7 @@ process SEGEMEHL_ALIGN { stub: prefix = task.ext.prefix ?: "${meta.id}" - def suffix = ( args.contains("-b") || args.contains("--bamabafixoida") ) ? "bam" : "sam" + suffix = ( args.contains("-b") || args.contains("--bamabafixoida") ) ? "bam" : "sam" """ mkdir -p $prefix touch ${prefix}/${prefix}.${suffix} diff --git a/modules/nf-core/segemehl/align/meta.yml b/modules/nf-core/segemehl/align/meta.yml index aaad17eb..fc8e43ba 100644 --- a/modules/nf-core/segemehl/align/meta.yml +++ b/modules/nf-core/segemehl/align/meta.yml @@ -11,7 +11,7 @@ tools: homepage: "https://www.bioinf.uni-leipzig.de/Software/segemehl/" documentation: "https://www.bioinf.uni-leipzig.de/Software/segemehl/" doi: "10.1186/gb-2014-15-2-r34" - licence: "GPL v3" + licence: ["GPL v3"] input: - meta: type: map @@ -36,19 +36,38 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - results: - type: directory + - alignment: + type: file description: | - Directory containing genomic alignments in SAM format + File containing genomic alignments in SAM format (please add "-b" flag to task.ext.args for BAM) - In addition to split-read alignments files when -S parameter used. - [ *.{sam,bam}, *.trns.txt, *.mult.bed, *.sngl.bed ] - pattern: "${meta.id}*" + pattern: "*.{sam,bam}" + - trans_alignments: + type: file + description: | + Custom text file containing all single split alignments predicted to be in trans + (optional, only if -S flag is set in task.ext.args) + pattern: "*.trns.txt" + - single_bed: + type: file + description: | + Bed file containing all single splice events predicted + in the split read alignments. + (optional, only if -S flag is set in task.ext.args) + pattern: "*.sngl.bed" + - multi_bed: + type: file + description: | + Bed file containing all splice events predicted + in the split read alignments. + (optional, only if -S flag is set in task.ext.args) + pattern: "*.mult.bed" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@BarryDigby" + - "@nictru" maintainers: - - "@BarryDigby" + - "@nictru" diff --git a/modules/nf-core/segemehl/align/tests/main.nf.test b/modules/nf-core/segemehl/align/tests/main.nf.test new file mode 100644 index 00000000..c1b4921e --- /dev/null +++ b/modules/nf-core/segemehl/align/tests/main.nf.test @@ -0,0 +1,140 @@ +nextflow_process { + + name "Test Process SEGEMEHL_ALIGN" + script "../main.nf" + process "SEGEMEHL_ALIGN" + tag "modules" + tag "modules_nfcore" + tag "segemehl" + tag "segemehl/align" + tag "segemehl/index" + + setup { + run("SEGEMEHL_INDEX") { + script "../../../segemehl/index/main.nf" + process { + """ + input[0] = Channel.of([ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + } + + test("homo_sapiens - single_end") { + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = SEGEMEHL_INDEX.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.alignment[0][1]).exists() }, + { assert snapshot(process.out.versions).match("homo_sapiens - single_end - versions") } + ) + } + } + + test("homo_sapiens - paired_end") { + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = SEGEMEHL_INDEX.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.alignment[0][1]).exists() }, + { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - versions") } + ) + } + } + + test("homo_sapiens - split - single_end") { + config "./split.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = SEGEMEHL_INDEX.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.alignment[0][1]).exists() }, + { assert path(process.out.trans_alignments[0][1]).exists() }, + { assert path(process.out.multi_bed[0][1]).exists() }, + { assert path(process.out.single_bed[0][1]).exists() }, + { assert snapshot(process.out.versions).match("homo_sapiens - split - single_end - versions") } + ) + } + } + + test("homo_sapiens - split - paired_end") { + config "./split.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = SEGEMEHL_INDEX.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.alignment[0][1]).exists() }, + { assert path(process.out.trans_alignments[0][1]).exists() }, + { assert path(process.out.multi_bed[0][1]).exists() }, + { assert path(process.out.single_bed[0][1]).exists() }, + { assert snapshot(process.out.versions).match("homo_sapiens - split - paired_end - versions") } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/segemehl/align/tests/main.nf.test.snap b/modules/nf-core/segemehl/align/tests/main.nf.test.snap new file mode 100644 index 00000000..c914bc3d --- /dev/null +++ b/modules/nf-core/segemehl/align/tests/main.nf.test.snap @@ -0,0 +1,50 @@ +{ + "homo_sapiens - paired_end - versions": { + "content": [ + [ + "versions.yml:md5,0c6afcd6ae65e27a0ea87f5b42c853eb" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-05-30T12:58:05.434115758" + }, + "homo_sapiens - single_end - versions": { + "content": [ + [ + "versions.yml:md5,0c6afcd6ae65e27a0ea87f5b42c853eb" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-05-30T12:57:56.488707635" + }, + "homo_sapiens - split - single_end - versions": { + "content": [ + [ + "versions.yml:md5,0c6afcd6ae65e27a0ea87f5b42c853eb" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-05-30T13:06:11.217385877" + }, + "homo_sapiens - split - paired_end - versions": { + "content": [ + [ + "versions.yml:md5,0c6afcd6ae65e27a0ea87f5b42c853eb" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-05-30T13:06:29.757385118" + } +} \ No newline at end of file diff --git a/modules/nf-core/segemehl/align/tests/split.config b/modules/nf-core/segemehl/align/tests/split.config new file mode 100644 index 00000000..d4f6aab8 --- /dev/null +++ b/modules/nf-core/segemehl/align/tests/split.config @@ -0,0 +1,5 @@ +process{ + withName: SEGEMEHL_ALIGN { + ext.args = "-S" + } +} \ No newline at end of file diff --git a/modules/nf-core/segemehl/align/tests/tags.yml b/modules/nf-core/segemehl/align/tests/tags.yml new file mode 100644 index 00000000..6e7bf26e --- /dev/null +++ b/modules/nf-core/segemehl/align/tests/tags.yml @@ -0,0 +1,2 @@ +segemehl/align: + - modules/nf-core/segemehl/align/** diff --git a/modules/nf-core/tximeta/tximport/templates/tximport.r b/modules/nf-core/tximeta/tximport/templates/tximport.r index 92f1a9e8..40d79eb9 100755 --- a/modules/nf-core/tximeta/tximport/templates/tximport.r +++ b/modules/nf-core/tximeta/tximport/templates/tximport.r @@ -169,9 +169,7 @@ if ("tx2gene" %in% names(transcript_info) && !is.null(transcript_info\$tx2gene)) list(obj = gse, slot = "length", suffix = "gene_lengths.tsv"), list(obj = gse, slot = "abundance", suffix = "gene_tpm.tsv"), list(obj = gse, slot = "counts", suffix = "gene_counts.tsv"), - list(obj = gse.ls, slot = "abundance", suffix = "gene_tpm_length_scaled.tsv"), list(obj = gse.ls, slot = "counts", suffix = "gene_counts_length_scaled.tsv"), - list(obj = gse.s, slot = "abundance", suffix = "gene_tpm_scaled.tsv"), list(obj = gse.s, slot = "counts", suffix = "gene_counts_scaled.tsv") )) } diff --git a/modules/nf-core/tximeta/tximport/tests/main.nf.test.snap b/modules/nf-core/tximeta/tximport/tests/main.nf.test.snap index fe972d09..3cd0ee9e 100644 --- a/modules/nf-core/tximeta/tximport/tests/main.nf.test.snap +++ b/modules/nf-core/tximeta/tximport/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:54.169267" + "timestamp": "2024-05-28T12:35:50.683744" }, "lengths_gene_kallisto - stub": { "content": [ @@ -31,7 +31,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:20.838048" + "timestamp": "2024-05-28T12:35:16.126128" }, "counts_gene_scaled_salmon - stub": { "content": [ @@ -48,7 +48,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:54.139493" + "timestamp": "2024-05-28T12:35:50.654405" }, "counts_gene_kallisto - stub": { "content": [ @@ -65,7 +65,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:20.823542" + "timestamp": "2024-05-28T12:35:16.112898" }, "lengths_transcript_salmon - stub": { "content": [ @@ -82,7 +82,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:54.157265" + "timestamp": "2024-05-28T12:35:50.67148" }, "versions_salmon - stub": { "content": [ @@ -94,7 +94,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:54.175019" + "timestamp": "2024-05-28T12:35:50.690592" }, "counts_gene_length_scaled_kallisto": { "content": [ @@ -111,7 +111,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:04.116135" + "timestamp": "2024-05-28T12:34:59.621599" }, "lengths_transcript_salmon": { "content": [ @@ -128,7 +128,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:37.664041" + "timestamp": "2024-05-28T12:35:32.876208" }, "counts_transcript_kallisto": { "content": [ @@ -145,7 +145,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:04.162273" + "timestamp": "2024-05-28T12:34:59.62725" }, "counts_transcript_kallisto - stub": { "content": [ @@ -162,7 +162,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:20.834743" + "timestamp": "2024-05-28T12:35:16.122852" }, "counts_transcript_salmon": { "content": [ @@ -179,7 +179,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:37.652813" + "timestamp": "2024-05-28T12:35:32.866731" }, "lengths_gene_salmon - stub": { "content": [ @@ -196,7 +196,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:54.151603" + "timestamp": "2024-05-28T12:35:50.6654" }, "tpm_gene_salmon": { "content": [ @@ -213,7 +213,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:37.669821" + "timestamp": "2024-05-28T12:35:32.881193" }, "tpm_transcript_salmon": { "content": [ @@ -230,7 +230,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:37.674895" + "timestamp": "2024-05-28T12:35:32.886363" }, "tpm_gene_salmon - stub": { "content": [ @@ -247,7 +247,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:54.163303" + "timestamp": "2024-05-28T12:35:50.677538" }, "lengths_transcript_kallisto": { "content": [ @@ -264,7 +264,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:04.1686" + "timestamp": "2024-05-28T12:34:59.632822" }, "counts_gene_length_scaled_kallisto - stub": { "content": [ @@ -281,7 +281,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:20.827742" + "timestamp": "2024-05-28T12:35:16.11652" }, "tpm_gene_kallisto - stub": { "content": [ @@ -298,7 +298,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:20.846428" + "timestamp": "2024-05-28T12:35:16.133742" }, "counts_transcript_salmon - stub": { "content": [ @@ -315,7 +315,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:54.145564" + "timestamp": "2024-05-28T12:35:50.660144" }, "counts_gene_scaled_kallisto": { "content": [ @@ -332,7 +332,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:04.159638" + "timestamp": "2024-05-28T12:34:59.624732" }, "counts_gene_salmon": { "content": [ @@ -349,7 +349,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:37.636972" + "timestamp": "2024-05-28T12:35:32.852188" }, "versions_salmon": { "content": [ @@ -361,7 +361,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:37.680246" + "timestamp": "2024-05-28T12:35:32.892224" }, "counts_gene_length_scaled_salmon": { "content": [ @@ -378,7 +378,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:37.642848" + "timestamp": "2024-05-28T12:35:32.857451" }, "tpm_gene_kallisto": { "content": [ @@ -395,7 +395,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:04.172531" + "timestamp": "2024-05-28T12:34:59.636454" }, "lengths_transcript_kallisto - stub": { "content": [ @@ -412,7 +412,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:20.842475" + "timestamp": "2024-05-28T12:35:16.129712" }, "lengths_gene_kallisto": { "content": [ @@ -429,7 +429,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:04.16551" + "timestamp": "2024-05-28T12:34:59.630042" }, "counts_gene_scaled_kallisto - stub": { "content": [ @@ -446,7 +446,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:20.831518" + "timestamp": "2024-05-28T12:35:16.119638" }, "tpm_transcript_kallisto": { "content": [ @@ -463,7 +463,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:04.177955" + "timestamp": "2024-05-28T12:34:59.639525" }, "lengths_gene_salmon": { "content": [ @@ -480,7 +480,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:37.658624" + "timestamp": "2024-05-28T12:35:32.871162" }, "counts_gene_length_scaled_salmon - stub": { "content": [ @@ -497,7 +497,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:54.13369" + "timestamp": "2024-05-28T12:35:50.605613" }, "counts_gene_kallisto": { "content": [ @@ -514,7 +514,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:04.113216" + "timestamp": "2024-05-28T12:34:59.61832" }, "versions_kallisto": { "content": [ @@ -526,7 +526,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:04.181904" + "timestamp": "2024-05-28T12:34:59.642751" }, "counts_gene_salmon - stub": { "content": [ @@ -543,7 +543,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:54.127272" + "timestamp": "2024-05-28T12:35:50.598457" }, "versions_kallisto - stub": { "content": [ @@ -555,7 +555,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:20.86053" + "timestamp": "2024-05-28T12:35:16.141689" }, "tpm_transcript_kallisto - stub": { "content": [ @@ -572,7 +572,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:20.856075" + "timestamp": "2024-05-28T12:35:16.137716" }, "counts_gene_scaled_salmon": { "content": [ @@ -589,6 +589,6 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-11T11:35:37.647691" + "timestamp": "2024-05-28T12:35:32.862272" } } \ No newline at end of file From b81a30a9826388d2b693b606d531b96414bdc63e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 30 May 2024 14:12:14 +0200 Subject: [PATCH 259/491] Update segemehl unify call --- subworkflows/local/discovery/segemehl.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/discovery/segemehl.nf b/subworkflows/local/discovery/segemehl.nf index 5aa4b342..71669032 100644 --- a/subworkflows/local/discovery/segemehl.nf +++ b/subworkflows/local/discovery/segemehl.nf @@ -14,8 +14,8 @@ workflow SEGEMEHL { index = index ?: INDEX( fasta ).index ALIGN( reads, fasta, index ) - UNIFY( ALIGN.out.results - .map{ meta, results -> [ meta + [tool: "segemehl"], results ] }, [] ) + UNIFY( ALIGN.out.single_bed + .map{ meta, bed -> [ meta + [tool: "segemehl"], bed ] }, [] ) ch_versions = ch_versions.mix(ALIGN.out.versions) ch_versions = ch_versions.mix(UNIFY.out.versions) From 0a98534fd6a368dd7c643ef38e82e0b96dbacc0b Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 31 May 2024 13:04:46 +0200 Subject: [PATCH 260/491] Add support for ext.args in ciriquant --- modules/local/ciriquant/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/local/ciriquant/main.nf b/modules/local/ciriquant/main.nf index 5c96fe14..c1c29bfb 100644 --- a/modules/local/ciriquant/main.nf +++ b/modules/local/ciriquant/main.nf @@ -47,7 +47,8 @@ process CIRIQUANT { --config config.yml \\ --no-gene \\ -o ${prefix} \\ - -p ${prefix} + -p ${prefix} \\ + ${args} cat <<-END_VERSIONS > versions.yml "${task.process}": From 0cc85b036de4a7d9c74e109216c39b4caa5c999a Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 31 May 2024 13:51:03 +0200 Subject: [PATCH 261/491] Add strandedness to samplesheet --- assets/schema_input.json | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/assets/schema_input.json b/assets/schema_input.json index fe551cb8..7e9257a0 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -26,6 +26,13 @@ "exists": true, "pattern": "^\\S+\\.f(ast)?q\\.gz$", "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" + }, + "strandedness": { + "type": "string", + "enum": ["unstranded", "forward", "reverse", "auto"], + "default": "auto", + "errorMessage": "Strandedness must be one of 'unstranded', 'forward', 'reverse' or 'auto'", + "meta": ["strandedness"] } }, "required": ["sample", "fastq_1"] From 30af702000fb90ec112240d620976639eeb75735 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 31 May 2024 14:03:27 +0200 Subject: [PATCH 262/491] Add support for strandedness in ciriquant --- modules/local/ciriquant/main.nf | 3 +++ 1 file changed, 3 insertions(+) diff --git a/modules/local/ciriquant/main.nf b/modules/local/ciriquant/main.nf index c1c29bfb..db228929 100644 --- a/modules/local/ciriquant/main.nf +++ b/modules/local/ciriquant/main.nf @@ -26,6 +26,8 @@ process CIRIQUANT { def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" def VERSION = '2.1.0' + def strandedness = meta.strandedness ?: 'auto' + def library_type = strandedness == 'auto' ? '' : strandedness == 'unstranded' ? '-l 0' : strandedness == 'forward' ? '-l 1' : '-l 2' """ BWA=`which bwa` HISAT2=`which hisat2` @@ -48,6 +50,7 @@ process CIRIQUANT { --no-gene \\ -o ${prefix} \\ -p ${prefix} \\ + ${library_type} \\ ${args} cat <<-END_VERSIONS > versions.yml From 9c5889989200b6781fcbbb7cfeca186395c5a794 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 31 May 2024 20:29:07 +0200 Subject: [PATCH 263/491] Revise DCC parameters --- modules/local/dcc/main.nf | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/modules/local/dcc/main.nf b/modules/local/dcc/main.nf index 9baad3ff..429d7dc5 100644 --- a/modules/local/dcc/main.nf +++ b/modules/local/dcc/main.nf @@ -22,13 +22,15 @@ process DCC { script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" + def strandedness = meta.strandedness ?: 'auto' + def strand_args = strandedness == 'auto' || strandedness == 'unstranded' ? '-N' : strandedness == 'forward' ? '' : '-ss' if(meta.single_end){ """ sed -i 's/^chr//g' $gtf mkdir ${prefix} && mv ${prefix}.Chimeric.out.junction ${prefix} && printf "${prefix}/${prefix}.Chimeric.out.junction" > samplesheet - DCC @samplesheet -D -an $gtf -Pi -ss -F -M -Nr 1 1 -fg -A $fasta -N -T ${task.cpus} + DCC @samplesheet -D -an $gtf -F -M -Nr 1 1 -A $fasta $strand_args -T ${task.cpus} awk '{print \$6}' CircCoordinates >> strand paste CircRNACount strand | tail -n +2 | awk -v OFS="\\t" '{print \$1,\$2,\$3,\$5,\$4}' >> ${prefix}.txt @@ -46,7 +48,7 @@ process DCC { mkdir ${prefix}_mate1 && mv ${prefix}_mate1.Chimeric.out.junction ${prefix}_mate1 && printf "${prefix}_mate1/${prefix}_mate1.Chimeric.out.junction" > mate1file mkdir ${prefix}_mate2 && mv ${prefix}_mate2.Chimeric.out.junction ${prefix}_mate2 && printf "${prefix}_mate2/${prefix}_mate2.Chimeric.out.junction" > mate2file - DCC @samplesheet -mt1 @mate1file -mt2 @mate2file -D -an $gtf -Pi -ss -F -M -Nr 1 1 -fg -A $fasta -N -T ${task.cpus} + DCC @samplesheet -mt1 @mate1file -mt2 @mate2file -D -an $gtf -Pi -F -M -Nr 1 1 -A $fasta $strand_args -T ${task.cpus} awk '{print \$6}' CircCoordinates >> strand paste CircRNACount strand | tail -n +2 | awk -v OFS="\\t" '{print \$1,\$2,\$3,\$5,\$4}' >> ${prefix}.txt From f38c58cd5b13c61f646e6131f032a9fc7627d2d6 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 31 May 2024 20:43:19 +0200 Subject: [PATCH 264/491] Implement ext.args interface for find_circ --- modules/local/find_circ/find_circ/main.nf | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/modules/local/find_circ/find_circ/main.nf b/modules/local/find_circ/find_circ/main.nf index bd1bced2..3c367cf9 100644 --- a/modules/local/find_circ/find_circ/main.nf +++ b/modules/local/find_circ/find_circ/main.nf @@ -23,6 +23,8 @@ process FIND_CIRC { script: prefix = task.ext.prefix ?: "${meta.id}" + args = task.ext.args ?: "" + args2 = task.ext.args2 ?: "" def VERSION = '1.2' """ INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/.rev.1.bt2//"` @@ -37,8 +39,9 @@ process FIND_CIRC { --score-min=C,-15,0 \\ -q \\ -x \$INDEX \\ + $args \\ -U $anchors | \\ - find_circ.py --genome=$fasta --prefix=${prefix} --stats=${prefix}.sites.log --reads=${prefix}.sites.reads > ${prefix}.sites.bed + find_circ.py --genome=$fasta $args2 --prefix=${prefix} --stats=${prefix}.sites.log --reads=${prefix}.sites.reads > ${prefix}.sites.bed cat <<-END_VERSIONS > versions.yml "${task.process}": From ca15b3a91c97acd8ec301425a283c890d0e4129b Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 31 May 2024 20:50:07 +0200 Subject: [PATCH 265/491] Fix trimming indentation in modules.config --- conf/modules.config | 54 ++++++++++++++++++++++----------------------- 1 file changed, 27 insertions(+), 27 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index a1cd75c2..03c820e7 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -28,36 +28,36 @@ process { // TRIMMING courtesy of nf-core/rnaseq -if (!params.skip_trimming) { - process { - withName: '.*:FASTQC_TRIMGALORE:TRIMGALORE' { - ext.args = { - [ - "--fastqc_args '-t ${task.cpus}' ", - params.trim_nextseq > 0 ? "--nextseq ${params.trim_nextseq}" : '' - ].join(' ').trim() - } - publishDir = [ - [ - path: { "${params.outdir}/quality_control/trimgalore/fastqc" }, - mode: params.publish_dir_mode, - pattern: "*.{html,zip}" - ], - [ - path: { "${params.outdir}/quality_control/trimgalore" }, - mode: params.publish_dir_mode, - pattern: "*.fq.gz", - enabled: params.save_trimmed - ], - [ - path: { "${params.outdir}/quality_control/trimgalore" }, - mode: params.publish_dir_mode, - pattern: "*.txt" + if (!params.skip_trimming) { + process { + withName: '.*:FASTQC_TRIMGALORE:TRIMGALORE' { + ext.args = { + [ + "--fastqc_args '-t ${task.cpus}' ", + params.trim_nextseq > 0 ? "--nextseq ${params.trim_nextseq}" : '' + ].join(' ').trim() + } + publishDir = [ + [ + path: { "${params.outdir}/quality_control/trimgalore/fastqc" }, + mode: params.publish_dir_mode, + pattern: "*.{html,zip}" + ], + [ + path: { "${params.outdir}/quality_control/trimgalore" }, + mode: params.publish_dir_mode, + pattern: "*.fq.gz", + enabled: params.save_trimmed + ], + [ + path: { "${params.outdir}/quality_control/trimgalore" }, + mode: params.publish_dir_mode, + pattern: "*.txt" + ] ] - ] + } } } -} // PREPARE GENOME withName: CLEAN_FASTA { From 2b54d433bf21d7ea00d3276ce03bd60a29461020 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 31 May 2024 20:50:49 +0200 Subject: [PATCH 266/491] Move segemehl index location in modules.config --- conf/modules.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 03c820e7..1a8754f2 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -143,6 +143,8 @@ process { ] } + // circRNA + withName: '.*:SEGEMEHL:INDEX' { publishDir = [ path: { "${params.outdir}/references/index/segemehl" }, @@ -152,8 +154,6 @@ process { ] } - // circRNA - withName: '.*:SEGEMEHL:ALIGN' { ext.args = [ "", "-b", From 022d66e0c85d6b7db58aafc7c2833bccfc356ec0 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 31 May 2024 20:59:09 +0200 Subject: [PATCH 267/491] Add strandedness to bowtie2 calls --- conf/modules.config | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 1a8754f2..569cedf4 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -295,13 +295,9 @@ process { } withName: '.*:FIND_CIRC:ALIGN' { - ext.args = [ "", - "--very-sensitive", - "--mm", - "-D 20", - "--score-min=C,-15,0", - "-q" - ].join(' ').trim() + ext.args = { "--very-sensitive --mm -D 20 --score-min=C,-15,0 -q " + + (!meta.strandedness || meta.strandedness == 'unstranded' || meta.strandedness == 'auto' ? '' : + meta.strandedness == 'forward' ? ' --norc' : ' --nofw') } publishDir = [ path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, @@ -331,6 +327,8 @@ process { } withName: '.*:FIND_CIRC:MAIN' { + ext.args = { !meta.strandedness || meta.strandedness == 'unstranded' || meta.strandedness == 'auto' ? '' : + meta.strandedness == 'forward' ? ' --norc' : ' --nofw' } publishDir = [ path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, From a41eab1fcd68ba9585cc475f087ba69d4ef8ef71 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 31 May 2024 21:06:20 +0200 Subject: [PATCH 268/491] Add strandedness to find_circ --- modules/local/find_circ/find_circ/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/local/find_circ/find_circ/main.nf b/modules/local/find_circ/find_circ/main.nf index 3c367cf9..8a4ca128 100644 --- a/modules/local/find_circ/find_circ/main.nf +++ b/modules/local/find_circ/find_circ/main.nf @@ -25,6 +25,7 @@ process FIND_CIRC { prefix = task.ext.prefix ?: "${meta.id}" args = task.ext.args ?: "" args2 = task.ext.args2 ?: "" + def strand_arg = meta.strandedness && (meta.strandedness == 'forward' || meta.strandedness == 'reverse') ? "--stranded" : "" def VERSION = '1.2' """ INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/.rev.1.bt2//"` @@ -41,7 +42,7 @@ process FIND_CIRC { -x \$INDEX \\ $args \\ -U $anchors | \\ - find_circ.py --genome=$fasta $args2 --prefix=${prefix} --stats=${prefix}.sites.log --reads=${prefix}.sites.reads > ${prefix}.sites.bed + find_circ.py --genome=$fasta $strand_arg $args2 --prefix=${prefix} --stats=${prefix}.sites.log --reads=${prefix}.sites.reads > ${prefix}.sites.bed cat <<-END_VERSIONS > versions.yml "${task.process}": From 8957a7ee752f63ee031eaf27fa51d1551bcaeef3 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sun, 9 Jun 2024 15:26:49 +0200 Subject: [PATCH 269/491] Add strandedness documentation --- docs/usage.md | 27 ++++++++++++++------------- 1 file changed, 14 insertions(+), 13 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 5c6337d5..e84dc944 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -24,21 +24,22 @@ The pipeline will auto-detect whether a sample is single- or paired-end using th A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice. ```csv title="samplesheet.csv" -sample,fastq_1,fastq_2 -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz -CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz -CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz -TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz, -TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz, -TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz, -TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz, +sample,fastq_1,fastq_2,strandedness +CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz, +CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz, +CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz, +TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz,, +TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz,, +TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz,, +TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,, ``` -| Column | Description | -| --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | -| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | -| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| Column | Description | +| -------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | +| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| `strandedness` | Strandedness of the library. Options are `auto`, `unstranded`, `forward`, `reverse`. Default is `auto`. | An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. From c65e604d913e3657f6f5bef065acb08e556df726 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sun, 9 Jun 2024 15:33:17 +0200 Subject: [PATCH 270/491] Add samplesheet validation for strandedness of runs of the same sample --- docs/usage.md | 22 +++++++++---------- .../utils_nfcore_circrna_pipeline/main.nf | 6 +++++ 2 files changed, 17 insertions(+), 11 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index e84dc944..c5312fa6 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -25,21 +25,21 @@ A final samplesheet file consisting of both single- and paired-end data may look ```csv title="samplesheet.csv" sample,fastq_1,fastq_2,strandedness -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz, +CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,auto CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz, CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz, -TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz,, -TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz,, -TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz,, -TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,, +TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz,,forward +TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz,,reverse +TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz,,unstranded +TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,,unstranded ``` -| Column | Description | -| -------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | -| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | -| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | -| `strandedness` | Strandedness of the library. Options are `auto`, `unstranded`, `forward`, `reverse`. Default is `auto`. | +| Column | Description | +| -------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | +| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| `strandedness` | Strandedness of the library. Options are `auto`, `unstranded`, `forward`, `reverse`. Default is `auto`. Make sure to use the same strandedness for each library/run of the same sample. | An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. diff --git a/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf b/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf index 15c32930..646b5476 100644 --- a/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_circrna_pipeline/main.nf @@ -170,6 +170,12 @@ def validateInputSamplesheet(input) { error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") } + // Check that multiple runs of the same sample are of the same strandedness i.e. auto / unstranded / forward / reverse + def strandedness_ok = metas.collect{ it.strandedness }.unique().size == 1 + if (!strandedness_ok) { + error("Please check input samplesheet -> Multiple runs of a sample must be of the same strandedness: ${metas[0].id}") + } + return [ metas[0], fastqs ] } // From 0ea2e7538c0768e168998946666ffd847e319928 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sun, 9 Jun 2024 15:40:03 +0200 Subject: [PATCH 271/491] Update modules --- modules.json | 20 +- modules/nf-core/bwa/index/meta.yml | 2 +- .../nf-core/samtools/faidx/environment.yml | 4 +- modules/nf-core/samtools/faidx/main.nf | 4 +- .../samtools/faidx/tests/main.nf.test.snap | 30 +-- .../nf-core/samtools/flagstat/environment.yml | 4 +- modules/nf-core/samtools/flagstat/main.nf | 4 +- .../samtools/flagstat/tests/main.nf.test.snap | 6 +- .../nf-core/samtools/idxstats/environment.yml | 4 +- modules/nf-core/samtools/idxstats/main.nf | 4 +- .../samtools/idxstats/tests/main.nf.test.snap | 6 +- .../nf-core/samtools/index/environment.yml | 4 +- modules/nf-core/samtools/index/main.nf | 4 +- .../samtools/index/tests/main.nf.test.snap | 18 +- modules/nf-core/samtools/sort/environment.yml | 4 +- modules/nf-core/samtools/sort/main.nf | 4 +- .../nf-core/samtools/sort/tests/main.nf.test | 16 +- .../samtools/sort/tests/main.nf.test.snap | 198 +++++++----------- .../nf-core/samtools/stats/environment.yml | 4 +- modules/nf-core/samtools/stats/main.nf | 4 +- .../samtools/stats/tests/main.nf.test.snap | 24 +-- modules/nf-core/samtools/view/environment.yml | 4 +- modules/nf-core/samtools/view/main.nf | 4 +- .../samtools/view/tests/main.nf.test.snap | 36 ++-- .../tests/main.nf.test.snap | 12 +- 25 files changed, 196 insertions(+), 228 deletions(-) diff --git a/modules.json b/modules.json index 6e535782..9f5b1a68 100644 --- a/modules.json +++ b/modules.json @@ -42,7 +42,7 @@ }, "bwa/index": { "branch": "master", - "git_sha": "086fa66260595e123b0ea47a6512539b72a9afa3", + "git_sha": "e0ff65e1fb313677de09f5f477ae3da30ce19b7b", "installed_by": ["modules"] }, "cat/cat": { @@ -127,37 +127,37 @@ }, "samtools/faidx": { "branch": "master", - "git_sha": "f153f1f10e1083c49935565844cccb7453021682", + "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", "installed_by": ["modules"] }, "samtools/flagstat": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", "installed_by": ["bam_stats_samtools"] }, "samtools/idxstats": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", "installed_by": ["bam_sort_stats_samtools", "modules"] }, "samtools/sort": { "branch": "master", - "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", + "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", "installed_by": ["bam_sort_stats_samtools", "modules"] }, "samtools/stats": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", "installed_by": ["bam_stats_samtools"] }, "samtools/view": { "branch": "master", - "git_sha": "0bd7d2333a88483aa0476acea172e9f5f6dd83bb", + "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", "installed_by": ["modules"] }, "segemehl/align": { @@ -201,12 +201,12 @@ "nf-core": { "bam_sort_stats_samtools": { "branch": "master", - "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", + "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", "installed_by": ["subworkflows"] }, "bam_stats_samtools": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", "installed_by": ["bam_sort_stats_samtools", "subworkflows"] }, "utils_nextflow_pipeline": { diff --git a/modules/nf-core/bwa/index/meta.yml b/modules/nf-core/bwa/index/meta.yml index 4c7d30f3..6bbc87a6 100644 --- a/modules/nf-core/bwa/index/meta.yml +++ b/modules/nf-core/bwa/index/meta.yml @@ -11,7 +11,7 @@ tools: BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome. homepage: http://bio-bwa.sourceforge.net/ - documentation: http://www.htslib.org/doc/samtools.html + documentation: https://bio-bwa.sourceforge.net/bwa.shtml arxiv: arXiv:1303.3997 licence: ["GPL-3.0-or-later"] input: diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml index 9c24eb0a..f8450fa5 100644 --- a/modules/nf-core/samtools/faidx/environment.yml +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -6,5 +6,5 @@ channels: - defaults dependencies: - - bioconda::htslib=1.19.1 - - bioconda::samtools=1.19.2 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index cfe7ad95..bdcdbc95 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FAIDX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : + 'biocontainers/samtools:1.20--h50ea8bc_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap index 3e651ef6..3223b72b 100644 --- a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap @@ -18,7 +18,7 @@ ], "3": [ - "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + "versions.yml:md5,2db78952923a61e05d50b95518b21856" ], "fa": [ @@ -36,7 +36,7 @@ ], "versions": [ - "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + "versions.yml:md5,2db78952923a61e05d50b95518b21856" ] } ], @@ -44,7 +44,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-18T16:22:39.412601" + "timestamp": "2024-05-28T15:42:14.779784761" }, "test_samtools_faidx_bgzip": { "content": [ @@ -71,7 +71,7 @@ ] ], "3": [ - "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + "versions.yml:md5,2db78952923a61e05d50b95518b21856" ], "fa": [ @@ -95,7 +95,7 @@ ] ], "versions": [ - "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + "versions.yml:md5,2db78952923a61e05d50b95518b21856" ] } ], @@ -103,7 +103,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-18T16:23:22.427966" + "timestamp": "2024-05-28T15:42:20.256633877" }, "test_samtools_faidx_fasta": { "content": [ @@ -124,7 +124,7 @@ ], "3": [ - "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + "versions.yml:md5,2db78952923a61e05d50b95518b21856" ], "fa": [ [ @@ -142,7 +142,7 @@ ], "versions": [ - "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + "versions.yml:md5,2db78952923a61e05d50b95518b21856" ] } ], @@ -150,7 +150,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-18T16:24:04.107537" + "timestamp": "2024-05-28T15:42:25.632577273" }, "test_samtools_faidx_stub_fasta": { "content": [ @@ -171,7 +171,7 @@ ], "3": [ - "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + "versions.yml:md5,2db78952923a61e05d50b95518b21856" ], "fa": [ [ @@ -189,7 +189,7 @@ ], "versions": [ - "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + "versions.yml:md5,2db78952923a61e05d50b95518b21856" ] } ], @@ -197,7 +197,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-18T16:24:45.868463" + "timestamp": "2024-05-28T15:42:31.058424849" }, "test_samtools_faidx_stub_fai": { "content": [ @@ -218,7 +218,7 @@ ], "3": [ - "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + "versions.yml:md5,2db78952923a61e05d50b95518b21856" ], "fa": [ @@ -236,7 +236,7 @@ ], "versions": [ - "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + "versions.yml:md5,2db78952923a61e05d50b95518b21856" ] } ], @@ -244,6 +244,6 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-03-18T16:25:27.550554" + "timestamp": "2024-05-28T15:42:36.479929617" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index bd57cb54..68b81558 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index eb5f5252..754d84b7 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FLAGSTAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : + 'biocontainers/samtools:1.20--h50ea8bc_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap index a76fc27e..e9f85efa 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap @@ -20,13 +20,13 @@ "versions": { "content": [ [ - "versions.yml:md5,fd0030ce49ab3a92091ad80260226452" + "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:11:44.299617452" + "timestamp": "2024-05-28T15:41:52.516253882" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index 174973b8..eb6c8809 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index a544026f..2ea2a5cc 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_IDXSTATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : + 'biocontainers/samtools:1.20--h50ea8bc_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap index a7050bdc..4eacdb90 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "versions": { "content": [ [ - "versions.yml:md5,613dde56f108418039ffcdeeddba397a" + "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:16:50.147462763" + "timestamp": "2024-05-28T15:46:46.617989517" }, "idxstats": { "content": [ diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index a5e50649..260d516b 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index dc14f98d..b523c21b 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : + 'biocontainers/samtools:1.20--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 3dc8e7de..52756e85 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -2,26 +2,26 @@ "crai_versions": { "content": [ [ - "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:12:00.324667957" + "timestamp": "2024-05-28T15:42:04.203740976" }, "csi_versions": { "content": [ [ - "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:12:07.885103162" + "timestamp": "2024-05-28T15:42:09.57475878" }, "crai": { "content": [ @@ -62,13 +62,13 @@ "bai_versions": { "content": [ [ - "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:11:51.641425452" + "timestamp": "2024-05-28T15:41:57.929287369" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index 4d898e48..36a12eab 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index fc374f98..596c6f7e 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : + 'biocontainers/samtools:1.20--h50ea8bc_0' }" input: tuple val(meta) , path(bam) diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index 8360e2b1..fb38ed9b 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -30,7 +30,11 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.bam, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } } + ).match("test_bam") + } ) } } @@ -44,11 +48,11 @@ nextflow_process { """ input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) ]) input[1] = Channel.of([ [ id:'fasta' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]) """ } @@ -57,7 +61,11 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.bam, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } } + ).match("test_cram") + } ) } } diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index 38477656..5a27de1d 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -1,68 +1,21 @@ { "cram": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,bc0b7c25da26384a006ed84cc9e4da23" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.csi:md5,8d4e836c2fed6c0bf874d5e8cdba5831" - ] - ], - "4": [ - "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" - ], - "bam": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,bc0b7c25da26384a006ed84cc9e4da23" - ] - ], - "crai": [ - - ], - "cram": [ - - ], - "csi": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.csi:md5,8d4e836c2fed6c0bf874d5e8cdba5831" - ] - ], - "versions": [ - "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,21c992d59615936b99f2ad008aa54400" ] - } + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-03-04T15:08:00.830294" + "timestamp": "2024-05-31T08:13:54.512837189" }, "bam_stub_bam": { "content": [ @@ -70,85 +23,92 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nextflow": "24.04.2" + }, + "timestamp": "2024-05-31T07:29:00.761845507" + }, + "test_cram": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,22b2093be34a7637f5fbc84272b89d06" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" }, - "timestamp": "2024-02-12T19:21:04.364044" + "timestamp": "2024-05-31T09:16:51.924951855" + }, + "test_bam": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,21c992d59615936b99f2ad008aa54400" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-05-31T08:28:12.15952312" }, "bam_stub_versions": { "content": [ [ - "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" + "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-13T16:15:00.20800281" + "timestamp": "2024-05-31T07:29:00.765038811" }, "bam": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,bc0b7c25da26384a006ed84cc9e4da23" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.csi:md5,8d4e836c2fed6c0bf874d5e8cdba5831" - ] - ], - "4": [ - "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" - ], - "bam": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,bc0b7c25da26384a006ed84cc9e4da23" - ] - ], - "crai": [ - - ], - "cram": [ - - ], - "csi": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.csi:md5,8d4e836c2fed6c0bf874d5e8cdba5831" - ] - ], - "versions": [ - "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,21c992d59615936b99f2ad008aa54400" ] - } + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-03-04T15:07:48.773803" + "timestamp": "2024-05-31T08:13:48.538030517" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index 67bb0ca4..1cc83bd9 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 52b00f4b..982bc28e 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_STATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : + 'biocontainers/samtools:1.20--h50ea8bc_0' }" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap index 1b7c9ba4..2747fd6c 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -8,11 +8,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,01812900aa4027532906c5d431114233" + "test.stats:md5,c9d39b38c22de2057fc2f89949090975" ] ], "1": [ - "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9" + "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" ], "stats": [ [ @@ -20,19 +20,19 @@ "id": "test", "single_end": false }, - "test.stats:md5,01812900aa4027532906c5d431114233" + "test.stats:md5,c9d39b38c22de2057fc2f89949090975" ] ], "versions": [ - "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9" + "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:15:25.562429714" + "timestamp": "2024-05-28T15:45:24.403941966" }, "bam": { "content": [ @@ -43,11 +43,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,5d8681bf541199898c042bf400391d59" + "test.stats:md5,d522a1fa016b259d6a55620ae53dcd63" ] ], "1": [ - "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9" + "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" ], "stats": [ [ @@ -55,18 +55,18 @@ "id": "test", "single_end": false }, - "test.stats:md5,5d8681bf541199898c042bf400391d59" + "test.stats:md5,d522a1fa016b259d6a55620ae53dcd63" ] ], "versions": [ - "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9" + "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:15:07.857611509" + "timestamp": "2024-05-28T15:45:06.711251947" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml index b0676f33..150c3777 100644 --- a/modules/nf-core/samtools/view/environment.yml +++ b/modules/nf-core/samtools/view/environment.yml @@ -4,5 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::samtools=1.20 + - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index 5a8989d6..38df8576 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_VIEW { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : + 'biocontainers/samtools:1.20--h50ea8bc_0' }" input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap index f55943a7..eb0c577c 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap @@ -56,14 +56,14 @@ "bam_stub_versions": { "content": [ [ - "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1" + "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:13:09.713353823" + "timestamp": "2024-05-28T15:43:20.390692583" }, "cram_to_bam_index_cram": { "content": [ @@ -208,14 +208,14 @@ "cram_to_bam_index_qname_versions": { "content": [ [ - "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1" + "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:13:03.935041046" + "timestamp": "2024-05-28T15:43:15.007493874" }, "cram_to_bam_bam": { "content": [ @@ -240,14 +240,14 @@ "cram_to_bam_index_versions": { "content": [ [ - "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1" + "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:12:55.910685496" + "timestamp": "2024-05-28T15:43:09.472376824" }, "cram_to_bam_bai": { "content": [ @@ -264,14 +264,14 @@ "cram_to_bam_versions": { "content": [ [ - "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1" + "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:12:47.715221169" + "timestamp": "2024-05-28T15:43:04.080050906" }, "cram_bam": { "content": [ @@ -358,14 +358,14 @@ "bam_versions": { "content": [ [ - "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1" + "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:12:31.692607421" + "timestamp": "2024-05-28T15:42:52.978954857" }, "cram_to_bam_index_qname_cram": { "content": [ @@ -430,14 +430,14 @@ "cram_versions": { "content": [ [ - "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1" + "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:12:39.913411036" + "timestamp": "2024-05-28T15:42:58.400776109" }, "bam_sam": { "content": [ diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap index 6645a092..db063837 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap @@ -43,15 +43,15 @@ "id": "test", "single_end": false }, - "test.stats:md5,cb0bf2b79de52fdf0c61e80efcdb0bb4" + "test.stats:md5,d32de3b3716a11039cef2367c3c1a56e" ] ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:44:38.553256801" + "timestamp": "2024-05-29T07:47:44.044172487" }, "test_bam_sort_stats_samtools_paired_end_stats": { "content": [ @@ -61,15 +61,15 @@ "id": "test", "single_end": false }, - "test.stats:md5,d7796222a087b9bb97f631f1c21b9c95" + "test.stats:md5,cca83e4fc9406fc3875b5e60055d6574" ] ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:44:48.355870518" + "timestamp": "2024-05-29T07:47:51.426232891" }, "test_bam_sort_stats_samtools_single_end_idxstats": { "content": [ From 8150c43055c65172b5a85c83809cde8c3075043c Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 10 Jun 2024 12:29:21 +0200 Subject: [PATCH 272/491] Add new STATISTICAL_TESTS subworkflow --- subworkflows/local/quantification.nf | 1 + subworkflows/local/statistical_tests.nf | 11 +++++++++++ workflows/circrna/main.nf | 12 +++++++++++- 3 files changed, 23 insertions(+), 1 deletion(-) create mode 100644 subworkflows/local/statistical_tests.nf diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index ee9ad8be..bc33dbf1 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -121,6 +121,7 @@ workflow QUANTIFICATION { ) emit: + se = MERGE_EXPERIMENTS.out.merged gene_counts = JOIN_GENE_COUNTS.out.csv gene_tpm = JOIN_GENE_TPM.out.csv tx_counts = JOIN_TX_COUNTS.out.csv diff --git a/subworkflows/local/statistical_tests.nf b/subworkflows/local/statistical_tests.nf new file mode 100644 index 00000000..149d6f53 --- /dev/null +++ b/subworkflows/local/statistical_tests.nf @@ -0,0 +1,11 @@ +workflow STATISTICAL_TESTS { + take: + ch_quantification + + main: + ch_versions = Channel.empty() + + ch_quantification.view() + + +} \ No newline at end of file diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 4da9fe94..839b3af6 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -31,7 +31,7 @@ include { PREPARE_GENOME } from '../../subworkflows/local/prep include { CIRCRNA_DISCOVERY } from '../../subworkflows/local/circrna_discovery' include { QUANTIFICATION } from '../../subworkflows/local/quantification' include { MIRNA_PREDICTION } from '../../subworkflows/local/mirna_prediction' -include { DIFFERENTIAL_EXPRESSION } from '../../subworkflows/local/differential_expression' +include { STATISTICAL_TESTS } from '../../subworkflows/local/statistical_tests' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -182,6 +182,15 @@ workflow CIRCRNA { ch_versions = ch_versions.mix(MIRNA_PREDICTION.out.versions) + // + // 5. Statistical tests + // + + STATISTICAL_TESTS( + QUANTIFICATION.out.se + ) + + /* // // 5. Differential expression tests // @@ -204,6 +213,7 @@ workflow CIRCRNA { ch_versions = ch_versions.mix(DIFFERENTIAL_EXPRESSION.out.versions) ch_multiqc_files = ch_multiqc_files.mix(DIFFERENTIAL_EXPRESSION.out.reports) + */ // // Collate and save software versions From 7ef6b03ed5d726e49f307277444869ca93fb3832 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 10 Jun 2024 13:38:03 +0200 Subject: [PATCH 273/491] Implement CIRCTEST_PREPARE --- bin/prepare_circ_test.R | 69 ------------------- .../local/circtest/prepare/environment.yml | 5 ++ modules/local/circtest/prepare/main.nf | 34 ++++----- .../circtest/prepare/templates/prepare.R | 30 ++++++++ subworkflows/local/statistical_tests.nf | 9 ++- workflows/circrna/main.nf | 5 +- 6 files changed, 59 insertions(+), 93 deletions(-) delete mode 100755 bin/prepare_circ_test.R create mode 100644 modules/local/circtest/prepare/environment.yml create mode 100644 modules/local/circtest/prepare/templates/prepare.R diff --git a/bin/prepare_circ_test.R b/bin/prepare_circ_test.R deleted file mode 100755 index 95057f19..00000000 --- a/bin/prepare_circ_test.R +++ /dev/null @@ -1,69 +0,0 @@ -#!/usr/bin/env Rscript - -## Author: Barry Digby -## License: MIT - -circ_mat = read.table("merged_counts.tsv", header=T, sep="\t", check.names = FALSE, stringsAsFactors = F, row.names = "ID") -gene_mat = read.table("gene_count_matrix.csv", sep=",", header=T, row.names="gene_id", stringsAsFactors = F) -map = read.table("circrna_host-gene.txt", header = F, sep="\t", stringsAsFactors = F) - -# some circrnas do not have a host gene. -map <- na.omit(map) -colnames(map) <- c("circrna", "gene") - -# resolve multiple host genes by creating a new 'map' dataframe -# to enforce 1-1 mapping. - -new_circ = c() -new_gene = c() - -for(i in 1:nrow(map)){ - row <- map[i,] - circ <- row$circrna - gene <- row$gene - - # multiple host genes? - multiple_genes <- unlist(strsplit(gene, ",")) - #print(multiple_genes) - if(length(multiple_genes) > 1){ - for(gene in multiple_genes){ - new_circ <- c(new_circ, circ) - new_gene <- c(new_gene, gene) - } - } - new_circ <- c(new_circ, circ) - new_gene <- c(new_gene, gene) -} - -new_map <- data.frame(new_circ, new_gene) - -#create circTest dataframe. really odd formatting..! -new_circ_mat <- circ_mat[c(new_map$new_circ),] - -# unique names for duplicated circrna ids, resolve below -Chr <- c() -Start <- c() -End <- c() -for(i in 1:nrow(new_circ_mat)){ - row <- new_circ_mat[i,] - print(rownames(row)) - chr_ <- unlist(strsplit(rownames(row), ':'))[1] - coords <- unlist(strsplit(rownames(row), ':'))[2] - start_ <- unlist(strsplit(coords, '-'))[1] - end_ <- unlist(strsplit(coords, '-'))[2] - - Chr <- c(Chr, chr_) - Start <- c(Start, start_) - End <- c(End, end_) - -} - -Gene <- new_map$new_gene -circ_csv <- data.frame(Chr, Start, End, Gene, new_circ_mat) -# DROP the rownames, do not write to file. - -gene_csv <- gene_mat[c(new_map$new_gene),] -gene_csv <- data.frame(Chr, Start, End, Gene, gene_csv) - -write.csv(circ_csv, "circ.csv", quote=F, row.names = FALSE) -write.csv(gene_csv, "linear.csv", quote=F, row.names = FALSE) diff --git a/modules/local/circtest/prepare/environment.yml b/modules/local/circtest/prepare/environment.yml new file mode 100644 index 00000000..602dc60d --- /dev/null +++ b/modules/local/circtest/prepare/environment.yml @@ -0,0 +1,5 @@ +name: circtest_prepare +channels: + - conda-forge +dependencies: + - conda-forge::r-base=4.2.1 \ No newline at end of file diff --git a/modules/local/circtest/prepare/main.nf b/modules/local/circtest/prepare/main.nf index 834c6063..e41b6c46 100644 --- a/modules/local/circtest/prepare/main.nf +++ b/modules/local/circtest/prepare/main.nf @@ -1,32 +1,26 @@ -process PREPARE_CLR_TEST { - label 'process_medium' +process CIRCTEST_PREPARE { + label 'process_low' - conda "conda-forge::r-base=4.2.2 conda-forge::r-aod=1.3.2 conda-forge::r-ggplot2=3.4.0 conda-forge::r-plyr=1.8.8" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-c79b00aa4647c739dbe7e8480789d3ba67988f2e:0' : - 'biocontainers/mulled-v2-c79b00aa4647c739dbe7e8480789d3ba67988f2e:0' }" + 'https://depot.galaxyproject.org/singularity/biocontainers/r-base:4.2.1' : + 'biocontainers/r-base:4.2.1' }" input: - path(gene_matrix) - path(circrna_matrix) - path(circ_host_map) - path(gtf) + tuple val(meta), path(circ_counts) + tuple val(meta2), path(gene_counts) output: - path "circ.csv" , emit: circular - path "linear.csv" , emit: linear - path "versions.yml", emit: versions + tuple val(meta), path('*_circs.tsv'), emit: circ_counts + tuple val(meta), path('*_genes.tsv'), emit: gene_counts + + path "versions.yml" , emit: versions + when: task.ext.when == null || task.ext.when script: - """ - prepare_circ_test.R - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//') - END_VERSIONS - """ + prefix = task.ext.prefix ?: meta.id + template 'prepare.R' } diff --git a/modules/local/circtest/prepare/templates/prepare.R b/modules/local/circtest/prepare/templates/prepare.R new file mode 100644 index 00000000..96ad9bd2 --- /dev/null +++ b/modules/local/circtest/prepare/templates/prepare.R @@ -0,0 +1,30 @@ +#!/usr/bin/env Rscript + +circ = read.table("${circ_counts}", header=T, sep="\\t", check.names = FALSE) +gene = read.table("${gene_counts}", header=T, sep="\\t", check.names = FALSE, row.names = 1) + +gene = gene[circ\$gene_id, -1] +circ = circ[, -2] + +write.table(circ, "${prefix}_circs.tsv", sep="\\t", quote=F, row.names=F) +write.table(gene, "${prefix}_genes.tsv", sep="\\t", quote=F, row.names=T) + +################################################ +################################################ +## VERSIONS FILE ## +################################################ +################################################ + +r.version <- strsplit(version[['version.string']], ' ')[[1]][3] + +writeLines( + c( + '"${task.process}":', + paste(' r-base:', r.version) + ), +'versions.yml') + +################################################ +################################################ +################################################ +################################################ \ No newline at end of file diff --git a/subworkflows/local/statistical_tests.nf b/subworkflows/local/statistical_tests.nf index 149d6f53..1b822a4c 100644 --- a/subworkflows/local/statistical_tests.nf +++ b/subworkflows/local/statistical_tests.nf @@ -1,11 +1,14 @@ +include { CIRCTEST_PREPARE } from '../../modules/local/circtest/prepare' + workflow STATISTICAL_TESTS { take: ch_quantification + ch_gene_counts + ch_circ_counts + ch_phenotype main: ch_versions = Channel.empty() - ch_quantification.view() - - + CIRCTEST_PREPARE(ch_circ_counts, ch_gene_counts) } \ No newline at end of file diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 839b3af6..18021678 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -187,7 +187,10 @@ workflow CIRCRNA { // STATISTICAL_TESTS( - QUANTIFICATION.out.se + QUANTIFICATION.out.se, + QUANTIFICATION.out.gene_counts, + QUANTIFICATION.out.circular_tx_counts, + ch_phenotype ) /* From 5893d6dcb0e5c3c766d14d476ebd688f965bfc36 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 11 Jun 2024 10:49:36 +0200 Subject: [PATCH 274/491] Implement circTest --- assets/schema_phenotype.json | 23 +++++++ .../local/circtest/{test => circtest}/main.nf | 21 ++----- .../circtest/circtest/templates/circtest.R | 63 ++++++++----------- .../circtest/prepare/templates/prepare.R | 15 +++-- nextflow_schema.json | 11 ++-- subworkflows/local/statistical_tests.nf | 9 ++- 6 files changed, 78 insertions(+), 64 deletions(-) create mode 100644 assets/schema_phenotype.json rename modules/local/circtest/{test => circtest}/main.nf (50%) rename bin/circ_test.R => modules/local/circtest/circtest/templates/circtest.R (91%) diff --git a/assets/schema_phenotype.json b/assets/schema_phenotype.json new file mode 100644 index 00000000..bdeeaef8 --- /dev/null +++ b/assets/schema_phenotype.json @@ -0,0 +1,23 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "$id": "https://raw.githubusercontent.com/nf-core/circrna/master/assets/schema_phenotype.json", + "title": "nf-core/circrna pipeline - params.phenotype schema", + "description": "Schema for the file provided with params.phenotype", + "type": "array", + "items": { + "type": "object", + "properties": { + "sample": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Sample name must be provided and cannot contain spaces" + }, + "condition": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Condition name must be provided and cannot contain spaces" + } + }, + "required": ["sample", "condition"] + } +} diff --git a/modules/local/circtest/test/main.nf b/modules/local/circtest/circtest/main.nf similarity index 50% rename from modules/local/circtest/test/main.nf rename to modules/local/circtest/circtest/main.nf index c7add5e6..cbe33474 100644 --- a/modules/local/circtest/test/main.nf +++ b/modules/local/circtest/circtest/main.nf @@ -1,4 +1,4 @@ -process CIRCTEST { +process CIRCTEST_CIRCTEST { label 'process_medium' conda "conda-forge::r-base=4.2.2 conda-forge::r-aod=1.3.2 conda-forge::r-ggplot2=3.4.0 conda-forge::r-plyr=1.8.8" @@ -7,9 +7,9 @@ process CIRCTEST { 'biocontainers/mulled-v2-c79b00aa4647c739dbe7e8480789d3ba67988f2e:0' }" input: - path(circ_csv) - path(linear_csv) - tuple val(meta), path(phenotype) + tuple val(meta) , path(circ_counts) + tuple val(meta2), path(gene_counts) + tuple val(meta3), path(phenotype) output: path "*" , emit: results @@ -19,15 +19,6 @@ process CIRCTEST { task.ext.when == null || task.ext.when script: - """ - circ_test.R $circ_csv $linear_csv $phenotype - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//') - aod: \$(Rscript -e "library(aod); cat(as.character(packageVersion('aod')))") - ggplot2: \$(Rscript -e "library(ggplot2); cat(as.character(packageVersion('ggplot2')))") - plyr: \$(Rscript -e "library(plyr); cat(as.character(packageVersion('plyr')))") - END_VERSIONS - """ + prefix = task.ext.prefix ?: meta.id + template 'circtest.R' } diff --git a/bin/circ_test.R b/modules/local/circtest/circtest/templates/circtest.R similarity index 91% rename from bin/circ_test.R rename to modules/local/circtest/circtest/templates/circtest.R index 3e9ea6af..13b4f167 100755 --- a/bin/circ_test.R +++ b/modules/local/circtest/circtest/templates/circtest.R @@ -46,13 +46,13 @@ summarySE <- function(data=NULL, measurevar, groupvars=NULL, na.rm=FALSE, # Rename the "mean" column datac <- rename(datac, c("mean" = measurevar)) - datac$se <- datac$sd / sqrt(datac$N) # Calculate standard error of the mean + datac\$se <- datac\$sd / sqrt(datac\$N) # Calculate standard error of the mean # Confidence interval multiplier for standard error # Calculate t-statistic for confidence interval: # e.g., if conf.interval is .95, use .975 (above/below), and use df=N-1 - ciMult <- qt(conf.interval/2 + .5, datac$N-1) - datac$ci <- datac$se * ciMult + ciMult <- qt(conf.interval/2 + .5, datac\$N-1) + datac\$ci <- datac\$se * ciMult return(datac) } @@ -144,7 +144,7 @@ Circ.ratioplot <- function(Circ,Linear,CircCoordinates = None,plotrow='1',size=2 theme(legend.text=element_text(size=size)) + theme(plot.title = element_text(size=size)) + theme(axis.text.y = element_text(margin=margin(5,5,10,5,"pt")))+ - ggtitle(paste("Annotation: ", genename, "\nChr ", toString(Circ[plotrow,circle_description]),sep="")) + + ggtitle(paste("Annotation: ", genename, "\\nChr ", toString(Circ[plotrow,circle_description]),sep="")) + ylab("circRNA/(circRNA + Linear RNA)") + xlab("Sample") + geom_errorbar(aes(ymin=Ratio, ymax=Ratio+se), width=.2 , size=2) + @@ -329,6 +329,8 @@ Circ.test <- function(Circ, Linear, CircCoordinates=None, group, alpha=0.05, plo # groups if ( length(group) != ncol(Circ)-length(circle_description) ){ + print(length(group)) + print(ncol(Circ)-length(circle_description)) stop("length of 'group' must be equal to the number of samples of 'Circ' and 'Linear'. ") } group <- factor(group) @@ -364,7 +366,7 @@ Circ.test <- function(Circ, Linear, CircCoordinates=None, group, alpha=0.05, plo tmp_rations <- data.frame(Ratio=as.numeric(Circ[i,-circle_description])/(as.numeric(Linear[i,-circle_description])+as.numeric(Circ[i,-circle_description])), group=group) for (rep_group in seq(1,max(as.numeric(levels(group))),1)){ - tmp_df[i, paste("group_",rep_group,"_ratio_mean",sep="")] <- mean(na.omit(unlist(tmp_rations[tmp_rations$group==rep_group,1]))) + tmp_df[i, paste("group_",rep_group,"_ratio_mean",sep="")] <- mean(na.omit(unlist(tmp_rations[tmp_rations\$group==rep_group,1]))) } # Constract data frame @@ -382,7 +384,7 @@ Circ.test <- function(Circ, Linear, CircCoordinates=None, group, alpha=0.05, plo } message(paste(counter, "candidates processed in total")) - Circ$direction <- direction + Circ\$direction <- direction p.adj <- p.adjust(p.val,n=sum(!is.na(p.val)),'BH') # select significant ones sig_dat <- Circ[p.adj<=alpha & !is.na(p.adj),] @@ -418,40 +420,25 @@ Circ.test <- function(Circ, Linear, CircCoordinates=None, group, alpha=0.05, plo ) } -## MY CODE +## MAIN -args = commandArgs(trailingOnly = TRUE) +circs = read.table("${circ_counts}", header=T, sep="\\t") +genes = read.table("${gene_counts}", header=T, sep="\\t") +pheno = read.csv ("${phenotype}" , header=T, row.names = "sample") -circ = read.table(args[1], header=T, sep=",") -linear = read.table(args[2], header=T, sep=",") -pheno = read.table(args[3], header=T, sep=",", row.names = "Sample_ID") +circs <- Circ.filter(circ = circs, linear = genes, filter.sample = 2, filter.count = 5, percentage = 0.00001) +genes <- genes[rownames(circs),] +description <- c(1) +pheno <- pheno[colnames(circs[,-description]),,drop=FALSE] -# No need to enforce any filtering for circTest. -# 'filter.sample' - this has been applied to called circs using the 'tool.filter' param -# 'filter.count' - this has been applied to called circs using bsj_filter param -# 'percentage' - set to extremely low value (do not want to discard circRNAs - let the user inspect themselves). +print(head(circs)) +print(head(genes)) -# Need to apply the phenotype csv file correctly to circtest. -n_covars <- ncol(pheno) -if( n_covars == 2){ - covariate_1 <- as.factor(pheno[,1]) - covariate_2 <- as.factor(pheno[,2]) -}else{ - covariate_1 <- as.factor(pheno[,1]) -} - -n_reps <- as.numeric(table(covariate_1)[1]) - -Circ_filtered <- Circ.filter(circ = circ, linear = linear, Nreplicates = n_reps, filter.sample = 1, filter.count = 1, percentage = 0.00001, circle_description = c(1:4)) -Linear_filtered <- linear[rownames(Circ_filtered),] - - -# groups must be numerically encoded -group = as.numeric(covariate_1) -test <- Circ.test(Circ_filtered, Linear_filtered, group=group, circle_description = c(1:4)) -write.table(test$summary_table, "summary_table.txt", row.names=F) +test <- Circ.test(circs, genes, group=pheno\$condition, circle_description = description) +write.table(test\$summary_table, "${prefix}_summary.txt", row.names=F) +q() # Apply pheno to output once more.. @@ -461,14 +448,14 @@ if( n_covars == 2 ){ group_indicator2 <- as.character(covariate_2) pdf("circ_linear_ratio_plots.pdf", width = 8, height = 10) - for (i in rownames(test$summary_table)) { + for (i in rownames(test\$summary_table)) { Circ.ratioplot(Circ_filtered, Linear_filtered, plotrow=i, groupindicator1=groupindicator1, groupindicator2 = group_indicator2, circle_description = c(1:4) ) } dev.off() pdf("circ_linear_line_plots.pdf", width = 8, height = 10) - for (i in rownames(test$summary_table)) { + for (i in rownames(test\$summary_table)) { Circ.lineplot(Circ_filtered, Linear_filtered, plotrow=i, groupindicator1=group_indicator1, groupindicator2 = group_indicator2, circle_description = c(1:4) ) } @@ -479,14 +466,14 @@ if( n_covars == 2 ){ group_indicator1 <- as.character(covariate_1) pdf("circ_linear_ratio_plots.pdf", width = 8, height = 10) - for (i in rownames(test$summary_table)) { + for (i in rownames(test\$summary_table)) { Circ.ratioplot(Circ_filtered, Linear_filtered, plotrow=i, groupindicator1=group_indicator1, lab_legend = colnames(pheno)[1], circle_description = c(1:4) ) } dev.off() pdf("circ_linear_line_plots.pdf", width = 8, height = 10) - for (i in rownames(test$summary_table)) { + for (i in rownames(test\$summary_table)) { Circ.lineplot(Circ_filtered, Linear_filtered, plotrow=i, groupindicator1=group_indicator1, circle_description = c(1:4) ) } diff --git a/modules/local/circtest/prepare/templates/prepare.R b/modules/local/circtest/prepare/templates/prepare.R index 96ad9bd2..5eb2c55e 100644 --- a/modules/local/circtest/prepare/templates/prepare.R +++ b/modules/local/circtest/prepare/templates/prepare.R @@ -1,12 +1,15 @@ #!/usr/bin/env Rscript -circ = read.table("${circ_counts}", header=T, sep="\\t", check.names = FALSE) -gene = read.table("${gene_counts}", header=T, sep="\\t", check.names = FALSE, row.names = 1) +circ <- read.table("${circ_counts}", header=T, sep="\\t", check.names = FALSE) +gene <- read.table("${gene_counts}", header=T, sep="\\t", check.names = FALSE, row.names = 1) -gene = gene[circ\$gene_id, -1] -circ = circ[, -2] +gene <- gene[circ\$gene_id, ] -write.table(circ, "${prefix}_circs.tsv", sep="\\t", quote=F, row.names=F) +rownames(circ) <- circ\$tx +rownames(gene) <- rownames(circ) +circ\$tx <- NULL + +write.table(circ, "${prefix}_circs.tsv", sep="\\t", quote=F, row.names=T) write.table(gene, "${prefix}_genes.tsv", sep="\\t", quote=F, row.names=T) ################################################ @@ -27,4 +30,4 @@ writeLines( ################################################ ################################################ ################################################ -################################################ \ No newline at end of file +################################################ diff --git a/nextflow_schema.json b/nextflow_schema.json index 2aaea8bb..9bd91654 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -32,11 +32,14 @@ }, "phenotype": { "type": "string", - "description": "Phenotype CSV file specifying the experimental design for DESeq2.", - "fa_icon": "fas fa-file-csv", + "format": "file-path", + "exists": true, + "schema": "assets/schema_phenotype.json", "mimetype": "text/csv", - "help_text": "There are two rules for providing the phenotype CSV file. 1) The phenotype 'sample' column must match the sample sheets 'sample' column. 2) The response variable containing the phenotype of primary interest in the experiment must have the column name condition. All other columns included in the file are controlled for in the `DESeq2` design. \n\n| sample \t| condition \t| replicate \t|\n|-----------\t|-----------\t|-----------\t|\n| control_1 \t| ctr \t| 1 \t|\n| control_2 \t| ctr \t| 2 \t|\n| control_3 \t| ctr \t| 3 \t|\n| treated_1 \t| trt \t| 1 \t|\n| treated_2 \t| trt \t| 2 \t|\n| treated_3 \t| trt \t| 3 \t|\n\nThe above phenotype file will identify differentially expressed circRNAs/mRNAs between control and treatment cells, whilst controlling for the effect of variation between replicates: ` ~ replicates + condition`", - "pattern": "\\.csv$" + "pattern": "^\\S+\\.csv$", + "description": "Phenotype CSV file specifying the experimental design.", + "help_text": "There are two rules for providing the phenotype CSV file. 1) The 'sample' column must match the sample sheets 'sample' column. 2) The response variable containing the phenotype of primary interest in the experiment must have the column name condition. All other columns included in the file are controlled for in the `DESeq2` design. \n\n| sample \t| condition \t| replicate \t|\n|-----------\t|-----------\t|-----------\t|\n| control_1 \t| ctr \t| 1 \t|\n| control_2 \t| ctr \t| 2 \t|\n| control_3 \t| ctr \t| 3 \t|\n| treated_1 \t| trt \t| 1 \t|\n| treated_2 \t| trt \t| 2 \t|\n| treated_3 \t| trt \t| 3 \t|\n\nThe above phenotype file will identify differentially expressed circRNAs/mRNAs between control and treatment cells, whilst controlling for the effect of variation between replicates: ` ~ replicates + condition`", + "fa_icon": "fas fa-file-csv" } } }, diff --git a/subworkflows/local/statistical_tests.nf b/subworkflows/local/statistical_tests.nf index 1b822a4c..3c977f9a 100644 --- a/subworkflows/local/statistical_tests.nf +++ b/subworkflows/local/statistical_tests.nf @@ -1,4 +1,5 @@ -include { CIRCTEST_PREPARE } from '../../modules/local/circtest/prepare' +include { CIRCTEST_PREPARE } from '../../modules/local/circtest/prepare' +include { CIRCTEST_CIRCTEST } from '../../modules/local/circtest/circtest' workflow STATISTICAL_TESTS { take: @@ -11,4 +12,10 @@ workflow STATISTICAL_TESTS { ch_versions = Channel.empty() CIRCTEST_PREPARE(ch_circ_counts, ch_gene_counts) + ch_versions = ch_versions.mix(CIRCTEST_PREPARE.out.versions) + + CIRCTEST_CIRCTEST(CIRCTEST_PREPARE.out.circ_counts, + CIRCTEST_PREPARE.out.gene_counts, + ch_phenotype) + } \ No newline at end of file From 9c5906d82682a334cd4976f0257994e74050e5b8 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 11 Jun 2024 11:09:25 +0200 Subject: [PATCH 275/491] Fix circtest problems --- modules/local/circtest/circtest/main.nf | 4 +- .../circtest/circtest/templates/circtest.R | 107 ++++++++++-------- 2 files changed, 63 insertions(+), 48 deletions(-) diff --git a/modules/local/circtest/circtest/main.nf b/modules/local/circtest/circtest/main.nf index cbe33474..e9367be2 100644 --- a/modules/local/circtest/circtest/main.nf +++ b/modules/local/circtest/circtest/main.nf @@ -12,8 +12,8 @@ process CIRCTEST_CIRCTEST { tuple val(meta3), path(phenotype) output: - path "*" , emit: results - path "versions.yml", emit: versions + path "${prefix}_summary.txt", emit: summary + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/circtest/circtest/templates/circtest.R b/modules/local/circtest/circtest/templates/circtest.R index 13b4f167..6f36f7fa 100755 --- a/modules/local/circtest/circtest/templates/circtest.R +++ b/modules/local/circtest/circtest/templates/circtest.R @@ -432,53 +432,68 @@ genes <- genes[rownames(circs),] description <- c(1) pheno <- pheno[colnames(circs[,-description]),,drop=FALSE] -print(head(circs)) -print(head(genes)) - -test <- Circ.test(circs, genes, group=pheno\$condition, circle_description = description) +test <- Circ.test(circs, genes, group=as.numeric(as.factor(pheno\$condition)), circle_description = description) write.table(test\$summary_table, "${prefix}_summary.txt", row.names=F) -q() - # Apply pheno to output once more.. -if( n_covars == 2 ){ - - group_indicator1 <- as.character(covariate_1) - group_indicator2 <- as.character(covariate_2) - - pdf("circ_linear_ratio_plots.pdf", width = 8, height = 10) - for (i in rownames(test\$summary_table)) { - Circ.ratioplot(Circ_filtered, Linear_filtered, plotrow=i, groupindicator1=groupindicator1, groupindicator2 = group_indicator2, - circle_description = c(1:4) ) - } - dev.off() - - pdf("circ_linear_line_plots.pdf", width = 8, height = 10) - for (i in rownames(test\$summary_table)) { - Circ.lineplot(Circ_filtered, Linear_filtered, plotrow=i, groupindicator1=group_indicator1, groupindicator2 = group_indicator2, - circle_description = c(1:4) ) - } - dev.off() - -}else{ - - group_indicator1 <- as.character(covariate_1) - - pdf("circ_linear_ratio_plots.pdf", width = 8, height = 10) - for (i in rownames(test\$summary_table)) { - Circ.ratioplot(Circ_filtered, Linear_filtered, plotrow=i, groupindicator1=group_indicator1, - lab_legend = colnames(pheno)[1], circle_description = c(1:4) ) - } - dev.off() - - pdf("circ_linear_line_plots.pdf", width = 8, height = 10) - for (i in rownames(test\$summary_table)) { - Circ.lineplot(Circ_filtered, Linear_filtered, plotrow=i, groupindicator1=group_indicator1, - circle_description = c(1:4) ) - } - dev.off() -} - -# include variables, makes life easier in case user wishes to report bugs to workflow. -save.image("circ_test.RData") +# if( n_covars == 2 ){ +# +# group_indicator1 <- as.character(covariate_1) +# group_indicator2 <- as.character(covariate_2) +# +# pdf("circ_linear_ratio_plots.pdf", width = 8, height = 10) +# for (i in rownames(test\$summary_table)) { +# Circ.ratioplot(Circ_filtered, Linear_filtered, plotrow=i, groupindicator1=groupindicator1, groupindicator2 = group_indicator2, +# circle_description = c(1:4) ) +# } +# dev.off() +# +# pdf("circ_linear_line_plots.pdf", width = 8, height = 10) +# for (i in rownames(test\$summary_table)) { +# Circ.lineplot(Circ_filtered, Linear_filtered, plotrow=i, groupindicator1=group_indicator1, groupindicator2 = group_indicator2, +# circle_description = c(1:4) ) +# } +# dev.off() +# +# }else{ +# +# group_indicator1 <- as.character(covariate_1) +# +# pdf("circ_linear_ratio_plots.pdf", width = 8, height = 10) +# for (i in rownames(test\$summary_table)) { +# Circ.ratioplot(Circ_filtered, Linear_filtered, plotrow=i, groupindicator1=group_indicator1, +# lab_legend = colnames(pheno)[1], circle_description = c(1:4) ) +# } +# dev.off() +# +# pdf("circ_linear_line_plots.pdf", width = 8, height = 10) +# for (i in rownames(test\$summary_table)) { +# Circ.lineplot(Circ_filtered, Linear_filtered, plotrow=i, groupindicator1=group_indicator1, +# circle_description = c(1:4) ) +# } +# dev.off() +# } + +################################################ +################################################ +## VERSIONS FILE ## +################################################ +################################################ + +r.version <- strsplit(version[['version.string']], ' ')[[1]][3] + +writeLines( + c( + '"${task.process}":', + paste(' r-base:', r.version), + paste(' aod:', packageVersion('aod')), + paste(' plyr:', packageVersion('plyr')), + paste(' ggplot2:', packageVersion('ggplot2')) + ), +'versions.yml') + +################################################ +################################################ +################################################ +################################################ From 21236c891a3171774e86590cd26545372a20cad7 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 11 Jun 2024 11:23:00 +0200 Subject: [PATCH 276/491] Re-enable circtest plots --- modules/local/circtest/circtest/main.nf | 6 ++- .../circtest/circtest/templates/circtest.R | 54 ++++++------------- 2 files changed, 19 insertions(+), 41 deletions(-) diff --git a/modules/local/circtest/circtest/main.nf b/modules/local/circtest/circtest/main.nf index e9367be2..beaf10c1 100644 --- a/modules/local/circtest/circtest/main.nf +++ b/modules/local/circtest/circtest/main.nf @@ -12,8 +12,10 @@ process CIRCTEST_CIRCTEST { tuple val(meta3), path(phenotype) output: - path "${prefix}_summary.txt", emit: summary - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}_summary.txt"), emit: summary + tuple val(meta), path("*.pdf") , emit: plots + + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/circtest/circtest/templates/circtest.R b/modules/local/circtest/circtest/templates/circtest.R index 6f36f7fa..b1633c53 100755 --- a/modules/local/circtest/circtest/templates/circtest.R +++ b/modules/local/circtest/circtest/templates/circtest.R @@ -435,45 +435,21 @@ pheno <- pheno[colnames(circs[,-description]),,drop=FALSE] test <- Circ.test(circs, genes, group=as.numeric(as.factor(pheno\$condition)), circle_description = description) write.table(test\$summary_table, "${prefix}_summary.txt", row.names=F) -# Apply pheno to output once more.. - -# if( n_covars == 2 ){ -# -# group_indicator1 <- as.character(covariate_1) -# group_indicator2 <- as.character(covariate_2) -# -# pdf("circ_linear_ratio_plots.pdf", width = 8, height = 10) -# for (i in rownames(test\$summary_table)) { -# Circ.ratioplot(Circ_filtered, Linear_filtered, plotrow=i, groupindicator1=groupindicator1, groupindicator2 = group_indicator2, -# circle_description = c(1:4) ) -# } -# dev.off() -# -# pdf("circ_linear_line_plots.pdf", width = 8, height = 10) -# for (i in rownames(test\$summary_table)) { -# Circ.lineplot(Circ_filtered, Linear_filtered, plotrow=i, groupindicator1=group_indicator1, groupindicator2 = group_indicator2, -# circle_description = c(1:4) ) -# } -# dev.off() -# -# }else{ -# -# group_indicator1 <- as.character(covariate_1) -# -# pdf("circ_linear_ratio_plots.pdf", width = 8, height = 10) -# for (i in rownames(test\$summary_table)) { -# Circ.ratioplot(Circ_filtered, Linear_filtered, plotrow=i, groupindicator1=group_indicator1, -# lab_legend = colnames(pheno)[1], circle_description = c(1:4) ) -# } -# dev.off() -# -# pdf("circ_linear_line_plots.pdf", width = 8, height = 10) -# for (i in rownames(test\$summary_table)) { -# Circ.lineplot(Circ_filtered, Linear_filtered, plotrow=i, groupindicator1=group_indicator1, -# circle_description = c(1:4) ) -# } -# dev.off() -# } + +pdf("circ_linear_ratio_plots.pdf", width = 8, height = 10) +for (i in rownames(test\$summary_table)) { + Circ.ratioplot(circs, genes, plotrow=i, groupindicator1=pheno\$condition, + lab_legend = condition, circle_description = c(1:4) ) +} +dev.off() + +pdf("circ_linear_line_plots.pdf", width = 8, height = 10) +for (i in rownames(test\$summary_table)) { + Circ.lineplot(circs, genes, plotrow=i, groupindicator1=pheno\$condition, + circle_description = description ) +} +dev.off() + ################################################ ################################################ From 69f82c08a6466ff0d0dfd2ce6eed34a34df7562e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 11 Jun 2024 11:34:31 +0200 Subject: [PATCH 277/491] Fix circtest plot problem --- modules/local/circtest/circtest/templates/circtest.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/circtest/circtest/templates/circtest.R b/modules/local/circtest/circtest/templates/circtest.R index b1633c53..debdf039 100755 --- a/modules/local/circtest/circtest/templates/circtest.R +++ b/modules/local/circtest/circtest/templates/circtest.R @@ -439,7 +439,7 @@ write.table(test\$summary_table, "${prefix}_summary.txt", row.names=F) pdf("circ_linear_ratio_plots.pdf", width = 8, height = 10) for (i in rownames(test\$summary_table)) { Circ.ratioplot(circs, genes, plotrow=i, groupindicator1=pheno\$condition, - lab_legend = condition, circle_description = c(1:4) ) + lab_legend = 'condition', circle_description = description ) } dev.off() From d2839a315a88987403d4b072e4771811d778a67e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 11 Jun 2024 11:53:21 +0200 Subject: [PATCH 278/491] Remove artifacts of old differential expression analysis --- bin/DEA.R | 621 ------------------ bin/annotate_outputs.sh | 143 ---- bin/check_empty.sh | 28 - modules/local/annotation/parent_gene/main.nf | 53 -- subworkflows/local/differential_expression.nf | 75 --- 5 files changed, 920 deletions(-) delete mode 100755 bin/DEA.R delete mode 100755 bin/annotate_outputs.sh delete mode 100755 bin/check_empty.sh delete mode 100644 modules/local/annotation/parent_gene/main.nf delete mode 100644 subworkflows/local/differential_expression.nf diff --git a/bin/DEA.R b/bin/DEA.R deleted file mode 100755 index ea5960b7..00000000 --- a/bin/DEA.R +++ /dev/null @@ -1,621 +0,0 @@ -#!/usr/bin/env Rscript - -## Author: Barry Digby -## License: MIT - -get_args <- function(){ - - argp <- arg_parser( - description="this script is designed to automate DESeq2 analysis for circRNA nextflow script", - hide.opts=TRUE) - - argp <- add_argument( - parser=argp, - arg="gene_counts", - short="g", - help="gene_count_matrix.csv produced by prepDE.py downstream of Stringtie quant with -e flag", - default="gene_count_matrix.csv") - - argp <- add_argument( - parser=argp, - arg="phenotype", - short="p", - help="file containing sample metadata information to guide the design", - default="phenotype.csv") - - argp <- add_argument( - parser=argp, - arg="circRNA", - short="c", - help="circRNA counts matrix", - default="merged_counts.bed") - - argp <- add_argument( - parser=argp, - arg="species", - short="s", - help="species ID", - default="hsa") - - argp <- add_argument( - parser=argp, - arg="map", - short="m", - help="ensDB", - "default"="ensemblDatabase.txt") - - argv <- parse_args( - parser=argp, - argv = commandArgs(trailingOnly = TRUE)) - - return(argv) - -} - -giveError <- function(message){ - cat(paste("\n", message, sep="")) - quit() -} - -usage <- function(){giveError("USAGE: DEA.R ")} - - -stage_data <- function(gene_counts, phenotype, circRNA, species, map){ - - inputdata <- list() - - dbmap <- read.table(map, sep="\t", header=T, quote="", stringsAsFactors=FALSE) - gene_mat <- read.csv(gene_counts, row.names="gene_id", check.names=F) - circ <- read.table(circRNA, sep ="\t", header = T, stringsAsFactors=FALSE) - - # Merge circRNA genomic loci to ID - circ$circ <- with(circ, paste0(chr, sep=":", start, sep="-", end, sep=":", strand)) - rownames(circ) <- circ$circ - circ <- subset(circ, select=-c(chr, start, end, strand, circ)) - - # R converts '-' to '.' in colnames here and results in failures. - # If you need to make this 'smarter' check that colnames contains '.', - # compare gsub to colnames(gene_mat), then apply. - colnames(circ) <- gsub("\\.", "-", colnames(circ)) - - ## add pseudocount of 1 - gene_mat <- gene_mat + 1 - circ <- circ + 1 - - inputdata$pheno <- checkinputdata(phenotype) - cols <- rownames(inputdata$pheno) - - if(identical(rownames(inputdata$pheno), colnames(gene_mat))){ - circ <- circ[, cols,] - }else{ - giveError(c("Samples in phenotype file do not match sequencing sample names.\n", - "Please check that phenotype samples match gene_count_matrix.csv headers.\n", - "*Make sure they are sorted in alphabetical order:", - "tail -n +2 phenotype.txt | sort -k1,1\n\n")) - } - - inputdata$gene <- gene_mat - inputdata$circ <- circ - inputdata$design <- makedesign(inputdata$pheno) - inputdata$species <- species - inputdata$map <- dbmap - - inputdata$gene <- ens2symbol(inputdata$gene, inputdata) - - save.image(file='inputdata.RData') - - return(inputdata) -} - - -checkinputdata <- function(phenotype){ - - # Stage phenotype file - pheno <- read.csv(phenotype, row.names=1, header = T, stringsAsFactors = T) - - # Check if there are at least 3 replicates (DESeq2 fails if < 3) - if(min(table(pheno$condition)) >= 3){ - print("Suitable sample size for DE analysis") - }else{ - giveError("Not enough samples per condition to perform DE analysis!") - } - - ## check if all columns are factors. If numeric, convert to factor. - factor_cols <- sapply(pheno, is.factor) - if(all(factor_cols) == TRUE){ - print("All columns in phenotype are factors and suitable for analysis.") - }else{ - numeric_cols <- sapply(pheno, is.numeric) - names <- colnames(pheno)[numeric_cols] - print(paste0("Column(s) ", names, " is numeric. Converting to factor.")) - pheno[numeric_cols] <- as.data.frame(lapply(pheno[numeric_cols], factor)) - final_check <- sapply(pheno, is.factor) - if(all(final_check) == TRUE){ - print("Finished coverting to factor") - }else{ - giveError("Error in converting to factors. See checkinputdata function.") - } - } - - return(pheno) - -} - - - -makedesign <- function(phenotype){ - - # Covariates i.e explanatory variables. - covariates <- names(phenotype)[which(!names(phenotype) %in% c("condition"))] - design <- formula(paste("~", paste(c(covariates, "condition"), sep="", collapse=" + "))) - return(design) - -} - - - - -ens2symbol <- function(mat, inputdata){ - - ## designed to work on input gene_count_matrix.csv file - ## everything else downstream no longer needs to be converted - - mat <- as.data.frame(mat) - map <- inputdata$map - species <- inputdata$species - - if(all(grepl(pattern="^ENSG", rownames(mat)))){ - filter = "ensembl_gene_id" - if(all(grepl(pattern=".", rownames(mat)))){ - filter = "ensembl_gene_id_version" - } - }else{ - filter = "external_gene_name" - } - - if(filter == "external_gene_name"){ - print("Using external gene name as gene symbol") - }else{ - print("Setting up Mart to convert ENS IDs to gene symbols") - ## set up Mart - mart_call <- as.character(subset(map$command, map$species == species)) - print("ENS2SYMBOL") - mart <- eval(str2expression(mart_call)) - } - - ## now go about converting ENS2SYMBOL - if(filter == "ensembl_gene_id"){ - - mat$ensembl_gene_id <- rownames(mat) - info <- getBM(attributes=c("ensembl_gene_id","external_gene_name"), - filters = c("ensembl_gene_id"), - values = mat$ensembl_gene_id, - mart = mart, - useCache=FALSE) - - tmp <- merge(mat, info, by="ensembl_gene_id") - tmp$external_gene_name <- make.names(tmp$external_gene_name, unique = T) - rownames(tmp) <- tmp$external_gene_name - tmp <- subset(tmp, select=-c(ensembl_gene_id, external_gene_name)) - - mat <- tmp - print("input mat ensembl gene id detected and converted") - return(mat) - }else if(filter == "ensembl_gene_id_version"){ - - mat$ensembl_gene_id_version <- rownames(mat) - info <- getBM(attributes=c("ensembl_gene_id_version","external_gene_name"), - filters = c("ensembl_gene_id_version"), - values = mat$ensembl_gene_id_version, - mart = mart, - useCache=FALSE) - - tmp <- merge(mat, info, by="ensembl_gene_id_version") - tmp$external_gene_name <- make.names(tmp$external_gene_name, unique = T) - rownames(tmp) <- tmp$external_gene_name - tmp <- subset(tmp, select=-c(ensembl_gene_id_version, external_gene_name)) - - mat <- tmp - print("input mat ensembl gene id version detected and converted") - return(mat) - }else{ - print("NO change made to input mat ") - return(mat) - } - -} - -get_upregulated <- function(df){ - - key <- intersect(rownames(df)[which(df$log2FoldChange>=1)], rownames(df)[which(df$pvalue<=0.05)]) - results <- as.data.frame((df)[which(rownames(df) %in% key),]) - return(results) - -} - -get_downregulated <- function(df){ - - key <- intersect(rownames(df)[which(df$log2FoldChange<=-1)], rownames(df)[which(df$pvalue<=0.05)]) - results <- as.data.frame((df)[which(rownames(df) %in% key),]) - return(results) - -} - -# Data type provided at end of script to activate RNA-Seq / circRNA analysis. -DESeq2 <- function(inputdata, data_type){ - - if(data_type == "RNA-Seq"){ - outdir <- "RNA-Seq/" - - dds <- DESeqDataSetFromMatrix( - countData=inputdata$gene, - colData=inputdata$pheno, - design = inputdata$design) - - levels <- as.character(unique(inputdata$pheno$condition)) - for(level in levels){ - reference <- level - contrasts <- levels[levels != paste0(reference)] - dds$condition <- relevel(dds$condition, ref = paste0(reference)) - dds <- DESeq(dds, quiet=TRUE) - - DESeq2_plots(dds, outdir) - - for(var in contrasts){ - contrast <- paste(var, "vs", reference, sep="_") - DEG <- getDESeqDEAbyContrast(dds, contrast, reference, var, outdir, inputdata) - } - - save.image(file='RNA-Seq.RData') - - } - }else if(data_type == "circRNA"){ - outdir <- "circRNA/" - - ## use gene sizeFactors - tmp <- DESeqDataSetFromMatrix( - countData=inputdata$gene, - colData=inputdata$pheno, - design = inputdata$design) - tmp <- DESeq(tmp, quiet=TRUE) - - sizefactors <- estimateSizeFactorsForMatrix(counts(tmp)) - rm(tmp) - - dds <- DESeqDataSetFromMatrix( - countData=round(inputdata$circ), - colData=inputdata$pheno, - design = inputdata$design) - - levels <- as.character(unique(inputdata$pheno$condition)) - for(level in levels){ - reference <- level - contrasts <- levels[levels != paste0(reference)] - dds$condition <- relevel(dds$condition, ref = paste0(reference)) - dds <- DESeq(dds, quiet=TRUE) - sizeFactors(dds) <- sizefactors - - DESeq2_plots(dds, outdir) - - for(var in contrasts){ - contrast <- paste(var, "vs", reference, sep="_") - DEG <- getDESeqDEAbyContrast(dds, contrast, reference, var, outdir) - } - - save.image(file='circRNA.RData') - } - }else{ - giveError("Data type not provided correctly, check end of script") - } - return(DEG) -} - - -getDESeqDEAbyContrast <- function(dds, contrast, reference, var, outdir, inputdata) { - - res <- results(dds, filterFun=ihw, alpha=0.05, contrast=c("condition", var, reference)) - cat('\n\nSummary data from DESeq2 for ', contrast, ':', sep="") - summary(res) - - ma_plot(res, contrast, outdir) - - up_regulated <- get_upregulated(res) - down_regulated <- get_downregulated(res) - - de_up <- rownames(up_regulated) - de_down <- rownames(down_regulated) - de <- c(de_up, de_down) - cts <- counts(dds, normalized=T) - - # attempt boxplots here - if(outdir == "circRNA/"){ - make_boxplots(de, cts, contrast) - } - - log2 <- log2(cts +1) - global_heatmap(de, log2, contrast, outdir) - - if(outdir == "RNA-Seq/"){ - up_regulated <- tibble::rownames_to_column(up_regulated, "ID") - down_regulated <- tibble::rownames_to_column(down_regulated, "ID") - }else{ - up_regulated <- tibble::rownames_to_column(up_regulated, "ID") - down_regulated <- tibble::rownames_to_column(down_regulated, "ID") - } - - dir <- paste(outdir, contrast, sep="") - dir.create(dir) - write.table(up_regulated, file.path(dir, paste("DESeq2", contrast, "up_regulated_differential_expression.txt", sep="_")), sep="\t", row.names=F, quote=F) - write.table(down_regulated, file.path(dir, paste("DESeq2", contrast, "down_regulated_differential_expression.txt", sep="_")), sep="\t", row.names=F, quote=F) - - res_df <- as.data.frame(res) - - volcano_plot(res_df, contrast, outdir) - - pdf(file.path(dir, paste("DESeq2", contrast, "fold_change_distribution.pdf", sep="_")), width=8, height=8) - hist(res$log2FoldChange, breaks=50, col="seagreen", xlab=paste("(Fold change)", contrast, sep=" "), main="Distribution of differential expression fold change") - abline(v=c(-1,1), col="black", lwd=2, lty=2) - legend("topright", "Fold change <-1 and >1", lwd=2, lty=2) - dev.off() - - pdf(file.path(dir, paste("DESeq2", contrast, "pvalue_distribution.pdf", sep="_")), width=8, height=8) - hist(res$pvalue, breaks=50, col="seagreen", xlab=paste("P-Value (Fold change)", contrast, sep=" "), main="Distribution of P-Values") - abline(v=c(0.05),col="black",lwd=2,lty=2) - legend("topright", "P-Value <0.05",lwd=2,lty=2) - dev.off() - - pdf(file.path(dir, paste("DESeq2", contrast, "Adj_pvalue_distribution.pdf", sep="_")), width=8, height=8) - hist(res$padj, breaks=50, col="seagreen", xlab=paste("P-Adj (Fold change)", contrast, sep=" "), main="Distribution of AdjP-Values") - abline(v=c(0.05),col="black",lwd=2,lty=2) - legend("top", "P-Adj <0.05",lwd=2,lty=2) - dev.off() -} - - -DESeq2_plots <- function(dds, outdir){ - - dir.create("DESeq2_QC") - dir.create(paste("DESeq2_QC/", outdir, sep="")) - dir=paste("DESeq2_QC/", outdir, sep="") - - pdf(file.path(dir, "DESeq2_dispersion.pdf"), width=8, height=8) - plotDispEsts(dds) - dev.off() - - counts <- counts(dds, normalized=T) - - if(outdir == "RNA-Seq/"){ - counts <- ens2symbol(counts, inputdata) - log2 <- log2(counts + 1) - }else{ - counts <- as.data.frame(counts) - log2 <- log2(counts + 1) - } - - write_counts <- tibble::rownames_to_column(counts, "ID") - write_log2 <- tibble::rownames_to_column(log2, "ID") - - write.table(write_counts, file.path(outdir, "DESeq2_normalized_counts.txt"), sep="\t", quote=F, row.names = F) - write.table(write_log2, file.path(outdir, "DESeq2_log2_transformed_counts.txt"), sep="\t", quote=F, row.names = F) - - sample_to_sample_heatmap(log2, outdir) - sample_to_sample_dendogram(log2, outdir) - PCA_plot(log2, outdir) - -} - - -ma_plot <- function(res, contrast, outdir){ - dir <- paste(outdir, contrast, sep="") - dir.create(dir) - pdf(file.path(dir, paste("DESeq2", contrast, "MA_plot.pdf", sep="_")), width=8, height=8) - plotMA(res) - dev.off() - -} - -sample_to_sample_heatmap <- function(log2, outdir){ - - dir.create("DESeq2_QC") - dir.create(paste("DESeq2_QC/", outdir, sep="")) - dir=paste("DESeq2_QC/", outdir, sep="") - - sampleDists <- dist(t(log2)) - sampleDistMatrix <- as.matrix(sampleDists) - pdf(file.path(dir, "DESeq2_sample_heatmap.pdf"), width=8, height=8) - pheatmap(mat=sampleDistMatrix, - clustering_distance_rows=sampleDists, - clustering_distance_cols=sampleDists, - col=colorRampPalette( rev(brewer.pal(9, "Blues")) )(255), - fontsize_row=8) - dev.off() - -} - - - -sample_to_sample_dendogram <- function(log2, outdir){ - - dir.create("DESeq2_QC") - dir.create(paste("DESeq2_QC/", outdir, sep="")) - dir=paste("DESeq2_QC/", outdir, sep="") - - d=t(log2) - d=dist(d) - hc=hclust(d, method="complete") - print("test hclust") - print(head(d)) - pdf(file.path(dir, "DESeq2_sample_dendogram.pdf")) - plot(hc) - dev.off() - -} - - -PCA_plot <- function(log2, outdir){ - - p <- pca(log2, metadata=inputdata$pheno) - - for(exp_var in names(inputdata$pheno)){ - dir.create("DESeq2_QC") - dir=paste("DESeq2_QC/", outdir, sep="") - pdf(file.path(dir, paste("DESeq2", exp_var, "PCA.pdf", sep="_"))) - biplot <- biplot(p, - colby=paste(exp_var), - hline=0, - vline=0, - legendPosition="right", - legendLabSize=12, - legendIconSize=8, - lab = TRUE, - labSize = 0.0, - drawConnectors=FALSE, - title="PCA bi-plot", - subtitle="PC1 vs. PC2") - plot(biplot) - dev.off() - } -} - - -volcano_plot <- function(res, contrast, outdir){ - - res <- na.omit(res) - - min_width <- min(res$log2FoldChange) - max_width <- max(res$log2FoldChange) - symmetric_plot <- max(max_width, abs(min_width)) - min_width <- symmetric_plot * -1 - max_width <- symmetric_plot - max_height <- -log10(min(res[res$pvalue>0, 5])) - - up <- subset(res, res$log2FoldChange > 1 & res$pvalue <= 0.05) - up <- up[order(-up$log2FoldChange),] - up_list <- head(rownames(up), n=10L) - - down <- subset(res, res$log2FoldChange < 1 & res$pvalue <= 0.05) - down <- down[order(down$log2FoldChange),] - down_list <- head(rownames(down), n=10L) - - plot_top_20 <- c(up_list, down_list) - - dir <- paste(outdir, contrast, sep="") - dir.create(dir) - pdf(file.path(dir, paste("DESeq2", contrast, "volcano_plot.pdf", sep="_"))) - p <- EnhancedVolcano(res, - lab=rownames(res), - x="log2FoldChange", - y="pvalue", - selectLab=FALSE, - drawConnectors=FALSE, - FCcutoff=1.0, - pCutoff=0.05, - title="Volcano Plot", - subtitle=paste(contrast), - #legendVisible=F, - caption = paste0('Total Genes = ', nrow(res)), - xlim=c(min_width, max_width), - ylim=c(0, max_height), - pointSize = 1.5) - plot(p) - dev.off() - -} - - -global_heatmap <- function(de, log2, contrast, outdir){ - - # Split contrast e.g normal_vs_tumor -> "normal", "tumor" - levels <- unlist(strsplit(contrast, "_vs_")) - pheno <- inputdata$pheno - # subset phenotype file for contrast samples - pheno_subset <- subset(pheno, pheno$condition %in% levels) - # check it worked? - #print(pheno_subset) - # subset log2 counts for contrast samples - mat <- log2[,rownames(pheno_subset)] - # subset de genes/circRNAs - mat <- mat[de,] - # Perform scaling and centering on DE expr data - mat <- t(mat) - mat <- scale(mat, center=T) - mat <- t(mat) - - dir <- paste(outdir, contrast, sep="") - dir.create(dir) - pdf(file.path(dir, paste("DESeq2", contrast, "heatmap.pdf", sep="_"))) - pheatmap(mat, - annotation_col=pheno_subset, - color=greenred(75), - cluster_rows = T, - show_rownames = F) - dev.off() - -} - - - -make_boxplots <- function(de, cts, contrast){ - - pheno <- inputdata$pheno - levels <- unlist(strsplit(contrast, "_vs_")) - pheno_subset <- subset(pheno, pheno$condition %in% levels) - # subset counts for levels of interest - counts <- cts[,rownames(pheno_subset)] - # subset for de genes - counts <- as.data.frame(counts[de,]) - dir.create("boxplots") - dir.create(paste("boxplots/", contrast, sep="")) - dir=paste("boxplots/", contrast, sep="") - for( i in 1:nrow(counts)){ - circ_id <- rownames(counts[i,]); - mat <- as.data.frame(t(counts[i,])); - mat <- cbind(mat, pheno_subset); - names <- c("counts", "condition"); - colnames(mat) <- names; - - p1 <- ggboxplot(mat, x="condition", y="counts", - fill="condition", palette = "npg", - title = paste(circ_id), - ylab = "normalized counts", xlab="", - add = c("dotplot"), - add.params = list(size=0.5, jitter=0.1), - legend = "none", - bxp.errorbar = T, - bxp.errorbar.width = 0.2, width=0.3, - ggtheme = theme_classic()) + - rotate_x_text(angle = 0) + - theme(plot.title = element_text(face = "bold", size=16, hjust = 0.5)) + - theme(axis.text.x = element_text( colour = "black", size=14)) + - theme(axis.title.y = element_text(size=14, face = "italic")) + - theme(axis.title.x = element_blank()) + - theme(axis.text.y = element_text(color = "black", size=10)) - - pdf(file.path(dir, paste(circ_id, "boxplot.pdf", sep="_"))) - plot(p1) - dev.off() - } -} - - -options(error=function()traceback(2)) -suppressPackageStartupMessages(library("argparser")) -suppressPackageStartupMessages(library("biomaRt")) -suppressPackageStartupMessages(library("DESeq2")) -suppressPackageStartupMessages(library("dplyr")) -suppressPackageStartupMessages(library("EnhancedVolcano")) -suppressPackageStartupMessages(library("ggplot2")) -suppressPackageStartupMessages(library("ggpubr")) -suppressPackageStartupMessages(library("gplots")) -suppressPackageStartupMessages(library("IHW")) -suppressPackageStartupMessages(library("PCAtools")) -suppressPackageStartupMessages(library("pheatmap")) -suppressPackageStartupMessages(library("RColorBrewer")) - -arg <- get_args() - -inputdata <- stage_data(arg$gene_counts, arg$phenotype, arg$circRNA, arg$species, arg$map) -dir.create("RNA-Seq") -dir.create("circRNA") -x <- DESeq2(inputdata, "RNA-Seq") -y <- DESeq2(inputdata, "circRNA") diff --git a/bin/annotate_outputs.sh b/bin/annotate_outputs.sh deleted file mode 100755 index 3c2054f2..00000000 --- a/bin/annotate_outputs.sh +++ /dev/null @@ -1,143 +0,0 @@ -#!/usr/bin/env bash - -echo "====================================================================================" -echo "[nf-core/circrna]: circRNA annotation script " -echo "[nf-core/circrna]: Author: Barry Digby " -echo "[nf-core/circrna]: Institution: National University of Ireland, Galway " -echo "[nf-core/circrna]: " -echo "[nf-core/circrna]: MIT license " -echo "====================================================================================" - -mkdir -p bed12 - -EB=$1 - -while IFS='' read -r line; do - - name=$(echo $line | awk '{print $4}') - count=$(echo $line | awk '{print $5}') - touch ${name}.bed - echo "$line" >> ${name}.bed_tmp - sed 's/[\t]*$//' ${name}.bed_tmp > ${name}.bed && rm ${name}.bed_tmp - - bedtools intersect -a filt.gtf -b ${name}.bed -s -f 1.00 > ${name}.gtf - - start=$(echo $line | awk '{print $2}') - stop=$(echo $line | awk '{print $3}') - - echo "[nf-core/circrna]: Starting analysis for: $name" - - # is the gtf file NOT (-s) empty? i.e did it overlap biotypes? - if [[ -s ${name}.gtf ]]; - then - - echo "[nf-core/circrna]: $name overlaps features in GTF file" - echo "[nf-core/circrna]: Inspecting Genes..." - - gene_id=$(awk -F'gene_id ' '{print $2}' ${name}.gtf | \ - awk -F';' '{print $1}' | sed 's/"//g' | sort -u | paste -s -d, -) - - tx_id=$(awk -F'transcript_id ' '{print $2}' ${name}.gtf | \ - awk -F';' '{print $1}' | sed 's/"//g' | sort -u | paste -s -d, -) - - echo "[nf-core/circrna]: Overlapping Gene IDs: $gene_id" - echo "[nf-core/circrna]: Converting to BED12" - - gtfToGenePred ${name}.gtf ${name}.genepred - genePredToBed ${name}.genepred ${name}_predtobed.bed - - # Attempting perfect exon boundary overlaps - echo "[nf-core/circrna]: Attempting to fit circRNA to gene exon boundaries" - awk -v OFS="\t" -v start="$start" -v stop="$stop" \ - '{if($2==start && $3==stop) print $0}' ${name}_predtobed.bed | \ - sort -rnk10 | head -n 1 > ${name}.bed12.bed - - # Resulting file not empty? i.e perfectly overlapped with exon boundaries? - if [[ -s ${name}.bed12.bed ]]; - then - echo "[nf-core/circrna]: ${name} fits gene exons, is a circRNA" - type="circRNA" - else - - echo "[nf-core/circrna]: circRNA overlaps exons, but not boundaries" - echo "[nf-core/circrna]: Investigating if EIciRNA or acceptable to take underlying transcript" - echo "[nf-core/circrna]: Retrying with longest underlying transcript" - - awk -v OFS="\t" '{$13 = $3 - $2; print}' ${name}_predtobed.bed | \ - sort -rnk13 | cut -f13 --complement | head -n 1 > ${name}.bed12.bed_tmp - - tx_len=$(awk -v OFS="\t" '{$13 = $3 - $2; print}' ${name}_predtobed.bed | \ - sort -rnk13 | awk '{print $13}' | head -n 1) - - circ_len=$(awk -v OFS="\t" '{$7 = $3 - $2; print}' ${name}.bed | awk '{print $7}') - - echo "[nf-core/circrna]: Best transcript length: $tx_len" - echo "[nf-core/circrna]: $name length: $circ_len" - - difference=$(($circ_len - $tx_len)) - - if [[ $difference -gt $EB ]]; - then - - echo "[nf-core/circrna]: Transcript exon boundaries more than ${EB}bp off $name" - echo "[nf-core/circrna]: Treating as EIciRNA" - - type="EIciRNA" - block_count=1 - block_size=$(($stop-$start)) - rgb="0,0,0" - block_start=0 - awk -v OFS="\t" -v thick=$start -v rgb=$rgb -v count=$block_count -v start=$block_start -v size=$block_size \ - '{print $0, thick, thick, rgb, count, size, start}' ${name}.bed > ${name}.bed12.bed - rm ${name}.bed12.bed_tmp - else - - echo "[nf-core/circrna]: Transcript exon boundaries within ${EB}bp ${name}" - echo "[nf-core/circrna]: Treating ${name} as circRNA." - type="circRNA" - mv ${name}.bed12.bed_tmp ${name}.bed12.bed - fi - fi - else - - echo "[nf-core/circrna]: $name returned no GTF overlaps." - echo "[nf-core/circrna]: Treating as an intronic circRNA" - - gene_id="NA" - tx_id="NA" - type="ciRNA" - block_count=1 - block_size=$(($stop-$start)) - rgb="0,0,0" - block_start=0 - awk -v OFS="\t" -v thick=$start -v rgb=$rgb -v count=$block_count -v start=$block_start -v size=$block_size \ - '{print $0, thick, thick, rgb, count, size, start}' ${name}.bed > ${name}.bed12.bed - fi - # add type, geneid tx_id and count - awk -v type="$type" -v gene="$gene_id" -v tx="$tx_id" -v count="$count" 'BEGIN{FS=OFS="\t"}{$5=count;$13=type;$14=gene;$15=tx}1' ${name}.bed12.bed > ${name}.bed12.bed_tmp - awk -v OFS="\t" -v name=$name '{$4 = name; print}' ${name}.bed12.bed_tmp > ${name}.bed12.bed_tmp1 - - rm ${name}.bed12.bed - rm ${name}.bed12.bed_tmp - mv ${name}.bed12.bed_tmp1 ${name}.bed12.bed - echo "[nf-core/circrna]: cleaning up intermediate files" - rm -f ${name}.gtf - rm -f ${name}.genepred - rm -f ${name}_predtobed.bed - rm -f ${name}.bed - - cp ${name}.bed12.bed bed12/ - rm -rf ${name}.bed12.bed - echo "====================================================================================" - echo "====================================================================================" - -done < circs.bed - -# remove the trailing commas that appear on end of Exon Size, Exon Starts (col 11, 12) -cat bed12/*.bed12.bed > master_bed12.bed.tmp - -awk 'BEGIN{FS=OFS="\t"} {gsub(/,$/,"",$11);gsub(/,$/,"",$12)} 1' master_bed12.bed.tmp > master_bed12.bed && rm master_bed12.bed.tmp - -echo " Thank you for using nf-core/circrna! - Barry " -echo "====================================================================================" -echo "====================================================================================" diff --git a/bin/check_empty.sh b/bin/check_empty.sh deleted file mode 100755 index 8f28e88c..00000000 --- a/bin/check_empty.sh +++ /dev/null @@ -1,28 +0,0 @@ -#!/usr/bin/env bash - -## When consolidating tool outputs for a sample, check if any are empty. -## This will prevent R from throwing errors -## Author: Barry Digby -## License: MIT - -for i in *bed; do - - if [[ -s $i ]]; - then - : - else - echo "${i}" >> remove_empty_sample.txt - fi - -done - -## sample.csv contains all tool bed files by default -mv samples.csv checkme.csv - -## if there are empty tool outputs then remove them from samples.csv and rewrite. -if [[ -s remove_empty_sample.txt ]]; -then - grep -vf remove_empty_sample.txt checkme.csv > samples.csv -else - mv checkme.csv samples.csv -fi diff --git a/modules/local/annotation/parent_gene/main.nf b/modules/local/annotation/parent_gene/main.nf deleted file mode 100644 index 21f0b892..00000000 --- a/modules/local/annotation/parent_gene/main.nf +++ /dev/null @@ -1,53 +0,0 @@ -process PARENT_GENE { - label 'process_high' - - conda "bioconda::ucsc-gtftogenepred=377 bioconda::ucsc-genepredtobed=377 bioconda::bedtools=2.27.0" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-d7ee3552d06d8acebbc660507b48487c7369e221:07daadbfe8182aa3c974c7b78924d5c8730b922d-0' : - 'biocontainers/mulled-v2-d7ee3552d06d8acebbc660507b48487c7369e221:07daadbfe8182aa3c974c7b78924d5c8730b922d-0' }" - - input: - path circrna_matrix - path gtf - path biotypes - val exon_boundary - - output: - path "circrna_host-gene.txt" , emit: circ_host_map - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def VERSION = '377' - """ - # remove redundant biotypes from GTF. - grep -vf $biotypes $gtf > filt.gtf - - # generate circrna BED file. - tail -n +2 $circrna_matrix | awk '{print \$1}' > IDs.txt - - # ID_to_BED - while IFS='' read -r line; do - name=\$(echo \$line) - chr=\$(echo \$line | cut -d: -f1) - start=\$(echo \$line | cut -d- -f1 | cut -d: -f2) - stop=\$(echo \$line | cut -d- -f2 | cut -d: -f1) - sign=\$(echo \$line | cut -d: -f3) - echo -e "\$chr\\t\$start\\t\$stop\\t\$name\\t0\\t\$sign" >> \${name}.bed - done < IDs.txt - - cat *.bed > merged.txt && rm IDs.txt && rm *.bed && mv merged.txt circs.bed - - # Re-use annotation script to identify the host gene. - annotate_outputs.sh $exon_boundary &> annotation.log - awk -v OFS="\\t" '{print \$4, \$14}' master_bed12.bed > circrna_host-gene.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") - ucsc: $VERSION - END_VERSIONS - """ -} diff --git a/subworkflows/local/differential_expression.nf b/subworkflows/local/differential_expression.nf deleted file mode 100644 index d4199b86..00000000 --- a/subworkflows/local/differential_expression.nf +++ /dev/null @@ -1,75 +0,0 @@ -include { HISAT2_ALIGN } from '../../modules/nf-core/hisat2/align/main' -include { STRINGTIE_STRINGTIE } from '../../modules/nf-core/stringtie/stringtie/main' -include { STRINGTIE_PREPDE } from '../../modules/local/stringtie/prepde/main' -include { PARENT_GENE } from '../../modules/local/annotation/parent_gene/main' -include { PREPARE_CLR_TEST } from '../../modules/local/circtest/prepare/main' -include { CIRCTEST } from '../../modules/local/circtest/test/main' -include { DESEQ2_DIFFERENTIAL_EXPRESSION } from '../../modules/local/deseq2/differential_expression/main' -include { BAM_SORT_STATS_SAMTOOLS } from '../nf-core/bam_sort_stats_samtools/main' - -workflow DIFFERENTIAL_EXPRESSION { - - take: - reads - ch_gtf - ch_fasta - hisat2_index - splice_sites - phenotype - counts_bed - counts_tsv - species - ensembl_map - exon_boundary - - main: - ch_versions = Channel.empty() - qc_reports = Channel.empty() - - fasta = ch_fasta.map{ meta, fasta -> fasta } - gtf = ch_gtf.map{ meta, gtf -> gtf } - - // - // LINEAR RNA ALIGNEMT WORKFLOW: - // - - HISAT2_ALIGN( reads, hisat2_index, splice_sites ) - BAM_SORT_STATS_SAMTOOLS( HISAT2_ALIGN.out.bam, ch_fasta ) - STRINGTIE_STRINGTIE( BAM_SORT_STATS_SAMTOOLS.out.bam, gtf ) - STRINGTIE_PREPDE( STRINGTIE_STRINGTIE.out.transcript_gtf.map{ meta, gtf -> return [ gtf ] }.collect() ) - - qc_reports = qc_reports.mix(HISAT2_ALIGN.out.summary.map{ meta, log -> log}) - qc_reports = qc_reports.mix(BAM_SORT_STATS_SAMTOOLS.out.stats.map{ meta, stats -> stats}) - qc_reports = qc_reports.mix(BAM_SORT_STATS_SAMTOOLS.out.flagstat.map{ meta, flagstat -> flagstat}) - qc_reports = qc_reports.mix(BAM_SORT_STATS_SAMTOOLS.out.idxstats.map{ meta, idxstats -> idxstats}) - - - // - // Circular, Linear Differential Expression - // - - DESEQ2_DIFFERENTIAL_EXPRESSION( STRINGTIE_PREPDE.out.gene_matrix, phenotype, counts_bed, species, ensembl_map ) - - // - // CircRNA - Host Gene Ratio tests - // - - ch_biotypes = Channel.fromPath("${projectDir}/bin/unwanted_biotypes.txt") - - PARENT_GENE( counts_tsv, gtf, ch_biotypes.collect(), exon_boundary ) - PREPARE_CLR_TEST( STRINGTIE_PREPDE.out.gene_matrix, counts_tsv, PARENT_GENE.out.circ_host_map, gtf ) - CIRCTEST( PREPARE_CLR_TEST.out.circular, PREPARE_CLR_TEST.out.linear, phenotype ) - - ch_versions = ch_versions.mix(HISAT2_ALIGN.out.versions) - ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS.out.versions) - ch_versions = ch_versions.mix(STRINGTIE_STRINGTIE.out.versions) - ch_versions = ch_versions.mix(STRINGTIE_PREPDE.out.versions) - ch_versions = ch_versions.mix(DESEQ2_DIFFERENTIAL_EXPRESSION.out.versions) - ch_versions = ch_versions.mix(PARENT_GENE.out.versions) - ch_versions = ch_versions.mix(PREPARE_CLR_TEST.out.versions) - ch_versions = ch_versions.mix(CIRCTEST.out.versions) - - emit: - versions = ch_versions - reports = qc_reports -} From b67e980fda09fb2775be33e7e870eff933818958 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 11 Jun 2024 14:41:02 +0200 Subject: [PATCH 279/491] Simplify annotation module --- modules/local/annotation/{full_annotation => }/main.nf | 0 subworkflows/local/discovery/annotation.nf | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) rename modules/local/annotation/{full_annotation => }/main.nf (100%) diff --git a/modules/local/annotation/full_annotation/main.nf b/modules/local/annotation/main.nf similarity index 100% rename from modules/local/annotation/full_annotation/main.nf rename to modules/local/annotation/main.nf diff --git a/subworkflows/local/discovery/annotation.nf b/subworkflows/local/discovery/annotation.nf index d865a5da..518260b6 100644 --- a/subworkflows/local/discovery/annotation.nf +++ b/subworkflows/local/discovery/annotation.nf @@ -1,5 +1,5 @@ include { BEDTOOLS_INTERSECT as INTERSECT } from '../../../modules/nf-core/bedtools/intersect' -include { ANNOTATION as ANNOTATE } from '../../../modules/local/annotation/full_annotation' +include { ANNOTATION as ANNOTATE } from '../../../modules/local/annotation' include { GNU_SORT as COMBINE_BEDS } from '../../../modules/nf-core/gnu/sort' include { GAWK as REMOVE_SCORE_STRAND } from '../../../modules/nf-core/gawk' include { GNU_SORT as COMBINE_GTFS } from '../../../modules/nf-core/gnu/sort' From 6fdc23d8a02672c6a18f966977f32577bdde81b4 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 11 Jun 2024 14:54:03 +0200 Subject: [PATCH 280/491] Switch annotation to template syntax --- modules/local/annotation/main.nf | 22 +++------ .../local/annotation/templates}/annotation.py | 46 ++++++++++++++----- 2 files changed, 41 insertions(+), 27 deletions(-) rename {bin => modules/local/annotation/templates}/annotation.py (75%) diff --git a/modules/local/annotation/main.nf b/modules/local/annotation/main.nf index 207cd463..a5b6d77a 100644 --- a/modules/local/annotation/main.nf +++ b/modules/local/annotation/main.nf @@ -12,22 +12,12 @@ process ANNOTATION { val(exon_boundary) output: - tuple val(meta), path("${out_bed}"), emit: bed - tuple val(meta), path("${out_gtf}"), emit: gtf - path "versions.yml", emit: versions + tuple val(meta), path("${prefix}.bed"), emit: bed + tuple val(meta), path("${prefix}.gtf"), emit: gtf - script: - prefix = task.ext.prefix ?: "${meta.id}.annotation" - out_bed = "${prefix}.bed" - out_gtf = "${prefix}.gtf" - """ - annotation.py --input ${intersection} --exon_boundary ${exon_boundary} --output_bed ${out_bed} --output_gtf ${out_gtf} + path "versions.yml" , emit: versions - cat <<-END_VERSIONS > versions.yml - "${task.process}": - python: \$(python --version | sed 's/Python //g') - pandas: \$(python -c "import pandas; print(pandas.__version__)") - numpy: \$(python -c "import numpy; print(numpy.__version__)") - END_VERSIONS - """ + script: + prefix = task.ext.prefix ?: meta.id + template 'annotation.py' } diff --git a/bin/annotation.py b/modules/local/annotation/templates/annotation.py similarity index 75% rename from bin/annotation.py rename to modules/local/annotation/templates/annotation.py index 877ed877..6cd1d68d 100755 --- a/bin/annotation.py +++ b/modules/local/annotation/templates/annotation.py @@ -2,16 +2,27 @@ import pandas as pd import numpy as np -import argparse +import platform import csv -parser = argparse.ArgumentParser(description='Annotate circRNAs') -parser.add_argument('--input', type=str, help='Path to the input file') -parser.add_argument('--exon_boundary', type=int, help='Exon boundary') -parser.add_argument('--output_bed', type=str, help='Path to the output bed file') -parser.add_argument('--output_gtf', type=str, help='Path to the output gtf') +def format_yaml_like(data: dict, indent: int = 0) -> str: + """Formats a dictionary to a YAML-like string. -args = parser.parse_args() + Args: + data (dict): The dictionary to format. + indent (int): The current indentation level. + + Returns: + str: A string formatted as YAML. + """ + yaml_str = "" + for key, value in data.items(): + spaces = " " * indent + if isinstance(value, dict): + yaml_str += f"{spaces}{key}:\\n{format_yaml_like(value, indent + 1)}" + else: + yaml_str += f"{spaces}{key}: {value}\\n" + return yaml_str columns = { @@ -28,9 +39,9 @@ attributes = ['gene_id', 'gene_name', 'transcript_id'] -exon_boundary = args.exon_boundary +exon_boundary = int("${exon_boundary}") -df = pd.read_csv(args.input, sep="\t", header=None, usecols=columns.keys()) +df = pd.read_csv("${intersection}", sep="\\t", header=None, usecols=columns.keys()) df = df.rename(columns=columns) # Extract circRNAs without match @@ -99,7 +110,7 @@ def determine_type(row): # Sort by chr, start, end df = df.sort_values(['chr', 'start', 'end']) -df.to_csv(args.output_bed, sep='\t', index=False, header=False) +df.to_csv("${prefix}.bed", sep='\\t', index=False, header=False) # Convert to GTF df['source'] = 'circRNA' @@ -109,4 +120,17 @@ def determine_type(row): gtf_order = ['chr', 'source', 'type', 'start', 'end', 'score', 'strand', 'frame', 'attributes'] df = df[gtf_order] -df.to_csv(args.output_gtf, sep='\t', index=False, header=False, quoting=csv.QUOTE_NONE) +df.to_csv("${prefix}.gtf", sep='\\t', index=False, header=False, quoting=csv.QUOTE_NONE) + +# Versions + +versions = { + "${task.process}": { + "python": platform.python_version(), + "pandas": pd.__version__, + "numpy": np.__version__ + } +} + +with open("versions.yml", "w") as f: + f.write(format_yaml_like(versions)) From a87569b2f2f53b7ea53a78a04bcf0cb2ae4713cb Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 11 Jun 2024 14:59:11 +0200 Subject: [PATCH 281/491] Remove unused combine_quantification script --- bin/combine_quantification.py | 16 ---------------- 1 file changed, 16 deletions(-) delete mode 100755 bin/combine_quantification.py diff --git a/bin/combine_quantification.py b/bin/combine_quantification.py deleted file mode 100755 index dd0b1307..00000000 --- a/bin/combine_quantification.py +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env python3 - -import argparse -import pandas as pd -import os - -parser = argparse.ArgumentParser(description='Merge quantification files into a single file') -parser.add_argument('--inputs', type=str, nargs='+', help='List input files to merge') -parser.add_argument('--output', type=str, help='Path to output combined quantification file') - -args = parser.parse_args() - -dfs = [pd.read_csv(f, sep='\t', index_col=[0, 1]) for f in args.inputs] -df_combined = pd.concat(dfs, axis=1, sort=True) - -df_combined.to_csv(args.output, sep='\t') From fa7cc09cac1c9e8a2fdc6b23d238a0df9278dbe0 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 11 Jun 2024 15:05:17 +0200 Subject: [PATCH 282/491] Switch merge_samples to template syntax --- bin/merge_samples.py | 29 ---------- .../local/count_matrix/merge_samples/main.nf | 11 +--- .../merge_samples/templates/merge_samples.py | 53 +++++++++++++++++++ 3 files changed, 55 insertions(+), 38 deletions(-) delete mode 100755 bin/merge_samples.py create mode 100755 modules/local/count_matrix/merge_samples/templates/merge_samples.py diff --git a/bin/merge_samples.py b/bin/merge_samples.py deleted file mode 100755 index f50fe3db..00000000 --- a/bin/merge_samples.py +++ /dev/null @@ -1,29 +0,0 @@ -#!/usr/bin/env python3 - -import argparse -import pandas as pd -import os - -parser = argparse.ArgumentParser(description='Merge counts across tools for a single sample') -parser.add_argument('--beds', type=str, nargs='+', help='List of bed files to merge') -parser.add_argument('--out_bed', type=str, help='Output bed file') -parser.add_argument('--out_tsv', type=str, help='Output tsv file') - -args = parser.parse_args() - -columns = ['chr', 'start', 'end', 'name', 'count', 'strand'] -dfs = {os.path.basename(bed).split('.')[0]: pd.read_csv(bed, - sep='\t', - header=None, - index_col=["chr", "start", "end", "strand"], - usecols=["chr", "start", "end", "strand", "count"], - names=columns) for bed in args.beds} - -dfs = [df.rename(columns={'count': sample}) for sample, df in dfs.items()] -df = pd.concat(dfs, axis=1) -df = df.fillna(0) -df.to_csv(args.out_bed, sep='\t', header=True, index=True) - -df.index = df.index.map(lambda x: f'{x[0]}:{x[1]}-{x[2]}:{x[3]}') -df.index.name = 'ID' -df.to_csv(args.out_tsv, sep='\t') diff --git a/modules/local/count_matrix/merge_samples/main.nf b/modules/local/count_matrix/merge_samples/main.nf index b286c757..410d2097 100644 --- a/modules/local/count_matrix/merge_samples/main.nf +++ b/modules/local/count_matrix/merge_samples/main.nf @@ -12,16 +12,9 @@ process MERGE_SAMPLES { output: path("merged_counts.bed") , emit: counts_bed path("merged_counts.tsv") , emit: counts_tsv + path "versions.yml" , emit: versions script: - """ - merge_samples.py --beds ${beds} --out_bed merged_counts.bed --out_tsv merged_counts.tsv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - python: \$(python --version | sed 's/Python //g') - pandas: \$(python -c "import pandas; print(pandas.__version__)") - END_VERSIONS - """ + template "merge_samples.py" } diff --git a/modules/local/count_matrix/merge_samples/templates/merge_samples.py b/modules/local/count_matrix/merge_samples/templates/merge_samples.py new file mode 100755 index 00000000..010eb616 --- /dev/null +++ b/modules/local/count_matrix/merge_samples/templates/merge_samples.py @@ -0,0 +1,53 @@ +#!/usr/bin/env python3 + +import platform +import pandas as pd +import os + +def format_yaml_like(data: dict, indent: int = 0) -> str: + """Formats a dictionary to a YAML-like string. + + Args: + data (dict): The dictionary to format. + indent (int): The current indentation level. + + Returns: + str: A string formatted as YAML. + """ + yaml_str = "" + for key, value in data.items(): + spaces = " " * indent + if isinstance(value, dict): + yaml_str += f"{spaces}{key}:\\n{format_yaml_like(value, indent + 1)}" + else: + yaml_str += f"{spaces}{key}: {value}\\n" + return yaml_str + +columns = ['chr', 'start', 'end', 'name', 'count', 'strand'] +dfs = {os.path.basename(bed).split('.')[0]: pd.read_csv(bed, + sep='\t', + header=None, + index_col=["chr", "start", "end", "strand"], + usecols=["chr", "start", "end", "strand", "count"], + names=columns) for bed in "${beds}".split()} + +dfs = [df.rename(columns={'count': sample}) for sample, df in dfs.items()] +df = pd.concat(dfs, axis=1) +df = df.fillna(0) +df.to_csv("merged_counts.bed", sep='\\t', header=True, index=True) + +df.index = df.index.map(lambda x: f'{x[0]}:{x[1]}-{x[2]}:{x[3]}') +df.index.name = 'ID' +df.to_csv("merged_counts.tsv", sep='\\t') + +# Versions + +versions = { + "${task.process}": { + "python": platform.python_version(), + "pandas": pd.__version__ + } +} + +with open("versions.yml", "w") as f: + f.write(format_yaml_like(versions)) From f3e63fda741b81eb64add683f6df7b6ab30dc4a1 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 11 Jun 2024 15:24:02 +0200 Subject: [PATCH 283/491] Switch to template syntax in merge_tools --- bin/merge_tools.py | 24 --------- .../local/count_matrix/merge_tools/main.nf | 12 +---- .../merge_tools/templates/merge_tools.py | 52 +++++++++++++++++++ 3 files changed, 54 insertions(+), 34 deletions(-) delete mode 100755 bin/merge_tools.py create mode 100755 modules/local/count_matrix/merge_tools/templates/merge_tools.py diff --git a/bin/merge_tools.py b/bin/merge_tools.py deleted file mode 100755 index 3d6a1396..00000000 --- a/bin/merge_tools.py +++ /dev/null @@ -1,24 +0,0 @@ -#!/usr/bin/env python3 - -import argparse -import pandas as pd - -parser = argparse.ArgumentParser(description='Merge counts across tools for a single sample') -parser.add_argument('--beds', type=str, nargs='+', help='List of bed files to merge') -parser.add_argument('--tool_filter', type=int, help='Minimum number of tools to keep a circRNA') -parser.add_argument('--duplicates_fun', type=str, help='Function to apply to duplicates', choices=['sum', 'mean', 'max', 'min']) -parser.add_argument('--output', type=str, help='Output file') - -args = parser.parse_args() - -columns = ['chr', 'start', 'end', 'name', 'count', 'strand'] -dfs = [pd.read_csv(bed, sep='\t', header=None, names=columns) for bed in args.beds] -df = pd.concat(dfs) - -df['tool_count'] = 1 -df = df.groupby(['chr', 'start', 'end', 'strand', 'name']).agg({'count': args.duplicates_fun, - 'tool_count': 'sum'}).reset_index() -df = df[df['tool_count'] >= args.tool_filter] - -df = df[columns] -df.to_csv(args.output, sep='\t', index=False, header=False) diff --git a/modules/local/count_matrix/merge_tools/main.nf b/modules/local/count_matrix/merge_tools/main.nf index 17f8556f..dc80f483 100644 --- a/modules/local/count_matrix/merge_tools/main.nf +++ b/modules/local/count_matrix/merge_tools/main.nf @@ -15,16 +15,8 @@ process MERGE_TOOLS { output: tuple val(meta), path("${meta.id}.merged.bed"), emit: merged - path "versions.yml" , emit: versions + path "versions.yml" , emit: versions script: - """ - merge_tools.py --beds ${beds} --tool_filter ${tool_filter} --duplicates_fun ${duplicates_fun} --output ${meta.id}.merged.bed - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - python: \$(python --version | sed 's/Python //g') - pandas: \$(python -c "import pandas; print(pandas.__version__)") - END_VERSIONS - """ + template 'merge_tools.py' } diff --git a/modules/local/count_matrix/merge_tools/templates/merge_tools.py b/modules/local/count_matrix/merge_tools/templates/merge_tools.py new file mode 100755 index 00000000..debb85bf --- /dev/null +++ b/modules/local/count_matrix/merge_tools/templates/merge_tools.py @@ -0,0 +1,52 @@ +#!/usr/bin/env python3 + +import platform +import pandas as pd + +def format_yaml_like(data: dict, indent: int = 0) -> str: + """Formats a dictionary to a YAML-like string. + + Args: + data (dict): The dictionary to format. + indent (int): The current indentation level. + + Returns: + str: A string formatted as YAML. + """ + yaml_str = "" + for key, value in data.items(): + spaces = " " * indent + if isinstance(value, dict): + yaml_str += f"{spaces}{key}:\\n{format_yaml_like(value, indent + 1)}" + else: + yaml_str += f"{spaces}{key}: {value}\\n" + return yaml_str + +duplicates_fun = "${duplicates_fun}" + +if duplicates_fun not in ['sum', 'mean', 'max', 'min']: + raise ValueError(f"Invalid value for duplicates_fun: {duplicates_fun}") + +columns = ['chr', 'start', 'end', 'name', 'count', 'strand'] +dfs = [pd.read_csv(bed, sep='\t', header=None, names=columns) for bed in "${beds}".split()] +df = pd.concat(dfs) + +df['tool_count'] = 1 +df = df.groupby(['chr', 'start', 'end', 'strand', 'name']).agg({'count': duplicates_fun, + 'tool_count': 'sum'}).reset_index() +df = df[df['tool_count'] >= int("${tool_filter}")] + +df = df[columns] +df.to_csv("${meta.id}.merged.bed", sep='\t', index=False, header=False) + +# Versions + +versions = { + "${task.process}": { + "python": platform.python_version(), + "pandas": pd.__version__ + } +} + +with open("versions.yml", "w") as f: + f.write(format_yaml_like(versions)) From 4a49a485db7410736f0d3ba6697c7c355859a38d Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 11 Jun 2024 15:34:32 +0200 Subject: [PATCH 284/491] Remove custom DESeq2 module --- bin/ensembl_database_map.txt | 18 ------ .../deseq2/differential_expression/main.nf | 55 ------------------- 2 files changed, 73 deletions(-) delete mode 100755 bin/ensembl_database_map.txt delete mode 100644 modules/local/deseq2/differential_expression/main.nf diff --git a/bin/ensembl_database_map.txt b/bin/ensembl_database_map.txt deleted file mode 100755 index 86e6bb55..00000000 --- a/bin/ensembl_database_map.txt +++ /dev/null @@ -1,18 +0,0 @@ -species command -cel useMart(biomart = "ensembl", dataset = "celegans_gene_ensembl", host="https://www.ensembl.org", archive=FALSE) -hsa useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl", host="https://www.ensembl.org", archive=FALSE) -mmu useMart(biomart = "ensembl", dataset = "mmusculus_gene_ensembl", host="https://www.ensembl.org", archive=FALSE) -ath useMart(biomart = "plants_mart", dataset = "athaliana_eg_gene", host="plants.ensembl.org", archive=FALSE) -bta useMart(biomart = "ensembl", dataset = "btaurus_gene_ensembl", host="https://www.ensembl.org", archive=FALSE) -cfa useMart(biomart = "ensembl", dataset = "clfamiliaris_gene_ensembl", host="https://www.ensembl.org", archive=FALSE) -dre useMart(biomart = "ensembl", dataset = "drerio_gene_ensembl", host="https://www.ensembl.org", archive=FALSE) -dme useMart(biomart = "ensembl", dataset = "dmelanogaster_gene_ensembl", host="https://www.ensembl.org", archive=FALSE) -eca useMart(biomart = "ensembl", dataset = "ecaballus_gene_ensembl", host="https://www.ensembl.org", archive=FALSE) -gga useMart(biomart = "ensembl", dataset = "ggallus_gene_ensembl", host="https://www.ensembl.org", archive=FALSE) -osa useMart(biomart = "plants_mart", dataset = "osativa_eg_gene", host="plants.ensembl.org", archive=FALSE) -ptr useMart(biomart = "ensembl", dataset = "ptroglodytes_gene_ensembl", host="https://www.ensembl.org", archive=FALSE) -rno useMart(biomart = "ensembl", dataset = "rnorvegicus_gene_ensembl", host="https://www.ensembl.org", archive=FALSE) -sbi useMart(biomart = "plants_mart", dataset = "sbicolor_eg_gene", host="plants.ensembl.org", archive=FALSE) -ssc useMart(biomart = "ensembl", dataset = "sscrofa_gene_ensembl", host="https://www.ensembl.org", archive=FALSE) -zma useMart(biomart = "plants_mart", dataset = "zmays_eg_gene", host="plants.ensembl.org", archive=FALSE) -mml useMart(biomart = "ensembl", dataset = "mmulatta_gene_ensembl", host="https://www.ensembl.org", archive=FALSE) diff --git a/modules/local/deseq2/differential_expression/main.nf b/modules/local/deseq2/differential_expression/main.nf deleted file mode 100644 index 560df2fc..00000000 --- a/modules/local/deseq2/differential_expression/main.nf +++ /dev/null @@ -1,55 +0,0 @@ -process DESEQ2_DIFFERENTIAL_EXPRESSION { - label 'process_medium' - - conda "r-base=3.6.3 conda-forge::r-argparser=0.6 conda-forge::r-dplyr=1.0.5 conda-forge::r-ggplot2=3.3.3 r-ggpubr=0.4.0 conda-forge::r-gplots=3.1.1 conda-forge::r-pheatmap=1.0.12 r-plyr=1.8.6 r-pvclust=2.2_0 r-rcolorbrewer=1.1_2 conda-forge::r-circlize=0.4.12 bioconductor-biomart=2.42.0 bioconductor-complexheatmap=2.2.0 bioconductor-deseq2=1.26.0 bioconductor-enhancedvolcano=1.4.0 bioconductor-ihw=1.14.0 bioconductor-org.hs.eg.db=3.10.0 bioconductor-pcatools=1.2.0 bioconductor-tximport=1.14.0" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-04b2ef814c9c6ab8c196c3e372521b88160dc260:e0cb4046baee3fd35fdbf883ba8af34e3e8af2e8-0' : - 'biocontainers/mulled-v2-04b2ef814c9c6ab8c196c3e372521b88160dc260:e0cb4046baee3fd35fdbf883ba8af34e3e8af2e8-0' }" - - input: - path(gene_matrix) - tuple val(meta), path(phenotype) - path(circrna_matrix) - val(species) - path(biomart_keys) - - output: - path "circRNA" , emit: circular_results - path "RNA-Seq" , emit: linear_results - path "DESeq2_QC" , emit: deseq2_qc - path "versions.yml", emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - """ - ## prepDE && circRNA counts headers are sorted such that uppercase preceedes lowercase i.e Z before a - ## reformat the phenotype file to match the order of the samples. - head -n 1 $phenotype > header - tail -n +2 $phenotype | LC_COLLATE=C sort > sorted_pheno - cat header sorted_pheno > tmp && rm phenotype.csv && mv tmp phenotype.csv - - DEA.R $gene_matrix $phenotype $circrna_matrix $species ensembl_database_map.txt - mv boxplots/ circRNA/ - mv *.RData DESeq2_QC/ - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//') - argparser: \$(Rscript -e "library(argparser); cat(as.character(packageVersion('argparser')))") - biomart: \$(Rscript -e "library(biomaRt); cat(as.character(packageVersion('biomaRt')))") - deseq2: \$(Rscript -e "library(DESeq2); cat(as.character(packageVersion('DESeq2')))") - dplyr: \$(Rscript -e "library(dplyr); cat(as.character(packageVersion('dplyr')))") - enhancedvolcano: \$(Rscript -e "library(EnhancedVolcano); cat(as.character(packageVersion('EnhancedVolcano')))") - gplots: \$(Rscript -e "library(gplots); cat(as.character(packageVersion('gplots')))") - ggplot2: \$(Rscript -e "library(ggplot2); cat(as.character(packageVersion('ggplot2')))") - ggpubr: \$(Rscript -e "library(ggpubr); cat(as.character(packageVersion('ggpubr')))") - ihw: \$(Rscript -e "library(IHW); cat(as.character(packageVersion('IHW')))") - pvclust: \$(Rscript -e "library(pvclust); cat(as.character(packageVersion('pvclust')))") - pcatools: \$(Rscript -e "library(PCAtools); cat(as.character(packageVersion('PCAtools')))") - pheatmap: \$(Rscript -e "library(pheatmap); cat(as.character(packageVersion('pheatmap')))") - rcolorbrewer: \$(Rscript -e "library(RColorBrewer); cat(as.character(packageVersion('RColorBrewer')))") - END_VERSIONS - """ -} From ec9198bf6bfd0d99c2020150059524b5e7b7ad85 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 11 Jun 2024 15:34:44 +0200 Subject: [PATCH 285/491] Remove DIFFERENTIAL_EXPRESSION traces --- workflows/circrna/main.nf | 20 -------------------- 1 file changed, 20 deletions(-) diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 18021678..be782faa 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -194,26 +194,6 @@ workflow CIRCRNA { ) /* - // - // 5. Differential expression tests - // - - ch_ensembl_database_map = params.module.contains('differential_expression') ? Channel.fromPath("${projectDir}/bin/ensembl_database_map.txt") : Channel.empty() - - DIFFERENTIAL_EXPRESSION( - FASTQC_TRIMGALORE.out.reads, - ch_gtf, - ch_fasta, - hisat2_index, - PREPARE_GENOME.out.splice_sites, - ch_phenotype, - CIRCRNA_DISCOVERY.out.counts_bed, - CIRCRNA_DISCOVERY.out.counts_tsv, - ch_species, - ch_ensembl_database_map, - params.exon_boundary - ) - ch_versions = ch_versions.mix(DIFFERENTIAL_EXPRESSION.out.versions) ch_multiqc_files = ch_multiqc_files.mix(DIFFERENTIAL_EXPRESSION.out.reports) */ From 344104858e0120a61a0a6b3058f560f8144e05f0 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 11 Jun 2024 15:46:26 +0200 Subject: [PATCH 286/491] Remove unwanted biotypes --- bin/unwanted_biotypes.txt | 55 --------------------------------------- 1 file changed, 55 deletions(-) delete mode 100755 bin/unwanted_biotypes.txt diff --git a/bin/unwanted_biotypes.txt b/bin/unwanted_biotypes.txt deleted file mode 100755 index ef5a6b2b..00000000 --- a/bin/unwanted_biotypes.txt +++ /dev/null @@ -1,55 +0,0 @@ -IG_C_gene -IG_D_gene -IG_J_gene -IG_LV_gene -IG_V_gene -TR_C_gene -TR_J_gene -TR_V_gene -TR_D_gene -IG_pseudogene -IG_C_pseudogene -IG_J_pseudogene -IG_V_pseudogene -TR_V_pseudogene -TR_J_pseudogene -Mt_rRNA -Mt_tRNA -miRNA -misc_RNA -rRNA -scRNA -snRNA -snoRNA -ribozyme -sRNA -scaRNA -TEC -Mt_tRNA_pseudogene -tRNA_pseudogene -snoRNA_pseudogene -snRNA_pseudogene -scRNA_pseudogene -rRNA_pseudogene -misc_RNA_pseudogene -miRNA_pseudogene -vaultRNA/vault_RNA -disrupted_domain -macro_lncRNA -artifact -unitary_pseudogene -GL000009.2 -GL000194.1 -GL000195.1 -GL000205.2 -GL000213.1 -GL000218.1 -GL000219.1 -KI270711.1 -KI270713.1 -KI270721.1 -KI270726.1 -KI270727.1 -KI270728.1 -KI270731.1 -KI270734.1 From abd9dcd8de435ef2b47e74965431d2f979fd4da2 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 11 Jun 2024 16:04:57 +0200 Subject: [PATCH 287/491] Fix linting problems --- conf/modules.config | 85 ------------------------- subworkflows/local/statistical_tests.nf | 7 +- workflows/circrna/main.nf | 6 +- 3 files changed, 7 insertions(+), 91 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 569cedf4..6752d858 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -689,89 +689,4 @@ process { pattern: "*.txt" ] } - - // DIFF EXP - - withName: HISAT2_ALIGN { - ext.when = { params.module.split(',').contains('differential_expression') } - ext.args = ["", - "--dta", - "--no-spliced-alignment" - ].join(' ').trim() - publishDir = [ - path: { "${params.outdir}/differential_expression/intermediates/hisat2/" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates, - ] - } - - withName: SAMTOOLS_SORT { - ext.when = { params.module.split(',').contains('differential_expression') } - ext.prefix = { "${meta.id}.sorted" } - publishDir = [ - path: { "${params.outdir}/differential_expression/intermediates/hisat2/" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates, - pattern: "*.bam" - ] - } - - withName: STRINGTIE_STRINGTIE { - ext.when = { params.module.split(',').contains('differential_expression') } - ext.args = "-e" - publishDir = [ - path: { "${params.outdir}/differential_expression/intermediates/stringtie/" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates - ] - } - - withName: STRINGTIE_PREPDE { - ext.when = { params.module.split(',').contains('differential_expression') } - publishDir = [ - path: { "${params.outdir}/differential_expression/RNA-Seq/" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates - ] - } - - withName: DESEQ2_DIFFERENTIAL_EXPRESSION { - ext.when = { params.module.split(',').contains('differential_expression') } - publishDir = [ - path: { "${params.outdir}/differential_expression/" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: PARENT_GENE { - ext.when = { params.module.split(',').contains('differential_expression') } - publishDir = [ - path: { "${params.outdir}/differential_expression/circular_linear_ratio_test" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: PREPARE_CLR_TEST { - ext.when = { params.module.split(',').contains('differential_expression') } - publishDir = [ - path: { "${params.outdir}/differential_expression/circular_linear_ratio_test" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: CIRCTEST { - ext.when = { params.module.split(',').contains('differential_expression') } - publishDir = [ - path: { "${params.outdir}/differential_expression/circular_linear_ratio_test" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } } diff --git a/subworkflows/local/statistical_tests.nf b/subworkflows/local/statistical_tests.nf index 3c977f9a..332f9ac7 100644 --- a/subworkflows/local/statistical_tests.nf +++ b/subworkflows/local/statistical_tests.nf @@ -7,7 +7,7 @@ workflow STATISTICAL_TESTS { ch_gene_counts ch_circ_counts ch_phenotype - + main: ch_versions = Channel.empty() @@ -17,5 +17,8 @@ workflow STATISTICAL_TESTS { CIRCTEST_CIRCTEST(CIRCTEST_PREPARE.out.circ_counts, CIRCTEST_PREPARE.out.gene_counts, ch_phenotype) + ch_versions = ch_versions.mix(CIRCTEST_CIRCTEST.out.versions) -} \ No newline at end of file + emit: + versions = ch_versions +} diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index be782faa..0b74ace1 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -193,10 +193,8 @@ workflow CIRCRNA { ch_phenotype ) - /* - ch_versions = ch_versions.mix(DIFFERENTIAL_EXPRESSION.out.versions) - ch_multiqc_files = ch_multiqc_files.mix(DIFFERENTIAL_EXPRESSION.out.reports) - */ + ch_versions = ch_versions.mix(STATISTICAL_TESTS.out.versions) + // // Collate and save software versions From ffbada60f3d7cc87d14e7a608c678c32be22b601 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 11 Jun 2024 16:07:16 +0200 Subject: [PATCH 288/491] Prettier --- modules/local/circtest/prepare/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/circtest/prepare/environment.yml b/modules/local/circtest/prepare/environment.yml index 602dc60d..02becc7c 100644 --- a/modules/local/circtest/prepare/environment.yml +++ b/modules/local/circtest/prepare/environment.yml @@ -2,4 +2,4 @@ name: circtest_prepare channels: - conda-forge dependencies: - - conda-forge::r-base=4.2.1 \ No newline at end of file + - conda-forge::r-base=4.2.1 From 2d259c38ff51689fafca50fc3ed5706bcd10dd6e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Wed, 12 Jun 2024 09:18:16 +0200 Subject: [PATCH 289/491] Remove traces of differential_expression in docs --- README.md | 5 +- docs/output.md | 184 ++----------------------------------------------- docs/usage.md | 47 ++----------- 3 files changed, 13 insertions(+), 223 deletions(-) diff --git a/README.md b/README.md index fe77e560..b289dbf1 100644 --- a/README.md +++ b/README.md @@ -22,7 +22,7 @@ ## Introduction -**nf-core/circrna** is a bioinformatics best-practice analysis pipeline for Quantification, miRNA target prediction and differential expression analysis of circular RNAs. +**nf-core/circrna** is a bioinformatics best-practice analysis pipeline for BSJ detection, quantification, annotation and miRNA target prediction of circular RNAs. The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! @@ -50,7 +50,6 @@ On release, automated continuous integration tests run the pipeline on a full-si - [`miRanda`](http://cbio.mskcc.org/miRNA2003/miranda.html) - [`TargetScan`](http://www.targetscan.org/cgi-bin/targetscan/data_download.vert72.cgi) - Filter results, miRNAs must be called by both tools -- Differential expression analysis [`DESeq2`](https://bioconductor.org/packages/release/bioc/html/DESeq2.html) - Circular - Linear ratio tests ['CircTest'](https://github.com/dieterich-lab/CircTest) diff --git a/nextflow_schema.json b/nextflow_schema.json index 2196197e..9d814605 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -37,7 +37,7 @@ "schema": "assets/schema_phenotype.json", "mimetype": "text/csv", "pattern": "^\\S+\\.csv$", - "description": "Phenotype CSV file specifying the experimental design.", + "description": "Phenotype CSV file specifying the experimental design. If provided, the pipeline will run CIRCTEST.", "help_text": "There are two rules for providing the phenotype CSV file. 1) The 'sample' column must match the sample sheets 'sample' column. 2) The response variable containing the phenotype of primary interest in the experiment must have the column name condition. All other columns included in the file are controlled for in the `DESeq2` design. \n\n| sample \t| condition \t| replicate \t|\n|-----------\t|-----------\t|-----------\t|\n| control_1 \t| ctr \t| 1 \t|\n| control_2 \t| ctr \t| 2 \t|\n| control_3 \t| ctr \t| 3 \t|\n| treated_1 \t| trt \t| 1 \t|\n| treated_2 \t| trt \t| 2 \t|\n| treated_3 \t| trt \t| 3 \t|\n\nThe above phenotype file will identify differentially expressed circRNAs/mRNAs between control and treatment cells, whilst controlling for the effect of variation between replicates: ` ~ replicates + condition`", "fa_icon": "fas fa-file-csv" } From 9f9e967c20c406b9ae59479ccded73e684e5b199 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 14 Jun 2024 13:30:21 +0200 Subject: [PATCH 299/491] Update documentation for enabling miRNA prediction --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 722e9df3..2d3f427b 100644 --- a/README.md +++ b/README.md @@ -46,7 +46,7 @@ On release, automated continuous integration tests run the pipeline on a full-si - Export mature spliced length as FASTA file - Annotate parent gene, underlying transcripts. - circRNA count matrix -- miRNA target prediction +- miRNA target prediction (only if the `mature` parameter is provided) - [`miRanda`](http://cbio.mskcc.org/miRNA2003/miranda.html) - [`TargetScan`](http://www.targetscan.org/cgi-bin/targetscan/data_download.vert72.cgi) - Filter results, miRNAs must be called by both tools From a0fb084fd4accde02bf9753bec9033ee5c332b3c Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 14 Jun 2024 14:31:57 +0200 Subject: [PATCH 300/491] Update README --- README.md | 57 ++++++++++++++------------------------ docs/images/metro-map.png | Bin 0 -> 289348 bytes 2 files changed, 21 insertions(+), 36 deletions(-) create mode 100644 docs/images/metro-map.png diff --git a/README.md b/README.md index 2d3f427b..b769e066 100644 --- a/README.md +++ b/README.md @@ -30,64 +30,49 @@ On release, automated continuous integration tests run the pipeline on a full-si ## Pipeline summary +![Metro Map](./docs/images/metro-map.png) + - Raw read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) - Adapter trimming ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)) -- MultiQC report [`MultiQC`](http://multiqc.info/) -- circRNA quantification -- [`CIRIquant`](https://github.com/Kevinzjy/CIRIquant) -- [`STAR 2-Pass mode`](https://github.com/alexdobin/STAR) - - [`CIRCexplorer2`](https://circexplorer2.readthedocs.io/en/latest/) - - [`circRNA finder`](https://github.com/orzechoj/circRNA_finder) - - [`DCC`](https://github.com/dieterich-lab/DCC) -- [`find circ`](https://github.com/marvin-jens/find_circ) -- [`MapSplice`](http://www.netlab.uky.edu/p/bioinfo/MapSplice2) -- [`Segemehl`](https://www.bioinf.uni-leipzig.de/Software/segemehl/) +- BSJ detection + - [`CIRIquant`](https://github.com/Kevinzjy/CIRIquant) + - [`STAR 2-Pass mode`](https://github.com/alexdobin/STAR) + - [`CIRCexplorer2`](https://circexplorer2.readthedocs.io/en/latest/) + - [`circRNA finder`](https://github.com/orzechoj/circRNA_finder) + - [`DCC`](https://github.com/dieterich-lab/DCC) + - [`find circ`](https://github.com/marvin-jens/find_circ) + - [`MapSplice`](http://www.netlab.uky.edu/p/bioinfo/MapSplice2) + - [`Segemehl`](https://www.bioinf.uni-leipzig.de/Software/segemehl/) - circRNA annotation -- Export mature spliced length as FASTA file -- Annotate parent gene, underlying transcripts. -- circRNA count matrix -- miRNA target prediction (only if the `mature` parameter is provided) +- Extract circRNA sequences and build circular transcriptome +- Merge circular transcriptome with linear transcriptome derived from provided GTF +- Quantification of combined circular and linear transcriptome + - [`psirc-quant`](https://github.com/Christina-hshi/psirc) +- miRNA binding affinity analysis (only if the `mature` parameter is provided) - [`miRanda`](http://cbio.mskcc.org/miRNA2003/miranda.html) - [`TargetScan`](http://www.targetscan.org/cgi-bin/targetscan/data_download.vert72.cgi) - - Filter results, miRNAs must be called by both tools -- Circular - circRNA-Host ratio tests ['CircTest'](https://github.com/dieterich-lab/CircTest) (only if the `phenotype` parameter is provided) - - +- Statistical tests (only if the `phenotype` parameter is provided) + - [`CircTest`](https://github.com/dieterich-lab/CircTest) +- MultiQC report [`MultiQC`](http://multiqc.info/) ## Usage > [!NOTE] > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. - - Now, you can run the pipeline using: -```bash -nextflow run nf-core/circrna \ - --input samplesheet.csv \ - --outdir \ - --genome GRCh37 \ - -profile \ - --tool 'ciriquant' \ - --bsj_reads 2 -``` - ```bash nextflow run nf-core/circrna \ -profile \ diff --git a/docs/images/metro-map.png b/docs/images/metro-map.png new file mode 100644 index 0000000000000000000000000000000000000000..2f4f8af8970272b3404fdd5684c0e563b0e2289b GIT binary patch literal 289348 zcmeEvbySpl)U_fZAR-_jjnb`jgF#6u-3`jnNH?f7C`hNEbaxFP-H5;pjnX~z(0tFJ zzSsMGdSCBd-=E&KT+ZS;&-~(?efHkxj0PykNnl|RV_dj!0ZU5q!DHaJ+zS_wWiF!v zKk3Wok^_FbX!ls+-i7>L(xnR*C@)AoxU1x(vpRwHMtP_TZNqAj3`Ze5gpxir^;YVz zrV?kW9#8r3uDXG&jEqb$OJM?z-ZIydLa%hxDHy)IltLjLzJL{U&MkRgopPx$}S z+s{AL2pJh-j{ILf{p*?~#YFX3@WsXc{p!E(SyZow{68PT1#cx_1CRBUo_~MbzduW4 z$m)MTziWRE;7CQkxhSr 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Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration except for parameters; see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). + +## Samplesheet input +You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row as shown in the examples below. ```bash -nextflow run nf-core/circrna -profile test, +--input '[path to samplesheet file]' ``` -# Running the pipeline +### Multiple runs of the same sample -The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes: +The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes. If you set the strandedness value to `auto` the pipeline will use the tool-defaults throughout the pipeline. ```csv title="samplesheet.csv" -sample,fastq_1,fastq_2 -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz -CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz -CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz +sample,fastq_1,fastq_2,strandedness +CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,auto +CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz,auto +CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz,auto ``` ### Full samplesheet -The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 3 columns to match those defined in the table below. +The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 4 columns to match those defined in the table below. A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice. ```csv title="samplesheet.csv" sample,fastq_1,fastq_2,strandedness -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,auto -CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz, -CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz, -TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz,,forward +CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,forward +CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz,forward +CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz,forward +TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz,,reverse TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz,,reverse -TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz,,unstranded -TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,,unstranded +TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz,,reverse +TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,,reverse ``` -| Column | Description | -| -------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | -| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | -| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | -| `strandedness` | Strandedness of the library. Options are `auto`, `unstranded`, `forward`, `reverse`. Default is `auto`. Make sure to use the same strandedness for each library/run of the same sample. | +| Column | Description | +| -------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | +| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| `strandedness` | Sample strand-specificity. Must be one of `unstranded`, `forward`, `reverse` or `auto`. | An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. @@ -48,9 +57,19 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```bash -nextflow run nf-core/circrna --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker +nextflow run \ + nf-core/circrna \ + --input \ + --outdir \ + --gtf \ + --fasta \ + --igenomes_ignore \ + --genome null \ + -profile docker ``` +> **NB:** Loading iGenomes configuration remains the default for reasons of consistency with other workflows, but should be disabled when not using iGenomes, applying the recommended usage above. + This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. Note that the pipeline will create the following files in your working directory: @@ -115,7 +134,7 @@ If you wish to share such profile (such as upload as supplementary material for Input data can be passed to `nf-core/circrna` using a CSV file containing the absolute paths to input fastq files. -The headers of the CSV file must be: `sample,fastq_1,fastq_2`. +The header of the CSV file must at least contain the `sample` and `fastq_1` columns. The `fastq_2` column is optional and only required for paired-end data. With an additional `strandness` column, the user can specify the strandedness of the library. The `sample` column should contain a unique identifier for each sample, and the `fastq_1` and `fastq_2` columns should contain the paths to the input fastq files. Valid examples for fastq input data in a CSV file is given below: @@ -128,7 +147,6 @@ Valid examples for fastq input data in a CSV file is given below: | TCGA-EJ-5518-01A | /data/afbbc370-5970-43d3-b9f8-f40f8e649bb6_gdc_realn_rehead_R1.fastq.gz | /data/afbbc370-5970-43d3-b9f8-f40f8e649bb6_gdc_realn_rehead_R2.fastq.gz | | TCGA-KK-A8I4-01A | /data/81254692-ee1e-4985-bd0a-4929eed4c620_gdc_realn_rehead_R1.fastq.gz | /data/81254692-ee1e-4985-bd0a-4929eed4c620_gdc_realn_rehead_R2.fastq.gz | -> Do not leave any cell empty in the CSV file. ## Phenotype file From 1d6668878587c26d21d9751fc0f3929f9ebd602b Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 14 Jun 2024 14:55:57 +0200 Subject: [PATCH 302/491] Update nextflow schema order --- nextflow_schema.json | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 9d814605..e8229303 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -543,19 +543,19 @@ }, "allOf": [ { - "$ref": "#/definitions/alignment_options" + "$ref": "#/definitions/input_output_options" }, { - "$ref": "#/definitions/input_output_options" + "$ref": "#/definitions/reference_genome_options" }, { - "$ref": "#/definitions/discovery_options" + "$ref": "#/definitions/read_trimming_options" }, { - "$ref": "#/definitions/reference_genome_options" + "$ref": "#/definitions/alignment_options" }, { - "$ref": "#/definitions/read_trimming_options" + "$ref": "#/definitions/discovery_options" }, { "$ref": "#/definitions/institutional_config_options" From ee159a2ed61b62905e123cd6799d69f13ac724f8 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 14 Jun 2024 15:04:09 +0200 Subject: [PATCH 303/491] Update ouput docs --- docs/output.md | 53 +++++++++++++++++++++++++------------------------- 1 file changed, 27 insertions(+), 26 deletions(-) diff --git a/docs/output.md b/docs/output.md index f20ae72d..aef45d17 100644 --- a/docs/output.md +++ b/docs/output.md @@ -2,45 +2,46 @@ ## Introduction -This documentation describes the output of `nf-core/circrna` for the test dataset which runs all modules in the workflow. +:::warning +This page has not been updated for a long time and might not align with the current pipeline output. We are working on updating it. +If you have questions regarding the pipeline output, feel free to reach out in the [nf-core slack](https://nfcore.slack.com/channels/circrna) channel. +::: -A full run of the workflow will produce the following directory output structure: +This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report generated from the [full-sized test dataset](https://github.com/nf-core/test-datasets/tree/circrna) for the pipeline using a command similar to the one below: -```console -|-- results/ - |-- circrna_discovery - |-- mirna_prediction - |-- multiqc - |-- pipeline_info - |-- quality_control - |-- references +```bash +nextflow run nf-core/circrna -profile test_full, ``` +The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory. + ## Pipeline Overview The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: - Raw read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) - Adapter trimming ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)) -- MultiQC report [`MultiQC`](http://multiqc.info/) -- circRNA quantification -- [`CIRIquant`](https://github.com/Kevinzjy/CIRIquant) -- [`STAR 2-Pass mode`](https://github.com/alexdobin/STAR) - - [`CIRCexplorer2`](https://circexplorer2.readthedocs.io/en/latest/) - - [`circRNA finder`](https://github.com/orzechoj/circRNA_finder) - - [`DCC`](https://github.com/dieterich-lab/DCC) -- [`find circ`](https://github.com/marvin-jens/find_circ) -- [`MapSplice`](http://www.netlab.uky.edu/p/bioinfo/MapSplice2) -- [`Segemehl`](https://www.bioinf.uni-leipzig.de/Software/segemehl/) +- BSJ detection + - [`CIRIquant`](https://github.com/Kevinzjy/CIRIquant) + - [`STAR 2-Pass mode`](https://github.com/alexdobin/STAR) + - [`CIRCexplorer2`](https://circexplorer2.readthedocs.io/en/latest/) + - [`circRNA finder`](https://github.com/orzechoj/circRNA_finder) + - [`DCC`](https://github.com/dieterich-lab/DCC) + - [`find circ`](https://github.com/marvin-jens/find_circ) + - [`MapSplice`](http://www.netlab.uky.edu/p/bioinfo/MapSplice2) + - [`Segemehl`](https://www.bioinf.uni-leipzig.de/Software/segemehl/) - circRNA annotation -- Export mature spliced length as FASTA file -- Annotate parent gene, underlying transcripts. -- circRNA count matrix -- miRNA target prediction +- Extract circRNA sequences and build circular transcriptome +- Merge circular transcriptome with linear transcriptome derived from provided GTF +- Quantification of combined circular and linear transcriptome + - [`psirc-quant`](https://github.com/Christina-hshi/psirc) +- miRNA binding affinity analysis (only if the `mature` parameter is provided) - [`miRanda`](http://cbio.mskcc.org/miRNA2003/miranda.html) - [`TargetScan`](http://www.targetscan.org/cgi-bin/targetscan/data_download.vert72.cgi) - - Filter results, miRNAs must be called by both tools -- Circular - Linear ratio tests ['CircTest'](https://github.com/dieterich-lab/CircTest) +- Statistical tests (only if the `phenotype` parameter is provided) + - [`CircTest`](https://github.com/dieterich-lab/CircTest) +- MultiQC report [`MultiQC`](http://multiqc.info/) + ## Quality Control From ab74eb5e56eadc64ed59f003f7b88d99bf4c0903 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 14 Jun 2024 15:05:40 +0200 Subject: [PATCH 304/491] Prettier --- README.md | 2 +- docs/output.md | 1 - docs/usage.md | 2 +- 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 2c75af9d..e3d02d62 100644 --- a/README.md +++ b/README.md @@ -60,7 +60,6 @@ On release, automated continuous integration tests run the pipeline on a full-si > [!NOTE] > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. - First, prepare a samplesheet with your input data that looks as follows: ```csv title="samplesheet.csv" @@ -68,6 +67,7 @@ sample,fastq_1,fastq_2 CONTROL,CONTROL_R1.fastq.gz,CONTROL_R2.fastq.gz TREATMENT,TREATMENT_R1.fastq.gz,TREATMENT_R2.fastq.gz ``` + Each row represents a fastq file (single-end) or a pair of fastq files (paired end). Now, you can run the pipeline using: diff --git a/docs/output.md b/docs/output.md index aef45d17..fdd9bf48 100644 --- a/docs/output.md +++ b/docs/output.md @@ -42,7 +42,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [`CircTest`](https://github.com/dieterich-lab/CircTest) - MultiQC report [`MultiQC`](http://multiqc.info/) - ## Quality Control ### FastQC diff --git a/docs/usage.md b/docs/usage.md index 0db384c2..137fb841 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -9,6 +9,7 @@ Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration except for parameters; see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). ## Samplesheet input + You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row as shown in the examples below. ```bash @@ -147,7 +148,6 @@ Valid examples for fastq input data in a CSV file is given below: | TCGA-EJ-5518-01A | /data/afbbc370-5970-43d3-b9f8-f40f8e649bb6_gdc_realn_rehead_R1.fastq.gz | /data/afbbc370-5970-43d3-b9f8-f40f8e649bb6_gdc_realn_rehead_R2.fastq.gz | | TCGA-KK-A8I4-01A | /data/81254692-ee1e-4985-bd0a-4929eed4c620_gdc_realn_rehead_R1.fastq.gz | /data/81254692-ee1e-4985-bd0a-4929eed4c620_gdc_realn_rehead_R2.fastq.gz | - ## Phenotype file The CSV file provided via the `phenotype` parameter can be used to provide additional metadata about the samples in the input CSV file. If provided, it needs to at least contain a column called `sample` which corresponds to the `sample` column in the input CSV file and a column called `condition`. The `condition` column will be used to group samples for the [CircTest](https://github.com/dieterich-lab/CircTest) functionality. All metadata columns will be included in the result `SummarizedExperiment` RDS file. From b8474a0fb3e9d296c0bda3e35a953b8d279fc696 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 17 Jun 2024 19:27:35 +0200 Subject: [PATCH 305/491] Add annotations parameter and pass it to the according position --- assets/schema_annotation.json | 32 ++++++++++++++++++++++ main.nf | 2 ++ nextflow.config | 1 + nextflow_schema.json | 11 ++++++++ subworkflows/local/circrna_discovery.nf | 3 +- subworkflows/local/discovery/annotation.nf | 3 ++ workflows/circrna/main.nf | 2 ++ 7 files changed, 53 insertions(+), 1 deletion(-) create mode 100644 assets/schema_annotation.json diff --git a/assets/schema_annotation.json b/assets/schema_annotation.json new file mode 100644 index 00000000..fa0b63db --- /dev/null +++ b/assets/schema_annotation.json @@ -0,0 +1,32 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "$id": "https://raw.githubusercontent.com/nf-core/circrna/master/assets/schema_annotation.json", + "title": "nf-core/circrna pipeline - params.annotation schema", + "description": "Schema for the file provided with params.annotation", + "type": "array", + "items": { + "type": "object", + "properties": { + "name": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Annotation file name must be provided and cannot contain spaces" + }, + "file": { + "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.bed$", + "errorMessage": "Annotation file must be provided and must be a BED file" + }, + "min_overlap": { + "type": "number", + "minimum": 0, + "maximum": 1, + "default": 0.9, + "errorMessage": "Minimum overlap must be a number between 0 and 1" + } + }, + "required": ["name", "file"] + } +} diff --git a/main.nf b/main.nf index 7717ffc7..438b11ec 100644 --- a/main.nf +++ b/main.nf @@ -61,6 +61,7 @@ workflow NFCORE_CIRCRNA { ch_mature = params.mature ? Channel.value([[id: "mature"], file(params.mature, checkIfExists:true)]) : Channel.empty() ch_phenotype = params.phenotype ? Channel.value([[id: "phenotype"], file(params.phenotype, checkIfExists:true)]) : Channel.empty() ch_species = params.phenotype ? Channel.value(params.species_id) : Channel.empty() + ch_annotations = Channel.fromSamplesheet("annotations") CIRCRNA ( ch_samplesheet, @@ -68,6 +69,7 @@ workflow NFCORE_CIRCRNA { ch_fasta, ch_gtf, ch_mature, + ch_annotations, ch_species, ch_versions ) diff --git a/nextflow.config b/nextflow.config index 7fdfaeaa..e2c6308d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -13,6 +13,7 @@ params { input = null outdir = null phenotype = null + annotation = null // workflow options tool = 'circexplorer2' diff --git a/nextflow_schema.json b/nextflow_schema.json index e8229303..c1b06562 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -40,6 +40,17 @@ "description": "Phenotype CSV file specifying the experimental design. If provided, the pipeline will run CIRCTEST.", "help_text": "There are two rules for providing the phenotype CSV file. 1) The 'sample' column must match the sample sheets 'sample' column. 2) The response variable containing the phenotype of primary interest in the experiment must have the column name condition. All other columns included in the file are controlled for in the `DESeq2` design. \n\n| sample \t| condition \t| replicate \t|\n|-----------\t|-----------\t|-----------\t|\n| control_1 \t| ctr \t| 1 \t|\n| control_2 \t| ctr \t| 2 \t|\n| control_3 \t| ctr \t| 3 \t|\n| treated_1 \t| trt \t| 1 \t|\n| treated_2 \t| trt \t| 2 \t|\n| treated_3 \t| trt \t| 3 \t|\n\nThe above phenotype file will identify differentially expressed circRNAs/mRNAs between control and treatment cells, whilst controlling for the effect of variation between replicates: ` ~ replicates + condition`", "fa_icon": "fas fa-file-csv" + }, + "annotation": { + "type": "string", + "format": "file-path", + "exists": true, + "schema": "assets/schema_annotation.json", + "mimetype": "text/csv", + "pattern": "^\\S+\\.csv$", + "description": "Path to a CSV file containing BED files that should be used for annotation.", + "help_text": "The annotation file should be a CSV file with the following columns: `name`, `file` and `min_overlap`. The `name` column should contain a unique identifier for the annotation, the `file` column should contain the path to the BED file and the `min_overlap` column should contain the minimum overlap required for a circRNA to be considered as overlapping with the annotation. The `min_overlap` column is optional and defaults to 0.9 if not provided.", + "fa_icon": "fas fa-file-csv" } } }, diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index a8ae043a..91d6fbcc 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -30,6 +30,7 @@ workflow CIRCRNA_DISCOVERY { chromosomes hisat2_index star_index + ch_annotations bsj_reads tool_filter duplicates_fun @@ -140,7 +141,7 @@ workflow CIRCRNA_DISCOVERY { // ANNOTATION WORKFLOW: // - ANNOTATION( ch_bed_incl_merged, gtf, exon_boundary ) + ANNOTATION( ch_bed_incl_merged, gtf, exon_boundary, ch_annotations ) ch_versions = ch_versions.mix(ANNOTATION.out.versions) // diff --git a/subworkflows/local/discovery/annotation.nf b/subworkflows/local/discovery/annotation.nf index 518260b6..87b2446b 100644 --- a/subworkflows/local/discovery/annotation.nf +++ b/subworkflows/local/discovery/annotation.nf @@ -9,6 +9,7 @@ workflow ANNOTATION { regions gtf exon_boundary + ch_annotations main: ch_versions = Channel.empty() @@ -16,6 +17,8 @@ workflow ANNOTATION { INTERSECT( regions.combine(gtf), [[], []]) ANNOTATE( INTERSECT.out.intersect, exon_boundary ) + ch_annotations.view() + ch_bed_merged = ANNOTATE.out.bed.filter{ meta, bed -> meta.tool == "merged" } ch_gtf_merged = ANNOTATE.out.gtf.filter{ meta, gtf -> meta.tool == "merged" } diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 11783898..6df3470e 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -58,6 +58,7 @@ workflow CIRCRNA { ch_fasta ch_gtf ch_mature + ch_annotations ch_species ch_versions @@ -143,6 +144,7 @@ workflow CIRCRNA { chromosomes, hisat2_index, star_index, + ch_annotations, params.bsj_reads, params.tool_filter, params.duplicates_fun, From 30e28ddbc1bb2ac99ba825b64f905297c187b779 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 17 Jun 2024 19:30:51 +0200 Subject: [PATCH 306/491] Make annotations parameter optional --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index 438b11ec..9d50c5f4 100644 --- a/main.nf +++ b/main.nf @@ -61,7 +61,7 @@ workflow NFCORE_CIRCRNA { ch_mature = params.mature ? Channel.value([[id: "mature"], file(params.mature, checkIfExists:true)]) : Channel.empty() ch_phenotype = params.phenotype ? Channel.value([[id: "phenotype"], file(params.phenotype, checkIfExists:true)]) : Channel.empty() ch_species = params.phenotype ? Channel.value(params.species_id) : Channel.empty() - ch_annotations = Channel.fromSamplesheet("annotations") + ch_annotations = params.annotations ? Channel.fromSamplesheet("annotations") : Channel.empty() CIRCRNA ( ch_samplesheet, From a3f165cb1de9dd43c0409739d710df3cf6fed314 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 17 Jun 2024 19:56:00 +0200 Subject: [PATCH 307/491] Unify annotation naming --- conf/modules.config | 9 --------- main.nf | 4 ++-- subworkflows/local/circrna_discovery.nf | 4 ++-- subworkflows/local/discovery/annotation.nf | 14 +++++++------- workflows/circrna/main.nf | 4 ++-- 5 files changed, 13 insertions(+), 22 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 05169f07..40cfece6 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -562,15 +562,6 @@ process { ext.suffix = {"${meta.tool}.filtered.bed"} } - withName: ANNOTATION { - ext.prefix = { "${meta.id}.${meta.tool}.annotated" } - publishDir = [ - path: { "${params.outdir}/circrna_discovery/${meta.tool}/${meta.id}" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - withName: UPSET_SAMPLES { ext.when = { params.tool.split(',').length > 1 } } diff --git a/main.nf b/main.nf index 9d50c5f4..022b6be8 100644 --- a/main.nf +++ b/main.nf @@ -61,7 +61,7 @@ workflow NFCORE_CIRCRNA { ch_mature = params.mature ? Channel.value([[id: "mature"], file(params.mature, checkIfExists:true)]) : Channel.empty() ch_phenotype = params.phenotype ? Channel.value([[id: "phenotype"], file(params.phenotype, checkIfExists:true)]) : Channel.empty() ch_species = params.phenotype ? Channel.value(params.species_id) : Channel.empty() - ch_annotations = params.annotations ? Channel.fromSamplesheet("annotations") : Channel.empty() + ch_annotation = params.annotation ? Channel.fromSamplesheet("annotation") : Channel.empty() CIRCRNA ( ch_samplesheet, @@ -69,7 +69,7 @@ workflow NFCORE_CIRCRNA { ch_fasta, ch_gtf, ch_mature, - ch_annotations, + ch_annotation, ch_species, ch_versions ) diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 91d6fbcc..2a163ce7 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -30,7 +30,7 @@ workflow CIRCRNA_DISCOVERY { chromosomes hisat2_index star_index - ch_annotations + ch_annotation bsj_reads tool_filter duplicates_fun @@ -141,7 +141,7 @@ workflow CIRCRNA_DISCOVERY { // ANNOTATION WORKFLOW: // - ANNOTATION( ch_bed_incl_merged, gtf, exon_boundary, ch_annotations ) + ANNOTATION( ch_bed_incl_merged, gtf, exon_boundary, ch_annotation ) ch_versions = ch_versions.mix(ANNOTATION.out.versions) // diff --git a/subworkflows/local/discovery/annotation.nf b/subworkflows/local/discovery/annotation.nf index 87b2446b..c9e0dfa8 100644 --- a/subworkflows/local/discovery/annotation.nf +++ b/subworkflows/local/discovery/annotation.nf @@ -1,5 +1,5 @@ include { BEDTOOLS_INTERSECT as INTERSECT } from '../../../modules/nf-core/bedtools/intersect' -include { ANNOTATION as ANNOTATE } from '../../../modules/local/annotation' +include { ANNOTATION as GTF_ANNOTATION } from '../../../modules/local/annotation' include { GNU_SORT as COMBINE_BEDS } from '../../../modules/nf-core/gnu/sort' include { GAWK as REMOVE_SCORE_STRAND } from '../../../modules/nf-core/gawk' include { GNU_SORT as COMBINE_GTFS } from '../../../modules/nf-core/gnu/sort' @@ -9,25 +9,25 @@ workflow ANNOTATION { regions gtf exon_boundary - ch_annotations + ch_annotation main: ch_versions = Channel.empty() INTERSECT( regions.combine(gtf), [[], []]) - ANNOTATE( INTERSECT.out.intersect, exon_boundary ) + GTF_ANNOTATION( INTERSECT.out.intersect, exon_boundary ) - ch_annotations.view() + ch_annotation.view() - ch_bed_merged = ANNOTATE.out.bed.filter{ meta, bed -> meta.tool == "merged" } - ch_gtf_merged = ANNOTATE.out.gtf.filter{ meta, gtf -> meta.tool == "merged" } + ch_bed_merged = GTF_ANNOTATION.out.bed.filter{ meta, bed -> meta.tool == "merged" } + ch_gtf_merged = GTF_ANNOTATION.out.gtf.filter{ meta, gtf -> meta.tool == "merged" } COMBINE_BEDS(ch_bed_merged.map{ meta, bed -> bed}.collect().map{[[id: "annotation"], it]}) REMOVE_SCORE_STRAND( COMBINE_BEDS.out.sorted, []) COMBINE_GTFS(ch_gtf_merged.map{ meta, gtf -> gtf}.collect().map{[[id: "annotation"], it]}) ch_versions = ch_versions.mix(INTERSECT.out.versions) - ch_versions = ch_versions.mix(ANNOTATE.out.versions) + ch_versions = ch_versions.mix(GTF_ANNOTATION.out.versions) ch_versions = ch_versions.mix(COMBINE_BEDS.out.versions) ch_versions = ch_versions.mix(REMOVE_SCORE_STRAND.out.versions) ch_versions = ch_versions.mix(COMBINE_GTFS.out.versions) diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 6df3470e..a16fb752 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -58,7 +58,7 @@ workflow CIRCRNA { ch_fasta ch_gtf ch_mature - ch_annotations + ch_annotation ch_species ch_versions @@ -144,7 +144,7 @@ workflow CIRCRNA { chromosomes, hisat2_index, star_index, - ch_annotations, + ch_annotation, params.bsj_reads, params.tool_filter, params.duplicates_fun, From 706e797de17af356040fcfd8e82d89013b9bc69d Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 18 Jun 2024 10:24:13 +0200 Subject: [PATCH 308/491] First database annotation implementation --- assets/schema_annotation.json | 6 ++-- conf/modules.config | 15 ++++++++++ subworkflows/local/discovery/annotation.nf | 32 ++++++++++++++++------ 3 files changed, 43 insertions(+), 10 deletions(-) diff --git a/assets/schema_annotation.json b/assets/schema_annotation.json index fa0b63db..4158373d 100644 --- a/assets/schema_annotation.json +++ b/assets/schema_annotation.json @@ -10,7 +10,8 @@ "name": { "type": "string", "pattern": "^\\S+$", - "errorMessage": "Annotation file name must be provided and cannot contain spaces" + "errorMessage": "Annotation file name must be provided and cannot contain spaces", + "meta": ["id"] }, "file": { "type": "string", @@ -24,7 +25,8 @@ "minimum": 0, "maximum": 1, "default": 0.9, - "errorMessage": "Minimum overlap must be a number between 0 and 1" + "errorMessage": "Minimum overlap must be a number between 0 and 1", + "meta": ["min_overlap"] } }, "required": ["name", "file"] diff --git a/conf/modules.config b/conf/modules.config index 40cfece6..3929576c 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -575,6 +575,21 @@ process { ext.suffix = "intersect.bed" } + withName: '.*:ANNOTATION:INGEST_DATABASE_NAMES' { + ext.args = { "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \"${meta.id}:\" + \$4, \$5, \$6 }'" } + ext.suffix = "named.bed" + } + + withName: '.*:ANNOTATION:DATABASE_ANNOTATION' { + ext.args = { "-f ${meta.min_overlap} -r -loj" } + ext.suffix = "annotated.bed" + } + + withName: '.*:ANNOTATION:COMBINE_DATABASES' { + ext.args = "-k 1,1 -k2,2n -k3,3n -u" + ext.suffix = "combined.bed" + } + withName: '.*:ANNOTATION:COMBINE_BEDS' { ext.args = "-k 1,1 -k2,2n -k3,3n -u" ext.suffix = "combined.bed" diff --git a/subworkflows/local/discovery/annotation.nf b/subworkflows/local/discovery/annotation.nf index c9e0dfa8..d6277f04 100644 --- a/subworkflows/local/discovery/annotation.nf +++ b/subworkflows/local/discovery/annotation.nf @@ -1,8 +1,11 @@ -include { BEDTOOLS_INTERSECT as INTERSECT } from '../../../modules/nf-core/bedtools/intersect' -include { ANNOTATION as GTF_ANNOTATION } from '../../../modules/local/annotation' -include { GNU_SORT as COMBINE_BEDS } from '../../../modules/nf-core/gnu/sort' -include { GAWK as REMOVE_SCORE_STRAND } from '../../../modules/nf-core/gawk' -include { GNU_SORT as COMBINE_GTFS } from '../../../modules/nf-core/gnu/sort' +include { BEDTOOLS_INTERSECT as INTERSECT } from '../../../modules/nf-core/bedtools/intersect' +include { ANNOTATION as GTF_ANNOTATION } from '../../../modules/local/annotation' +include { GAWK as INGEST_DATABASE_NAMES } from '../../../modules/nf-core/gawk' +include { GNU_SORT as COMBINE_DATABASES } from '../../../modules/nf-core/gnu/sort' +include { BEDTOOLS_INTERSECT as DATABASE_ANNOTATION } from '../../../modules/nf-core/bedtools/intersect' +include { GNU_SORT as COMBINE_BEDS } from '../../../modules/nf-core/gnu/sort' +include { GAWK as REMOVE_SCORE_STRAND } from '../../../modules/nf-core/gawk' +include { GNU_SORT as COMBINE_GTFS } from '../../../modules/nf-core/gnu/sort' workflow ANNOTATION { take: @@ -14,20 +17,33 @@ workflow ANNOTATION { main: ch_versions = Channel.empty() - INTERSECT( regions.combine(gtf), [[], []]) + INTERSECT( regions.combine(gtf), [[], []] ) GTF_ANNOTATION( INTERSECT.out.intersect, exon_boundary ) - ch_annotation.view() - ch_bed_merged = GTF_ANNOTATION.out.bed.filter{ meta, bed -> meta.tool == "merged" } ch_gtf_merged = GTF_ANNOTATION.out.gtf.filter{ meta, gtf -> meta.tool == "merged" } + INGEST_DATABASE_NAMES( ch_annotation, [] ) + DATABASE_ANNOTATION( ch_bed_merged.combine(INGEST_DATABASE_NAMES.out.output) + .map{ meta1, regions, meta2, database -> + [meta1 + [id: "${meta1.id}:${meta2.id}", + sample: meta1.id, + db: meta2.id, + min_overlap: meta2.min_overlap], regions, database] }, + [[], []]) + COMBINE_DATABASES( DATABASE_ANNOTATION.out.intersect + .map{ meta, annotated -> [[id: meta.sample], annotated] } + .groupTuple()) + COMBINE_BEDS(ch_bed_merged.map{ meta, bed -> bed}.collect().map{[[id: "annotation"], it]}) REMOVE_SCORE_STRAND( COMBINE_BEDS.out.sorted, []) COMBINE_GTFS(ch_gtf_merged.map{ meta, gtf -> gtf}.collect().map{[[id: "annotation"], it]}) ch_versions = ch_versions.mix(INTERSECT.out.versions) ch_versions = ch_versions.mix(GTF_ANNOTATION.out.versions) + ch_versions = ch_versions.mix(INGEST_DATABASE_NAMES.out.versions) + ch_versions = ch_versions.mix(COMBINE_DATABASES.out.versions) + ch_versions = ch_versions.mix(DATABASE_ANNOTATION.out.versions) ch_versions = ch_versions.mix(COMBINE_BEDS.out.versions) ch_versions = ch_versions.mix(REMOVE_SCORE_STRAND.out.versions) ch_versions = ch_versions.mix(COMBINE_GTFS.out.versions) From 8ecd3cd9de8d6f6454e702b01245ec2ede9b7fdf Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 18 Jun 2024 10:58:37 +0200 Subject: [PATCH 309/491] Fix per-sample DB annotation --- conf/modules.config | 12 +++++++++--- subworkflows/local/discovery/annotation.nf | 4 +++- 2 files changed, 12 insertions(+), 4 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 3929576c..5ae54e6e 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -576,18 +576,24 @@ process { } withName: '.*:ANNOTATION:INGEST_DATABASE_NAMES' { - ext.args = { "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \"${meta.id}:\" + \$4, \$5, \$6 }'" } + ext.args = { "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \"${meta.id}:\" \$4, \$5, \$6 }'" } ext.suffix = "named.bed" } withName: '.*:ANNOTATION:DATABASE_ANNOTATION' { - ext.args = { "-f ${meta.min_overlap} -r -loj" } + ext.args = { "-f ${meta.min_overlap} -r -loj -wa -wb" } ext.suffix = "annotated.bed" } + withName: '.*:ANNOTATION:CLEAN_DATABASE_ANNOTATION' { + // Keep first 10 columns and the 14th column + ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$4, \$5, \$6, \$7, \$8, \$9, \$10, \$14 }'" + ext.suffix = "cleaned_db.bed" + } + withName: '.*:ANNOTATION:COMBINE_DATABASES' { ext.args = "-k 1,1 -k2,2n -k3,3n -u" - ext.suffix = "combined.bed" + ext.suffix = "combined_dbs.bed" } withName: '.*:ANNOTATION:COMBINE_BEDS' { diff --git a/subworkflows/local/discovery/annotation.nf b/subworkflows/local/discovery/annotation.nf index d6277f04..c3e55b55 100644 --- a/subworkflows/local/discovery/annotation.nf +++ b/subworkflows/local/discovery/annotation.nf @@ -3,6 +3,7 @@ include { ANNOTATION as GTF_ANNOTATION } from '../../../modules/loc include { GAWK as INGEST_DATABASE_NAMES } from '../../../modules/nf-core/gawk' include { GNU_SORT as COMBINE_DATABASES } from '../../../modules/nf-core/gnu/sort' include { BEDTOOLS_INTERSECT as DATABASE_ANNOTATION } from '../../../modules/nf-core/bedtools/intersect' +include { GAWK as CLEAN_DATABASE_ANNOTATION } from '../../../modules/nf-core/gawk' include { GNU_SORT as COMBINE_BEDS } from '../../../modules/nf-core/gnu/sort' include { GAWK as REMOVE_SCORE_STRAND } from '../../../modules/nf-core/gawk' include { GNU_SORT as COMBINE_GTFS } from '../../../modules/nf-core/gnu/sort' @@ -31,7 +32,8 @@ workflow ANNOTATION { db: meta2.id, min_overlap: meta2.min_overlap], regions, database] }, [[], []]) - COMBINE_DATABASES( DATABASE_ANNOTATION.out.intersect + CLEAN_DATABASE_ANNOTATION( DATABASE_ANNOTATION.out.intersect, [] ) + COMBINE_DATABASES( CLEAN_DATABASE_ANNOTATION.out.output .map{ meta, annotated -> [[id: meta.sample], annotated] } .groupTuple()) From 6a97b0ccd3707152f075b42216fd0eead9f5bbce Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 18 Jun 2024 11:43:47 +0200 Subject: [PATCH 310/491] Change database intersection strategy --- conf/modules.config | 15 +------ modules/local/annotation/main.nf | 2 +- .../local/annotation/templates/annotation.py | 2 +- subworkflows/local/discovery/annotation.nf | 40 +++++++++---------- 4 files changed, 23 insertions(+), 36 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 5ae54e6e..307ea313 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -570,7 +570,7 @@ process { ext.when = { params.tool.split(',').length > 1 } } - withName: '.*:ANNOTATION:INTERSECT' { + withName: '.*:ANNOTATION:INTERSECT_GTF' { ext.args = "-loj" ext.suffix = "intersect.bed" } @@ -580,22 +580,11 @@ process { ext.suffix = "named.bed" } - withName: '.*:ANNOTATION:DATABASE_ANNOTATION' { + withName: '.*:ANNOTATION:INTERSECT_DATABASE' { ext.args = { "-f ${meta.min_overlap} -r -loj -wa -wb" } ext.suffix = "annotated.bed" } - withName: '.*:ANNOTATION:CLEAN_DATABASE_ANNOTATION' { - // Keep first 10 columns and the 14th column - ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$4, \$5, \$6, \$7, \$8, \$9, \$10, \$14 }'" - ext.suffix = "cleaned_db.bed" - } - - withName: '.*:ANNOTATION:COMBINE_DATABASES' { - ext.args = "-k 1,1 -k2,2n -k3,3n -u" - ext.suffix = "combined_dbs.bed" - } - withName: '.*:ANNOTATION:COMBINE_BEDS' { ext.args = "-k 1,1 -k2,2n -k3,3n -u" ext.suffix = "combined.bed" diff --git a/modules/local/annotation/main.nf b/modules/local/annotation/main.nf index a5b6d77a..c06f03b9 100644 --- a/modules/local/annotation/main.nf +++ b/modules/local/annotation/main.nf @@ -8,7 +8,7 @@ process ANNOTATION { 'biocontainers/pandas:1.5.2' }" input: - tuple val(meta), path(intersection) + tuple val(meta), path(gtf_intersection), path(db_intersections) val(exon_boundary) output: diff --git a/modules/local/annotation/templates/annotation.py b/modules/local/annotation/templates/annotation.py index 6cd1d68d..f45e3ae8 100755 --- a/modules/local/annotation/templates/annotation.py +++ b/modules/local/annotation/templates/annotation.py @@ -41,7 +41,7 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: exon_boundary = int("${exon_boundary}") -df = pd.read_csv("${intersection}", sep="\\t", header=None, usecols=columns.keys()) +df = pd.read_csv("${gtf_intersection}", sep="\\t", header=None, usecols=columns.keys()) df = df.rename(columns=columns) # Extract circRNAs without match diff --git a/subworkflows/local/discovery/annotation.nf b/subworkflows/local/discovery/annotation.nf index c3e55b55..88cc5c76 100644 --- a/subworkflows/local/discovery/annotation.nf +++ b/subworkflows/local/discovery/annotation.nf @@ -1,8 +1,8 @@ -include { BEDTOOLS_INTERSECT as INTERSECT } from '../../../modules/nf-core/bedtools/intersect' -include { ANNOTATION as GTF_ANNOTATION } from '../../../modules/local/annotation' +include { BEDTOOLS_INTERSECT as INTERSECT_GTF } from '../../../modules/nf-core/bedtools/intersect' +include { ANNOTATION as ANNOTATE } from '../../../modules/local/annotation' include { GAWK as INGEST_DATABASE_NAMES } from '../../../modules/nf-core/gawk' include { GNU_SORT as COMBINE_DATABASES } from '../../../modules/nf-core/gnu/sort' -include { BEDTOOLS_INTERSECT as DATABASE_ANNOTATION } from '../../../modules/nf-core/bedtools/intersect' +include { BEDTOOLS_INTERSECT as INTERSECT_DATABASE } from '../../../modules/nf-core/bedtools/intersect' include { GAWK as CLEAN_DATABASE_ANNOTATION } from '../../../modules/nf-core/gawk' include { GNU_SORT as COMBINE_BEDS } from '../../../modules/nf-core/gnu/sort' include { GAWK as REMOVE_SCORE_STRAND } from '../../../modules/nf-core/gawk' @@ -18,34 +18,32 @@ workflow ANNOTATION { main: ch_versions = Channel.empty() - INTERSECT( regions.combine(gtf), [[], []] ) - GTF_ANNOTATION( INTERSECT.out.intersect, exon_boundary ) - - ch_bed_merged = GTF_ANNOTATION.out.bed.filter{ meta, bed -> meta.tool == "merged" } - ch_gtf_merged = GTF_ANNOTATION.out.gtf.filter{ meta, gtf -> meta.tool == "merged" } - + INTERSECT_GTF( regions.combine(gtf), [[], []] ) INGEST_DATABASE_NAMES( ch_annotation, [] ) - DATABASE_ANNOTATION( ch_bed_merged.combine(INGEST_DATABASE_NAMES.out.output) + INTERSECT_DATABASE( regions.combine(INGEST_DATABASE_NAMES.out.output) .map{ meta1, regions, meta2, database -> - [meta1 + [id: "${meta1.id}:${meta2.id}", - sample: meta1.id, - db: meta2.id, + [[id: "${meta1.id}:${meta2.id}", + original_meta: meta1, min_overlap: meta2.min_overlap], regions, database] }, [[], []]) - CLEAN_DATABASE_ANNOTATION( DATABASE_ANNOTATION.out.intersect, [] ) - COMBINE_DATABASES( CLEAN_DATABASE_ANNOTATION.out.output - .map{ meta, annotated -> [[id: meta.sample], annotated] } - .groupTuple()) + + ANNOTATE( INTERSECT_GTF.out.intersect + .join(INTERSECT_DATABASE.out.intersect + .map{ meta, bed -> [meta.original_meta, bed] } + .groupTuple()), + exon_boundary ) + + ch_bed_merged = ANNOTATE.out.bed.filter{ meta, bed -> meta.tool == "merged" } + ch_gtf_merged = ANNOTATE.out.gtf.filter{ meta, gtf -> meta.tool == "merged" } COMBINE_BEDS(ch_bed_merged.map{ meta, bed -> bed}.collect().map{[[id: "annotation"], it]}) REMOVE_SCORE_STRAND( COMBINE_BEDS.out.sorted, []) COMBINE_GTFS(ch_gtf_merged.map{ meta, gtf -> gtf}.collect().map{[[id: "annotation"], it]}) - ch_versions = ch_versions.mix(INTERSECT.out.versions) - ch_versions = ch_versions.mix(GTF_ANNOTATION.out.versions) + ch_versions = ch_versions.mix(INTERSECT_GTF.out.versions) ch_versions = ch_versions.mix(INGEST_DATABASE_NAMES.out.versions) - ch_versions = ch_versions.mix(COMBINE_DATABASES.out.versions) - ch_versions = ch_versions.mix(DATABASE_ANNOTATION.out.versions) + ch_versions = ch_versions.mix(INTERSECT_DATABASE.out.versions) + ch_versions = ch_versions.mix(ANNOTATE.out.versions) ch_versions = ch_versions.mix(COMBINE_BEDS.out.versions) ch_versions = ch_versions.mix(REMOVE_SCORE_STRAND.out.versions) ch_versions = ch_versions.mix(COMBINE_GTFS.out.versions) From b511c0cf24df8958c29dd6ef3ca12066ab823f8e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 18 Jun 2024 11:52:14 +0200 Subject: [PATCH 311/491] Make sure databases are optional --- subworkflows/local/discovery/annotation.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/discovery/annotation.nf b/subworkflows/local/discovery/annotation.nf index 88cc5c76..7c9801b6 100644 --- a/subworkflows/local/discovery/annotation.nf +++ b/subworkflows/local/discovery/annotation.nf @@ -30,7 +30,8 @@ workflow ANNOTATION { ANNOTATE( INTERSECT_GTF.out.intersect .join(INTERSECT_DATABASE.out.intersect .map{ meta, bed -> [meta.original_meta, bed] } - .groupTuple()), + .groupTuple(), remainder: true) + .map{ meta, gtf_intersection, db_intersections -> [meta, gtf_intersection, db_intersections ?: []]}, exon_boundary ) ch_bed_merged = ANNOTATE.out.bed.filter{ meta, bed -> meta.tool == "merged" } From b4c2f4969a9b5af012bd029bd7ad4b2091c859b4 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 18 Jun 2024 12:31:46 +0200 Subject: [PATCH 312/491] Add db annotation to annotation python script --- modules/local/annotation/templates/annotation.py | 11 +++++++++++ subworkflows/local/discovery/annotation.nf | 2 +- 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/modules/local/annotation/templates/annotation.py b/modules/local/annotation/templates/annotation.py index f45e3ae8..479980b1 100755 --- a/modules/local/annotation/templates/annotation.py +++ b/modules/local/annotation/templates/annotation.py @@ -107,6 +107,17 @@ def determine_type(row): df = pd.concat([df, df_intergenic], axis=0) +db_colnames = ['chr', 'start', 'end', 'name', 'score', 'strand', 'db_chr', 'db_start', 'db_end', 'db_name', 'db_score', 'db_strand'] +db_usecols = ['chr', 'start', 'end', 'name', 'score', 'strand', 'db_name'] +df_databases = pd.concat([pd.read_csv(db_path, sep="\\t", header=0, names=db_colnames, usecols=db_usecols) for db_path in "${db_intersections}".split()]) + +# Group by chr, start, end, name, score, strand, and aggregate the db_name to csv string +df_databases = df_databases.groupby(['chr', 'start', 'end', 'name', 'score', 'strand']).aggregate({ + 'db_name': lambda x: ",".join(x) if len(x) > 0 else "." +}) + +df = df.merge(df_databases, how='left', on=['chr', 'start', 'end', 'name', 'score', 'strand']) + # Sort by chr, start, end df = df.sort_values(['chr', 'start', 'end']) diff --git a/subworkflows/local/discovery/annotation.nf b/subworkflows/local/discovery/annotation.nf index 7c9801b6..da2c7b99 100644 --- a/subworkflows/local/discovery/annotation.nf +++ b/subworkflows/local/discovery/annotation.nf @@ -22,7 +22,7 @@ workflow ANNOTATION { INGEST_DATABASE_NAMES( ch_annotation, [] ) INTERSECT_DATABASE( regions.combine(INGEST_DATABASE_NAMES.out.output) .map{ meta1, regions, meta2, database -> - [[id: "${meta1.id}:${meta2.id}", + [[id: "${meta1.id}-${meta2.id}", original_meta: meta1, min_overlap: meta2.min_overlap], regions, database] }, [[], []]) From cbaf4fd8053c8ca8d0dee20691fafdc48ec0bc76 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 18 Jun 2024 12:56:44 +0200 Subject: [PATCH 313/491] Fix first row length bug --- conf/modules.config | 2 +- modules/local/annotation/templates/annotation.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 307ea313..ab9245e2 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -596,7 +596,7 @@ process { } withName: '.*:ANNOTATION:REMOVE_SCORE_STRAND' { - ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3, \".\", \".\", \$7, \$8, \$9, \$10 }'" + ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3, \".\", \".\", \$7, \$8, \$9, \$10, \$11 }'" ext.suffix = "tidy.bed" } diff --git a/modules/local/annotation/templates/annotation.py b/modules/local/annotation/templates/annotation.py index 479980b1..9bb3519d 100755 --- a/modules/local/annotation/templates/annotation.py +++ b/modules/local/annotation/templates/annotation.py @@ -109,7 +109,7 @@ def determine_type(row): db_colnames = ['chr', 'start', 'end', 'name', 'score', 'strand', 'db_chr', 'db_start', 'db_end', 'db_name', 'db_score', 'db_strand'] db_usecols = ['chr', 'start', 'end', 'name', 'score', 'strand', 'db_name'] -df_databases = pd.concat([pd.read_csv(db_path, sep="\\t", header=0, names=db_colnames, usecols=db_usecols) for db_path in "${db_intersections}".split()]) +df_databases = pd.concat([pd.read_csv(db_path, sep="\\t", names=db_colnames, usecols=db_usecols) for db_path in "${db_intersections}".split()]) # Group by chr, start, end, name, score, strand, and aggregate the db_name to csv string df_databases = df_databases.groupby(['chr', 'start', 'end', 'name', 'score', 'strand']).aggregate({ From 8999212aae6026c51d0d9d5da08f1133b6a9d5f7 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 18 Jun 2024 13:13:10 +0200 Subject: [PATCH 314/491] Make sure annotation input is optional --- .../local/annotation/templates/annotation.py | 26 ++++++++++++------- 1 file changed, 17 insertions(+), 9 deletions(-) diff --git a/modules/local/annotation/templates/annotation.py b/modules/local/annotation/templates/annotation.py index 9bb3519d..91121d78 100755 --- a/modules/local/annotation/templates/annotation.py +++ b/modules/local/annotation/templates/annotation.py @@ -107,16 +107,24 @@ def determine_type(row): df = pd.concat([df, df_intergenic], axis=0) -db_colnames = ['chr', 'start', 'end', 'name', 'score', 'strand', 'db_chr', 'db_start', 'db_end', 'db_name', 'db_score', 'db_strand'] -db_usecols = ['chr', 'start', 'end', 'name', 'score', 'strand', 'db_name'] -df_databases = pd.concat([pd.read_csv(db_path, sep="\\t", names=db_colnames, usecols=db_usecols) for db_path in "${db_intersections}".split()]) +db_intersections = "${db_intersections}".split() +has_db = len(db_intersections) > 0 -# Group by chr, start, end, name, score, strand, and aggregate the db_name to csv string -df_databases = df_databases.groupby(['chr', 'start', 'end', 'name', 'score', 'strand']).aggregate({ - 'db_name': lambda x: ",".join(x) if len(x) > 0 else "." -}) +if has_db: + db_colnames = ['chr', 'start', 'end', 'name', 'score', 'strand', 'db_chr', 'db_start', 'db_end', 'db_name', 'db_score', 'db_strand'] + db_usecols = ['chr', 'start', 'end', 'name', 'score', 'strand', 'db_name'] + df_databases = pd.concat([pd.read_csv(db_path, sep="\\t", names=db_colnames, usecols=db_usecols) for db_path in db_intersections]) + + # Group by chr, start, end, name, score, strand, and aggregate the db_name to list + df_databases = df_databases.groupby(['chr', 'start', 'end', 'name', 'score', 'strand']).aggregate({ + 'db_name': lambda x: ",".join([val for val in x if val != '.']) + }) + + df_databases['db_name'] = df_databases['db_name'].apply(lambda x: x if x else '.') -df = df.merge(df_databases, how='left', on=['chr', 'start', 'end', 'name', 'score', 'strand']) + df = df.merge(df_databases, how='left', on=['chr', 'start', 'end', 'name', 'score', 'strand']) +else: + df['db_name'] = "." # Sort by chr, start, end df = df.sort_values(['chr', 'start', 'end']) @@ -126,7 +134,7 @@ def determine_type(row): # Convert to GTF df['source'] = 'circRNA' df['frame'] = '.' -df['attributes'] = 'gene_id "' + df['gene_id'] + '"; gene_name "' + df['gene_name'] + '"; transcript_id "circ_' + df['name'] + '";' +df['attributes'] = 'gene_id "' + df['gene_id'] + '"; gene_name "' + df['gene_name'] + '"; transcript_id "circ_' + df['name'] + '"; db_ids "' + df['db_name'] + '";' gtf_order = ['chr', 'source', 'type', 'start', 'end', 'score', 'strand', 'frame', 'attributes'] df = df[gtf_order] From fab59a31e6af998289be2681447aaf463d472099 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Wed, 19 Jun 2024 09:30:19 +0200 Subject: [PATCH 315/491] Use psirc bioconda package --- modules/local/psirc/index/environment.yml | 6 ++++++ modules/local/psirc/index/main.nf | 8 +++++--- modules/local/psirc/quant/environment.yml | 6 ++++++ modules/local/psirc/quant/main.nf | 8 +++++--- 4 files changed, 22 insertions(+), 6 deletions(-) create mode 100644 modules/local/psirc/index/environment.yml create mode 100644 modules/local/psirc/quant/environment.yml diff --git a/modules/local/psirc/index/environment.yml b/modules/local/psirc/index/environment.yml new file mode 100644 index 00000000..e0303603 --- /dev/null +++ b/modules/local/psirc/index/environment.yml @@ -0,0 +1,6 @@ +name: psirc_index +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::psirc=1.0.0 diff --git a/modules/local/psirc/index/main.nf b/modules/local/psirc/index/main.nf index 7c10a533..b975d414 100644 --- a/modules/local/psirc/index/main.nf +++ b/modules/local/psirc/index/main.nf @@ -2,7 +2,10 @@ process PSIRC_INDEX { tag "${meta.id}" label 'process_high' - container "registry.hub.docker.com/bigdatainbiomedicine/psirc" + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/psirc:1.0.0--he1fd2f9_0' : + 'biocontainers/psirc:1.0.0--he1fd2f9_0' }" input: tuple val(meta), path(fasta) @@ -12,13 +15,12 @@ process PSIRC_INDEX { path "versions.yml", emit: versions script: - def VERSION = '1.0' """ psirc-quant index -i psirc.index --make-unique $fasta cat <<-END_VERSIONS > versions.yml "${task.process}": - psirc-quant: $VERSION + psirc-quant: \$(psirc-quant version | sed -n 's/^psirc-quant, version \\([0-9.]*\\).*$/\\1/p') END_VERSIONS """ } diff --git a/modules/local/psirc/quant/environment.yml b/modules/local/psirc/quant/environment.yml new file mode 100644 index 00000000..222b4e89 --- /dev/null +++ b/modules/local/psirc/quant/environment.yml @@ -0,0 +1,6 @@ +name: psirc_quant +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::psirc=1.0.0 diff --git a/modules/local/psirc/quant/main.nf b/modules/local/psirc/quant/main.nf index edecc8f9..20cddf32 100644 --- a/modules/local/psirc/quant/main.nf +++ b/modules/local/psirc/quant/main.nf @@ -2,7 +2,10 @@ process PSIRC_QUANT { tag "${meta.id}" label 'process_high' - container "registry.hub.docker.com/bigdatainbiomedicine/psirc" + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/psirc:1.0.0--he1fd2f9_0' : + 'biocontainers/psirc:1.0.0--he1fd2f9_0' }" input: tuple val(meta), path(reads) @@ -19,13 +22,12 @@ process PSIRC_QUANT { def single_end = meta.single_end ? "--single -l 76 -s 20" : "" def genomebam = gtf ? "--genomebam -g $gtf" : "" def chromosomes = chrom_sizes ? "-c $chrom_sizes" : "" - def VERSION = '1.0' """ psirc-quant quant -t $task.cpus -i $index -o $meta.id $single_end $reads -b $bootstrap_samples $genomebam $chromosomes cat <<-END_VERSIONS > versions.yml "${task.process}": - psirc-quant: $VERSION + psirc-quant: \$(psirc-quant version | sed -n 's/^psirc-quant, version \\([0-9.]*\\).*$/\\1/p') END_VERSIONS """ } From 8311bab8356d2e825d1412172d089929556bef57 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Wed, 19 Jun 2024 09:35:14 +0200 Subject: [PATCH 316/491] Escape problematic $ --- modules/local/psirc/quant/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/psirc/quant/main.nf b/modules/local/psirc/quant/main.nf index 20cddf32..862e9ccd 100644 --- a/modules/local/psirc/quant/main.nf +++ b/modules/local/psirc/quant/main.nf @@ -27,7 +27,7 @@ process PSIRC_QUANT { cat <<-END_VERSIONS > versions.yml "${task.process}": - psirc-quant: \$(psirc-quant version | sed -n 's/^psirc-quant, version \\([0-9.]*\\).*$/\\1/p') + psirc-quant: \$(psirc-quant version | sed -n 's/^psirc-quant, version \\([0-9.]*\\).*\$/\\1/p') END_VERSIONS """ } From 9b57e7f2caab961aa3c1eab2169cda93cf1ba8e9 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Wed, 19 Jun 2024 09:41:11 +0200 Subject: [PATCH 317/491] Fix problematic $ also in psirc index --- modules/local/psirc/index/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/psirc/index/main.nf b/modules/local/psirc/index/main.nf index b975d414..c0cae596 100644 --- a/modules/local/psirc/index/main.nf +++ b/modules/local/psirc/index/main.nf @@ -20,7 +20,7 @@ process PSIRC_INDEX { cat <<-END_VERSIONS > versions.yml "${task.process}": - psirc-quant: \$(psirc-quant version | sed -n 's/^psirc-quant, version \\([0-9.]*\\).*$/\\1/p') + psirc-quant: \$(psirc-quant version | sed -n 's/^psirc-quant, version \\([0-9.]*\\).*\$/\\1/p') END_VERSIONS """ } From fbabe351540646c7d8796e07d9df46e88d255031 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sun, 23 Jun 2024 08:59:16 +0200 Subject: [PATCH 318/491] Implement GTF filtering --- conf/modules.config | 4 + modules/local/gtf_filter/main.nf | 24 +++++ .../local/gtf_filter/templates/gtf_filter.py | 94 +++++++++++++++++++ subworkflows/local/prepare_genome.nf | 24 +++-- workflows/circrna/main.nf | 1 + 5 files changed, 138 insertions(+), 9 deletions(-) create mode 100644 modules/local/gtf_filter/main.nf create mode 100644 modules/local/gtf_filter/templates/gtf_filter.py diff --git a/conf/modules.config b/conf/modules.config index ab9245e2..0885b37e 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -70,6 +70,10 @@ process { ] } + withName: GTF_FILTER { + ext.suffix = "filtered.gtf" + } + withName: SEQKIT_SPLIT { ext.args = "-i --by-id-prefix \"\"" publishDir = [ diff --git a/modules/local/gtf_filter/main.nf b/modules/local/gtf_filter/main.nf new file mode 100644 index 00000000..4606b97e --- /dev/null +++ b/modules/local/gtf_filter/main.nf @@ -0,0 +1,24 @@ +process GTF_FILTER { + tag "$fasta" + + conda "conda-forge::python=3.9.5" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/python:3.9--1' : + 'biocontainers/python:3.9--1' }" + + input: + tuple val(meta), path(fasta) + tuple val(meta2), path(gtf) + + output: + tuple val(meta), path("${prefix}.${suffix}"), emit: filtered + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + prefix = task.ext.prefix ?: meta.id + suffix = task.ext.suffix ?: "gtf" + template 'gtf_filter.py' +} diff --git a/modules/local/gtf_filter/templates/gtf_filter.py b/modules/local/gtf_filter/templates/gtf_filter.py new file mode 100644 index 00000000..f82d8055 --- /dev/null +++ b/modules/local/gtf_filter/templates/gtf_filter.py @@ -0,0 +1,94 @@ +#!/usr/bin/env python + +# Written by Olga Botvinnik with subsequent reworking by Jonathan Manning and Nico Trummer. +# Released under the MIT license. + +import logging +import re +import statistics +import platform +from typing import Set + +# Create a logger +logging.basicConfig(format="%(name)s - %(asctime)s %(levelname)s: %(message)s") +logger = logging.getLogger("fasta_gtf_filter") +logger.setLevel(logging.INFO) + +def format_yaml_like(data: dict, indent: int = 0) -> str: + """Formats a dictionary to a YAML-like string. + + Args: + data (dict): The dictionary to format. + indent (int): The current indentation level. + + Returns: + str: A string formatted as YAML. + """ + yaml_str = "" + for key, value in data.items(): + spaces = " " * indent + if isinstance(value, dict): + yaml_str += f"{spaces}{key}:\\n{format_yaml_like(value, indent + 1)}" + else: + yaml_str += f"{spaces}{key}: {value}\\n" + return yaml_str + + +def extract_fasta_seq_names(fasta_name: str) -> Set[str]: + """Extracts the sequence names from a FASTA file.""" + with open(fasta_name) as fasta: + return {line[1:].split(None, 1)[0] for line in fasta if line.startswith(">")} + + +def tab_delimited(file: str) -> float: + """Check if file is tab-delimited and return median number of tabs.""" + with open(file, "r") as f: + data = f.read(102400) + return statistics.median(line.count("\t") for line in data.split("\n")) + + +def filter_gtf(fasta: str, gtf_in: str, filtered_gtf_out: str, skip_transcript_id_check: bool) -> None: + """Filter GTF file based on FASTA sequence names.""" + if tab_delimited(gtf_in) != 8: + raise ValueError("Invalid GTF file: Expected 9 tab-separated columns.") + + seq_names_in_genome = extract_fasta_seq_names(fasta) + logger.info(f"Extracted chromosome sequence names from {fasta}") + logger.debug("All sequence IDs from FASTA: " + ", ".join(sorted(seq_names_in_genome))) + + seq_names_in_gtf = set() + try: + with open(gtf_in) as gtf, open(filtered_gtf_out, "w") as out: + line_count = 0 + for line in gtf: + seq_name = line.split("\t")[0] + seq_names_in_gtf.add(seq_name) # Add sequence name to the set + + if seq_name in seq_names_in_genome: + if skip_transcript_id_check or re.search(r'transcript_id "([^"]+)"', line): + out.write(line) + line_count += 1 + + if line_count == 0: + raise ValueError("All GTF lines removed by filters") + + except IOError as e: + logger.error(f"File operation failed: {e}") + return + + logger.debug("All sequence IDs from GTF: " + ", ".join(sorted(seq_names_in_gtf))) + logger.info(f"Extracted {line_count} matching sequences from {gtf_in} into {filtered_gtf_out}") + + +filter_gtf("${fasta}", "${gtf}", "${prefix}.${suffix}", False) + +# Versions + +versions = { + "${task.process}": { + "python": platform.python_version() + } +} + +with open("versions.yml", "w") as f: + f.write(format_yaml_like(versions)) diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 473d314b..715ce125 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -1,12 +1,13 @@ -include { SEQKIT_SPLIT } from '../../modules/local/seqkit/split' -include { BOWTIE_BUILD } from '../../modules/nf-core/bowtie/build' -include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build' -include { BWA_INDEX } from '../../modules/nf-core/bwa/index' +include { GTF_FILTER } from '../../modules/local/gtf_filter' +include { SEQKIT_SPLIT } from '../../modules/local/seqkit/split' +include { BOWTIE_BUILD } from '../../modules/nf-core/bowtie/build' +include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build' +include { BWA_INDEX } from '../../modules/nf-core/bwa/index' include { HISAT2_EXTRACTSPLICESITES } from '../../modules/nf-core/hisat2/extractsplicesites' -include { HISAT2_BUILD } from '../../modules/nf-core/hisat2/build' -include { STAR_GENOMEGENERATE } from '../../modules/nf-core/star/genomegenerate' -include { GAWK as CLEAN_FASTA } from '../../modules/nf-core/gawk' -include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx' +include { HISAT2_BUILD } from '../../modules/nf-core/hisat2/build' +include { STAR_GENOMEGENERATE } from '../../modules/nf-core/star/genomegenerate' +include { GAWK as CLEAN_FASTA } from '../../modules/nf-core/gawk' +include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx' workflow PREPARE_GENOME { @@ -26,6 +27,9 @@ workflow PREPARE_GENOME { ch_versions = ch_versions.mix(CLEAN_FASTA.out.versions) } + GTF_FILTER(ch_fasta, ch_gtf) + ch_gtf = GTF_FILTER.out.filtered + SEQKIT_SPLIT(ch_fasta) BOWTIE_BUILD(ch_fasta.map{ meta, fasta -> fasta }) @@ -43,7 +47,8 @@ workflow PREPARE_GENOME { SAMTOOLS_FAIDX(ch_fasta, [[], []]) // Collect versions - ch_versions = ch_versions.mix(SEQKIT_SPLIT.out.versions, + ch_versions = ch_versions.mix(GTF_FILTER.out.versions, + SEQKIT_SPLIT.out.versions, BOWTIE_BUILD.out.versions, BOWTIE2_BUILD.out.versions, BWA_INDEX.out.versions, @@ -53,6 +58,7 @@ workflow PREPARE_GENOME { SAMTOOLS_FAIDX.out.versions) emit: + gtf = ch_gtf faidx = SAMTOOLS_FAIDX.out.fai bowtie = params.bowtie ?: BOWTIE_BUILD.out.index bowtie2 = params.bowtie2 ? Channel.value([[id: "bowtie2"], file(params.bowtie2, checkIfExists: true)]) : BOWTIE2_BUILD.out.index.collect() diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index a16fb752..0d852ae7 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -112,6 +112,7 @@ workflow CIRCRNA { ch_gtf ) + ch_gtf = PREPARE_GENOME.out.gtf bowtie_index = PREPARE_GENOME.out.bowtie bowtie2_index = PREPARE_GENOME.out.bowtie2 bwa_index = PREPARE_GENOME.out.bwa From 15ffbb0338116ce06a494717d93e4f1905df90a2 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sun, 23 Jun 2024 09:02:14 +0200 Subject: [PATCH 319/491] Escape backslashes --- modules/local/gtf_filter/templates/gtf_filter.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/gtf_filter/templates/gtf_filter.py b/modules/local/gtf_filter/templates/gtf_filter.py index f82d8055..20343cef 100644 --- a/modules/local/gtf_filter/templates/gtf_filter.py +++ b/modules/local/gtf_filter/templates/gtf_filter.py @@ -44,7 +44,7 @@ def tab_delimited(file: str) -> float: """Check if file is tab-delimited and return median number of tabs.""" with open(file, "r") as f: data = f.read(102400) - return statistics.median(line.count("\t") for line in data.split("\n")) + return statistics.median(line.count("\\t") for line in data.split("\\n")) def filter_gtf(fasta: str, gtf_in: str, filtered_gtf_out: str, skip_transcript_id_check: bool) -> None: @@ -61,7 +61,7 @@ def filter_gtf(fasta: str, gtf_in: str, filtered_gtf_out: str, skip_transcript_i with open(gtf_in) as gtf, open(filtered_gtf_out, "w") as out: line_count = 0 for line in gtf: - seq_name = line.split("\t")[0] + seq_name = line.split("\\t")[0] seq_names_in_gtf.add(seq_name) # Add sequence name to the set if seq_name in seq_names_in_genome: From 50226e88623c85f61d51ecd624363680df5842d5 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 24 Jun 2024 09:56:12 +0200 Subject: [PATCH 320/491] Fix pandas references --- modules/local/annotation/environment.yml | 5 +++++ modules/local/annotation/main.nf | 2 +- modules/local/count_matrix/merge_tools/environment.yml | 5 +++++ modules/local/count_matrix/merge_tools/main.nf | 2 +- 4 files changed, 12 insertions(+), 2 deletions(-) create mode 100644 modules/local/annotation/environment.yml create mode 100644 modules/local/count_matrix/merge_tools/environment.yml diff --git a/modules/local/annotation/environment.yml b/modules/local/annotation/environment.yml new file mode 100644 index 00000000..8c311352 --- /dev/null +++ b/modules/local/annotation/environment.yml @@ -0,0 +1,5 @@ +name: annotation +channels: + - conda-forge +dependencies: + - pandas=1.5.2 diff --git a/modules/local/annotation/main.nf b/modules/local/annotation/main.nf index c06f03b9..1f20cc72 100644 --- a/modules/local/annotation/main.nf +++ b/modules/local/annotation/main.nf @@ -2,7 +2,7 @@ process ANNOTATION { tag "$meta.id:$meta.tool" label 'process_single' - conda "bioconda::pandas=1.5.2" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : 'biocontainers/pandas:1.5.2' }" diff --git a/modules/local/count_matrix/merge_tools/environment.yml b/modules/local/count_matrix/merge_tools/environment.yml new file mode 100644 index 00000000..796e68fc --- /dev/null +++ b/modules/local/count_matrix/merge_tools/environment.yml @@ -0,0 +1,5 @@ +name: merge_tools +channels: + - conda-forge +dependencies: + - pandas=1.5.2 diff --git a/modules/local/count_matrix/merge_tools/main.nf b/modules/local/count_matrix/merge_tools/main.nf index dc80f483..cdd3f2c0 100644 --- a/modules/local/count_matrix/merge_tools/main.nf +++ b/modules/local/count_matrix/merge_tools/main.nf @@ -2,7 +2,7 @@ process MERGE_TOOLS { tag "$meta.id" label "process_single" - conda "bioconda::pandas=1.5.2" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : 'biocontainers/pandas:1.5.2' }" From 81adab0398e3e530234b98675a3bcd34ccd58af3 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 24 Jun 2024 10:13:34 +0200 Subject: [PATCH 321/491] Remove problematic r-base singularity image --- modules/local/circtest/prepare/main.nf | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/modules/local/circtest/prepare/main.nf b/modules/local/circtest/prepare/main.nf index e41b6c46..bfc32b4e 100644 --- a/modules/local/circtest/prepare/main.nf +++ b/modules/local/circtest/prepare/main.nf @@ -2,9 +2,7 @@ process CIRCTEST_PREPARE { label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/biocontainers/r-base:4.2.1' : - 'biocontainers/r-base:4.2.1' }" + container "biocontainers/r-base:4.2.1" input: tuple val(meta), path(circ_counts) From bed731cf1b6b4d8b77ce379415aa045ce860358f Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 24 Jun 2024 10:24:05 +0200 Subject: [PATCH 322/491] Add missing environment yml files --- modules/local/quantification/split_types/environment.yml | 6 ++++++ modules/local/quantification/transcriptome/environment.yml | 6 ++++++ 2 files changed, 12 insertions(+) create mode 100644 modules/local/quantification/split_types/environment.yml create mode 100644 modules/local/quantification/transcriptome/environment.yml diff --git a/modules/local/quantification/split_types/environment.yml b/modules/local/quantification/split_types/environment.yml new file mode 100644 index 00000000..0c6dab50 --- /dev/null +++ b/modules/local/quantification/split_types/environment.yml @@ -0,0 +1,6 @@ +name: split_types +channels: + - conda-forge + - bioconda +dependencies: + - gawk=5.1.0 diff --git a/modules/local/quantification/transcriptome/environment.yml b/modules/local/quantification/transcriptome/environment.yml new file mode 100644 index 00000000..b07ac902 --- /dev/null +++ b/modules/local/quantification/transcriptome/environment.yml @@ -0,0 +1,6 @@ +name: transcriptome +channels: + - conda-forge + - bioconda +dependencies: + - gffread=0.12.1 From bc8acdf4d3cd746b57ea77fed4f4f97b87c90dc1 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 24 Jun 2024 10:28:41 +0200 Subject: [PATCH 323/491] Add another missing environment yml --- modules/local/count_matrix/merge_samples/environment.yml | 5 +++++ modules/local/count_matrix/merge_samples/main.nf | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) create mode 100644 modules/local/count_matrix/merge_samples/environment.yml diff --git a/modules/local/count_matrix/merge_samples/environment.yml b/modules/local/count_matrix/merge_samples/environment.yml new file mode 100644 index 00000000..d5f9e211 --- /dev/null +++ b/modules/local/count_matrix/merge_samples/environment.yml @@ -0,0 +1,5 @@ +name: merge_samples +channels: + - conda-forge +dependencies: + - pandas=1.5.2 diff --git a/modules/local/count_matrix/merge_samples/main.nf b/modules/local/count_matrix/merge_samples/main.nf index 410d2097..8f8d3789 100644 --- a/modules/local/count_matrix/merge_samples/main.nf +++ b/modules/local/count_matrix/merge_samples/main.nf @@ -1,7 +1,7 @@ process MERGE_SAMPLES { label "process_single" - conda "bioconda::pandas=1.5.2" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : 'biocontainers/pandas:1.5.2' }" From 900e1fc9c036ad55e6eaf1d291e324939b49f9e9 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 25 Jun 2024 08:28:42 +0200 Subject: [PATCH 324/491] Add tximeta environment.yml --- modules/local/tximeta/tximeta/environment.yml | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 modules/local/tximeta/tximeta/environment.yml diff --git a/modules/local/tximeta/tximeta/environment.yml b/modules/local/tximeta/tximeta/environment.yml new file mode 100644 index 00000000..be4bcd30 --- /dev/null +++ b/modules/local/tximeta/tximeta/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +name: "tximeta_tximeta" +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::bioconductor-tximeta=1.20.1" From c3783b9acb0c69399a7d4ccd4e6f145fd9a9da40 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 25 Jun 2024 08:37:26 +0200 Subject: [PATCH 325/491] Fix GTF sorting --- conf/modules.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index ab9245e2..b236e177 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -591,7 +591,7 @@ process { } withName: '.*:ANNOTATION:COMBINE_GTFS' { - ext.args = "-k 1,1 -k3,3n -k4,4n -u" + ext.args = "-k 1,1 -k4,4n -k5,5n -u" ext.suffix = "combined.gtf" } @@ -612,7 +612,7 @@ process { } withName: COMBINE_TRANSCRIPTOME_GTFS { - ext.args = "-k 1,1 -k3,3n -k4,4n" + ext.args = "-k 1,1 -k4,4n -k5,5n" ext.suffix = "gtf" } From cb72c91b1ea0e470bf75146d47b3928a74bf10a1 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 25 Jun 2024 09:24:32 +0200 Subject: [PATCH 326/491] Fix typo on merge_experiments conda environment --- modules/local/quantification/merge_experiments/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/quantification/merge_experiments/main.nf b/modules/local/quantification/merge_experiments/main.nf index 9e14df7e..32fadcd8 100644 --- a/modules/local/quantification/merge_experiments/main.nf +++ b/modules/local/quantification/merge_experiments/main.nf @@ -2,7 +2,7 @@ process MERGE_EXPERIMENTS { tag "$meta.id" label "process_medium" - conda "${moduleDir}/environment.yaml" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-rtracklayer:1.62.0--r43ha9d7317_0' : 'biocontainers/bioconductor-rtracklayer:1.62.0--r43ha9d7317_0' }" From 6c73c83b9b31f93394bff80bb83f81c50616bd4c Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 25 Jun 2024 10:03:51 +0200 Subject: [PATCH 327/491] Fix merge_experiments environment definition --- modules/local/quantification/merge_experiments/environment.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/modules/local/quantification/merge_experiments/environment.yml b/modules/local/quantification/merge_experiments/environment.yml index cfc21aba..b27efe1e 100644 --- a/modules/local/quantification/merge_experiments/environment.yml +++ b/modules/local/quantification/merge_experiments/environment.yml @@ -4,6 +4,5 @@ name: "fishpond_swish" channels: - conda-forge - bioconda - - defaults dependencies: - - "bioconda::bioconductor-rtracklayer==1.62.0--r43ha9d7317_0" + - "biocnda::bioconductor-rtracklayer=1.62.0" From aaebb740f7575fb3fe60f349e42168fd66b106d5 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 25 Jun 2024 10:04:36 +0200 Subject: [PATCH 328/491] Fix typo --- modules/local/quantification/merge_experiments/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/quantification/merge_experiments/environment.yml b/modules/local/quantification/merge_experiments/environment.yml index b27efe1e..07f95f05 100644 --- a/modules/local/quantification/merge_experiments/environment.yml +++ b/modules/local/quantification/merge_experiments/environment.yml @@ -5,4 +5,4 @@ channels: - conda-forge - bioconda dependencies: - - "biocnda::bioconductor-rtracklayer=1.62.0" + - "bioconda::bioconductor-rtracklayer=1.62.0" From 34a3a80d4d372820a759956eda5bac21d2d7a2dc Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 27 Jun 2024 09:51:06 +0200 Subject: [PATCH 329/491] Fix circexplorer2 count location --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index b236e177..369b900d 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -263,7 +263,7 @@ process { } withName: '.*:CIRCEXPLORER2:UNIFY' { - ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$10, \$6 }'" + ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$13, \$6 }'" ext.suffix = "circexplorer2.bed" publishDir = [ path: { "${params.outdir}/circrna_discovery/circexplorer2/${meta.id}" }, From 5b25150f3d0a4c50bd46e4a8d5e557cd7492db54 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 15 Jul 2024 15:50:24 +0200 Subject: [PATCH 330/491] Use nf core module for gtffilter functionality --- modules.json | 5 + modules/local/gtf_filter/main.nf | 24 ---- .../nf-core/custom/gtffilter/environment.yml | 9 ++ modules/nf-core/custom/gtffilter/main.nf | 37 +++++ modules/nf-core/custom/gtffilter/meta.yml | 51 +++++++ .../custom/gtffilter/templates/gtffilter.py} | 66 +++++++-- .../custom/gtffilter/tests/main.nf.test | 115 +++++++++++++++ .../custom/gtffilter/tests/main.nf.test.snap | 134 ++++++++++++++++++ .../nf-core/custom/gtffilter/tests/tags.yml | 2 + subworkflows/local/prepare_genome.nf | 26 ++-- 10 files changed, 418 insertions(+), 51 deletions(-) delete mode 100644 modules/local/gtf_filter/main.nf create mode 100644 modules/nf-core/custom/gtffilter/environment.yml create mode 100644 modules/nf-core/custom/gtffilter/main.nf create mode 100644 modules/nf-core/custom/gtffilter/meta.yml rename modules/{local/gtf_filter/templates/gtf_filter.py => nf-core/custom/gtffilter/templates/gtffilter.py} (50%) create mode 100644 modules/nf-core/custom/gtffilter/tests/main.nf.test create mode 100644 modules/nf-core/custom/gtffilter/tests/main.nf.test.snap create mode 100644 modules/nf-core/custom/gtffilter/tests/tags.yml diff --git a/modules.json b/modules.json index 3792423c..007ae30d 100644 --- a/modules.json +++ b/modules.json @@ -80,6 +80,11 @@ "git_sha": "de45447d060b8c8b98575bc637a4a575fd0638e1", "installed_by": ["modules"] }, + "custom/gtffilter": { + "branch": "master", + "git_sha": "7888e16f3c8678dfc5d59c899f79b7286271f177", + "installed_by": ["modules"] + }, "custom/tx2gene": { "branch": "master", "git_sha": "ec155021a9104441bf6a9bae3b55d1b5b0bfdb3a", diff --git a/modules/local/gtf_filter/main.nf b/modules/local/gtf_filter/main.nf deleted file mode 100644 index 4606b97e..00000000 --- a/modules/local/gtf_filter/main.nf +++ /dev/null @@ -1,24 +0,0 @@ -process GTF_FILTER { - tag "$fasta" - - conda "conda-forge::python=3.9.5" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.9--1' : - 'biocontainers/python:3.9--1' }" - - input: - tuple val(meta), path(fasta) - tuple val(meta2), path(gtf) - - output: - tuple val(meta), path("${prefix}.${suffix}"), emit: filtered - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - prefix = task.ext.prefix ?: meta.id - suffix = task.ext.suffix ?: "gtf" - template 'gtf_filter.py' -} diff --git a/modules/nf-core/custom/gtffilter/environment.yml b/modules/nf-core/custom/gtffilter/environment.yml new file mode 100644 index 00000000..115f4123 --- /dev/null +++ b/modules/nf-core/custom/gtffilter/environment.yml @@ -0,0 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +name: "custom_gtffilter" +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - "conda-forge::python=3.9.5" diff --git a/modules/nf-core/custom/gtffilter/main.nf b/modules/nf-core/custom/gtffilter/main.nf new file mode 100644 index 00000000..e921d94f --- /dev/null +++ b/modules/nf-core/custom/gtffilter/main.nf @@ -0,0 +1,37 @@ +process CUSTOM_GTFFILTER { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/python:3.9--1' : + 'biocontainers/python:3.9--1' }" + + input: + tuple val(meta), path(gtf) + tuple val(meta2), path(fasta) + + output: + tuple val(meta), path("*.gtf"), emit: gtf + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + prefix = task.ext.prefix ?: "${meta.id}" + suffix = task.ext.suffix ?: "gtf" + (gtf.extension == 'gz' ? '.gz' : '') + template 'gtffilter.py' + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + suffix = task.ext.suffix ?: "gtf" + (gtf.extension == 'gz' ? '.gz' : '') + """ + touch ${prefix}.${suffix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version 2>&1 | cut -d ' ' -f 2) + END_VERSIONS + """ +} diff --git a/modules/nf-core/custom/gtffilter/meta.yml b/modules/nf-core/custom/gtffilter/meta.yml new file mode 100644 index 00000000..2c869221 --- /dev/null +++ b/modules/nf-core/custom/gtffilter/meta.yml @@ -0,0 +1,51 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "custom_gtffilter" +description: Filter a gtf file to keep only regions that are located on a chromosome represented in a given fasta file +keywords: + - gtf + - fasta + - filter +tools: + - "gtffilter": + description: "Filter a gtf file to keep only regions that are located on a chromosome represented in a given fasta file" + tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/gtffilter/main.nf" + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + + - gtf: + type: file + description: GTF file + pattern: "*.{gtf}" + + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fasta,fa}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + + - gtf: + type: file + description: Filtered GTF file + pattern: "*.{gtf}" + + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@nictru" +maintainers: + - "@nictru" diff --git a/modules/local/gtf_filter/templates/gtf_filter.py b/modules/nf-core/custom/gtffilter/templates/gtffilter.py similarity index 50% rename from modules/local/gtf_filter/templates/gtf_filter.py rename to modules/nf-core/custom/gtffilter/templates/gtffilter.py index 20343cef..764ec2ef 100644 --- a/modules/local/gtf_filter/templates/gtf_filter.py +++ b/modules/nf-core/custom/gtffilter/templates/gtffilter.py @@ -1,10 +1,30 @@ #!/usr/bin/env python # Written by Olga Botvinnik with subsequent reworking by Jonathan Manning and Nico Trummer. -# Released under the MIT license. + +# MIT License + +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: + +# The above copyright notice and this permission notice shall be included in all +# copies or substantial portions of the Software. + +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +# SOFTWARE. import logging import re +import gzip import statistics import platform from typing import Set @@ -14,6 +34,7 @@ logger = logging.getLogger("fasta_gtf_filter") logger.setLevel(logging.INFO) + def format_yaml_like(data: dict, indent: int = 0) -> str: """Formats a dictionary to a YAML-like string. @@ -36,8 +57,18 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: def extract_fasta_seq_names(fasta_name: str) -> Set[str]: """Extracts the sequence names from a FASTA file.""" - with open(fasta_name) as fasta: - return {line[1:].split(None, 1)[0] for line in fasta if line.startswith(">")} + + is_gz = fasta_name.endswith(".gz") + open_fn = gzip.open if is_gz else open + + with open_fn(fasta_name) as fasta: + sequences = set() + for line in fasta: + line = line.decode("utf-8") if is_gz else line + if line.startswith(">"): + sequences.add(line[1:].split(None, 1)[0]) + + return sequences def tab_delimited(file: str) -> float: @@ -47,26 +78,35 @@ def tab_delimited(file: str) -> float: return statistics.median(line.count("\\t") for line in data.split("\\n")) -def filter_gtf(fasta: str, gtf_in: str, filtered_gtf_out: str, skip_transcript_id_check: bool) -> None: +def filter_gtf( + fasta: str, gtf_in: str, filtered_gtf_out: str, skip_transcript_id_check: bool +) -> None: """Filter GTF file based on FASTA sequence names.""" if tab_delimited(gtf_in) != 8: raise ValueError("Invalid GTF file: Expected 9 tab-separated columns.") seq_names_in_genome = extract_fasta_seq_names(fasta) logger.info(f"Extracted chromosome sequence names from {fasta}") - logger.debug("All sequence IDs from FASTA: " + ", ".join(sorted(seq_names_in_genome))) + logger.debug( + "All sequence IDs from FASTA: " + ", ".join(sorted(seq_names_in_genome)) + ) seq_names_in_gtf = set() try: - with open(gtf_in) as gtf, open(filtered_gtf_out, "w") as out: + is_gz = gtf_in.endswith(".gz") + open_fn = gzip.open if is_gz else open + with open_fn(gtf_in) as gtf, open_fn(filtered_gtf_out, "wb" if is_gz else "w") as out: line_count = 0 for line in gtf: + line = line.decode("utf-8") if is_gz else line seq_name = line.split("\\t")[0] seq_names_in_gtf.add(seq_name) # Add sequence name to the set if seq_name in seq_names_in_genome: - if skip_transcript_id_check or re.search(r'transcript_id "([^"]+)"', line): - out.write(line) + if skip_transcript_id_check or re.search( + r'transcript_id "([^"]+)"', line + ): + out.write(line.encode() if is_gz else line) line_count += 1 if line_count == 0: @@ -77,18 +117,16 @@ def filter_gtf(fasta: str, gtf_in: str, filtered_gtf_out: str, skip_transcript_i return logger.debug("All sequence IDs from GTF: " + ", ".join(sorted(seq_names_in_gtf))) - logger.info(f"Extracted {line_count} matching sequences from {gtf_in} into {filtered_gtf_out}") + logger.info( + f"Extracted {line_count} matching sequences from {gtf_in} into {filtered_gtf_out}" + ) filter_gtf("${fasta}", "${gtf}", "${prefix}.${suffix}", False) # Versions -versions = { - "${task.process}": { - "python": platform.python_version() - } -} +versions = {"${task.process}": {"python": platform.python_version()}} with open("versions.yml", "w") as f: f.write(format_yaml_like(versions)) diff --git a/modules/nf-core/custom/gtffilter/tests/main.nf.test b/modules/nf-core/custom/gtffilter/tests/main.nf.test new file mode 100644 index 00000000..252d11a1 --- /dev/null +++ b/modules/nf-core/custom/gtffilter/tests/main.nf.test @@ -0,0 +1,115 @@ +nextflow_process { + + name "Test Process CUSTOM_GTFFILTER" + script "../main.nf" + process "CUSTOM_GTFFILTER" + + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "custom/gtffilter" + + test("test_custom_gtffilter") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ] + input[1] = [ + [ id: 'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_custom_gtffilter_gzip") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ] + input[1] = [ + [ id: 'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_custom_gtffilter - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ] + input[1] = [ + [ id: 'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_custom_gtffilter_gzip - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ] + input[1] = [ + [ id: 'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/custom/gtffilter/tests/main.nf.test.snap b/modules/nf-core/custom/gtffilter/tests/main.nf.test.snap new file mode 100644 index 00000000..787dd42e --- /dev/null +++ b/modules/nf-core/custom/gtffilter/tests/main.nf.test.snap @@ -0,0 +1,134 @@ +{ + "test_custom_gtffilter_gzip": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.gtf:md5,aa8b2aa1e0b5fbbba3b04d471e1b0535" + ] + ], + "1": [ + "versions.yml:md5,39c43040514c93566d2e3dca39e54cf2" + ], + "gtf": [ + [ + { + "id": "test" + }, + "test.gtf:md5,aa8b2aa1e0b5fbbba3b04d471e1b0535" + ] + ], + "versions": [ + "versions.yml:md5,39c43040514c93566d2e3dca39e54cf2" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-15T14:23:11.091273747" + }, + "test_custom_gtffilter": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.gtf:md5,aa8b2aa1e0b5fbbba3b04d471e1b0535" + ] + ], + "1": [ + "versions.yml:md5,39c43040514c93566d2e3dca39e54cf2" + ], + "gtf": [ + [ + { + "id": "test" + }, + "test.gtf:md5,aa8b2aa1e0b5fbbba3b04d471e1b0535" + ] + ], + "versions": [ + "versions.yml:md5,39c43040514c93566d2e3dca39e54cf2" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-15T14:23:03.654104046" + }, + "test_custom_gtffilter_gzip - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,4547ffaa530b6d65b2dd1f607d7f85e3" + ], + "gtf": [ + [ + { + "id": "test" + }, + "test.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,4547ffaa530b6d65b2dd1f607d7f85e3" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-15T14:23:24.216284615" + }, + "test_custom_gtffilter - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,4547ffaa530b6d65b2dd1f607d7f85e3" + ], + "gtf": [ + [ + { + "id": "test" + }, + "test.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,4547ffaa530b6d65b2dd1f607d7f85e3" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-15T14:23:17.765499066" + } +} \ No newline at end of file diff --git a/modules/nf-core/custom/gtffilter/tests/tags.yml b/modules/nf-core/custom/gtffilter/tests/tags.yml new file mode 100644 index 00000000..34dda217 --- /dev/null +++ b/modules/nf-core/custom/gtffilter/tests/tags.yml @@ -0,0 +1,2 @@ +custom/gtffilter: + - "modules/nf-core/custom/gtffilter/**" diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 715ce125..76fe152d 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -1,13 +1,13 @@ -include { GTF_FILTER } from '../../modules/local/gtf_filter' -include { SEQKIT_SPLIT } from '../../modules/local/seqkit/split' -include { BOWTIE_BUILD } from '../../modules/nf-core/bowtie/build' -include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build' -include { BWA_INDEX } from '../../modules/nf-core/bwa/index' -include { HISAT2_EXTRACTSPLICESITES } from '../../modules/nf-core/hisat2/extractsplicesites' -include { HISAT2_BUILD } from '../../modules/nf-core/hisat2/build' -include { STAR_GENOMEGENERATE } from '../../modules/nf-core/star/genomegenerate' -include { GAWK as CLEAN_FASTA } from '../../modules/nf-core/gawk' -include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx' +include { CUSTOM_GTFFILTER as GTFFILTER } from '../../modules/nf-core/custom/gtffilter' +include { SEQKIT_SPLIT } from '../../modules/local/seqkit/split' +include { BOWTIE_BUILD } from '../../modules/nf-core/bowtie/build' +include { BOWTIE2_BUILD } from '../../modules/nf-core/bowtie2/build' +include { BWA_INDEX } from '../../modules/nf-core/bwa/index' +include { HISAT2_EXTRACTSPLICESITES } from '../../modules/nf-core/hisat2/extractsplicesites' +include { HISAT2_BUILD } from '../../modules/nf-core/hisat2/build' +include { STAR_GENOMEGENERATE } from '../../modules/nf-core/star/genomegenerate' +include { GAWK as CLEAN_FASTA } from '../../modules/nf-core/gawk' +include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx' workflow PREPARE_GENOME { @@ -27,8 +27,8 @@ workflow PREPARE_GENOME { ch_versions = ch_versions.mix(CLEAN_FASTA.out.versions) } - GTF_FILTER(ch_fasta, ch_gtf) - ch_gtf = GTF_FILTER.out.filtered + GTFFILTER(ch_gtf, ch_fasta) + ch_gtf = GTFFILTER.out.gtf SEQKIT_SPLIT(ch_fasta) @@ -47,7 +47,7 @@ workflow PREPARE_GENOME { SAMTOOLS_FAIDX(ch_fasta, [[], []]) // Collect versions - ch_versions = ch_versions.mix(GTF_FILTER.out.versions, + ch_versions = ch_versions.mix(GTFFILTER.out.versions, SEQKIT_SPLIT.out.versions, BOWTIE_BUILD.out.versions, BOWTIE2_BUILD.out.versions, From 853e9dab978488d0347350297056d52cf6459eb2 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 15 Jul 2024 15:53:18 +0200 Subject: [PATCH 331/491] Rename GTFFILTER module accession --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 0885b37e..6252fa89 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -70,7 +70,7 @@ process { ] } - withName: GTF_FILTER { + withName: GTFFILTER { ext.suffix = "filtered.gtf" } From 73bf5e4998cc12f08b9ca8c34141eb7c62be5c85 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Mon, 15 Jul 2024 16:26:52 +0200 Subject: [PATCH 332/491] Update GTFFILTER module --- modules.json | 2 +- modules/nf-core/custom/gtffilter/main.nf | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules.json b/modules.json index 007ae30d..8a2d096a 100644 --- a/modules.json +++ b/modules.json @@ -82,7 +82,7 @@ }, "custom/gtffilter": { "branch": "master", - "git_sha": "7888e16f3c8678dfc5d59c899f79b7286271f177", + "git_sha": "a0aee18374b7f072aa0f89f4d66f5a3a9f8176d2", "installed_by": ["modules"] }, "custom/tx2gene": { diff --git a/modules/nf-core/custom/gtffilter/main.nf b/modules/nf-core/custom/gtffilter/main.nf index e921d94f..b682ff8c 100644 --- a/modules/nf-core/custom/gtffilter/main.nf +++ b/modules/nf-core/custom/gtffilter/main.nf @@ -12,8 +12,8 @@ process CUSTOM_GTFFILTER { tuple val(meta2), path(fasta) output: - tuple val(meta), path("*.gtf"), emit: gtf - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.${suffix}"), emit: gtf + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when From 342964d9d51732bd68a0bf579de842880d68dbe9 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 1 Aug 2024 10:55:57 +0200 Subject: [PATCH 333/491] Add filter for circular RNAs to find_circ --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 40a6398c..ed733627 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -343,7 +343,7 @@ process { withName: '.*:FIND_CIRC:UNIFY' { // Keep only rows with UNAMBIGUOUS_BP and ANCHOR_UNIQUE in $18 - ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (\$18 ~ /UNAMBIGUOUS_BP/ && \$18 ~ /ANCHOR_UNIQUE/) { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$5, \$6 } }'" + ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (\$18 ~ /CIRCULAR/ && \$18 ~ /UNAMBIGUOUS_BP/ && \$18 ~ /ANCHOR_UNIQUE/) { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$5, \$6 } }'" ext.suffix = "find_circ.bed" publishDir = [ path: { "${params.outdir}/circrna_discovery/find_circ/${meta.id}" }, From 3be2733652701c021ebb08bcc5f6a9d3ded57f07 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 1 Aug 2024 10:57:48 +0200 Subject: [PATCH 334/491] Update comment --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index ed733627..ec811890 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -342,7 +342,7 @@ process { } withName: '.*:FIND_CIRC:UNIFY' { - // Keep only rows with UNAMBIGUOUS_BP and ANCHOR_UNIQUE in $18 + // Keep only rows with CIRCULAR, UNAMBIGUOUS_BP and ANCHOR_UNIQUE in $18 ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (\$18 ~ /CIRCULAR/ && \$18 ~ /UNAMBIGUOUS_BP/ && \$18 ~ /ANCHOR_UNIQUE/) { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$5, \$6 } }'" ext.suffix = "find_circ.bed" publishDir = [ From a66fcd3800bf3ae30a89394e4d1b3f155c542722 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 12 Jul 2024 10:53:44 +0200 Subject: [PATCH 335/491] Add error message for empty intersections --- modules/local/annotation/templates/annotation.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/modules/local/annotation/templates/annotation.py b/modules/local/annotation/templates/annotation.py index 91121d78..20ea682c 100755 --- a/modules/local/annotation/templates/annotation.py +++ b/modules/local/annotation/templates/annotation.py @@ -41,7 +41,10 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: exon_boundary = int("${exon_boundary}") -df = pd.read_csv("${gtf_intersection}", sep="\\t", header=None, usecols=columns.keys()) +try: + df = pd.read_csv("${gtf_intersection}", sep="\\t", header=None, usecols=columns.keys()) +except pd.errors.EmptyDataError: + raise ValueError("Intersection between circRNAs and GTF file is empty.") df = df.rename(columns=columns) # Extract circRNAs without match From 02a19f2b6ba30cf16d2e42e71bb6c11aaf15bda2 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 12 Jul 2024 10:58:17 +0200 Subject: [PATCH 336/491] Add docs for GTF required attributes --- nextflow_schema.json | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow_schema.json b/nextflow_schema.json index c1b06562..64df9eb1 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -216,6 +216,7 @@ "fa_icon": "fas fa-address-book", "mimetype": "text/plain", "description": "Path to reference GTF file.", + "help_text": "This parameter is *mandatory* if `--genome` is not specified. Needs to contain the following attributes: `gene_id`, `transcript_id` and `gene_name`.", "pattern": "\\.gtf$" }, "mature": { From 2e3d66732edbf494379b54ac3c3d6839e5ce1a5c Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 12 Jul 2024 11:15:03 +0200 Subject: [PATCH 337/491] Add check for presence of attributes in annotation intersection --- modules/local/annotation/templates/annotation.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/local/annotation/templates/annotation.py b/modules/local/annotation/templates/annotation.py index 20ea682c..eb0aadd0 100755 --- a/modules/local/annotation/templates/annotation.py +++ b/modules/local/annotation/templates/annotation.py @@ -58,6 +58,13 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: # Convert attributes to a dictionary df['attributes'] = df['attributes'].apply(lambda row: dict([[value.strip(r'"') for value in entry.strip().split(' ', 1)] for entry in row.split(';') if entry])) +# Make sure all attributes are present +df_incomplete = df['attributes'].apply(lambda row: ", ".join([key for key in attributes if key not in row])) +if len(df_incomplete) > 0: + counts = df_incomplete.value_counts() + counts.name = 'count' + counts.index.name = 'missing' + raise ValueError(f"The following attributes are missing in the intersection file:\\n\\n{counts.to_frame()}") # Keep only the attributes we want df['attributes'] = df['attributes'].apply(lambda row: {key: row[key] for key in attributes if key in row}) # Convert attributes to columns From 3a8e88c84ababea4ce20b98eb3983b573326aea1 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 12 Jul 2024 11:53:03 +0200 Subject: [PATCH 338/491] Fix bug in missing attribute check --- modules/local/annotation/templates/annotation.py | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/local/annotation/templates/annotation.py b/modules/local/annotation/templates/annotation.py index eb0aadd0..b0ff285b 100755 --- a/modules/local/annotation/templates/annotation.py +++ b/modules/local/annotation/templates/annotation.py @@ -60,6 +60,7 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: df['attributes'] = df['attributes'].apply(lambda row: dict([[value.strip(r'"') for value in entry.strip().split(' ', 1)] for entry in row.split(';') if entry])) # Make sure all attributes are present df_incomplete = df['attributes'].apply(lambda row: ", ".join([key for key in attributes if key not in row])) +df_incomplete = df_incomplete[df_incomplete != ""] if len(df_incomplete) > 0: counts = df_incomplete.value_counts() counts.name = 'count' From b0086537b4c8627c13616d57145fb91ec00c243b Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 1 Aug 2024 22:46:39 +0200 Subject: [PATCH 339/491] Implement Segemehl grouping --- conf/modules.config | 5 +++++ subworkflows/local/discovery/segemehl.nf | 7 +++++-- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index ec811890..233c766b 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -184,6 +184,11 @@ process { ] } + withName: '.*:SEGEMEHL:GROUP' { + ext.summary_col = 5 + ext.args = "-g 1,2,3,4,6 -o count" + } + withName: '.*:STAR2PASS:PASS_1' { ext.when = { params.tool.split(',').contains('circexplorer2') || params.tool.split(',').contains('circrna_finder') } ext.args = [ "", diff --git a/subworkflows/local/discovery/segemehl.nf b/subworkflows/local/discovery/segemehl.nf index 71669032..10ac9b4c 100644 --- a/subworkflows/local/discovery/segemehl.nf +++ b/subworkflows/local/discovery/segemehl.nf @@ -1,7 +1,7 @@ include { SEGEMEHL_INDEX as INDEX } from '../../../modules/nf-core/segemehl/index' include { SEGEMEHL_ALIGN as ALIGN } from '../../../modules/nf-core/segemehl/align' include { GAWK as UNIFY } from '../../../modules/nf-core/gawk' - +include { BEDTOOLS_GROUPBY as GROUP } from '../../../modules/nf-core/bedtools/groupby' workflow SEGEMEHL { take: @@ -17,11 +17,14 @@ workflow SEGEMEHL { UNIFY( ALIGN.out.single_bed .map{ meta, bed -> [ meta + [tool: "segemehl"], bed ] }, [] ) + GROUP( UNIFY.out.output, 5 ) + ch_versions = ch_versions.mix(ALIGN.out.versions) ch_versions = ch_versions.mix(UNIFY.out.versions) + ch_versions = ch_versions.mix(GROUP.out.versions) emit: - bed = UNIFY.out.output + bed = GROUP.out.bed versions = ch_versions } From 9d799725f41a882c2da2fa38fee2e81ab2ad666e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 1 Aug 2024 22:47:45 +0200 Subject: [PATCH 340/491] Add bedtools groupby --- modules.json | 5 ++ .../nf-core/bedtools/groupby/environment.yml | 7 +++ modules/nf-core/bedtools/groupby/main.nf | 50 +++++++++++++++++++ modules/nf-core/bedtools/groupby/meta.yml | 47 +++++++++++++++++ 4 files changed, 109 insertions(+) create mode 100644 modules/nf-core/bedtools/groupby/environment.yml create mode 100644 modules/nf-core/bedtools/groupby/main.nf create mode 100644 modules/nf-core/bedtools/groupby/meta.yml diff --git a/modules.json b/modules.json index 8a2d096a..36315754 100644 --- a/modules.json +++ b/modules.json @@ -10,6 +10,11 @@ "git_sha": "cdcdd5e3d806f0ff3983c40c69e0b07bb44ec299", "installed_by": ["modules"] }, + "bedtools/groupby": { + "branch": "master", + "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", + "installed_by": ["modules"] + }, "bedtools/intersect": { "branch": "master", "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", diff --git a/modules/nf-core/bedtools/groupby/environment.yml b/modules/nf-core/bedtools/groupby/environment.yml new file mode 100644 index 00000000..dab99ea1 --- /dev/null +++ b/modules/nf-core/bedtools/groupby/environment.yml @@ -0,0 +1,7 @@ +name: bedtools_groupby +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/groupby/main.nf b/modules/nf-core/bedtools/groupby/main.nf new file mode 100644 index 00000000..063e7ba2 --- /dev/null +++ b/modules/nf-core/bedtools/groupby/main.nf @@ -0,0 +1,50 @@ +process BEDTOOLS_GROUPBY { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_0' : + 'biocontainers/bedtools:2.31.1--hf5e1c6e_0' }" + + input: + tuple val(meta), path(bed) + val(summary_col) + + output: + tuple val(meta), path('*.bed'), emit: bed + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}.grouped" + def summary_col = task.ext.summary_col ? "-c ${task.ext.summary_col}" : "-c 5" + if ("$bed" == "${prefix}.bed") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + bedtools \\ + groupby \\ + -i $bed \\ + ${summary_col} \\ + $args \\ + > ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ +} diff --git a/modules/nf-core/bedtools/groupby/meta.yml b/modules/nf-core/bedtools/groupby/meta.yml new file mode 100644 index 00000000..bcbc561a --- /dev/null +++ b/modules/nf-core/bedtools/groupby/meta.yml @@ -0,0 +1,47 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json +name: bedtools_groupby +description: Groups features in a BED file by given column(s) and computes summary statistics for each group to another column. +keywords: + - bed + - groupby + - bedtools +tools: + - bedtools: + description: | + A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. + documentation: https://bedtools.readthedocs.io/en/latest/content/tools/groupby.html + homepage: https://bedtools.readthedocs.io/en/latest/ + doi: 10.1093/bioinformatics/btq033 + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bed: + type: file + description: Input BED file + pattern: "*.{bed}" + - summary_column: + type: integer + description: Column to be summarized (1-based) +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bed: + type: file + description: Grouped by bed file with combined features + pattern: "*.{bed}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@mashehu" +maintainers: + - "@mashehu" From 50a18178ce4709536c84ca33f775bf602c118356 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 1 Aug 2024 23:01:03 +0200 Subject: [PATCH 341/491] Fix segemehl grouping --- conf/modules.config | 18 ++++++++++++------ subworkflows/local/discovery/segemehl.nf | 14 +++++++++----- 2 files changed, 21 insertions(+), 11 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 233c766b..df9fe0b3 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -171,10 +171,21 @@ process { ] } - withName: '.*:SEGEMEHL:UNIFY' { + withName: '.*:SEGEMEHL:EXTRACT' { // Keep only rows with ";C;" in column 4 // Print $1 $2 $3 $1:$2-$3 $5 $6 ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (\$4 ~ /;C;/) { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$5, \$6 } }'" + ext.suffix = "segemehl_extracted.bed" + } + + withName: '.*:SEGEMEHL:GROUP' { + ext.summary_col = 5 + ext.args = "-g 1,2,3,4,6 -o count" + ext.suffix = "segemehl_grouped.bed" + } + + withName: '.*:SEGEMEHL:UNIFY' { + ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$4, \$6, \$5 }'" ext.suffix = "segemehl.bed" publishDir = [ path: { "${params.outdir}/circrna_discovery/segemehl/${meta.id}" }, @@ -184,11 +195,6 @@ process { ] } - withName: '.*:SEGEMEHL:GROUP' { - ext.summary_col = 5 - ext.args = "-g 1,2,3,4,6 -o count" - } - withName: '.*:STAR2PASS:PASS_1' { ext.when = { params.tool.split(',').contains('circexplorer2') || params.tool.split(',').contains('circrna_finder') } ext.args = [ "", diff --git a/subworkflows/local/discovery/segemehl.nf b/subworkflows/local/discovery/segemehl.nf index 10ac9b4c..7c61e46d 100644 --- a/subworkflows/local/discovery/segemehl.nf +++ b/subworkflows/local/discovery/segemehl.nf @@ -1,7 +1,8 @@ include { SEGEMEHL_INDEX as INDEX } from '../../../modules/nf-core/segemehl/index' include { SEGEMEHL_ALIGN as ALIGN } from '../../../modules/nf-core/segemehl/align' -include { GAWK as UNIFY } from '../../../modules/nf-core/gawk' +include { GAWK as EXTRACT } from '../../../modules/nf-core/gawk' include { BEDTOOLS_GROUPBY as GROUP } from '../../../modules/nf-core/bedtools/groupby' +include { GAWK as UNIFY } from '../../../modules/nf-core/gawk' workflow SEGEMEHL { take: @@ -13,18 +14,21 @@ workflow SEGEMEHL { ch_versions = Channel.empty() index = index ?: INDEX( fasta ).index + ALIGN( reads, fasta, index ) - UNIFY( ALIGN.out.single_bed + EXTRACT( ALIGN.out.single_bed .map{ meta, bed -> [ meta + [tool: "segemehl"], bed ] }, [] ) - GROUP( UNIFY.out.output, 5 ) + GROUP( EXTRACT.out.output, 5 ) + UNIFY( GROUP.out.bed, [] ) ch_versions = ch_versions.mix(ALIGN.out.versions) - ch_versions = ch_versions.mix(UNIFY.out.versions) + ch_versions = ch_versions.mix(EXTRACT.out.versions) ch_versions = ch_versions.mix(GROUP.out.versions) + ch_versions = ch_versions.mix(UNIFY.out.versions) emit: - bed = GROUP.out.bed + bed = UNIFY.out.output versions = ch_versions } From 9fc67a1ff6f90475a2edb667ef71aaf2e22a3fa9 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 1 Aug 2024 23:17:32 +0200 Subject: [PATCH 342/491] Implement ordering of segemehl results --- conf/modules.config | 5 +++++ subworkflows/local/discovery/segemehl.nf | 5 ++++- 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index df9fe0b3..8fe2a0ea 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -178,6 +178,11 @@ process { ext.suffix = "segemehl_extracted.bed" } + withName: '.*:SEGEMEHL:SORT' { + ext.args = "-k1,1 -k2,2n -k3,3n -k4,4 -k6,6" + ext.suffix = "segemehl_sorted.bed" + } + withName: '.*:SEGEMEHL:GROUP' { ext.summary_col = 5 ext.args = "-g 1,2,3,4,6 -o count" diff --git a/subworkflows/local/discovery/segemehl.nf b/subworkflows/local/discovery/segemehl.nf index 7c61e46d..9e8e2c0d 100644 --- a/subworkflows/local/discovery/segemehl.nf +++ b/subworkflows/local/discovery/segemehl.nf @@ -1,6 +1,7 @@ include { SEGEMEHL_INDEX as INDEX } from '../../../modules/nf-core/segemehl/index' include { SEGEMEHL_ALIGN as ALIGN } from '../../../modules/nf-core/segemehl/align' include { GAWK as EXTRACT } from '../../../modules/nf-core/gawk' +include { GNU_SORT as SORT } from '../../../modules/nf-core/gnu/sort' include { BEDTOOLS_GROUPBY as GROUP } from '../../../modules/nf-core/bedtools/groupby' include { GAWK as UNIFY } from '../../../modules/nf-core/gawk' @@ -19,11 +20,13 @@ workflow SEGEMEHL { EXTRACT( ALIGN.out.single_bed .map{ meta, bed -> [ meta + [tool: "segemehl"], bed ] }, [] ) - GROUP( EXTRACT.out.output, 5 ) + SORT( EXTRACT.out.output ) + GROUP( SORT.out.sorted, 5 ) UNIFY( GROUP.out.bed, [] ) ch_versions = ch_versions.mix(ALIGN.out.versions) ch_versions = ch_versions.mix(EXTRACT.out.versions) + ch_versions = ch_versions.mix(SORT.out.versions) ch_versions = ch_versions.mix(GROUP.out.versions) ch_versions = ch_versions.mix(UNIFY.out.versions) From 08d56cc44cc1a41937ef643137dde5e32a210996 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 1 Aug 2024 23:17:44 +0200 Subject: [PATCH 343/491] Implement check for duplicates in tool results --- .../merge_tools/templates/merge_tools.py | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/modules/local/count_matrix/merge_tools/templates/merge_tools.py b/modules/local/count_matrix/merge_tools/templates/merge_tools.py index debb85bf..8e514993 100755 --- a/modules/local/count_matrix/merge_tools/templates/merge_tools.py +++ b/modules/local/count_matrix/merge_tools/templates/merge_tools.py @@ -28,7 +28,19 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: raise ValueError(f"Invalid value for duplicates_fun: {duplicates_fun}") columns = ['chr', 'start', 'end', 'name', 'count', 'strand'] -dfs = [pd.read_csv(bed, sep='\t', header=None, names=columns) for bed in "${beds}".split()] +columns_no_count = ['chr', 'start', 'end', 'name', 'strand'] +dfs = [] + +for bed_path in "${beds}".split(): + df = pd.read_csv(bed_path, sep='\\t', header=None, names=columns) + + # If there are duplicate rows, throw an error + if df.duplicated(subset=columns_no_count).any(): + print(df[df.duplicated(subset=columns_no_count)]) + raise ValueError("Duplicate rows found in input BED file: " + bed_path) + + dfs.append(df) + df = pd.concat(dfs) df['tool_count'] = 1 From 7d470e60c0690fd3a91550f480db924fab0a4a91 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 11:18:25 +0200 Subject: [PATCH 344/491] Implement custom BSJome generation --- conf/modules.config | 32 +++++++++++++++++++ subworkflows/local/circrna_discovery.nf | 41 ++++++++++++++++++++----- 2 files changed, 66 insertions(+), 7 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 8fe2a0ea..45a698b3 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -582,6 +582,38 @@ process { ext.suffix = {"${meta.tool}.filtered.bed"} } + withName: 'MASK_SCORES' { + // Take bed file and replace the score column with a dot + ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$4, \".\", \$6 }'" + ext.suffix = {"${meta.tool}.masked.bed"} + } + + withName: 'CONCAT_TOOLS_PER_SAMPLE' { + // GNU sort by columns 1,2,3,4,6 + ext.args = "-k1,1 -k2,2n -k3,3n -k4,4 -k6,6" + ext.suffix = {"sorted.bed"} + } + + withName: 'COUNT_TOOLS' { + // Count the number of tools that support each circRNA + ext.summary_col = 5 + ext.args = "-g 1,2,3,4,6 -o count" + ext.suffix = {"grouped.bed"} + } + + withName: 'FILTER_MIN_TOOLS' { + // Keep only rows with at least the minimum number of tools + // Replace the score column with a dot + ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (\$5 >= ${params.tool_filter}) { print \$1, \$2, \$3, \$4, \".\", \$6 } }'" + ext.suffix = {"filtered.bed"} + } + + withName: 'CONCAT_SAMPLES' { + // GNU sort by columns 1,2,3,4,6 + ext.args = "-k1,1 -k2,2n -k3,3n -k4,4 -k6,6 -u" + ext.suffix = {"sorted.bed"} + } + withName: UPSET_SAMPLES { ext.when = { params.tool.split(',').length > 1 } } diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 2a163ce7..6e682f06 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -1,11 +1,16 @@ // MODULES -include { GAWK as FILTER_BSJS } from '../../modules/nf-core/gawk' -include { MERGE_TOOLS } from '../../modules/local/count_matrix/merge_tools' -include { MERGE_SAMPLES } from '../../modules/local/count_matrix/merge_samples' -include { UPSET as UPSET_SAMPLES } from '../../modules/local/upset' -include { UPSET as UPSET_ALL } from '../../modules/local/upset' -include { BEDTOOLS_GETFASTA } from '../../modules/nf-core/bedtools/getfasta' -include { GAWK as ADD_BACKSPLICE } from '../../modules/nf-core/gawk' +include { GAWK as FILTER_BSJS } from '../../modules/nf-core/gawk' +include { GAWK as MASK_SCORES } from '../../modules/nf-core/gawk' +include { GNU_SORT as CONCAT_TOOLS_PER_SAMPLE } from '../../modules/nf-core/gnu/sort' +include { BEDTOOLS_GROUPBY as COUNT_TOOLS } from '../../modules/nf-core/bedtools/groupby' +include { GAWK as FILTER_MIN_TOOLS } from '../../modules/nf-core/gawk' +include { GNU_SORT as CONCAT_SAMPLES } from '../../modules/nf-core/gnu/sort' +include { MERGE_TOOLS } from '../../modules/local/count_matrix/merge_tools' +include { MERGE_SAMPLES } from '../../modules/local/count_matrix/merge_samples' +include { UPSET as UPSET_SAMPLES } from '../../modules/local/upset' +include { UPSET as UPSET_ALL } from '../../modules/local/upset' +include { BEDTOOLS_GETFASTA } from '../../modules/nf-core/bedtools/getfasta' +include { GAWK as ADD_BACKSPLICE } from '../../modules/nf-core/gawk' // SUBWORKFLOWS include { SEGEMEHL } from './discovery/segemehl' @@ -111,6 +116,28 @@ workflow CIRCRNA_DISCOVERY { // CREATE COUNT MATRIX // + MASK_SCORES( ch_bed, [] ) + ch_versions = ch_versions.mix(MASK_SCORES.out.versions) + + CONCAT_TOOLS_PER_SAMPLE( + MASK_SCORES.out.output.map{ meta, bed -> [ [id: meta.id], bed ] }.groupTuple() + ) + ch_versions = ch_versions.mix(CONCAT_TOOLS_PER_SAMPLE.out.versions) + + COUNT_TOOLS( CONCAT_TOOLS_PER_SAMPLE.out.sorted, 5 ) + ch_versions = ch_versions.mix(COUNT_TOOLS.out.versions) + + FILTER_MIN_TOOLS( COUNT_TOOLS.out.bed, [] ) + ch_versions = ch_versions.mix(FILTER_MIN_TOOLS.out.versions) + + ch_bsjome_per_sample = FILTER_MIN_TOOLS.out.output + + CONCAT_SAMPLES( + ch_bsjome_per_sample.map{ meta, bed -> [[id: "all"], bed] }.groupTuple() + ) + ch_versions = ch_versions.mix(CONCAT_SAMPLES.out.versions) + ch_bsjome = CONCAT_SAMPLES.out.sorted + MERGE_TOOLS( ch_bed.map{ meta, bed -> [ [id: meta.id], bed ] }.groupTuple(), tools_selected.size() > 1 ? tool_filter : 1, duplicates_fun ) MERGE_SAMPLES( MERGE_TOOLS.out.merged.map{ meta, bed -> bed }.collect() ) From 8719a3f821e31dbc8be68fcfbd554eeb7411de89 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 16:00:02 +0200 Subject: [PATCH 345/491] Extract annotation from discovery --- conf/modules.config | 6 -- modules/local/annotation/main.nf | 2 +- .../local/{discovery => }/annotation.nf | 43 ++++------- subworkflows/local/circrna_discovery.nf | 76 ++++++++----------- subworkflows/local/mirna_prediction.nf | 12 ++- workflows/circrna/main.nf | 33 +++++--- 6 files changed, 75 insertions(+), 97 deletions(-) rename subworkflows/local/{discovery => }/annotation.nf (51%) diff --git a/conf/modules.config b/conf/modules.config index 45a698b3..8f0bfc8d 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -655,12 +655,6 @@ process { withName: ADD_BACKSPLICE { ext.args = "'{ if (/^>/) { print \$0 } else { start = substr(\$0, 1, 25); print \$0 start } }'" ext.suffix = "backspliced.fa" - publishDir = [ - path: { "${params.outdir}/circrna_discovery/${meta.tool}/${meta.id}" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - pattern: "*.backspliced.fa" - ] } withName: COMBINE_TRANSCRIPTOME_GTFS { diff --git a/modules/local/annotation/main.nf b/modules/local/annotation/main.nf index 1f20cc72..7a698e40 100644 --- a/modules/local/annotation/main.nf +++ b/modules/local/annotation/main.nf @@ -1,5 +1,5 @@ process ANNOTATION { - tag "$meta.id:$meta.tool" + tag "$meta.id" label 'process_single' conda "${moduleDir}/environment.yml" diff --git a/subworkflows/local/discovery/annotation.nf b/subworkflows/local/annotation.nf similarity index 51% rename from subworkflows/local/discovery/annotation.nf rename to subworkflows/local/annotation.nf index da2c7b99..f1887d93 100644 --- a/subworkflows/local/discovery/annotation.nf +++ b/subworkflows/local/annotation.nf @@ -1,31 +1,33 @@ -include { BEDTOOLS_INTERSECT as INTERSECT_GTF } from '../../../modules/nf-core/bedtools/intersect' -include { ANNOTATION as ANNOTATE } from '../../../modules/local/annotation' -include { GAWK as INGEST_DATABASE_NAMES } from '../../../modules/nf-core/gawk' -include { GNU_SORT as COMBINE_DATABASES } from '../../../modules/nf-core/gnu/sort' -include { BEDTOOLS_INTERSECT as INTERSECT_DATABASE } from '../../../modules/nf-core/bedtools/intersect' -include { GAWK as CLEAN_DATABASE_ANNOTATION } from '../../../modules/nf-core/gawk' -include { GNU_SORT as COMBINE_BEDS } from '../../../modules/nf-core/gnu/sort' -include { GAWK as REMOVE_SCORE_STRAND } from '../../../modules/nf-core/gawk' -include { GNU_SORT as COMBINE_GTFS } from '../../../modules/nf-core/gnu/sort' +include { BEDTOOLS_INTERSECT as INTERSECT_GTF } from '../../modules/nf-core/bedtools/intersect' +include { GAWK as INGEST_DATABASE_NAMES } from '../../modules/nf-core/gawk' +include { GNU_SORT as COMBINE_DATABASES } from '../../modules/nf-core/gnu/sort' +include { BEDTOOLS_INTERSECT as INTERSECT_DATABASE } from '../../modules/nf-core/bedtools/intersect' +include { ANNOTATION as ANNOTATE } from '../../modules/local/annotation' workflow ANNOTATION { take: regions - gtf + ch_gtf exon_boundary ch_annotation main: ch_versions = Channel.empty() - INTERSECT_GTF( regions.combine(gtf), [[], []] ) + INTERSECT_GTF( regions.combine(ch_gtf.map{meta, gtf -> gtf}), [[], []] ) + ch_versions = ch_versions.mix(INTERSECT_GTF.out.versions) + INGEST_DATABASE_NAMES( ch_annotation, [] ) + ch_versions = ch_versions.mix(INGEST_DATABASE_NAMES.out.versions) + INTERSECT_DATABASE( regions.combine(INGEST_DATABASE_NAMES.out.output) .map{ meta1, regions, meta2, database -> [[id: "${meta1.id}-${meta2.id}", original_meta: meta1, min_overlap: meta2.min_overlap], regions, database] }, [[], []]) + ch_versions = ch_versions.mix(INTERSECT_DATABASE.out.versions) + ANNOTATE( INTERSECT_GTF.out.intersect .join(INTERSECT_DATABASE.out.intersect @@ -33,26 +35,11 @@ workflow ANNOTATION { .groupTuple(), remainder: true) .map{ meta, gtf_intersection, db_intersections -> [meta, gtf_intersection, db_intersections ?: []]}, exon_boundary ) - - ch_bed_merged = ANNOTATE.out.bed.filter{ meta, bed -> meta.tool == "merged" } - ch_gtf_merged = ANNOTATE.out.gtf.filter{ meta, gtf -> meta.tool == "merged" } - - COMBINE_BEDS(ch_bed_merged.map{ meta, bed -> bed}.collect().map{[[id: "annotation"], it]}) - REMOVE_SCORE_STRAND( COMBINE_BEDS.out.sorted, []) - COMBINE_GTFS(ch_gtf_merged.map{ meta, gtf -> gtf}.collect().map{[[id: "annotation"], it]}) - - ch_versions = ch_versions.mix(INTERSECT_GTF.out.versions) - ch_versions = ch_versions.mix(INGEST_DATABASE_NAMES.out.versions) - ch_versions = ch_versions.mix(INTERSECT_DATABASE.out.versions) ch_versions = ch_versions.mix(ANNOTATE.out.versions) - ch_versions = ch_versions.mix(COMBINE_BEDS.out.versions) - ch_versions = ch_versions.mix(REMOVE_SCORE_STRAND.out.versions) - ch_versions = ch_versions.mix(COMBINE_GTFS.out.versions) emit: - merged_bed = ch_bed_merged - bed = REMOVE_SCORE_STRAND.out.output - gtf = COMBINE_GTFS.out.sorted + bed = ANNOTATE.out.bed + gtf = ANNOTATE.out.gtf versions = ch_versions } diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 6e682f06..35205ac8 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -5,12 +5,9 @@ include { GNU_SORT as CONCAT_TOOLS_PER_SAMPLE } from '../../modules/nf-core/gnu/ include { BEDTOOLS_GROUPBY as COUNT_TOOLS } from '../../modules/nf-core/bedtools/groupby' include { GAWK as FILTER_MIN_TOOLS } from '../../modules/nf-core/gawk' include { GNU_SORT as CONCAT_SAMPLES } from '../../modules/nf-core/gnu/sort' -include { MERGE_TOOLS } from '../../modules/local/count_matrix/merge_tools' -include { MERGE_SAMPLES } from '../../modules/local/count_matrix/merge_samples' include { UPSET as UPSET_SAMPLES } from '../../modules/local/upset' include { UPSET as UPSET_ALL } from '../../modules/local/upset' include { BEDTOOLS_GETFASTA } from '../../modules/nf-core/bedtools/getfasta' -include { GAWK as ADD_BACKSPLICE } from '../../modules/nf-core/gawk' // SUBWORKFLOWS include { SEGEMEHL } from './discovery/segemehl' @@ -21,7 +18,6 @@ include { FIND_CIRC } from './discovery/find_circ' include { CIRIQUANT } from './discovery/ciriquant' include { DCC } from './discovery/dcc' include { MAPSPLICE } from './discovery/mapsplice' -include { ANNOTATION } from './discovery/annotation' workflow CIRCRNA_DISCOVERY { @@ -35,11 +31,7 @@ workflow CIRCRNA_DISCOVERY { chromosomes hisat2_index star_index - ch_annotation bsj_reads - tool_filter - duplicates_fun - exon_boundary main: ch_versions = Channel.empty() @@ -113,11 +105,12 @@ workflow CIRCRNA_DISCOVERY { ch_versions = ch_versions.mix(FILTER_BSJS.out.versions) // - // CREATE COUNT MATRIX + // MERGE BED FILES // MASK_SCORES( ch_bed, [] ) ch_versions = ch_versions.mix(MASK_SCORES.out.versions) + ch_bsj_bed_per_sample_tool = MASK_SCORES.out.output CONCAT_TOOLS_PER_SAMPLE( MASK_SCORES.out.output.map{ meta, bed -> [ [id: meta.id], bed ] }.groupTuple() @@ -129,24 +122,13 @@ workflow CIRCRNA_DISCOVERY { FILTER_MIN_TOOLS( COUNT_TOOLS.out.bed, [] ) ch_versions = ch_versions.mix(FILTER_MIN_TOOLS.out.versions) - - ch_bsjome_per_sample = FILTER_MIN_TOOLS.out.output + ch_bsj_bed_per_sample = FILTER_MIN_TOOLS.out.output CONCAT_SAMPLES( - ch_bsjome_per_sample.map{ meta, bed -> [[id: "all"], bed] }.groupTuple() + ch_bsj_bed_per_sample.map{ meta, bed -> [[id: "all"], bed] }.groupTuple() ) ch_versions = ch_versions.mix(CONCAT_SAMPLES.out.versions) - ch_bsjome = CONCAT_SAMPLES.out.sorted - - MERGE_TOOLS( ch_bed.map{ meta, bed -> [ [id: meta.id], bed ] }.groupTuple(), - tools_selected.size() > 1 ? tool_filter : 1, duplicates_fun ) - MERGE_SAMPLES( MERGE_TOOLS.out.merged.map{ meta, bed -> bed }.collect() ) - - ch_bed_incl_merged = ch_bed.mix( - MERGE_TOOLS.out.merged.map{ meta, bed -> [meta + [tool: "merged"], bed] }) - - ch_versions = ch_versions.mix(MERGE_TOOLS.out.versions) - ch_versions = ch_versions.mix(MERGE_SAMPLES.out.versions) + ch_bsj_bed_combined = CONCAT_SAMPLES.out.sorted // // UPSET PLOTS @@ -155,40 +137,42 @@ workflow CIRCRNA_DISCOVERY { UPSET_SAMPLES( ch_bed.map{ meta, bed -> [meta.id, meta.tool, bed]} .groupTuple() .map{ sample, tools, beds -> [[id: sample], tools, beds]} ) + ch_multiqc_files = ch_multiqc_files.mix(UPSET_SAMPLES.out.multiqc) + ch_versions = ch_versions.mix(UPSET_SAMPLES.out.versions) + UPSET_ALL( ch_bed.map{ meta, bed -> ["all", meta.tool, bed] } .groupTuple() .map{ sample, tools, beds -> [[id: sample], tools, beds]} ) - - ch_multiqc_files = ch_multiqc_files.mix(UPSET_SAMPLES.out.multiqc) ch_multiqc_files = ch_multiqc_files.mix(UPSET_ALL.out.multiqc) - ch_versions = ch_versions.mix(UPSET_SAMPLES.out.versions) ch_versions = ch_versions.mix(UPSET_ALL.out.versions) - // - // ANNOTATION WORKFLOW: - // - - ANNOTATION( ch_bed_incl_merged, gtf, exon_boundary, ch_annotation ) - ch_versions = ch_versions.mix(ANNOTATION.out.versions) - // // FASTA WORKFLOW: // - BEDTOOLS_GETFASTA( ANNOTATION.out.merged_bed, fasta ) - ADD_BACKSPLICE( BEDTOOLS_GETFASTA.out.fasta, []) - + BEDTOOLS_GETFASTA( + ch_bsj_bed_combined.mix(ch_bsj_bed_per_sample).mix(ch_bsj_bed_per_sample_tool), + fasta + ) ch_versions = ch_versions.mix(BEDTOOLS_GETFASTA.out.versions) - ch_versions = ch_versions.mix(ADD_BACKSPLICE.out.versions) + + ch_bsj_fasta = BEDTOOLS_GETFASTA.out.fasta.branch{ + meta, fasta -> + combined: meta.id == 'all' + per_sample_tool: meta.containsKey('tool') + per_sample: true + } emit: - circrna_bed12 = ANNOTATION.out.merged_bed - fasta = ADD_BACKSPLICE.out.output - annotation_bed = ANNOTATION.out.bed - annotation_gtf = ANNOTATION.out.gtf - counts_bed = MERGE_SAMPLES.out.counts_bed - counts_tsv = MERGE_SAMPLES.out.counts_tsv - - multiqc_files = ch_multiqc_files - versions = ch_versions + bsj_bed_combined = ch_bsj_bed_combined + bsj_fasta_combined = ch_bsj_fasta.combined + + bsj_bed_per_sample = ch_bsj_bed_per_sample + bsj_fasta_per_sample = ch_bsj_fasta.per_sample + + bsj_bed_per_sample_tool = ch_bsj_bed_per_sample_tool + bsj_fasta_per_sample_tool = ch_bsj_fasta.per_sample_tool + + multiqc_files = ch_multiqc_files + versions = ch_versions } diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index cdd6f86d..1bf7623f 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -1,7 +1,8 @@ -include { TARGETSCAN_DATABASE } from '../../modules/local/targetscan/database/main' -include { TARGETSCAN } from '../../modules/local/targetscan/predict/main' -include { MIRANDA } from '../../modules/nf-core/miranda/main' -include { MIRNA_TARGETS } from '../../modules/local/mirna_targets/main' +include { GAWK as ADD_BACKSPLICE } from '../../modules/nf-core/gawk' +include { TARGETSCAN_DATABASE } from '../../modules/local/targetscan/database/main' +include { TARGETSCAN } from '../../modules/local/targetscan/predict/main' +include { MIRANDA } from '../../modules/nf-core/miranda/main' +include { MIRNA_TARGETS } from '../../modules/local/mirna_targets/main' workflow MIRNA_PREDICTION{ @@ -13,6 +14,9 @@ workflow MIRNA_PREDICTION{ main: ch_versions = Channel.empty() + ADD_BACKSPLICE( circrna_fasta, [] ) + ch_versions = ch_versions.mix(ADD_BACKSPLICE.out.versions) + // // TARGETSCAN WORKFLOW: // diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 0d852ae7..aa7f4ea3 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -29,6 +29,7 @@ include { validateInputSamplesheet } from '../../subworkflows/local/util include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' include { PREPARE_GENOME } from '../../subworkflows/local/prepare_genome' include { CIRCRNA_DISCOVERY } from '../../subworkflows/local/circrna_discovery' +include { ANNOTATION } from '../../subworkflows/local/annotation' include { QUANTIFICATION } from '../../subworkflows/local/quantification' include { MIRNA_PREDICTION } from '../../subworkflows/local/mirna_prediction' include { STATISTICAL_TESTS } from '../../subworkflows/local/statistical_tests' @@ -145,27 +146,35 @@ workflow CIRCRNA { chromosomes, hisat2_index, star_index, - ch_annotation, params.bsj_reads, - params.tool_filter, - params.duplicates_fun, - params.exon_boundary ) ch_multiqc_files = ch_multiqc_files.mix(CIRCRNA_DISCOVERY.out.multiqc_files) ch_versions = ch_versions.mix(CIRCRNA_DISCOVERY.out.versions) // - // 3. Quantification + // 3. circRNA Annotation + // + + ANNOTATION( + CIRCRNA_DISCOVERY.out.bsj_bed_combined, + ch_gtf, + params.exon_boundary, + ch_annotation + ) + ch_versions = ch_versions.mix(ANNOTATION.out.versions) + + // + // 4. circRNA quantification // QUANTIFICATION( ch_gtf, ch_fasta, - CIRCRNA_DISCOVERY.out.counts_bed, + CIRCRNA_DISCOVERY.out.bsj_bed_combined, FASTQC_TRIMGALORE.out.reads, - CIRCRNA_DISCOVERY.out.annotation_bed, - CIRCRNA_DISCOVERY.out.annotation_gtf, + ANNOTATION.out.bed, + ANNOTATION.out.gtf, params.bootstrap_samples, ch_phenotype, PREPARE_GENOME.out.faidx @@ -174,19 +183,19 @@ workflow CIRCRNA { ch_versions = ch_versions.mix(QUANTIFICATION.out.versions) // - // 4. miRNA prediction + // 5. miRNA prediction // if (params.mature) { MIRNA_PREDICTION( - CIRCRNA_DISCOVERY.out.fasta, - CIRCRNA_DISCOVERY.out.circrna_bed12, + CIRCRNA_DISCOVERY.out.bsj_fasta_combined, + ANNOTATION.out.bed, ch_mature ) ch_versions = ch_versions.mix(MIRNA_PREDICTION.out.versions) } // - // 5. Statistical tests + // 6. Statistical tests // STATISTICAL_TESTS( From 8509cb015306e64c62aee5eb2a8454629b559a66 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 16:22:49 +0200 Subject: [PATCH 346/491] Fix bug in tool filtering --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 8f0bfc8d..4efbd418 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -604,7 +604,7 @@ process { withName: 'FILTER_MIN_TOOLS' { // Keep only rows with at least the minimum number of tools // Replace the score column with a dot - ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (\$5 >= ${params.tool_filter}) { print \$1, \$2, \$3, \$4, \".\", \$6 } }'" + ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (\$6 >= ${params.tool_filter}) { print \$1, \$2, \$3, \$4, \".\", \$5 } }'" ext.suffix = {"filtered.bed"} } From d26712ef1e433de1aaf34751d1331e821399b91f Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 17:15:53 +0200 Subject: [PATCH 347/491] Fix saveAs conditions --- conf/modules.config | 103 +++++++++++++++----------------------------- 1 file changed, 35 insertions(+), 68 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 4efbd418..41e0dd13 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -65,8 +65,7 @@ process { publishDir = [ path: { "${params.outdir}/references/clean_fasta" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_reference + saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null } ] } @@ -79,8 +78,7 @@ process { publishDir = [ path: { "${params.outdir}/references/chromosomes" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_reference + saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null } ] } @@ -89,8 +87,7 @@ process { publishDir = [ path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_reference + saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null } ] } @@ -99,8 +96,7 @@ process { publishDir = [ path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_reference + saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null } ] } @@ -109,8 +105,7 @@ process { publishDir = [ path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_reference + saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null } ] } @@ -119,8 +114,7 @@ process { publishDir = [ path: { "${params.outdir}/references/index/hisat2" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_reference + saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null } ] } @@ -129,8 +123,7 @@ process { publishDir = [ path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_reference + saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null } ] } @@ -142,8 +135,7 @@ process { publishDir = [ path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_reference + saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null } ] } @@ -153,8 +145,7 @@ process { publishDir = [ path: { "${params.outdir}/references/index/segemehl" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_reference + saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null } ] } @@ -164,10 +155,9 @@ process { "-S" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/circrna_discovery/segemehl/intermediates/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/segemehl/raw" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } @@ -193,7 +183,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$4, \$6, \$5 }'" ext.suffix = "segemehl.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/segemehl/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/segemehl/unified" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.segemehl.bed" @@ -216,8 +206,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/star/1st_pass" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } @@ -225,8 +214,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/star/sjdb" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } @@ -246,8 +234,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/star/2nd_pass" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } @@ -259,8 +246,7 @@ process { publishDir = [ path: { "${params.outdir}/references/circexplorer2" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_reference + saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null } ] } @@ -268,8 +254,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } @@ -277,8 +262,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } @@ -297,8 +281,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/circrna_finder/intermediates/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null }, pattern: "*.bed" ] } @@ -321,8 +304,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } @@ -332,8 +314,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } @@ -341,8 +322,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } @@ -352,8 +332,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } @@ -373,8 +352,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/ciriquant/intermediates/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } @@ -409,8 +387,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/dcc/intermediates/mate1/1st_pass" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } @@ -418,8 +395,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/dcc/intermediates/mate1/sjdb" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } @@ -440,8 +416,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/dcc/intermediates/mate1/2nd_pass" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } @@ -461,8 +436,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/dcc/intermediates/mate2/1st_pass" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } @@ -470,8 +444,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/dcc/intermediates/mate2/sjdb" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } @@ -492,8 +465,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/dcc/intermediates/mate2/2nd_pass" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } @@ -501,8 +473,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/dcc/intermediates/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } @@ -525,8 +496,7 @@ process { publishDir = [ path: { "${params.outdir}/references/mapsplice" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_reference + saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null } ] } @@ -542,8 +512,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } @@ -551,8 +520,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } @@ -560,8 +528,7 @@ process { publishDir = [ path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - enabled: params.save_intermediates + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] } From b45cea81abfcab53e8925a6dd14e93d7a47ad59e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 17:28:34 +0200 Subject: [PATCH 348/491] Fix some output definitions --- conf/modules.config | 24 +++++++++++------------- 1 file changed, 11 insertions(+), 13 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 41e0dd13..7ae54354 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -604,24 +604,22 @@ process { ext.suffix = "annotated.bed" } - withName: '.*:ANNOTATION:COMBINE_BEDS' { - ext.args = "-k 1,1 -k2,2n -k3,3n -u" - ext.suffix = "combined.bed" - } - - withName: '.*:ANNOTATION:COMBINE_GTFS' { - ext.args = "-k 1,1 -k4,4n -k5,5n -u" - ext.suffix = "combined.gtf" - } - - withName: '.*:ANNOTATION:REMOVE_SCORE_STRAND' { - ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3, \".\", \".\", \$7, \$8, \$9, \$10, \$11 }'" - ext.suffix = "tidy.bed" + withName: '.*:ANNOTATION:ANNOTATE' { + publishDir = [ + path: { "${params.outdir}/annotation" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] } withName: ADD_BACKSPLICE { ext.args = "'{ if (/^>/) { print \$0 } else { start = substr(\$0, 1, 25); print \$0 start } }'" ext.suffix = "backspliced.fa" + publishDir = [ + path: { "${params.outdir}/mirna_prediction" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] } withName: COMBINE_TRANSCRIPTOME_GTFS { From 11892e281e452404ce181976e0d1b6e781303b14 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 17:39:04 +0200 Subject: [PATCH 349/491] Add per-sample and combined output directories for discovery --- conf/modules.config | 29 +++++++++++++++++++++++++++-- 1 file changed, 27 insertions(+), 2 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 7ae54354..ac71479e 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -565,7 +565,12 @@ process { // Count the number of tools that support each circRNA ext.summary_col = 5 ext.args = "-g 1,2,3,4,6 -o count" - ext.suffix = {"grouped.bed"} + ext.suffix = {"tool_counts.bed"} + publishDir = [ + path: { "${params.outdir}/circrna_discovery/samples/${meta.id}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } + ] } withName: 'FILTER_MIN_TOOLS' { @@ -573,20 +578,40 @@ process { // Replace the score column with a dot ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (\$6 >= ${params.tool_filter}) { print \$1, \$2, \$3, \$4, \".\", \$5 } }'" ext.suffix = {"filtered.bed"} + publishDir = [ + path: { "${params.outdir}/circrna_discovery/samples/${meta.id}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] } withName: 'CONCAT_SAMPLES' { // GNU sort by columns 1,2,3,4,6 ext.args = "-k1,1 -k2,2n -k3,3n -k4,4 -k6,6 -u" - ext.suffix = {"sorted.bed"} + ext.suffix = {"combined.bed"} + publishDir = [ + path: { "${params.outdir}/circrna_discovery/combined" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] } withName: UPSET_SAMPLES { ext.when = { params.tool.split(',').length > 1 } + publishDir = [ + path: { "${params.outdir}/circrna_discovery/samples/${meta.id}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] } withName: UPSET_ALL { ext.when = { params.tool.split(',').length > 1 } + publishDir = [ + path: { "${params.outdir}/circrna_discovery/combined" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] } withName: '.*:ANNOTATION:INTERSECT_GTF' { From a0f3e731060212f14efab1c8ec5dbcb7ed3f44d0 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 17:44:07 +0200 Subject: [PATCH 350/491] Add tools subdirectory to discovery outdir --- conf/modules.config | 58 ++++++++++++++++++++++----------------------- 1 file changed, 29 insertions(+), 29 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index ac71479e..21241788 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -155,7 +155,7 @@ process { "-S" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/circrna_discovery/segemehl/raw" }, + path: { "${params.outdir}/circrna_discovery/tools/segemehl/raw" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -183,7 +183,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$4, \$6, \$5 }'" ext.suffix = "segemehl.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/segemehl/unified" }, + path: { "${params.outdir}/circrna_discovery/tools/segemehl/unified" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.segemehl.bed" @@ -204,7 +204,7 @@ process { "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/circrna_discovery/star/1st_pass" }, + path: { "${params.outdir}/circrna_discovery/tools/star/1st_pass" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -212,7 +212,7 @@ process { withName: '.*:STAR2PASS:SJDB' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/star/sjdb" }, + path: { "${params.outdir}/circrna_discovery/tools/star/sjdb" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -232,7 +232,7 @@ process { "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/circrna_discovery/star/2nd_pass" }, + path: { "${params.outdir}/circrna_discovery/tools/star/2nd_pass" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -252,7 +252,7 @@ process { withName: '.*:CIRCEXPLORER2:PARSE' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/circexplorer2/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -260,7 +260,7 @@ process { withName: '.*:CIRCEXPLORER2:ANNOTATE' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/circexplorer2/intermediates/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/circexplorer2/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -270,7 +270,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$13, \$6 }'" ext.suffix = "circexplorer2.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/circexplorer2/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/circexplorer2/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.circexplorer2.bed" @@ -279,7 +279,7 @@ process { withName: '.*:CIRCRNA_FINDER:MAIN' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/circrna_finder/intermediates/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/circrna_finder/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null }, pattern: "*.bed" @@ -290,7 +290,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$5, \$6 }'" ext.suffix = "circrna_finder.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/circrna_finder/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/circrna_finder/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.circrna_finder.bed" @@ -302,7 +302,7 @@ process { (!meta.strandedness || meta.strandedness == 'unstranded' || meta.strandedness == 'auto' ? '' : meta.strandedness == 'forward' ? ' --norc' : ' --nofw') } publishDir = [ - path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -312,7 +312,7 @@ process { ext.prefix = { "${meta.id}_unmapped" } ext.args = "-hf 4" publishDir = [ - path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -320,7 +320,7 @@ process { withName: '.*:FIND_CIRC:ANCHORS' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -330,7 +330,7 @@ process { ext.args = { !meta.strandedness || meta.strandedness == 'unstranded' || meta.strandedness == 'auto' ? '' : meta.strandedness == 'forward' ? ' --norc' : ' --nofw' } publishDir = [ - path: { "${params.outdir}/circrna_discovery/find_circ/intermediates/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -341,7 +341,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (\$18 ~ /CIRCULAR/ && \$18 ~ /UNAMBIGUOUS_BP/ && \$18 ~ /ANCHOR_UNIQUE/) { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$5, \$6 } }'" ext.suffix = "find_circ.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/find_circ/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/find_circ/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.find_circ.bed" @@ -350,7 +350,7 @@ process { withName: '.*:CIRIQUANT:MAIN' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/ciriquant/intermediates/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/ciriquant/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -364,7 +364,7 @@ process { ext.suffix = "ciriquant.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/ciriquant/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/ciriquant/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.ciriquant.bed" @@ -385,7 +385,7 @@ process { "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/circrna_discovery/dcc/intermediates/mate1/1st_pass" }, + path: { "${params.outdir}/circrna_discovery/tools/dcc/intermediates/mate1/1st_pass" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -393,7 +393,7 @@ process { withName: '.*:DCC:MATE1_SJDB' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/dcc/intermediates/mate1/sjdb" }, + path: { "${params.outdir}/circrna_discovery/tools/dcc/intermediates/mate1/sjdb" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -414,7 +414,7 @@ process { "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/circrna_discovery/dcc/intermediates/mate1/2nd_pass" }, + path: { "${params.outdir}/circrna_discovery/tools/dcc/intermediates/mate1/2nd_pass" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -434,7 +434,7 @@ process { "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/circrna_discovery/dcc/intermediates/mate2/1st_pass" }, + path: { "${params.outdir}/circrna_discovery/tools/dcc/intermediates/mate2/1st_pass" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -442,7 +442,7 @@ process { withName: '.*:DCC:MATE2_SJDB' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/dcc/intermediates/mate2/sjdb" }, + path: { "${params.outdir}/circrna_discovery/tools/dcc/intermediates/mate2/sjdb" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -463,7 +463,7 @@ process { "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/circrna_discovery/dcc/intermediates/mate2/2nd_pass" }, + path: { "${params.outdir}/circrna_discovery/tools/dcc/intermediates/mate2/2nd_pass" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -471,7 +471,7 @@ process { withName: '.*:DCC:MAIN' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/dcc/intermediates/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/dcc/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -481,7 +481,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$4, \$5, \$4 }'" ext.suffix = "dcc.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/dcc/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/dcc/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.dcc.bed" @@ -510,7 +510,7 @@ process { "--fusion-non-canonical" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/mapsplice/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -518,7 +518,7 @@ process { withName: '.*:MAPSPLICE:PARSE' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/mapsplice/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -526,7 +526,7 @@ process { withName: '.*:MAPSPLICE:ANNOTATE' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/mapsplice/intermediates/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/mapsplice/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -536,7 +536,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$10, \$6 }'" ext.suffix = "mapsplice.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/mapsplice/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/mapsplice/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.mapsplice.bed" From ea4ef3442ffc6c79748cd5ccfe40f8446acd6171 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 17:48:22 +0200 Subject: [PATCH 351/491] Implement separate processes for FASTA extraction --- subworkflows/local/circrna_discovery.nf | 47 +++++++++++++------------ 1 file changed, 24 insertions(+), 23 deletions(-) diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 35205ac8..b0ed9288 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -1,13 +1,15 @@ // MODULES -include { GAWK as FILTER_BSJS } from '../../modules/nf-core/gawk' -include { GAWK as MASK_SCORES } from '../../modules/nf-core/gawk' -include { GNU_SORT as CONCAT_TOOLS_PER_SAMPLE } from '../../modules/nf-core/gnu/sort' -include { BEDTOOLS_GROUPBY as COUNT_TOOLS } from '../../modules/nf-core/bedtools/groupby' -include { GAWK as FILTER_MIN_TOOLS } from '../../modules/nf-core/gawk' -include { GNU_SORT as CONCAT_SAMPLES } from '../../modules/nf-core/gnu/sort' -include { UPSET as UPSET_SAMPLES } from '../../modules/local/upset' -include { UPSET as UPSET_ALL } from '../../modules/local/upset' -include { BEDTOOLS_GETFASTA } from '../../modules/nf-core/bedtools/getfasta' +include { GAWK as FILTER_BSJS } from '../../modules/nf-core/gawk' +include { GAWK as MASK_SCORES } from '../../modules/nf-core/gawk' +include { GNU_SORT as CONCAT_TOOLS_PER_SAMPLE } from '../../modules/nf-core/gnu/sort' +include { BEDTOOLS_GROUPBY as COUNT_TOOLS } from '../../modules/nf-core/bedtools/groupby' +include { GAWK as FILTER_MIN_TOOLS } from '../../modules/nf-core/gawk' +include { GNU_SORT as CONCAT_SAMPLES } from '../../modules/nf-core/gnu/sort' +include { UPSET as UPSET_SAMPLES } from '../../modules/local/upset' +include { UPSET as UPSET_ALL } from '../../modules/local/upset' +include { BEDTOOLS_GETFASTA as FASTA_COMBINED } from '../../modules/nf-core/bedtools/getfasta' +include { BEDTOOLS_GETFASTA as FASTA_PER_SAMPLE } from '../../modules/nf-core/bedtools/getfasta' +include { BEDTOOLS_GETFASTA as FASTA_PER_SAMPLE_TOOL } from '../../modules/nf-core/bedtools/getfasta' // SUBWORKFLOWS include { SEGEMEHL } from './discovery/segemehl' @@ -150,28 +152,27 @@ workflow CIRCRNA_DISCOVERY { // FASTA WORKFLOW: // - BEDTOOLS_GETFASTA( - ch_bsj_bed_combined.mix(ch_bsj_bed_per_sample).mix(ch_bsj_bed_per_sample_tool), - fasta - ) - ch_versions = ch_versions.mix(BEDTOOLS_GETFASTA.out.versions) + FASTA_COMBINED( ch_bsj_bed_combined, fasta ) + ch_versions = ch_versions.mix(FASTA_COMBINED.out.versions) + ch_bsj_fasta_combined = FASTA_COMBINED.out.fasta - ch_bsj_fasta = BEDTOOLS_GETFASTA.out.fasta.branch{ - meta, fasta -> - combined: meta.id == 'all' - per_sample_tool: meta.containsKey('tool') - per_sample: true - } + FASTA_PER_SAMPLE( ch_bsj_bed_per_sample, fasta ) + ch_versions = ch_versions.mix(FASTA_PER_SAMPLE.out.versions) + ch_bsj_fasta_per_sample = FASTA_PER_SAMPLE.out.fasta + + FASTA_PER_SAMPLE_TOOL( ch_bsj_bed_per_sample_tool, fasta ) + ch_versions = ch_versions.mix(FASTA_PER_SAMPLE_TOOL.out.versions) + ch_bsj_fasta_per_sample_tool = FASTA_PER_SAMPLE_TOOL.out.fasta emit: bsj_bed_combined = ch_bsj_bed_combined - bsj_fasta_combined = ch_bsj_fasta.combined + bsj_fasta_combined = ch_bsj_fasta_combined bsj_bed_per_sample = ch_bsj_bed_per_sample - bsj_fasta_per_sample = ch_bsj_fasta.per_sample + bsj_fasta_per_sample = ch_bsj_fasta_per_sample bsj_bed_per_sample_tool = ch_bsj_bed_per_sample_tool - bsj_fasta_per_sample_tool = ch_bsj_fasta.per_sample_tool + bsj_fasta_per_sample_tool = ch_bsj_fasta_per_sample_tool multiqc_files = ch_multiqc_files versions = ch_versions From 8e7e441b800a5b016d63dac2a3f63e56c12e6815 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 18:00:18 +0200 Subject: [PATCH 352/491] Add fastas to discovery output --- conf/modules.config | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index 21241788..a1f4394b 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -614,6 +614,33 @@ process { ] } + withName: FASTA_COMBINED { + ext.suffix = "fasta" + publishDir = [ + path: { "${params.outdir}/circrna_discovery/combined" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: FASTA_PER_SAMPLE { + ext.suffix = "fasta" + publishDir = [ + path: { "${params.outdir}/circrna_discovery/samples/${meta.id}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: FASTA_PER_SAMPLE_TOOL { + ext.suffix = { "${meta.tool}.fasta" } + publishDir = [ + path: { "${params.outdir}/circrna_discovery/tools/${meta.tool}/${meta.id}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + withName: '.*:ANNOTATION:INTERSECT_GTF' { ext.args = "-loj" ext.suffix = "intersect.bed" From 4e9f4abcaaba5b4981fda5236471b9ab4183c96a Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 18:06:56 +0200 Subject: [PATCH 353/491] Add output directory for statistical tests --- conf/modules.config | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index a1f4394b..f3dbfd75 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -26,6 +26,14 @@ process { ] } + withName: CAT_FASTQ { + publishDir = [ + path: { "${params.outdir}/preprocessing/merged_samples" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + // TRIMMING courtesy of nf-core/rnaseq if (!params.skip_trimming) { @@ -749,4 +757,12 @@ process { pattern: "*.txt" ] } + + withName: CIRCTEST_CIRCTEST { + publishDir = [ + path: { "${params.outdir}/statistical_tests/circtest" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } } From 4e2ce6cca687bde955b775949179bdcce3718121 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 18:08:15 +0200 Subject: [PATCH 354/491] Handle output of circtest_prepare --- conf/modules.config | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index f3dbfd75..7f072016 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -758,6 +758,14 @@ process { ] } + withName: CIRCTEST_PREPARE { + publishDir = [ + path: { "${params.outdir}/statistical_tests/circtest" }, + mode: params.publish_dir_mode, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } + ] + } + withName: CIRCTEST_CIRCTEST { publishDir = [ path: { "${params.outdir}/statistical_tests/circtest" }, From ca5e4b664113706ac13f9c63deb9e8a7dccea8ae Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 20:22:42 +0200 Subject: [PATCH 355/491] Improve QC output directory structure --- conf/modules.config | 77 +++++++++++++++++++++++++++------------------ 1 file changed, 46 insertions(+), 31 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 7f072016..5bda6597 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -34,37 +34,34 @@ process { ] } - // TRIMMING courtesy of nf-core/rnaseq - - if (!params.skip_trimming) { - process { - withName: '.*:FASTQC_TRIMGALORE:TRIMGALORE' { - ext.args = { - [ - "--fastqc_args '-t ${task.cpus}' ", - params.trim_nextseq > 0 ? "--nextseq ${params.trim_nextseq}" : '' - ].join(' ').trim() - } - publishDir = [ - [ - path: { "${params.outdir}/quality_control/trimgalore/fastqc" }, - mode: params.publish_dir_mode, - pattern: "*.{html,zip}" - ], - [ - path: { "${params.outdir}/quality_control/trimgalore" }, - mode: params.publish_dir_mode, - pattern: "*.fq.gz", - enabled: params.save_trimmed - ], - [ - path: { "${params.outdir}/quality_control/trimgalore" }, - mode: params.publish_dir_mode, - pattern: "*.txt" - ] - ] - } + withName: '.*:FASTQC_TRIMGALORE:FASTQC' { + publishDir = [ + path: { "${params.outdir}/quality_control/fastqc" }, + mode: params.publish_dir_mode, + pattern: "*.{html,zip}" + ] + } + + withName: '.*:FASTQC_TRIMGALORE:TRIMGALORE' { + ext.args = { + [ + "--fastqc_args '-t ${task.cpus}' ", + params.trim_nextseq > 0 ? "--nextseq ${params.trim_nextseq}" : '' + ].join(' ').trim() } + publishDir = [ + [ + path: { "${params.outdir}/quality_control/trimgalore" }, + mode: params.publish_dir_mode, + pattern: "*.fq.gz", + enabled: params.save_trimmed + ], + [ + path: { "${params.outdir}/quality_control/trimgalore" }, + mode: params.publish_dir_mode, + pattern: "*.txt" + ] + ] } // PREPARE GENOME @@ -567,6 +564,11 @@ process { // GNU sort by columns 1,2,3,4,6 ext.args = "-k1,1 -k2,2n -k3,3n -k4,4 -k6,6" ext.suffix = {"sorted.bed"} + publishDir = [ + path: { "${params.outdir}/circrna_discovery/samples/${meta.id}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> null } // The same data will be published in COUNT_TOOLS in a better format + ] } withName: 'COUNT_TOOLS' { @@ -684,7 +686,12 @@ process { withName: COMBINE_TRANSCRIPTOME_GTFS { ext.args = "-k 1,1 -k4,4n -k5,5n" - ext.suffix = "gtf" + ext.suffix = "combined.gtf" + publishDir = [ + path: { "${params.outdir}/quantification" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] } withName: EXCLUDE_OVERLONG_TRANSCRIPTS { @@ -700,6 +707,14 @@ process { ext.suffix = "marked.fasta" } + withName: 'CUSTOM_TX2GENE' { + publishDir = [ + path: { "${params.outdir}/quantification/tx2gene" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + withName: ".*:JOIN_(GENE|TX)_(COUNTS|TPM)" { ext.args = "-f 1,2 -t" label = "process_medium" From f78404efdca51ea94af9658c001581a0cc519bfa Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 20:33:55 +0200 Subject: [PATCH 356/491] Unify discovery tool output directories --- conf/modules.config | 34 +++++++++++++++++++++++++++------- 1 file changed, 27 insertions(+), 7 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 5bda6597..45ea43b4 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -171,17 +171,32 @@ process { // Print $1 $2 $3 $1:$2-$3 $5 $6 ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (\$4 ~ /;C;/) { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$5, \$6 } }'" ext.suffix = "segemehl_extracted.bed" + publishDir = [ + path: { "${params.outdir}/circrna_discovery/tools/segemehl/extracted" }, + mode: params.publish_dir_mode, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } + ] } withName: '.*:SEGEMEHL:SORT' { ext.args = "-k1,1 -k2,2n -k3,3n -k4,4 -k6,6" ext.suffix = "segemehl_sorted.bed" + publishDir = [ + path: { "${params.outdir}/circrna_discovery/tools/segemehl/sorted" }, + mode: params.publish_dir_mode, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } + ] } withName: '.*:SEGEMEHL:GROUP' { ext.summary_col = 5 ext.args = "-g 1,2,3,4,6 -o count" ext.suffix = "segemehl_grouped.bed" + publishDir = [ + path: { "${params.outdir}/circrna_discovery/tools/segemehl/grouped" }, + mode: params.publish_dir_mode, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } + ] } withName: '.*:SEGEMEHL:UNIFY' { @@ -275,7 +290,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$13, \$6 }'" ext.suffix = "circexplorer2.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/circexplorer2/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/circexplorer2/unified" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.circexplorer2.bed" @@ -295,7 +310,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$5, \$6 }'" ext.suffix = "circrna_finder.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/circrna_finder/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/circrna_finder/unified" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.circrna_finder.bed" @@ -346,7 +361,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (\$18 ~ /CIRCULAR/ && \$18 ~ /UNAMBIGUOUS_BP/ && \$18 ~ /ANCHOR_UNIQUE/) { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$5, \$6 } }'" ext.suffix = "find_circ.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/find_circ/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/find_circ/unified" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.find_circ.bed" @@ -369,7 +384,7 @@ process { ext.suffix = "ciriquant.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/ciriquant/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/ciriquant/unified" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.ciriquant.bed" @@ -486,7 +501,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$4, \$5, \$4 }'" ext.suffix = "dcc.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/dcc/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/dcc/unified" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.dcc.bed" @@ -541,7 +556,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$10, \$6 }'" ext.suffix = "mapsplice.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/mapsplice/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/mapsplice/unified" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.mapsplice.bed" @@ -645,7 +660,7 @@ process { withName: FASTA_PER_SAMPLE_TOOL { ext.suffix = { "${meta.tool}.fasta" } publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/${meta.tool}/${meta.id}" }, + path: { "${params.outdir}/circrna_discovery/tools/${meta.tool}/fasta" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -697,6 +712,11 @@ process { withName: EXCLUDE_OVERLONG_TRANSCRIPTS { ext.args = "-v FS='\\t' -v OFS='\\t' '\$5-\$4 <= 10000 { print }'" ext.suffix = "filtered.gtf" + publishDir = [ + path: { "${params.outdir}/quantification" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] } withName: MARK_CIRCULAR { From 654caa5f0b62e4c5ac4856dbc88b39483189411f Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 21:09:31 +0200 Subject: [PATCH 357/491] Improve quantification outdir structure --- conf/modules.config | 39 +++++++++++++++++++++++++++++++++++---- 1 file changed, 35 insertions(+), 4 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 45ea43b4..4ead8236 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -76,6 +76,11 @@ process { withName: GTFFILTER { ext.suffix = "filtered.gtf" + publishDir = [ + path: { "${params.outdir}/references/filtered_gtf" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + ] } withName: SEQKIT_SPLIT { @@ -567,12 +572,22 @@ process { // Make sure score is higher or equal to the threshold ext.args = { "-v FS='\\t' -v OFS='\\t' '{ if (\$5 >= ${params.bsj_reads}) { print } }'" } ext.suffix = {"${meta.tool}.filtered.bed"} + publishDir = [ + path: { "${params.outdir}/circrna_discovery/tools/${meta.tool}/filtered" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + ] } withName: 'MASK_SCORES' { // Take bed file and replace the score column with a dot ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$4, \".\", \$6 }'" ext.suffix = {"${meta.tool}.masked.bed"} + publishDir = [ + path: { "${params.outdir}/circrna_discovery/tools/${meta.tool}/masked" }, + mode: params.publish_dir_mode, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } + ] } withName: 'CONCAT_TOOLS_PER_SAMPLE' { @@ -703,7 +718,7 @@ process { ext.args = "-k 1,1 -k4,4n -k5,5n" ext.suffix = "combined.gtf" publishDir = [ - path: { "${params.outdir}/quantification" }, + path: { "${params.outdir}/quantification/transcriptome" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -713,7 +728,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '\$5-\$4 <= 10000 { print }'" ext.suffix = "filtered.gtf" publishDir = [ - path: { "${params.outdir}/quantification" }, + path: { "${params.outdir}/quantification/transcriptome" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -727,6 +742,22 @@ process { ext.suffix = "marked.fasta" } + withName: PSIRC_INDEX { + publishDir = [ + path: { "${params.outdir}/references/psirc" }, + mode: params.publish_dir_mode, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null } + ] + } + + withName: PSIRC_QUANT { + publishDir = [ + path: { "${params.outdir}/quantification/psirc" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + withName: 'CUSTOM_TX2GENE' { publishDir = [ path: { "${params.outdir}/quantification/tx2gene" }, @@ -740,7 +771,7 @@ process { label = "process_medium" maxRetries = 3 publishDir = [ - path: { "${params.outdir}/quantification/" }, + path: { "${params.outdir}/quantification/matrices" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -748,7 +779,7 @@ process { withName: ".*:SPLIT_TYPES_(COUNTS|TPM)" { publishDir = [ - path: { "${params.outdir}/quantification/" }, + path: { "${params.outdir}/quantification/matrices" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] From 395febd9cfaf1d01fcb828758f55fad5d10032d6 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 21:21:23 +0200 Subject: [PATCH 358/491] Improve quantification outdir structure --- conf/modules.config | 24 ++++++++++++++++++++---- 1 file changed, 20 insertions(+), 4 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 4ead8236..2c460abe 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -752,7 +752,7 @@ process { withName: PSIRC_QUANT { publishDir = [ - path: { "${params.outdir}/quantification/psirc" }, + path: { "${params.outdir}/quantification/samples/${meta.id}/psirc" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -760,7 +760,23 @@ process { withName: 'CUSTOM_TX2GENE' { publishDir = [ - path: { "${params.outdir}/quantification/tx2gene" }, + path: { "${params.outdir}/quantification/transcriptome" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: TXIMETA_TXIMETA { + publishDir = [ + path: { "${params.outdir}/quantification/samples/${meta.id}/tximeta" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: TXIMETA_TXIMPORT { + publishDir = [ + path: { "${params.outdir}/quantification/samples/${meta.id}/tximport" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -771,7 +787,7 @@ process { label = "process_medium" maxRetries = 3 publishDir = [ - path: { "${params.outdir}/quantification/matrices" }, + path: { "${params.outdir}/quantification/combined" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -779,7 +795,7 @@ process { withName: ".*:SPLIT_TYPES_(COUNTS|TPM)" { publishDir = [ - path: { "${params.outdir}/quantification/matrices" }, + path: { "${params.outdir}/quantification/combined" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] From 45cfd02de5d5abc216bff3f789fd0d78394b5cff Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 21:37:20 +0200 Subject: [PATCH 359/491] Make some more outdir optimizations --- conf/modules.config | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index 2c460abe..51940524 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -34,6 +34,14 @@ process { ] } + withName: SAMTOOLS_FAIDX { + publishDir = [ + path: { "${params.outdir}/references/index/fasta" }, + mode: params.publish_dir_mode, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null } + ] + } + withName: '.*:FASTQC_TRIMGALORE:FASTQC' { publishDir = [ path: { "${params.outdir}/quality_control/fastqc" }, @@ -333,6 +341,14 @@ process { ] } + withName: '.*:FIND_CIRC:SAMTOOLS_INDEX' { + publishDir = [ + path: { "${params.outdir}/circrna_discovery/tools/find_circ/intermediates/${meta.id}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } + ] + } + withName: '.*:FIND_CIRC:SAMTOOLS_VIEW' { ext.prefix = { "${meta.id}_unmapped" } ext.args = "-hf 4" @@ -734,12 +750,25 @@ process { ] } + withName: TRANSCRIPTOME { + publishDir = [ + path: { "${params.outdir}/quantification/transcriptome" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + withName: MARK_CIRCULAR { // GAWK process that marks FASTA headers. // Leaves headers starting with "ENS" and non-header lines as is. // Adds "\tC" to the end of the header for all other headers ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (!/^>circ_/) { print } else { print \$1 \"\\tC\" } }'" ext.suffix = "marked.fasta" + publishDir = [ + path: { "${params.outdir}/quantification/transcriptome" }, + mode: params.publish_dir_mode, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } + ] } withName: PSIRC_INDEX { @@ -801,6 +830,14 @@ process { ] } + withName: MERGE_EXPERIMENTS { + publishDir = [ + path: { "${params.outdir}/quantification/combined" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + withName: TARGETSCAN_DATABASE { publishDir = [ path: { "${params.outdir}/references/targetscan" }, From dd682fb1ad6c96c12c45ec40f18df313d037ea62 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 21:41:35 +0200 Subject: [PATCH 360/491] Remove tool reference in mirna outdir --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 51940524..2ff7a549 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -870,7 +870,7 @@ process { withName: MIRNA_TARGETS { publishDir = [ - path: { "${params.outdir}/mirna_prediction/${meta.tool}" }, + path: { "${params.outdir}/mirna_prediction/combined" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.txt" From baf6d37ae2ee2bf508c9f94d61e86e17aa565b3f Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 22:20:07 +0200 Subject: [PATCH 361/491] Add annotation back to discovery --- conf/modules.config | 26 +++++++++++--- subworkflows/local/annotation.nf | 1 - subworkflows/local/circrna_discovery.nf | 45 ++++++++++++++++++++----- subworkflows/local/quantification.nf | 1 - workflows/circrna/main.nf | 29 +++++----------- 5 files changed, 67 insertions(+), 35 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 2ff7a549..13951291 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -697,24 +697,40 @@ process { ] } - withName: '.*:ANNOTATION:INTERSECT_GTF' { + withName: '.*:ANNOTATE_(COMBINED|PER_SAMPLE|PER_SAMPLE_TOOL):INTERSECT_GTF' { ext.args = "-loj" ext.suffix = "intersect.bed" } - withName: '.*:ANNOTATION:INGEST_DATABASE_NAMES' { + withName: '.*:ANNOTATE_(COMBINED|PER_SAMPLE|PER_SAMPLE_TOOL):INGEST_DATABASE_NAMES' { ext.args = { "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \"${meta.id}:\" \$4, \$5, \$6 }'" } ext.suffix = "named.bed" } - withName: '.*:ANNOTATION:INTERSECT_DATABASE' { + withName: '.*:ANNOTATE_(COMBINED|PER_SAMPLE|PER_SAMPLE_TOOL):INTERSECT_DATABASE' { ext.args = { "-f ${meta.min_overlap} -r -loj -wa -wb" } ext.suffix = "annotated.bed" } - withName: '.*:ANNOTATION:ANNOTATE' { + withName: '.*:ANNOTATE_COMBINED:ANNOTATE' { publishDir = [ - path: { "${params.outdir}/annotation" }, + path: { "${params.outdir}/circrna_discovery/combined" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: '.*:ANNOTATE_PER_SAMPLE:ANNOTATE' { + publishDir = [ + path: { "${params.outdir}/circrna_discovery/samples/${meta.id}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: '.*:ANNOTATE_PER_SAMPLE_TOOL:ANNOTATE' { + publishDir = [ + path: { "${params.outdir}/circrna_discovery/tools/${meta.tool}/annotated" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] diff --git a/subworkflows/local/annotation.nf b/subworkflows/local/annotation.nf index f1887d93..dea819a6 100644 --- a/subworkflows/local/annotation.nf +++ b/subworkflows/local/annotation.nf @@ -28,7 +28,6 @@ workflow ANNOTATION { [[], []]) ch_versions = ch_versions.mix(INTERSECT_DATABASE.out.versions) - ANNOTATE( INTERSECT_GTF.out.intersect .join(INTERSECT_DATABASE.out.intersect .map{ meta, bed -> [meta.original_meta, bed] } diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index b0ed9288..74485267 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -12,14 +12,17 @@ include { BEDTOOLS_GETFASTA as FASTA_PER_SAMPLE } from '../../modules/nf-co include { BEDTOOLS_GETFASTA as FASTA_PER_SAMPLE_TOOL } from '../../modules/nf-core/bedtools/getfasta' // SUBWORKFLOWS -include { SEGEMEHL } from './discovery/segemehl' -include { STAR2PASS } from './discovery/star2pass' -include { CIRCEXPLORER2 } from './discovery/circexplorer2' -include { CIRCRNA_FINDER } from './discovery/circrna_finder' -include { FIND_CIRC } from './discovery/find_circ' -include { CIRIQUANT } from './discovery/ciriquant' -include { DCC } from './discovery/dcc' -include { MAPSPLICE } from './discovery/mapsplice' +include { SEGEMEHL } from './discovery/segemehl' +include { STAR2PASS } from './discovery/star2pass' +include { CIRCEXPLORER2 } from './discovery/circexplorer2' +include { CIRCRNA_FINDER } from './discovery/circrna_finder' +include { FIND_CIRC } from './discovery/find_circ' +include { CIRIQUANT } from './discovery/ciriquant' +include { DCC } from './discovery/dcc' +include { MAPSPLICE } from './discovery/mapsplice' +include { ANNOTATION as ANNOTATE_COMBINED } from './annotation' +include { ANNOTATION as ANNOTATE_PER_SAMPLE } from './annotation' +include { ANNOTATION as ANNOTATE_PER_SAMPLE_TOOL } from './annotation' workflow CIRCRNA_DISCOVERY { @@ -27,6 +30,7 @@ workflow CIRCRNA_DISCOVERY { reads ch_fasta ch_gtf + ch_annotation bowtie_index bowtie2_index bwa_index @@ -34,6 +38,7 @@ workflow CIRCRNA_DISCOVERY { hisat2_index star_index bsj_reads + exon_boundary main: ch_versions = Channel.empty() @@ -148,6 +153,24 @@ workflow CIRCRNA_DISCOVERY { ch_multiqc_files = ch_multiqc_files.mix(UPSET_ALL.out.multiqc) ch_versions = ch_versions.mix(UPSET_ALL.out.versions) + // + // ANNOTATION + // + ANNOTATE_COMBINED( ch_bsj_bed_combined, ch_gtf, exon_boundary, ch_annotation ) + ch_versions = ch_versions.mix(ANNOTATE_COMBINED.out.versions) + ch_bsj_bed12_combined = ANNOTATE_COMBINED.out.bed + ch_bsj_gtf_combined = ANNOTATE_COMBINED.out.gtf + + ANNOTATE_PER_SAMPLE( ch_bsj_bed_per_sample, ch_gtf, exon_boundary, ch_annotation ) + ch_versions = ch_versions.mix(ANNOTATE_PER_SAMPLE.out.versions) + ch_bsj_bed12_per_sample = ANNOTATE_PER_SAMPLE.out.bed + ch_bsj_gtf_per_sample = ANNOTATE_PER_SAMPLE.out.gtf + + ANNOTATE_PER_SAMPLE_TOOL( ch_bsj_bed_per_sample_tool, ch_gtf, exon_boundary, ch_annotation ) + ch_versions = ch_versions.mix(ANNOTATE_PER_SAMPLE_TOOL.out.versions) + ch_bsj_bed12_per_sample_tool = ANNOTATE_PER_SAMPLE_TOOL.out.bed + ch_bsj_gtf_per_sample_tool = ANNOTATE_PER_SAMPLE_TOOL.out.gtf + // // FASTA WORKFLOW: // @@ -166,12 +189,18 @@ workflow CIRCRNA_DISCOVERY { emit: bsj_bed_combined = ch_bsj_bed_combined + bsj_bed12_combined = ch_bsj_bed12_combined + bsj_gtf_combined = ch_bsj_gtf_combined bsj_fasta_combined = ch_bsj_fasta_combined bsj_bed_per_sample = ch_bsj_bed_per_sample + bsj_bed12_per_sample = ch_bsj_bed12_per_sample + bsj_gtf_per_sample = ch_bsj_gtf_per_sample bsj_fasta_per_sample = ch_bsj_fasta_per_sample bsj_bed_per_sample_tool = ch_bsj_bed_per_sample_tool + bsj_bed12_per_sample_tool = ch_bsj_bed12_per_sample_tool + bsj_gtf_per_sample_tool = ch_bsj_gtf_per_sample_tool bsj_fasta_per_sample_tool = ch_bsj_fasta_per_sample_tool multiqc_files = ch_multiqc_files diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index 8b1fb10d..695fd524 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -19,7 +19,6 @@ workflow QUANTIFICATION { take: ch_gtf ch_fasta - counts reads circ_annotation_bed circ_annotation_gtf diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index aa7f4ea3..ffcc6e11 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -140,6 +140,7 @@ workflow CIRCRNA { FASTQC_TRIMGALORE.out.reads, ch_fasta, ch_gtf, + ch_annotation, bowtie_index, bowtie2_index, bwa_index, @@ -147,34 +148,22 @@ workflow CIRCRNA { hisat2_index, star_index, params.bsj_reads, + params.exon_boundary ) ch_multiqc_files = ch_multiqc_files.mix(CIRCRNA_DISCOVERY.out.multiqc_files) ch_versions = ch_versions.mix(CIRCRNA_DISCOVERY.out.versions) // - // 3. circRNA Annotation - // - - ANNOTATION( - CIRCRNA_DISCOVERY.out.bsj_bed_combined, - ch_gtf, - params.exon_boundary, - ch_annotation - ) - ch_versions = ch_versions.mix(ANNOTATION.out.versions) - - // - // 4. circRNA quantification + // 3. circRNA quantification // QUANTIFICATION( ch_gtf, ch_fasta, - CIRCRNA_DISCOVERY.out.bsj_bed_combined, FASTQC_TRIMGALORE.out.reads, - ANNOTATION.out.bed, - ANNOTATION.out.gtf, + CIRCRNA_DISCOVERY.out.bsj_bed12_combined, + CIRCRNA_DISCOVERY.out.bsj_gtf_combined, params.bootstrap_samples, ch_phenotype, PREPARE_GENOME.out.faidx @@ -183,19 +172,19 @@ workflow CIRCRNA { ch_versions = ch_versions.mix(QUANTIFICATION.out.versions) // - // 5. miRNA prediction + // 4. miRNA prediction // if (params.mature) { MIRNA_PREDICTION( CIRCRNA_DISCOVERY.out.bsj_fasta_combined, - ANNOTATION.out.bed, + CIRCRNA_DISCOVERY.out.bsj_bed_combined, ch_mature ) ch_versions = ch_versions.mix(MIRNA_PREDICTION.out.versions) } // - // 6. Statistical tests + // 5. Statistical tests // STATISTICAL_TESTS( @@ -215,7 +204,7 @@ workflow CIRCRNA { .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true) .set { ch_collated_versions } - // MODULE: MultiQC + // MultiQC ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty() ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo) : Channel.empty() summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") From 2ff430e2300f93176966977dca5b1fd16a9da398 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 22:27:29 +0200 Subject: [PATCH 362/491] Improve annotation output formatting --- conf/modules.config | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 13951291..cee4cb8d 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -699,7 +699,7 @@ process { withName: '.*:ANNOTATE_(COMBINED|PER_SAMPLE|PER_SAMPLE_TOOL):INTERSECT_GTF' { ext.args = "-loj" - ext.suffix = "intersect.bed" + ext.suffix = "intersect_gtf.bed" } withName: '.*:ANNOTATE_(COMBINED|PER_SAMPLE|PER_SAMPLE_TOOL):INGEST_DATABASE_NAMES' { @@ -709,7 +709,11 @@ process { withName: '.*:ANNOTATE_(COMBINED|PER_SAMPLE|PER_SAMPLE_TOOL):INTERSECT_DATABASE' { ext.args = { "-f ${meta.min_overlap} -r -loj -wa -wb" } - ext.suffix = "annotated.bed" + ext.suffix = "intersect_database.bed" + } + + withName: '.*:ANNOTATE_(COMBINED|PER_SAMPLE|PER_SAMPLE_TOOL):ANNOTATE' { + ext.prefix = { "${meta.id}.annotated" } } withName: '.*:ANNOTATE_COMBINED:ANNOTATE' { From c8fc5c3faa5ae457fde1be72add24abeee7326e3 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 22:37:22 +0200 Subject: [PATCH 363/491] Remove unnecessary outputs from circrna_discovery --- subworkflows/local/circrna_discovery.nf | 24 +++++++----------------- workflows/circrna/main.nf | 8 ++++---- 2 files changed, 11 insertions(+), 21 deletions(-) diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 74485267..de3077f2 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -188,21 +188,11 @@ workflow CIRCRNA_DISCOVERY { ch_bsj_fasta_per_sample_tool = FASTA_PER_SAMPLE_TOOL.out.fasta emit: - bsj_bed_combined = ch_bsj_bed_combined - bsj_bed12_combined = ch_bsj_bed12_combined - bsj_gtf_combined = ch_bsj_gtf_combined - bsj_fasta_combined = ch_bsj_fasta_combined - - bsj_bed_per_sample = ch_bsj_bed_per_sample - bsj_bed12_per_sample = ch_bsj_bed12_per_sample - bsj_gtf_per_sample = ch_bsj_gtf_per_sample - bsj_fasta_per_sample = ch_bsj_fasta_per_sample - - bsj_bed_per_sample_tool = ch_bsj_bed_per_sample_tool - bsj_bed12_per_sample_tool = ch_bsj_bed12_per_sample_tool - bsj_gtf_per_sample_tool = ch_bsj_gtf_per_sample_tool - bsj_fasta_per_sample_tool = ch_bsj_fasta_per_sample_tool - - multiqc_files = ch_multiqc_files - versions = ch_versions + bed = ch_bsj_bed_combined + bed12 = ch_bsj_bed12_combined + gtf = ch_bsj_gtf_combined + fasta = ch_bsj_fasta_combined + + multiqc_files = ch_multiqc_files + versions = ch_versions } diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index ffcc6e11..af779e8c 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -162,8 +162,8 @@ workflow CIRCRNA { ch_gtf, ch_fasta, FASTQC_TRIMGALORE.out.reads, - CIRCRNA_DISCOVERY.out.bsj_bed12_combined, - CIRCRNA_DISCOVERY.out.bsj_gtf_combined, + CIRCRNA_DISCOVERY.out.bed12, + CIRCRNA_DISCOVERY.out.gtf, params.bootstrap_samples, ch_phenotype, PREPARE_GENOME.out.faidx @@ -176,8 +176,8 @@ workflow CIRCRNA { // if (params.mature) { MIRNA_PREDICTION( - CIRCRNA_DISCOVERY.out.bsj_fasta_combined, - CIRCRNA_DISCOVERY.out.bsj_bed_combined, + CIRCRNA_DISCOVERY.out.fasta, + CIRCRNA_DISCOVERY.out.bed, ch_mature ) ch_versions = ch_versions.mix(MIRNA_PREDICTION.out.versions) From b19813a586c21922e200a10a5a4a91b7c8af8d8e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Fri, 2 Aug 2024 23:56:52 +0200 Subject: [PATCH 364/491] Fix bug in tool filtering --- conf/modules.config | 4 ++-- subworkflows/local/circrna_discovery.nf | 2 ++ 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index cee4cb8d..bd415410 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -632,8 +632,8 @@ process { withName: 'FILTER_MIN_TOOLS' { // Keep only rows with at least the minimum number of tools // Replace the score column with a dot - ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (\$6 >= ${params.tool_filter}) { print \$1, \$2, \$3, \$4, \".\", \$5 } }'" - ext.suffix = {"filtered.bed"} + ext.args = { "-v FS='\\t' -v OFS='\\t' '{ if (\$6 >= ${params.tool_filter}) { print \$1, \$2, \$3, \$4, \".\", \$5 } }'" } + ext.suffix = "filtered.bed" publishDir = [ path: { "${params.outdir}/circrna_discovery/samples/${meta.id}" }, mode: params.publish_dir_mode, diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index de3077f2..5c51f454 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -118,6 +118,7 @@ workflow CIRCRNA_DISCOVERY { MASK_SCORES( ch_bed, [] ) ch_versions = ch_versions.mix(MASK_SCORES.out.versions) ch_bsj_bed_per_sample_tool = MASK_SCORES.out.output + .filter{ meta, bed -> !bed.empty } CONCAT_TOOLS_PER_SAMPLE( MASK_SCORES.out.output.map{ meta, bed -> [ [id: meta.id], bed ] }.groupTuple() @@ -130,6 +131,7 @@ workflow CIRCRNA_DISCOVERY { FILTER_MIN_TOOLS( COUNT_TOOLS.out.bed, [] ) ch_versions = ch_versions.mix(FILTER_MIN_TOOLS.out.versions) ch_bsj_bed_per_sample = FILTER_MIN_TOOLS.out.output + .filter{ meta, bed -> !bed.empty } CONCAT_SAMPLES( ch_bsj_bed_per_sample.map{ meta, bed -> [[id: "all"], bed] }.groupTuple() From 1f00d9f56a5b0315e9dd45b96514dff873e768ee Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 00:28:23 +0200 Subject: [PATCH 365/491] Prevent pipeline from failing if no circRNAs are found --- modules/local/circtest/prepare/main.nf | 5 ++--- modules/local/circtest/prepare/templates/prepare.R | 10 ++++++++-- subworkflows/local/circrna_discovery.nf | 3 ++- 3 files changed, 12 insertions(+), 6 deletions(-) diff --git a/modules/local/circtest/prepare/main.nf b/modules/local/circtest/prepare/main.nf index bfc32b4e..4d3029c1 100644 --- a/modules/local/circtest/prepare/main.nf +++ b/modules/local/circtest/prepare/main.nf @@ -9,12 +9,11 @@ process CIRCTEST_PREPARE { tuple val(meta2), path(gene_counts) output: - tuple val(meta), path('*_circs.tsv'), emit: circ_counts - tuple val(meta), path('*_genes.tsv'), emit: gene_counts + tuple val(meta), path('*_circs.tsv'), emit: circ_counts, optional: true + tuple val(meta), path('*_genes.tsv'), emit: gene_counts, optional: true path "versions.yml" , emit: versions - when: task.ext.when == null || task.ext.when diff --git a/modules/local/circtest/prepare/templates/prepare.R b/modules/local/circtest/prepare/templates/prepare.R index 5eb2c55e..d5dcdebb 100644 --- a/modules/local/circtest/prepare/templates/prepare.R +++ b/modules/local/circtest/prepare/templates/prepare.R @@ -9,8 +9,14 @@ rownames(circ) <- circ\$tx rownames(gene) <- rownames(circ) circ\$tx <- NULL -write.table(circ, "${prefix}_circs.tsv", sep="\\t", quote=F, row.names=T) -write.table(gene, "${prefix}_genes.tsv", sep="\\t", quote=F, row.names=T) +if (nrow(circ) != nrow(gene)) { + stop("Number of rows in circ and gene counts do not match") +} + +if (nrow(circ) > 0) { + write.table(circ, "${prefix}_circs.tsv", sep="\\t", quote=F, row.names=T) + write.table(gene, "${prefix}_genes.tsv", sep="\\t", quote=F, row.names=T) +} ################################################ ################################################ diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index 5c51f454..cd7f7d79 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -131,7 +131,7 @@ workflow CIRCRNA_DISCOVERY { FILTER_MIN_TOOLS( COUNT_TOOLS.out.bed, [] ) ch_versions = ch_versions.mix(FILTER_MIN_TOOLS.out.versions) ch_bsj_bed_per_sample = FILTER_MIN_TOOLS.out.output - .filter{ meta, bed -> !bed.empty } + .filter{ meta, bed -> bed.size() > 0 } CONCAT_SAMPLES( ch_bsj_bed_per_sample.map{ meta, bed -> [[id: "all"], bed] }.groupTuple() @@ -158,6 +158,7 @@ workflow CIRCRNA_DISCOVERY { // // ANNOTATION // + ANNOTATE_COMBINED( ch_bsj_bed_combined, ch_gtf, exon_boundary, ch_annotation ) ch_versions = ch_versions.mix(ANNOTATE_COMBINED.out.versions) ch_bsj_bed12_combined = ANNOTATE_COMBINED.out.bed From 35ef315cf4182480840eac5ea35e74ca151881d0 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 08:59:06 +0200 Subject: [PATCH 366/491] Improve annotation output format --- conf/modules.config | 54 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index bd415410..fb251d3b 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -702,9 +702,39 @@ process { ext.suffix = "intersect_gtf.bed" } + withName: '.*:ANNOTATE_COMBINED:INTERSECT_GTF' { + publishDir = [ + path: { "${params.outdir}/circrna_discovery/combined" }, + mode: params.publish_dir_mode, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } + ] + } + + withName: '.*:ANNOTATE_PER_SAMPLE:INTERSECT_GTF' { + publishDir = [ + path: { "${params.outdir}/circrna_discovery/samples/${meta.id}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } + ] + } + + withName: '.*:ANNOTATE_PER_SAMPLE_TOOL:INTERSECT_GTF' { + publishDir = [ + path: { "${params.outdir}/circrna_discovery/tools/${meta.tool}/annotated" }, + mode: params.publish_dir_mode, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } + ] + } + withName: '.*:ANNOTATE_(COMBINED|PER_SAMPLE|PER_SAMPLE_TOOL):INGEST_DATABASE_NAMES' { ext.args = { "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \"${meta.id}:\" \$4, \$5, \$6 }'" } ext.suffix = "named.bed" + + publishDir = [ + path: { "${params.outdir}/references/named_databases" }, + mode: params.publish_dir_mode, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } + ] } withName: '.*:ANNOTATE_(COMBINED|PER_SAMPLE|PER_SAMPLE_TOOL):INTERSECT_DATABASE' { @@ -712,6 +742,30 @@ process { ext.suffix = "intersect_database.bed" } + withName: '.*:ANNOTATE_COMBINED:INTERSECT_DATABASE' { + publishDir = [ + path: { "${params.outdir}/circrna_discovery/combined" }, + mode: params.publish_dir_mode, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } + ] + } + + withName: '.*:ANNOTATE_PER_SAMPLE:INTERSECT_DATABASE' { + publishDir = [ + path: { "${params.outdir}/circrna_discovery/samples/${meta.id}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } + ] + } + + withName: '.*:ANNOTATE_PER_SAMPLE_TOOL:INTERSECT_DATABASE' { + publishDir = [ + path: { "${params.outdir}/circrna_discovery/tools/${meta.tool}/annotated" }, + mode: params.publish_dir_mode, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } + ] + } + withName: '.*:ANNOTATE_(COMBINED|PER_SAMPLE|PER_SAMPLE_TOOL):ANNOTATE' { ext.prefix = { "${meta.id}.annotated" } } From d153402dddc1c8f861dda3768e43db65118067ed Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 09:08:11 +0200 Subject: [PATCH 367/491] Remove traces of old merging functionality --- docs/usage.md | 4 -- .../merge_samples/environment.yml | 5 -- .../local/count_matrix/merge_samples/main.nf | 20 ------ .../merge_samples/templates/merge_samples.py | 53 --------------- .../count_matrix/merge_tools/environment.yml | 5 -- .../local/count_matrix/merge_tools/main.nf | 22 ------- .../merge_tools/templates/merge_tools.py | 64 ------------------- nextflow.config | 1 - nextflow_schema.json | 11 +--- 9 files changed, 2 insertions(+), 183 deletions(-) delete mode 100644 modules/local/count_matrix/merge_samples/environment.yml delete mode 100644 modules/local/count_matrix/merge_samples/main.nf delete mode 100755 modules/local/count_matrix/merge_samples/templates/merge_samples.py delete mode 100644 modules/local/count_matrix/merge_tools/environment.yml delete mode 100644 modules/local/count_matrix/merge_tools/main.nf delete mode 100755 modules/local/count_matrix/merge_tools/templates/merge_tools.py diff --git a/docs/usage.md b/docs/usage.md index 137fb841..978f2313 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -245,10 +245,6 @@ nextflow run nf-core/circrna \ > This filtering method is reflected in the circRNA count matrix. Per tool circRNA annotations are subject to back-splice read filtering only. -#### Handling duplicate circRNAs - -In the event a circRNA has been called by more than one quantification tool, the user can specify which aggregate function to apply to the duplicated circRNA. The accepted values are 'mean' and 'max', which are passed to the workflow using the `--duplicates_fun` parameter. - ## miRNA prediction The second module of `nf-core/circrna`, `mirna_prediction` analyses the mature spliced sequences of circRNAs to test for the presence of miRNA response elements using both `miRanda` and `TargetScan`. Results from both tools are consolidated and filtering methods are applied to produce robust miRNA target predictions of circRNAs in the dataset. diff --git a/modules/local/count_matrix/merge_samples/environment.yml b/modules/local/count_matrix/merge_samples/environment.yml deleted file mode 100644 index d5f9e211..00000000 --- a/modules/local/count_matrix/merge_samples/environment.yml +++ /dev/null @@ -1,5 +0,0 @@ -name: merge_samples -channels: - - conda-forge -dependencies: - - pandas=1.5.2 diff --git a/modules/local/count_matrix/merge_samples/main.nf b/modules/local/count_matrix/merge_samples/main.nf deleted file mode 100644 index 8f8d3789..00000000 --- a/modules/local/count_matrix/merge_samples/main.nf +++ /dev/null @@ -1,20 +0,0 @@ -process MERGE_SAMPLES { - label "process_single" - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : - 'biocontainers/pandas:1.5.2' }" - - input: - path(beds) - - output: - path("merged_counts.bed") , emit: counts_bed - path("merged_counts.tsv") , emit: counts_tsv - - path "versions.yml" , emit: versions - - script: - template "merge_samples.py" -} diff --git a/modules/local/count_matrix/merge_samples/templates/merge_samples.py b/modules/local/count_matrix/merge_samples/templates/merge_samples.py deleted file mode 100755 index 010eb616..00000000 --- a/modules/local/count_matrix/merge_samples/templates/merge_samples.py +++ /dev/null @@ -1,53 +0,0 @@ -#!/usr/bin/env python3 - -import platform -import pandas as pd -import os - -def format_yaml_like(data: dict, indent: int = 0) -> str: - """Formats a dictionary to a YAML-like string. - - Args: - data (dict): The dictionary to format. - indent (int): The current indentation level. - - Returns: - str: A string formatted as YAML. - """ - yaml_str = "" - for key, value in data.items(): - spaces = " " * indent - if isinstance(value, dict): - yaml_str += f"{spaces}{key}:\\n{format_yaml_like(value, indent + 1)}" - else: - yaml_str += f"{spaces}{key}: {value}\\n" - return yaml_str - -columns = ['chr', 'start', 'end', 'name', 'count', 'strand'] -dfs = {os.path.basename(bed).split('.')[0]: pd.read_csv(bed, - sep='\t', - header=None, - index_col=["chr", "start", "end", "strand"], - usecols=["chr", "start", "end", "strand", "count"], - names=columns) for bed in "${beds}".split()} - -dfs = [df.rename(columns={'count': sample}) for sample, df in dfs.items()] -df = pd.concat(dfs, axis=1) -df = df.fillna(0) -df.to_csv("merged_counts.bed", sep='\\t', header=True, index=True) - -df.index = df.index.map(lambda x: f'{x[0]}:{x[1]}-{x[2]}:{x[3]}') -df.index.name = 'ID' -df.to_csv("merged_counts.tsv", sep='\\t') - -# Versions - -versions = { - "${task.process}": { - "python": platform.python_version(), - "pandas": pd.__version__ - } -} - -with open("versions.yml", "w") as f: - f.write(format_yaml_like(versions)) diff --git a/modules/local/count_matrix/merge_tools/environment.yml b/modules/local/count_matrix/merge_tools/environment.yml deleted file mode 100644 index 796e68fc..00000000 --- a/modules/local/count_matrix/merge_tools/environment.yml +++ /dev/null @@ -1,5 +0,0 @@ -name: merge_tools -channels: - - conda-forge -dependencies: - - pandas=1.5.2 diff --git a/modules/local/count_matrix/merge_tools/main.nf b/modules/local/count_matrix/merge_tools/main.nf deleted file mode 100644 index cdd3f2c0..00000000 --- a/modules/local/count_matrix/merge_tools/main.nf +++ /dev/null @@ -1,22 +0,0 @@ -process MERGE_TOOLS { - tag "$meta.id" - label "process_single" - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : - 'biocontainers/pandas:1.5.2' }" - - input: - tuple val(meta), path(beds) - val(tool_filter) - val(duplicates_fun) - - output: - tuple val(meta), path("${meta.id}.merged.bed"), emit: merged - - path "versions.yml" , emit: versions - - script: - template 'merge_tools.py' -} diff --git a/modules/local/count_matrix/merge_tools/templates/merge_tools.py b/modules/local/count_matrix/merge_tools/templates/merge_tools.py deleted file mode 100755 index 8e514993..00000000 --- a/modules/local/count_matrix/merge_tools/templates/merge_tools.py +++ /dev/null @@ -1,64 +0,0 @@ -#!/usr/bin/env python3 - -import platform -import pandas as pd - -def format_yaml_like(data: dict, indent: int = 0) -> str: - """Formats a dictionary to a YAML-like string. - - Args: - data (dict): The dictionary to format. - indent (int): The current indentation level. - - Returns: - str: A string formatted as YAML. - """ - yaml_str = "" - for key, value in data.items(): - spaces = " " * indent - if isinstance(value, dict): - yaml_str += f"{spaces}{key}:\\n{format_yaml_like(value, indent + 1)}" - else: - yaml_str += f"{spaces}{key}: {value}\\n" - return yaml_str - -duplicates_fun = "${duplicates_fun}" - -if duplicates_fun not in ['sum', 'mean', 'max', 'min']: - raise ValueError(f"Invalid value for duplicates_fun: {duplicates_fun}") - -columns = ['chr', 'start', 'end', 'name', 'count', 'strand'] -columns_no_count = ['chr', 'start', 'end', 'name', 'strand'] -dfs = [] - -for bed_path in "${beds}".split(): - df = pd.read_csv(bed_path, sep='\\t', header=None, names=columns) - - # If there are duplicate rows, throw an error - if df.duplicated(subset=columns_no_count).any(): - print(df[df.duplicated(subset=columns_no_count)]) - raise ValueError("Duplicate rows found in input BED file: " + bed_path) - - dfs.append(df) - -df = pd.concat(dfs) - -df['tool_count'] = 1 -df = df.groupby(['chr', 'start', 'end', 'strand', 'name']).agg({'count': duplicates_fun, - 'tool_count': 'sum'}).reset_index() -df = df[df['tool_count'] >= int("${tool_filter}")] - -df = df[columns] -df.to_csv("${meta.id}.merged.bed", sep='\t', index=False, header=False) - -# Versions - -versions = { - "${task.process}": { - "python": platform.python_version(), - "pandas": pd.__version__ - } -} - -with open("versions.yml", "w") as f: - f.write(format_yaml_like(versions)) diff --git a/nextflow.config b/nextflow.config index e2c6308d..5e54776d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -19,7 +19,6 @@ params { tool = 'circexplorer2' bsj_reads = 0 tool_filter = 0 - duplicates_fun = 'mean' exon_boundary = 200 save_intermediates = false diff --git a/nextflow_schema.json b/nextflow_schema.json index 64df9eb1..45770cb8 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -81,17 +81,10 @@ "type": "integer", "fa_icon": "fas fa-intersection", "description": "Specify the minimum number of tools circRNAs must be called by to be output by the workflow.", - "help_text": "When multiple circRNA quantification tools have been provided to `--tool`, set a filtering method whereby circRNAs are output if they have been called by at least *n* quantification tools.\n\nSetting `--tool_filter` to 0/1 is the same as taking the union, all circRNAs are included in the output.\n\nSetting `--tool_filter` to 2 will output circRNAs that have been called by at least 2 quantification tools and so on.\n\nPlease note this is only reflected in the circRNA count matrix generated.", + "help_text": "When multiple circRNA quantification tools have been provided to `--tool`, set a filtering method whereby circRNAs are output if they have been called by at least *n* quantification tools.\n\nSetting `--tool_filter` to 0/1 is the same as taking the union, all circRNAs are included in the output.\n\nSetting `--tool_filter` to 2 will output circRNAs that have been called by at least 2 quantification tools and so on.", "default": 0, "minimum": 0, - "maximum": 6 - }, - "duplicates_fun": { - "type": "string", - "fa_icon": "fas fa-copy", - "description": "Aggregate function to apply to duplicate circRNAs when more than one quantification tool has been selected. Options: max, mean", - "default": "mean", - "enum": ["mean", "max"] + "maximum": 7 }, "save_intermediates": { "type": "boolean", From eeb1895153b0b107b6c3326f89c2d7245172d846 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 10:28:54 +0200 Subject: [PATCH 368/491] Make sure pipeline fails in an ordered way if no circRNAs are found --- modules/local/fail_on_empty/main.nf | 19 +++++++++++++++++++ subworkflows/local/circrna_discovery.nf | 23 +++++++++++++++++++++-- 2 files changed, 40 insertions(+), 2 deletions(-) create mode 100644 modules/local/fail_on_empty/main.nf diff --git a/modules/local/fail_on_empty/main.nf b/modules/local/fail_on_empty/main.nf new file mode 100644 index 00000000..277310ae --- /dev/null +++ b/modules/local/fail_on_empty/main.nf @@ -0,0 +1,19 @@ +process FAIL_ON_EMPTY { + tag "$meta.id" + + input: + tuple val(meta), path(bed) + path(waitFor, stageAs: 'waitFor*.txt') + + exec: + if (!bed) { + if (params.tool_filter <= 1) { + log.error "No circular RNAs were found by any tool in any sample.\n" + + "Please check the input data." + } else { + log.error "No circular RNAs were found by at least ${params.tool_filter} tools in any sample.\n" + + "Please check the input data or lower the tool_filter parameter." + } + exit 1 + } +} diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf index cd7f7d79..1447aa0a 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/circrna_discovery.nf @@ -10,6 +10,7 @@ include { UPSET as UPSET_ALL } from '../../modules/local include { BEDTOOLS_GETFASTA as FASTA_COMBINED } from '../../modules/nf-core/bedtools/getfasta' include { BEDTOOLS_GETFASTA as FASTA_PER_SAMPLE } from '../../modules/nf-core/bedtools/getfasta' include { BEDTOOLS_GETFASTA as FASTA_PER_SAMPLE_TOOL } from '../../modules/nf-core/bedtools/getfasta' +include { FAIL_ON_EMPTY } from '../../modules/local/fail_on_empty' // SUBWORKFLOWS include { SEGEMEHL } from './discovery/segemehl' @@ -143,13 +144,15 @@ workflow CIRCRNA_DISCOVERY { // UPSET PLOTS // - UPSET_SAMPLES( ch_bed.map{ meta, bed -> [meta.id, meta.tool, bed]} + UPSET_SAMPLES( ch_bsj_bed_per_sample_tool + .map{ meta, bed -> [meta.id, meta.tool, bed]} .groupTuple() .map{ sample, tools, beds -> [[id: sample], tools, beds]} ) ch_multiqc_files = ch_multiqc_files.mix(UPSET_SAMPLES.out.multiqc) ch_versions = ch_versions.mix(UPSET_SAMPLES.out.versions) - UPSET_ALL( ch_bed.map{ meta, bed -> ["all", meta.tool, bed] } + UPSET_ALL( ch_bsj_bed_per_sample_tool + .map{ meta, bed -> ["all", meta.tool, bed] } .groupTuple() .map{ sample, tools, beds -> [[id: sample], tools, beds]} ) ch_multiqc_files = ch_multiqc_files.mix(UPSET_ALL.out.multiqc) @@ -190,6 +193,22 @@ workflow CIRCRNA_DISCOVERY { ch_versions = ch_versions.mix(FASTA_PER_SAMPLE_TOOL.out.versions) ch_bsj_fasta_per_sample_tool = FASTA_PER_SAMPLE_TOOL.out.fasta + // STOP PIPELINE IF NO CIRCULAR RNAs WERE FOUND + FAIL_ON_EMPTY( + ch_bsj_bed_combined.ifEmpty([[id: "empty"], []]), + // Make sure to wait for per-sample results + Channel.empty() + .mix(ch_bsj_bed12_combined) + .mix(ch_bsj_bed12_per_sample) + .mix(ch_bsj_bed12_per_sample_tool) + .mix(ch_bsj_fasta_combined) + .mix(ch_bsj_fasta_per_sample) + .mix(ch_bsj_fasta_per_sample_tool) + .mix(UPSET_SAMPLES.out.plot) + .map{ meta, f -> f } + .collect() + ) + emit: bed = ch_bsj_bed_combined bed12 = ch_bsj_bed12_combined From 9bf06090606e4aba0d1e2b2c24af4829d8cdb930 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 10:41:21 +0200 Subject: [PATCH 369/491] Improve error message for no circRNAs found --- modules/local/fail_on_empty/main.nf | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/modules/local/fail_on_empty/main.nf b/modules/local/fail_on_empty/main.nf index 277310ae..95916684 100644 --- a/modules/local/fail_on_empty/main.nf +++ b/modules/local/fail_on_empty/main.nf @@ -7,13 +7,13 @@ process FAIL_ON_EMPTY { exec: if (!bed) { - if (params.tool_filter <= 1) { - log.error "No circular RNAs were found by any tool in any sample.\n" + - "Please check the input data." - } else { - log.error "No circular RNAs were found by at least ${params.tool_filter} tools in any sample.\n" + - "Please check the input data or lower the tool_filter parameter." - } + log.error ((params.tool_filter <= 1 ? + "No circular RNAs were found by any tool in any sample.\n" : + "No circular RNAs were found by at least ${params.tool_filter} tools in any sample.\n") + + "Feel free to check the preliminary results in '${params.outdir}'\n" + + (params.save_intermediates ? "" : + "You can enable saving intermediate files by setting the parameter 'save_intermediates' to 'true'.")) + exit 1 } } From ccd0bda7eeb09ec86beff8bac122984e69338d77 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 10:42:45 +0200 Subject: [PATCH 370/491] Linting --- modules/local/fail_on_empty/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/local/fail_on_empty/main.nf b/modules/local/fail_on_empty/main.nf index 95916684..aa97b9e8 100644 --- a/modules/local/fail_on_empty/main.nf +++ b/modules/local/fail_on_empty/main.nf @@ -7,11 +7,11 @@ process FAIL_ON_EMPTY { exec: if (!bed) { - log.error ((params.tool_filter <= 1 ? - "No circular RNAs were found by any tool in any sample.\n" : + log.error ((params.tool_filter <= 1 ? + "No circular RNAs were found by any tool in any sample.\n" : "No circular RNAs were found by at least ${params.tool_filter} tools in any sample.\n") + "Feel free to check the preliminary results in '${params.outdir}'\n" + - (params.save_intermediates ? "" : + (params.save_intermediates ? "" : "You can enable saving intermediate files by setting the parameter 'save_intermediates' to 'true'.")) exit 1 From ddbd2f53e0020d6a52f183213156acdcf18ccf0e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 10:48:53 +0200 Subject: [PATCH 371/491] Update first section of introduction --- README.md | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/README.md b/README.md index e3d02d62..03e28b14 100644 --- a/README.md +++ b/README.md @@ -22,11 +22,7 @@ ## Introduction -**nf-core/circrna** is a bioinformatics best-practice analysis pipeline for back-splice junction (BSJ) detection, quantification, annotation and miRNA target prediction of circular RNAs. - -The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! - -On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/circrna/results). +**nf-core/circrna** is a bioinformatics pipeline that can be used to analyse total RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming, back-splice junction (BSJ) detection, annotation, quantification and miRNA target prediction of circular RNAs. ## Pipeline summary From f8ce1a644359421f644bd2cc14c925605e442d33 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 10:56:31 +0200 Subject: [PATCH 372/491] Update credits --- README.md | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 03e28b14..ad73c3cb 100644 --- a/README.md +++ b/README.md @@ -40,6 +40,8 @@ - [`MapSplice`](http://www.netlab.uky.edu/p/bioinfo/MapSplice2) - [`Segemehl`](https://www.bioinf.uni-leipzig.de/Software/segemehl/) - circRNA annotation + - Based on GTF file + - Based on database files (if provided) - Extract circRNA sequences and build circular transcriptome - Merge circular transcriptome with linear transcriptome derived from provided GTF - Quantification of combined circular and linear transcriptome @@ -108,15 +110,17 @@ For more details about the output files and reports, please refer to the ## Credits -nf-core/circrna was originally written by Barry Digby. +nf-core/circrna was originally written by [Barry Digby](https://github.com/BarryDigby). +It was later refactored, extended and improved by [Nico Trummer](https://github.com/nictru). -We thank the following people for their extensive assistance in the development of this pipeline: +We thank the following people for their extensive assistance in the development of this pipeline (in alphabetical order): -- @apeltzer -- @ewels -- @maxulysse -- @KevinMenden -- @bj-w +- [Alexander Peltzer](https://github.com/apeltzer) +- [Ben Whittle](https://github.com/bj-w) +- [Kevin Menden](https://github.com/KevinMenden) +- [Marieke Vromman](https://github.com/MariekeVromman) +- [Maxime Garcia](https://github.com/maxulysse) +- [Phil Ewels](https://github.com/ewels) ## Acknowledgements From 17c692d9fe2f81a16556812e1c1f995693a1e065 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 11:08:58 +0200 Subject: [PATCH 373/491] Restructure usage docs --- docs/usage.md | 194 +++++++++++++++++++++++--------------------------- 1 file changed, 90 insertions(+), 104 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 978f2313..be4519df 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -53,115 +53,23 @@ TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,,reverse An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. -## Running the pipeline - -The typical command for running the pipeline is as follows: - -```bash -nextflow run \ - nf-core/circrna \ - --input \ - --outdir \ - --gtf \ - --fasta \ - --igenomes_ignore \ - --genome null \ - -profile docker -``` - -> **NB:** Loading iGenomes configuration remains the default for reasons of consistency with other workflows, but should be disabled when not using iGenomes, applying the recommended usage above. - -This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. - -Note that the pipeline will create the following files in your working directory: - -```bash -work # Directory containing the nextflow working files - # Finished results in specified location (defined with --outdir) -.nextflow_log # Log file from Nextflow -# Other nextflow hidden files, eg. history of pipeline runs and old logs. -``` - -If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file. - -Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. - -:::warning -Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). -::: - -The above pipeline run specified with a params file in yaml format: - -```bash -nextflow run nf-core/circrna -profile docker -params-file params.yaml -``` - -with `params.yaml` containing: - -```yaml -input: './samplesheet.csv' -outdir: './results/' -genome: 'GRCh37' -<...> -``` - -You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). - -### Updating the pipeline - -When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: - -```bash -nextflow pull nf-core/circrna -``` - -When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. - -### Reproducibility - -It's a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. - -First, go to the [nf-core/circrna releases page](https://github.com/nf-core/circrna/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. - -This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. - -To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. - -:::tip -If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. -::: - -# Input specifications - -Input data can be passed to `nf-core/circrna` using a CSV file containing the absolute paths to input fastq files. - -The header of the CSV file must at least contain the `sample` and `fastq_1` columns. The `fastq_2` column is optional and only required for paired-end data. With an additional `strandness` column, the user can specify the strandedness of the library. The `sample` column should contain a unique identifier for each sample, and the `fastq_1` and `fastq_2` columns should contain the paths to the input fastq files. - -Valid examples for fastq input data in a CSV file is given below: - -| sample | fastq_1 | fastq_2 | -| ---------------- | :---------------------------------------------------------------------- | ----------------------------------------------------------------------- | -| TCGA-EJ-7783-11A | /data/f4c1b2b1-ba1f-4355-a1ac-3e952cf351a5_gdc_realn_rehead_R1.fastq.gz | /data/f4c1b2b1-ba1f-4355-a1ac-3e952cf351a5_gdc_realn_rehead_R2.fastq.gz | -| TCGA-G9-6365-11A | /data/8a36555b-9e27-40ee-a8df-4b15d6580a02_gdc_realn_rehead_R1.fastq.gz | /data/8a36555b-9e27-40ee-a8df-4b15d6580a02_gdc_realn_rehead_R2.fastq.gz | -| TCGA-EJ-7782-11A | /data/8b3d4a3d-2bfa-48f8-b31f-901f49a5bf6b_gdc_realn_rehead_R1.fastq.gz | /data/8b3d4a3d-2bfa-48f8-b31f-901f49a5bf6b_gdc_realn_rehead_R2.fastq.gz | -| TCGA-CH-5772-01A | /data/b6546f66-3c13-4390-9643-d1fb3d660a2f_gdc_realn_rehead_R1.fastq.gz | /data/b6546f66-3c13-4390-9643-d1fb3d660a2f_gdc_realn_rehead_R2.fastq.gz | -| TCGA-EJ-5518-01A | /data/afbbc370-5970-43d3-b9f8-f40f8e649bb6_gdc_realn_rehead_R1.fastq.gz | /data/afbbc370-5970-43d3-b9f8-f40f8e649bb6_gdc_realn_rehead_R2.fastq.gz | -| TCGA-KK-A8I4-01A | /data/81254692-ee1e-4985-bd0a-4929eed4c620_gdc_realn_rehead_R1.fastq.gz | /data/81254692-ee1e-4985-bd0a-4929eed4c620_gdc_realn_rehead_R2.fastq.gz | - ## Phenotype file The CSV file provided via the `phenotype` parameter can be used to provide additional metadata about the samples in the input CSV file. If provided, it needs to at least contain a column called `sample` which corresponds to the `sample` column in the input CSV file and a column called `condition`. The `condition` column will be used to group samples for the [CircTest](https://github.com/dieterich-lab/CircTest) functionality. All metadata columns will be included in the result `SummarizedExperiment` RDS file. -A valid example of a `phenotype.csv` file (matching the TCGA example input CSV file above) is given: +A valid example of a `phenotype.csv` file (matching the "Full samplesheet") is given: + +```csv title="phenotype.csv" +sample,condition +CONTROL_REP1,control +CONTROL_REP2,control +CONTROL_REP3,control +TREATMENT_REP1,treatment +TREATMENT_REP2,treatment +TREATMENT_REP3,treatment +``` -| sample | condition | -| ---------------- | --------- | -| TCGA-EJ-7783-11A | control | -| TCGA-G9-6365-11A | control | -| TCGA-EJ-7782-11A | control | -| TCGA-CH-5772-01A | tumor | -| TCGA-EJ-5518-01A | tumor | -| TCGA-KK-A8I4-01A | tumor | +Note that `TREATMENT_REP3` only has one entry in the `phenotype.csv` file, even though it has two entries in the `samplesheet.csv` file. # Analysis modules @@ -261,6 +169,84 @@ nextflow run nf-core/circrna \ To view the outputs of the module, please see the output [documentation](https://nf-co.re/circrna/dev/output#mirna-prediction). +## Running the pipeline + +The typical command for running the pipeline is as follows: + +```bash +nextflow run \ + nf-core/circrna \ + --input \ + --outdir \ + --gtf \ + --fasta \ + --igenomes_ignore \ + --genome null \ + -profile docker +``` + +> **NB:** Loading iGenomes configuration remains the default for reasons of consistency with other workflows, but should be disabled when not using iGenomes, applying the recommended usage above. + +This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. + +Note that the pipeline will create the following files in your working directory: + +```bash +work # Directory containing the nextflow working files + # Finished results in specified location (defined with --outdir) +.nextflow_log # Log file from Nextflow +# Other nextflow hidden files, eg. history of pipeline runs and old logs. +``` + +If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file. + +Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. + +:::warning +Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). +::: + +The above pipeline run specified with a params file in yaml format: + +```bash +nextflow run nf-core/circrna -profile docker -params-file params.yaml +``` + +with `params.yaml` containing: + +```yaml +input: './samplesheet.csv' +outdir: './results/' +genome: 'GRCh37' +<...> +``` + +You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). + +### Updating the pipeline + +When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: + +```bash +nextflow pull nf-core/circrna +``` + +When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. + +### Reproducibility + +It's a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. + +First, go to the [nf-core/circrna releases page](https://github.com/nf-core/circrna/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. + +This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. + +To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. + +:::tip +If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. +::: + ## Core Nextflow arguments :::note From 19820980ca3a71e5fccb4ca2c03f4879fb269b40 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 11:16:01 +0200 Subject: [PATCH 374/491] Add plans for future implementations to README --- README.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/README.md b/README.md index ad73c3cb..875ce95c 100644 --- a/README.md +++ b/README.md @@ -24,6 +24,13 @@ **nf-core/circrna** is a bioinformatics pipeline that can be used to analyse total RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming, back-splice junction (BSJ) detection, annotation, quantification and miRNA target prediction of circular RNAs. +The pipeline is still under development, but the BSJ detection and quantification steps are already implemented and functional. The following features are planned to be implemented soon: +- Isoform-level circRNA detection and quantification +- circRNA-miRNA interaction analysis using [SPONGE](https://doi.org/10.1093/bioinformatics/btz314) and [spongEffects](https://doi.org/10.1093/bioinformatics/btad276) +- Improved downstream analyses + +If you want to contribute, feel free to create an issue or pull request on the [GitHub repository](https://github.com/nf-core/circrna) or join the [Slack channel](https://nf-co.re/join/slack). + ## Pipeline summary ![Metro Map](./docs/images/metro-map.png) From 9e9fdd9a69aa88882b25b9f4c3cff750a7f3f0be Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 11:22:22 +0200 Subject: [PATCH 375/491] Rename CIRCRNA_DISCOVERY to BSJ_DETECTION --- conf/modules.config | 106 +++++++++--------- docs/usage.md | 12 +- ...{circrna_discovery.nf => bsj_detection.nf} | 18 +-- .../circexplorer2.nf | 0 .../circrna_finder.nf | 0 .../ciriquant.nf | 0 .../{discovery => detection_tools}/dcc.nf | 0 .../find_circ.nf | 0 .../mapsplice.nf | 0 .../segemehl.nf | 0 .../star2pass.nf | 0 workflows/circrna/main.nf | 18 +-- 12 files changed, 74 insertions(+), 80 deletions(-) rename subworkflows/local/{circrna_discovery.nf => bsj_detection.nf} (91%) rename subworkflows/local/{discovery => detection_tools}/circexplorer2.nf (100%) rename subworkflows/local/{discovery => detection_tools}/circrna_finder.nf (100%) rename subworkflows/local/{discovery => detection_tools}/ciriquant.nf (100%) rename subworkflows/local/{discovery => detection_tools}/dcc.nf (100%) rename subworkflows/local/{discovery => detection_tools}/find_circ.nf (100%) rename subworkflows/local/{discovery => detection_tools}/mapsplice.nf (100%) rename subworkflows/local/{discovery => detection_tools}/segemehl.nf (100%) rename subworkflows/local/{discovery => detection_tools}/star2pass.nf (100%) diff --git a/conf/modules.config b/conf/modules.config index fb251d3b..d273ec07 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -173,7 +173,7 @@ process { "-S" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/segemehl/raw" }, + path: { "${params.outdir}/bsj_detection/tools/segemehl/raw" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -185,7 +185,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (\$4 ~ /;C;/) { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$5, \$6 } }'" ext.suffix = "segemehl_extracted.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/segemehl/extracted" }, + path: { "${params.outdir}/bsj_detection/tools/segemehl/extracted" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -195,7 +195,7 @@ process { ext.args = "-k1,1 -k2,2n -k3,3n -k4,4 -k6,6" ext.suffix = "segemehl_sorted.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/segemehl/sorted" }, + path: { "${params.outdir}/bsj_detection/tools/segemehl/sorted" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -206,7 +206,7 @@ process { ext.args = "-g 1,2,3,4,6 -o count" ext.suffix = "segemehl_grouped.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/segemehl/grouped" }, + path: { "${params.outdir}/bsj_detection/tools/segemehl/grouped" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -216,7 +216,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$4, \$6, \$5 }'" ext.suffix = "segemehl.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/segemehl/unified" }, + path: { "${params.outdir}/bsj_detection/tools/segemehl/unified" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.segemehl.bed" @@ -237,7 +237,7 @@ process { "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/star/1st_pass" }, + path: { "${params.outdir}/bsj_detection/tools/star/1st_pass" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -245,7 +245,7 @@ process { withName: '.*:STAR2PASS:SJDB' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/star/sjdb" }, + path: { "${params.outdir}/bsj_detection/tools/star/sjdb" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -265,7 +265,7 @@ process { "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/star/2nd_pass" }, + path: { "${params.outdir}/bsj_detection/tools/star/2nd_pass" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -285,7 +285,7 @@ process { withName: '.*:CIRCEXPLORER2:PARSE' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/circexplorer2/intermediates/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/tools/circexplorer2/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -293,7 +293,7 @@ process { withName: '.*:CIRCEXPLORER2:ANNOTATE' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/circexplorer2/intermediates/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/tools/circexplorer2/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -303,7 +303,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$13, \$6 }'" ext.suffix = "circexplorer2.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/circexplorer2/unified" }, + path: { "${params.outdir}/bsj_detection/tools/circexplorer2/unified" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.circexplorer2.bed" @@ -312,7 +312,7 @@ process { withName: '.*:CIRCRNA_FINDER:MAIN' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/circrna_finder/intermediates/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/tools/circrna_finder/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null }, pattern: "*.bed" @@ -323,7 +323,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$5, \$6 }'" ext.suffix = "circrna_finder.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/circrna_finder/unified" }, + path: { "${params.outdir}/bsj_detection/tools/circrna_finder/unified" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.circrna_finder.bed" @@ -335,7 +335,7 @@ process { (!meta.strandedness || meta.strandedness == 'unstranded' || meta.strandedness == 'auto' ? '' : meta.strandedness == 'forward' ? ' --norc' : ' --nofw') } publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/find_circ/intermediates/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/tools/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -343,7 +343,7 @@ process { withName: '.*:FIND_CIRC:SAMTOOLS_INDEX' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/find_circ/intermediates/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/tools/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -353,7 +353,7 @@ process { ext.prefix = { "${meta.id}_unmapped" } ext.args = "-hf 4" publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/find_circ/intermediates/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/tools/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -361,7 +361,7 @@ process { withName: '.*:FIND_CIRC:ANCHORS' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/find_circ/intermediates/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/tools/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -371,7 +371,7 @@ process { ext.args = { !meta.strandedness || meta.strandedness == 'unstranded' || meta.strandedness == 'auto' ? '' : meta.strandedness == 'forward' ? ' --norc' : ' --nofw' } publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/find_circ/intermediates/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/tools/find_circ/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -382,7 +382,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '{ if (\$18 ~ /CIRCULAR/ && \$18 ~ /UNAMBIGUOUS_BP/ && \$18 ~ /ANCHOR_UNIQUE/) { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$5, \$6 } }'" ext.suffix = "find_circ.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/find_circ/unified" }, + path: { "${params.outdir}/bsj_detection/tools/find_circ/unified" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.find_circ.bed" @@ -391,7 +391,7 @@ process { withName: '.*:CIRIQUANT:MAIN' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/ciriquant/intermediates/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/tools/ciriquant/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -405,7 +405,7 @@ process { ext.suffix = "ciriquant.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/ciriquant/unified" }, + path: { "${params.outdir}/bsj_detection/tools/ciriquant/unified" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.ciriquant.bed" @@ -426,7 +426,7 @@ process { "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/dcc/intermediates/mate1/1st_pass" }, + path: { "${params.outdir}/bsj_detection/tools/dcc/intermediates/mate1/1st_pass" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -434,7 +434,7 @@ process { withName: '.*:DCC:MATE1_SJDB' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/dcc/intermediates/mate1/sjdb" }, + path: { "${params.outdir}/bsj_detection/tools/dcc/intermediates/mate1/sjdb" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -455,7 +455,7 @@ process { "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/dcc/intermediates/mate1/2nd_pass" }, + path: { "${params.outdir}/bsj_detection/tools/dcc/intermediates/mate1/2nd_pass" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -475,7 +475,7 @@ process { "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/dcc/intermediates/mate2/1st_pass" }, + path: { "${params.outdir}/bsj_detection/tools/dcc/intermediates/mate2/1st_pass" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -483,7 +483,7 @@ process { withName: '.*:DCC:MATE2_SJDB' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/dcc/intermediates/mate2/sjdb" }, + path: { "${params.outdir}/bsj_detection/tools/dcc/intermediates/mate2/sjdb" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -504,7 +504,7 @@ process { "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/dcc/intermediates/mate2/2nd_pass" }, + path: { "${params.outdir}/bsj_detection/tools/dcc/intermediates/mate2/2nd_pass" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -512,7 +512,7 @@ process { withName: '.*:DCC:MAIN' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/dcc/intermediates/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/tools/dcc/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -522,7 +522,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$4, \$5, \$4 }'" ext.suffix = "dcc.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/dcc/unified" }, + path: { "${params.outdir}/bsj_detection/tools/dcc/unified" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.dcc.bed" @@ -551,7 +551,7 @@ process { "--fusion-non-canonical" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/mapsplice/intermediates/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/tools/mapsplice/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -559,7 +559,7 @@ process { withName: '.*:MAPSPLICE:PARSE' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/mapsplice/intermediates/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/tools/mapsplice/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -567,7 +567,7 @@ process { withName: '.*:MAPSPLICE:ANNOTATE' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/mapsplice/intermediates/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/tools/mapsplice/intermediates/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -577,7 +577,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3 \":\" \$6, \$10, \$6 }'" ext.suffix = "mapsplice.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/mapsplice/unified" }, + path: { "${params.outdir}/bsj_detection/tools/mapsplice/unified" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.mapsplice.bed" @@ -589,7 +589,7 @@ process { ext.args = { "-v FS='\\t' -v OFS='\\t' '{ if (\$5 >= ${params.bsj_reads}) { print } }'" } ext.suffix = {"${meta.tool}.filtered.bed"} publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/${meta.tool}/filtered" }, + path: { "${params.outdir}/bsj_detection/tools/${meta.tool}/filtered" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, ] @@ -600,7 +600,7 @@ process { ext.args = "-v FS='\\t' -v OFS='\\t' '{ print \$1, \$2, \$3, \$4, \".\", \$6 }'" ext.suffix = {"${meta.tool}.masked.bed"} publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/${meta.tool}/masked" }, + path: { "${params.outdir}/bsj_detection/tools/${meta.tool}/masked" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -611,7 +611,7 @@ process { ext.args = "-k1,1 -k2,2n -k3,3n -k4,4 -k6,6" ext.suffix = {"sorted.bed"} publishDir = [ - path: { "${params.outdir}/circrna_discovery/samples/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/samples/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> null } // The same data will be published in COUNT_TOOLS in a better format ] @@ -623,7 +623,7 @@ process { ext.args = "-g 1,2,3,4,6 -o count" ext.suffix = {"tool_counts.bed"} publishDir = [ - path: { "${params.outdir}/circrna_discovery/samples/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/samples/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -635,7 +635,7 @@ process { ext.args = { "-v FS='\\t' -v OFS='\\t' '{ if (\$6 >= ${params.tool_filter}) { print \$1, \$2, \$3, \$4, \".\", \$5 } }'" } ext.suffix = "filtered.bed" publishDir = [ - path: { "${params.outdir}/circrna_discovery/samples/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/samples/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -646,7 +646,7 @@ process { ext.args = "-k1,1 -k2,2n -k3,3n -k4,4 -k6,6 -u" ext.suffix = {"combined.bed"} publishDir = [ - path: { "${params.outdir}/circrna_discovery/combined" }, + path: { "${params.outdir}/bsj_detection/combined" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -655,7 +655,7 @@ process { withName: UPSET_SAMPLES { ext.when = { params.tool.split(',').length > 1 } publishDir = [ - path: { "${params.outdir}/circrna_discovery/samples/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/samples/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -664,7 +664,7 @@ process { withName: UPSET_ALL { ext.when = { params.tool.split(',').length > 1 } publishDir = [ - path: { "${params.outdir}/circrna_discovery/combined" }, + path: { "${params.outdir}/bsj_detection/combined" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -673,7 +673,7 @@ process { withName: FASTA_COMBINED { ext.suffix = "fasta" publishDir = [ - path: { "${params.outdir}/circrna_discovery/combined" }, + path: { "${params.outdir}/bsj_detection/combined" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -682,7 +682,7 @@ process { withName: FASTA_PER_SAMPLE { ext.suffix = "fasta" publishDir = [ - path: { "${params.outdir}/circrna_discovery/samples/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/samples/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -691,7 +691,7 @@ process { withName: FASTA_PER_SAMPLE_TOOL { ext.suffix = { "${meta.tool}.fasta" } publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/${meta.tool}/fasta" }, + path: { "${params.outdir}/bsj_detection/tools/${meta.tool}/fasta" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -704,7 +704,7 @@ process { withName: '.*:ANNOTATE_COMBINED:INTERSECT_GTF' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/combined" }, + path: { "${params.outdir}/bsj_detection/combined" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -712,7 +712,7 @@ process { withName: '.*:ANNOTATE_PER_SAMPLE:INTERSECT_GTF' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/samples/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/samples/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -720,7 +720,7 @@ process { withName: '.*:ANNOTATE_PER_SAMPLE_TOOL:INTERSECT_GTF' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/${meta.tool}/annotated" }, + path: { "${params.outdir}/bsj_detection/tools/${meta.tool}/annotated" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -744,7 +744,7 @@ process { withName: '.*:ANNOTATE_COMBINED:INTERSECT_DATABASE' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/combined" }, + path: { "${params.outdir}/bsj_detection/combined" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -752,7 +752,7 @@ process { withName: '.*:ANNOTATE_PER_SAMPLE:INTERSECT_DATABASE' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/samples/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/samples/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -760,7 +760,7 @@ process { withName: '.*:ANNOTATE_PER_SAMPLE_TOOL:INTERSECT_DATABASE' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/${meta.tool}/annotated" }, + path: { "${params.outdir}/bsj_detection/tools/${meta.tool}/annotated" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -772,7 +772,7 @@ process { withName: '.*:ANNOTATE_COMBINED:ANNOTATE' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/combined" }, + path: { "${params.outdir}/bsj_detection/combined" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -780,7 +780,7 @@ process { withName: '.*:ANNOTATE_PER_SAMPLE:ANNOTATE' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/samples/${meta.id}" }, + path: { "${params.outdir}/bsj_detection/samples/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -788,7 +788,7 @@ process { withName: '.*:ANNOTATE_PER_SAMPLE_TOOL:ANNOTATE' { publishDir = [ - path: { "${params.outdir}/circrna_discovery/tools/${meta.tool}/annotated" }, + path: { "${params.outdir}/bsj_detection/tools/${meta.tool}/annotated" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] diff --git a/docs/usage.md b/docs/usage.md index be4519df..a0071d87 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -71,17 +71,11 @@ TREATMENT_REP3,treatment Note that `TREATMENT_REP3` only has one entry in the `phenotype.csv` file, even though it has two entries in the `samplesheet.csv` file. -# Analysis modules - -`nf-core/circrna` provides 3 analysis modules to the user: - -1. BSJ detection -2. Joint quantification of circular and linear transcriptome -3. miRNA target prediction - ## circRNA discovery -The core module of `nf-core/circrna`, a user can utilise up to seven circRNA quantification tools to fully characterise the circRNA profile in samples. Currently, supported tools include `CIRCexplorer2`, `circRNA finder`, `CIRIquant`, `DCC`, `find circ` , `MapSplice` & `Segemehl` however, the authors of `nf-core/circrna` welcome contributions from authors of novel quantification tools to keep the workflow current. +The core module of `nf-core/circrna`, a user can utilise up to seven circRNA quantification tools to fully characterise the circRNA profile in samples. + +Currently, supported tools include `CIRCexplorer2`, `circRNA finder`, `CIRIquant`, `DCC`, `find circ` , `MapSplice` & `Segemehl` however, the authors of `nf-core/circrna` welcome contributions from authors of novel quantification tools to keep the workflow current. By default, `nf-core/circrna` runs the circRNA discovery analysis module. diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/bsj_detection.nf similarity index 91% rename from subworkflows/local/circrna_discovery.nf rename to subworkflows/local/bsj_detection.nf index 1447aa0a..7ebe8528 100644 --- a/subworkflows/local/circrna_discovery.nf +++ b/subworkflows/local/bsj_detection.nf @@ -13,19 +13,19 @@ include { BEDTOOLS_GETFASTA as FASTA_PER_SAMPLE_TOOL } from '../../modules/nf-co include { FAIL_ON_EMPTY } from '../../modules/local/fail_on_empty' // SUBWORKFLOWS -include { SEGEMEHL } from './discovery/segemehl' -include { STAR2PASS } from './discovery/star2pass' -include { CIRCEXPLORER2 } from './discovery/circexplorer2' -include { CIRCRNA_FINDER } from './discovery/circrna_finder' -include { FIND_CIRC } from './discovery/find_circ' -include { CIRIQUANT } from './discovery/ciriquant' -include { DCC } from './discovery/dcc' -include { MAPSPLICE } from './discovery/mapsplice' +include { SEGEMEHL } from './detection_tools/segemehl' +include { STAR2PASS } from './detection_tools/star2pass' +include { CIRCEXPLORER2 } from './detection_tools/circexplorer2' +include { CIRCRNA_FINDER } from './detection_tools/circrna_finder' +include { FIND_CIRC } from './detection_tools/find_circ' +include { CIRIQUANT } from './detection_tools/ciriquant' +include { DCC } from './detection_tools/dcc' +include { MAPSPLICE } from './detection_tools/mapsplice' include { ANNOTATION as ANNOTATE_COMBINED } from './annotation' include { ANNOTATION as ANNOTATE_PER_SAMPLE } from './annotation' include { ANNOTATION as ANNOTATE_PER_SAMPLE_TOOL } from './annotation' -workflow CIRCRNA_DISCOVERY { +workflow BSJ_DETECTION { take: reads diff --git a/subworkflows/local/discovery/circexplorer2.nf b/subworkflows/local/detection_tools/circexplorer2.nf similarity index 100% rename from subworkflows/local/discovery/circexplorer2.nf rename to subworkflows/local/detection_tools/circexplorer2.nf diff --git a/subworkflows/local/discovery/circrna_finder.nf b/subworkflows/local/detection_tools/circrna_finder.nf similarity index 100% rename from subworkflows/local/discovery/circrna_finder.nf rename to subworkflows/local/detection_tools/circrna_finder.nf diff --git a/subworkflows/local/discovery/ciriquant.nf b/subworkflows/local/detection_tools/ciriquant.nf similarity index 100% rename from subworkflows/local/discovery/ciriquant.nf rename to subworkflows/local/detection_tools/ciriquant.nf diff --git a/subworkflows/local/discovery/dcc.nf b/subworkflows/local/detection_tools/dcc.nf similarity index 100% rename from subworkflows/local/discovery/dcc.nf rename to subworkflows/local/detection_tools/dcc.nf diff --git a/subworkflows/local/discovery/find_circ.nf b/subworkflows/local/detection_tools/find_circ.nf similarity index 100% rename from subworkflows/local/discovery/find_circ.nf rename to subworkflows/local/detection_tools/find_circ.nf diff --git a/subworkflows/local/discovery/mapsplice.nf b/subworkflows/local/detection_tools/mapsplice.nf similarity index 100% rename from subworkflows/local/discovery/mapsplice.nf rename to subworkflows/local/detection_tools/mapsplice.nf diff --git a/subworkflows/local/discovery/segemehl.nf b/subworkflows/local/detection_tools/segemehl.nf similarity index 100% rename from subworkflows/local/discovery/segemehl.nf rename to subworkflows/local/detection_tools/segemehl.nf diff --git a/subworkflows/local/discovery/star2pass.nf b/subworkflows/local/detection_tools/star2pass.nf similarity index 100% rename from subworkflows/local/discovery/star2pass.nf rename to subworkflows/local/detection_tools/star2pass.nf diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index af779e8c..7a05e43b 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -28,7 +28,7 @@ include { validateInputSamplesheet } from '../../subworkflows/local/util include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' include { PREPARE_GENOME } from '../../subworkflows/local/prepare_genome' -include { CIRCRNA_DISCOVERY } from '../../subworkflows/local/circrna_discovery' +include { BSJ_DETECTION } from '../../subworkflows/local/bsj_detection' include { ANNOTATION } from '../../subworkflows/local/annotation' include { QUANTIFICATION } from '../../subworkflows/local/quantification' include { MIRNA_PREDICTION } from '../../subworkflows/local/mirna_prediction' @@ -133,10 +133,10 @@ workflow CIRCRNA { ch_multiqc_files = ch_multiqc_files.mix(FASTQC_TRIMGALORE.out.trim_log.collect{it[1]}.ifEmpty([])) // - // 2. circRNA Discovery + // 2. BSJ Discovery // - CIRCRNA_DISCOVERY( + BSJ_DETECTION( FASTQC_TRIMGALORE.out.reads, ch_fasta, ch_gtf, @@ -151,8 +151,8 @@ workflow CIRCRNA { params.exon_boundary ) - ch_multiqc_files = ch_multiqc_files.mix(CIRCRNA_DISCOVERY.out.multiqc_files) - ch_versions = ch_versions.mix(CIRCRNA_DISCOVERY.out.versions) + ch_multiqc_files = ch_multiqc_files.mix(BSJ_DETECTION.out.multiqc_files) + ch_versions = ch_versions.mix(BSJ_DETECTION.out.versions) // // 3. circRNA quantification @@ -162,8 +162,8 @@ workflow CIRCRNA { ch_gtf, ch_fasta, FASTQC_TRIMGALORE.out.reads, - CIRCRNA_DISCOVERY.out.bed12, - CIRCRNA_DISCOVERY.out.gtf, + BSJ_DETECTION.out.bed12, + BSJ_DETECTION.out.gtf, params.bootstrap_samples, ch_phenotype, PREPARE_GENOME.out.faidx @@ -176,8 +176,8 @@ workflow CIRCRNA { // if (params.mature) { MIRNA_PREDICTION( - CIRCRNA_DISCOVERY.out.fasta, - CIRCRNA_DISCOVERY.out.bed, + BSJ_DETECTION.out.fasta, + BSJ_DETECTION.out.bed, ch_mature ) ch_versions = ch_versions.mix(MIRNA_PREDICTION.out.versions) From 532c956b372a3224ea808d2abc1aefcf6f913595 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 11:30:17 +0200 Subject: [PATCH 376/491] Rename params.tool to params.tools --- conf/modules.config | 20 ++++++++++---------- nextflow.config | 2 +- nextflow_schema.json | 14 +++++++------- subworkflows/local/bsj_detection.nf | 2 +- subworkflows/local/prepare_genome.nf | 2 +- 5 files changed, 20 insertions(+), 20 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index d273ec07..99ace97d 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -101,7 +101,7 @@ process { } withName: BOWTIE_BUILD { - ext.when = { !params.bowtie && params.tool.split(',').contains('mapsplice') } + ext.when = { !params.bowtie && params.tools.split(',').contains('mapsplice') } publishDir = [ path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, @@ -110,7 +110,7 @@ process { } withName: BOWTIE2_BUILD { - ext.when = { !params.bowtie2 && params.tool.split(',').contains('find_circ') } + ext.when = { !params.bowtie2 && params.tools.split(',').contains('find_circ') } publishDir = [ path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, @@ -119,7 +119,7 @@ process { } withName: BWA_INDEX { - ext.when = { !params.bwa && params.tool.split(',').contains('ciriquant') } + ext.when = { !params.bwa && params.tools.split(',').contains('ciriquant') } publishDir = [ path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, @@ -128,7 +128,7 @@ process { } withName: HISAT2_EXTRACTSPLICESITES { - ext.when = { params.tool.split(',').contains('ciriquant') } + ext.when = { params.tools.split(',').contains('ciriquant') } publishDir = [ path: { "${params.outdir}/references/index/hisat2" }, mode: params.publish_dir_mode, @@ -137,7 +137,7 @@ process { } withName: HISAT2_BUILD { - ext.when = { params.tool.split(',').contains('ciriquant') } + ext.when = { params.tools.split(',').contains('ciriquant') } publishDir = [ path: { "${params.outdir}/references/index" }, mode: params.publish_dir_mode, @@ -146,7 +146,7 @@ process { } withName: STAR_GENOMEGENERATE { - ext.when = { !params.star && ( params.tool.split(',').contains('circexplorer2') || params.tool.split(',').contains('dcc') || params.tool.split(',').contains('circrna_finder') ) } + ext.when = { !params.star && ( params.tools.split(',').contains('circexplorer2') || params.tools.split(',').contains('dcc') || params.tools.split(',').contains('circrna_finder') ) } ext.args = [ "", params.sjdboverhang ? "--sjdbOverhang ${params.sjdboverhang}" : '', ].join(' ').trim() @@ -224,7 +224,7 @@ process { } withName: '.*:STAR2PASS:PASS_1' { - ext.when = { params.tool.split(',').contains('circexplorer2') || params.tool.split(',').contains('circrna_finder') } + ext.when = { params.tools.split(',').contains('circexplorer2') || params.tools.split(',').contains('circrna_finder') } ext.args = [ "", "--chimOutType Junctions WithinBAM", "--outSAMunmapped Within", @@ -253,7 +253,7 @@ process { withName: '.*:STAR2PASS:PASS_2' { ext.args = [ "", - params.tool.split(',').contains('circrna_finder') ? "--chimOutType Junctions SeparateSAMold" : "--chimOutType Junctions WithinBAM", + params.tools.split(',').contains('circrna_finder') ? "--chimOutType Junctions SeparateSAMold" : "--chimOutType Junctions WithinBAM", "--outSAMunmapped Within", "--outFilterType BySJout", "--outReadsUnmapped None", @@ -653,7 +653,7 @@ process { } withName: UPSET_SAMPLES { - ext.when = { params.tool.split(',').length > 1 } + ext.when = { params.tools.split(',').length > 1 } publishDir = [ path: { "${params.outdir}/bsj_detection/samples/${meta.id}" }, mode: params.publish_dir_mode, @@ -662,7 +662,7 @@ process { } withName: UPSET_ALL { - ext.when = { params.tool.split(',').length > 1 } + ext.when = { params.tools.split(',').length > 1 } publishDir = [ path: { "${params.outdir}/bsj_detection/combined" }, mode: params.publish_dir_mode, diff --git a/nextflow.config b/nextflow.config index 5e54776d..cdee4d4d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,7 +16,7 @@ params { annotation = null // workflow options - tool = 'circexplorer2' + tools = 'circexplorer2' bsj_reads = 0 tool_filter = 0 exon_boundary = 200 diff --git a/nextflow_schema.json b/nextflow_schema.json index 45770cb8..aebb0311 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -59,9 +59,9 @@ "type": "object", "fa_icon": "fas fa-circle-notch", "description": "Parameters for circrna discovery.", - "required": ["tool"], + "required": ["tools"], "properties": { - "tool": { + "tools": { "type": "string", "fa_icon": "fas fa-wrench", "description": "Comma separated list of circRNA quantification tools to use. Supported tools: ciriquant, circexplorer2, find_circ, circrna_finder, mapsplice, dcc, segemehl", @@ -74,16 +74,16 @@ "fa_icon": "fas fa-circle-notch", "description": "Minimum number of reads spanning circRNA back-splice junction required for circRNA to be output by workflow.", "help_text": "Filter low confidence circRNAs by removing circRNAs with read counts below a specified value. To disable, set the value to 0 (default).", - "default": 0, - "minimum": 0 + "default": 1, + "minimum": 1 }, "tool_filter": { "type": "integer", "fa_icon": "fas fa-intersection", "description": "Specify the minimum number of tools circRNAs must be called by to be output by the workflow.", - "help_text": "When multiple circRNA quantification tools have been provided to `--tool`, set a filtering method whereby circRNAs are output if they have been called by at least *n* quantification tools.\n\nSetting `--tool_filter` to 0/1 is the same as taking the union, all circRNAs are included in the output.\n\nSetting `--tool_filter` to 2 will output circRNAs that have been called by at least 2 quantification tools and so on.", - "default": 0, - "minimum": 0, + "help_text": "When multiple circRNA quantification tools have been provided to `--tool`, set a filtering method whereby circRNAs are output if they have been called by at least *n* quantification tools.\n\nSetting `--tool_filter` to 1 is the same as taking the union, all circRNAs are included in the output.\n\nSetting `--tool_filter` to 2 will output circRNAs that have been called by at least 2 quantification tools and so on.", + "default": 1, + "minimum": 1, "maximum": 7 }, "save_intermediates": { diff --git a/subworkflows/local/bsj_detection.nf b/subworkflows/local/bsj_detection.nf index 7ebe8528..5da9899f 100644 --- a/subworkflows/local/bsj_detection.nf +++ b/subworkflows/local/bsj_detection.nf @@ -58,7 +58,7 @@ workflow BSJ_DETECTION { // // DISCOVERY TOOLS: // - tools_selected = params.tool.split(',').collect{it.trim().toLowerCase()} + tools_selected = params.tools.split(',').collect{it.trim().toLowerCase()} if (tools_selected.size() == 0) { error 'No tools selected for circRNA discovery.' diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 76fe152d..cb87f6b4 100644 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -20,7 +20,7 @@ workflow PREPARE_GENOME { // MapSplice cannot deal with extra field in the fasta headers // this removes all additional fields in the headers of the input fasta file - if( params.tool.contains('mapsplice') ) { + if( params.tools.split(',').contains('mapsplice') ) { CLEAN_FASTA(ch_fasta, []) ch_fasta = CLEAN_FASTA.out.output From ac23046f1c24fb77ca11bb6421872ecf399b859c Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 11:40:33 +0200 Subject: [PATCH 377/491] Remove unused species_id parameter --- main.nf | 3 --- nextflow.config | 1 - nextflow_schema.json | 7 ------- workflows/circrna/main.nf | 1 - 4 files changed, 12 deletions(-) diff --git a/main.nf b/main.nf index 022b6be8..23b4c9c0 100644 --- a/main.nf +++ b/main.nf @@ -36,7 +36,6 @@ params.star = getGenomeAttribute('star') params.bowtie = getGenomeAttribute('bowtie') params.bowtie2 = getGenomeAttribute('bowtie2') params.mature = getGenomeAttribute('mature') -params.species_id = getGenomeAttribute('species_id') /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -60,7 +59,6 @@ workflow NFCORE_CIRCRNA { ch_gtf = Channel.value([[id: "gtf"], file(params.gtf, checkIfExists:true)]) ch_mature = params.mature ? Channel.value([[id: "mature"], file(params.mature, checkIfExists:true)]) : Channel.empty() ch_phenotype = params.phenotype ? Channel.value([[id: "phenotype"], file(params.phenotype, checkIfExists:true)]) : Channel.empty() - ch_species = params.phenotype ? Channel.value(params.species_id) : Channel.empty() ch_annotation = params.annotation ? Channel.fromSamplesheet("annotation") : Channel.empty() CIRCRNA ( @@ -70,7 +68,6 @@ workflow NFCORE_CIRCRNA { ch_gtf, ch_mature, ch_annotation, - ch_species, ch_versions ) diff --git a/nextflow.config b/nextflow.config index cdee4d4d..2080b90c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -34,7 +34,6 @@ params { hisat2_build_memory = '200.GB' segemehl = null save_reference = true - species_id = null // Trimming min_trimmed_reads = 10000 diff --git a/nextflow_schema.json b/nextflow_schema.json index aebb0311..0448bd36 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -220,13 +220,6 @@ "fa_icon": "fas fa-wheelchair", "default": null }, - "species_id": { - "type": "string", - "fa_icon": "fas fa-dog", - "description": "String identifying species.", - "help_text": "Check the igenomes.config file for species configured to work with nf-core/circrna", - "default": null - }, "bowtie": { "type": "string", "fa_icon": "fas fa-bold", diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 7a05e43b..4c1e76ea 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -60,7 +60,6 @@ workflow CIRCRNA { ch_gtf ch_mature ch_annotation - ch_species ch_versions main: From fde46d00ce42101495aab574fb712b680b492bdd Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 11:43:07 +0200 Subject: [PATCH 378/491] Apply parameter changes to test configs --- conf/full.config | 2 +- conf/test.config | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/conf/full.config b/conf/full.config index 4161771d..37cf7778 100644 --- a/conf/full.config +++ b/conf/full.config @@ -12,6 +12,6 @@ */ params { - tool = 'circexplorer2,ciriquant,find_circ,circrna_finder,mapsplice,dcc,segemehl' + tools = 'circexplorer2,ciriquant,find_circ,circrna_finder,mapsplice,dcc,segemehl' tool_filter = 2 } diff --git a/conf/test.config b/conf/test.config index 2f4323e2..6c40a460 100644 --- a/conf/test.config +++ b/conf/test.config @@ -24,10 +24,9 @@ params { fasta = "${params.test_data_base}/reference/chrI.fa" gtf = "${params.test_data_base}/reference/chrI.gtf" mature = "${params.test_data_base}/reference/mature.fa" - tool = "circexplorer2" + tools = "circexplorer2" phenotype = "${params.test_data_base}/phenotype.csv" skip_trimming = false outdir = "results/" bsj_reads = 2 - species_id = "cel" } From a8085274d81cd5a0c941fcd92cbb766589ffeae0 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 11:58:51 +0200 Subject: [PATCH 379/491] Change some default values --- nextflow.config | 6 +++--- nextflow_schema.json | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/nextflow.config b/nextflow.config index 2080b90c..d693ca69 100644 --- a/nextflow.config +++ b/nextflow.config @@ -17,9 +17,9 @@ params { // workflow options tools = 'circexplorer2' - bsj_reads = 0 - tool_filter = 0 - exon_boundary = 200 + bsj_reads = 1 + tool_filter = 1 + exon_boundary = 0 save_intermediates = false // References diff --git a/nextflow_schema.json b/nextflow_schema.json index 0448bd36..eb5452be 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -96,7 +96,7 @@ "type": "integer", "description": "Specify the distance at which the annotation script decides if a candidate is a circRNA or EI-circRNA.", "help_text": "During annotation, if one of the start or end position of a circular candidate imperfectly overlaps an exon boundary, the script will consider positions within 'exon_boundary' (default 200bp) to be an exonic circRNA. If they fall outside of this range, the candidate is assumed to be an exonic-intronic circRNA, and the entire underlying sequence is taken for miRNA analysis, as opposed to just the exonic sequences for canonical exonic circRNAs. ", - "default": 200 + "default": 0 } } }, From 9f6a709459612205b5bb0151627127b649297218 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 11:59:01 +0200 Subject: [PATCH 380/491] Finish updating usage docs --- docs/usage.md | 136 +++++++++++++++++--------------------------------- 1 file changed, 46 insertions(+), 90 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index a0071d87..6f694f6e 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -53,115 +53,71 @@ TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,,reverse An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. -## Phenotype file +## BSJ detection -The CSV file provided via the `phenotype` parameter can be used to provide additional metadata about the samples in the input CSV file. If provided, it needs to at least contain a column called `sample` which corresponds to the `sample` column in the input CSV file and a column called `condition`. The `condition` column will be used to group samples for the [CircTest](https://github.com/dieterich-lab/CircTest) functionality. All metadata columns will be included in the result `SummarizedExperiment` RDS file. +This part of the pipeline is responsible for the detection of back-splice junctions (BSJs) in the input data. The following tools are currently supported: +- `CIRCexplorer2` +- `circRNA finder` +- `CIRIquant` +- `DCC` +- `find circ` +- `MapSplice` +- `Segemehl` -A valid example of a `phenotype.csv` file (matching the "Full samplesheet") is given: +The tools to be used can be specified using the `tools` parameter. +Each of the tools also quantifies how many reads support each BSJ. You can specify a cutoff for the minimum number of reads supporting a BSJ using the `bsj_reads` parameter. +Additionally, the parameter `tool_filter` can be used to specify how many tools a BSJ has to be detected by to be considered as a valid hit. -```csv title="phenotype.csv" -sample,condition -CONTROL_REP1,control -CONTROL_REP2,control -CONTROL_REP3,control -TREATMENT_REP1,treatment -TREATMENT_REP2,treatment -TREATMENT_REP3,treatment -``` - -Note that `TREATMENT_REP3` only has one entry in the `phenotype.csv` file, even though it has two entries in the `samplesheet.csv` file. - -## circRNA discovery +For instructions on how to interpret the output of this section, please check out the [output documentation](https://nf-co.re/circrna/dev/output#bsj-detection). -The core module of `nf-core/circrna`, a user can utilise up to seven circRNA quantification tools to fully characterise the circRNA profile in samples. +## Annotation -Currently, supported tools include `CIRCexplorer2`, `circRNA finder`, `CIRIquant`, `DCC`, `find circ` , `MapSplice` & `Segemehl` however, the authors of `nf-core/circrna` welcome contributions from authors of novel quantification tools to keep the workflow current. +The annotation is generally based on the reference GTF file. It can also utilize BED files that are provided by the various circRNA databases. +The GTF-based annotation allows setting the parameter `exon_boundary` to specify a window around exons. If the BSJ is within this window, it will be annotated as a circRNA - otherwise, it will be annotated as an exon-intron circRNA (EI-circRNA). The default value is 0. -By default, `nf-core/circrna` runs the circRNA discovery analysis module. - -```bash -nextflow run nf-core/circrna \ - -profile \ - --genome 'GRCh37' \ - --input 'samples.csv' \ - --module 'circrna_discovery' -``` - -To view the outputs of the module, please see the output [documentation](https://nf-co.re/circrna/dev/output#circrna-quantification). - -> Please note that this module must be included for every run of the workflow - -### Tool selection - -The user may use one, all or any combination of circRNA quantification tools listed above in the analysis. To select which tools to use for the analysis, specify the `--tool` parameter in the configuration profile or pass it via the command line when running the workflow: - -```bash -nextflow run nf-core/circrna \ - -profile \ - --genome 'GRCh37' \ - --input 'samples.csv' \ - --tool 'ciriquant,dcc,find_circ' +For the database-based annotation, an additional sample sheet is required: +```csv title="annotation.csv" +name,file,min_overlap +db1,db1.bed,0.9 +db2,db2.bed,0.8 ``` -> When providing multiple tools, separate each entry with a comma. - -### circRNA filtering - -`nf-core/circrna` offers robust filtering of each called circRNA to reduce the number of spurious calls within the dataset. - -#### BSJ reads +| Column | Description | +| ------------ | --------------------------------------------------------------------------------------------- | +| `name` | Name of the database. This will be used as a prefix for the region names in the output files. | +| `file` | Path to the BED file. The file has to be a valid BED6 file. | +| `min_overlap`| Minimum bidirectional overlap required between the BSJ and the region in the BED file. | -The user can specify the minimum number of reads spanning the back-splice junction site required for a circRNA to be considered for further analysis. circRNAs with counts below this value will be filtered to remove from the results. +The output of the annotation step will be bundled with the outputs of the BSJ detection step. -To apply this filtering method, specify the `--bsj_reads` parameter in the configuration profile or pass it via the command line when running the workflow: - -```bash -nextflow run nf-core/circrna \ - -profile \ - --genome 'GRCh37' \ - --input 'samples.csv' \ - --phenotype 'phenotype.csv' \ - --tool 'ciriquant, dcc, find_circ' \ - --bsj_reads 2 -``` - -Disable the filter by setting the value to 0. - -#### Multiple tool filtering - -When more than one tool has been provided using the `--tool` parameter, the user can specify the minimum number of tools circRNAs must be called by using `--tool_filter`. Setting this parameter to 0 or 1 will result in the union being output, i.e no filtering is applied. Setting this parameter to 2 will output circRNAs that have been called by at least 2 quantification tools and so on. - -> The integer provided to the parameter must be less than or equal to the number of quantification tools provided to `--tool`. +## miRNA prediction -To apply this filtering method, specify the `--tool_filter` parameter in the configuration profile or pass it via the command line when running the workflow: +This section allows looking for miRNA binding sites in the circRNAs. The following tools are currently supported: +- `miRanda` +- `TargetScan` -```bash -nextflow run nf-core/circrna \ - -profile \ - --genome 'GRCh37' \ - --input 'samples.csv' \ - --tool 'ciriquant, dcc, find_circ' \ - --bsj_reads 2 \ - --tool_filter 2 -``` +This section will only be executed if the `mature` parameter is provided. The parameter should point to a FASTA file containing mature miRNA sequences. -> This filtering method is reflected in the circRNA count matrix. Per tool circRNA annotations are subject to back-splice read filtering only. +To view the outputs of the module, please see the output [documentation](https://nf-co.re/circrna/dev/output#mirna-prediction). -## miRNA prediction +## Statistical tests -The second module of `nf-core/circrna`, `mirna_prediction` analyses the mature spliced sequences of circRNAs to test for the presence of miRNA response elements using both `miRanda` and `TargetScan`. Results from both tools are consolidated and filtering methods are applied to produce robust miRNA target predictions of circRNAs in the dataset. +Currently, only [CircTest](https://github.com/dieterich-lab/CircTest) is supported for the statistical analysis of the circRNA expression data. The `phenotype` parameter is required for this step. -To invoke the module, specify the `--module` parameter via the configuration profile or pass it via the command line when running the workflow: +A valid example of a `phenotype.csv` file (matching the "Full samplesheet") is shown here: -```bash -nextflow run nf-core/circrna \ - -profile \ - --genome 'GRCh37' \ - --input 'samples.csv' \ - --module 'circrna_discovery,mirna_prediction' +```csv title="phenotype.csv" +sample,condition +CONTROL_REP1,control +CONTROL_REP2,control +CONTROL_REP3,control +TREATMENT_REP1,treatment +TREATMENT_REP2,treatment +TREATMENT_REP3,treatment ``` -To view the outputs of the module, please see the output [documentation](https://nf-co.re/circrna/dev/output#mirna-prediction). +Note that `TREATMENT_REP3` only has one entry in the `phenotype.csv` file, even though it has two entries in the `samplesheet.csv` file. +If the `phenotype` parameter is provided, the phenotype information will also be added to the `SummarizedExperiment` object, that results from the "Quantification" step. ## Running the pipeline From b0f797b37e67e63bfa6cffa536cca6250584d85e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 12:15:15 +0200 Subject: [PATCH 381/491] Add output directory structure documentation --- docs/output.md | 50 +++++++++++++++++++------------------------------- 1 file changed, 19 insertions(+), 31 deletions(-) diff --git a/docs/output.md b/docs/output.md index fdd9bf48..66a8f743 100644 --- a/docs/output.md +++ b/docs/output.md @@ -2,11 +2,6 @@ ## Introduction -:::warning -This page has not been updated for a long time and might not align with the current pipeline output. We are working on updating it. -If you have questions regarding the pipeline output, feel free to reach out in the [nf-core slack](https://nfcore.slack.com/channels/circrna) channel. -::: - This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report generated from the [full-sized test dataset](https://github.com/nf-core/test-datasets/tree/circrna) for the pipeline using a command similar to the one below: ```bash @@ -15,32 +10,25 @@ nextflow run nf-core/circrna -profile test_full, The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory. -## Pipeline Overview - -The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: - -- Raw read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) -- Adapter trimming ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)) -- BSJ detection - - [`CIRIquant`](https://github.com/Kevinzjy/CIRIquant) - - [`STAR 2-Pass mode`](https://github.com/alexdobin/STAR) - - [`CIRCexplorer2`](https://circexplorer2.readthedocs.io/en/latest/) - - [`circRNA finder`](https://github.com/orzechoj/circRNA_finder) - - [`DCC`](https://github.com/dieterich-lab/DCC) - - [`find circ`](https://github.com/marvin-jens/find_circ) - - [`MapSplice`](http://www.netlab.uky.edu/p/bioinfo/MapSplice2) - - [`Segemehl`](https://www.bioinf.uni-leipzig.de/Software/segemehl/) -- circRNA annotation -- Extract circRNA sequences and build circular transcriptome -- Merge circular transcriptome with linear transcriptome derived from provided GTF -- Quantification of combined circular and linear transcriptome - - [`psirc-quant`](https://github.com/Christina-hshi/psirc) -- miRNA binding affinity analysis (only if the `mature` parameter is provided) - - [`miRanda`](http://cbio.mskcc.org/miRNA2003/miranda.html) - - [`TargetScan`](http://www.targetscan.org/cgi-bin/targetscan/data_download.vert72.cgi) -- Statistical tests (only if the `phenotype` parameter is provided) - - [`CircTest`](https://github.com/dieterich-lab/CircTest) -- MultiQC report [`MultiQC`](http://multiqc.info/) +- references: Indices for various tools and intermediate reference genome files +- preprocessing: Per-sample concatenated FASTQ files +- quality_control: FastQC reports and TrimGalore reports +- bsj_detection + - combined: Combined BSJ calls across all samples + - samples: Per sample BSJ calls + - tools: Per tool and sample BSJ calls +- quantification + - combined: Quantification results for linear and circular transcripts across samples + - samples: Per sample quantification results + - transcriptome: Combined linear and circular transcriptome, based on GTF file and detected BSJs +- mirna_prediction + - miranda + - targetscan + - combined +- statistical_tests + - circtest +- multiqc +- pipeline_info ## Quality Control From 5bdd08bd2b2e283adbc0562a5af4eee7ff577e17 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 14:46:10 +0200 Subject: [PATCH 382/491] Add documentation for references output --- conf/modules.config | 20 +++++++++--------- docs/output.md | 51 ++++++++++++++++++++++++++++++--------------- 2 files changed, 44 insertions(+), 27 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 99ace97d..4f959433 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -76,7 +76,7 @@ process { withName: CLEAN_FASTA { ext.args2 = '\'/>/{ gsub(\$2, "",\$2);gsub(" ", "") };{print}\'' publishDir = [ - path: { "${params.outdir}/references/clean_fasta" }, + path: { "${params.outdir}/references/genome/clean_fasta" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null } ] @@ -85,16 +85,16 @@ process { withName: GTFFILTER { ext.suffix = "filtered.gtf" publishDir = [ - path: { "${params.outdir}/references/filtered_gtf" }, + path: { "${params.outdir}/references/genome/filtered_gtf" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null } ] } withName: SEQKIT_SPLIT { ext.args = "-i --by-id-prefix \"\"" publishDir = [ - path: { "${params.outdir}/references/chromosomes" }, + path: { "${params.outdir}/references/genome/chromosomes" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null } ] @@ -277,7 +277,7 @@ process { "-geneNameAsName2" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/references/circexplorer2" }, + path: { "${params.outdir}/references/bsj_detection/circexplorer2" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null } ] @@ -535,7 +535,7 @@ process { "-geneNameAsName2" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/references/mapsplice" }, + path: { "${params.outdir}/references/bsj_detection/mapsplice" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null } ] @@ -733,7 +733,7 @@ process { publishDir = [ path: { "${params.outdir}/references/named_databases" }, mode: params.publish_dir_mode, - saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } + saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null } ] } @@ -847,7 +847,7 @@ process { withName: PSIRC_INDEX { publishDir = [ - path: { "${params.outdir}/references/psirc" }, + path: { "${params.outdir}/references/index/psirc" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null } ] @@ -914,9 +914,9 @@ process { withName: TARGETSCAN_DATABASE { publishDir = [ - path: { "${params.outdir}/references/targetscan" }, + path: { "${params.outdir}/references/mirna_prediction/targetscan" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_reference ) ? filename : null }, pattern: "mature.txt" ] } diff --git a/docs/output.md b/docs/output.md index 66a8f743..cf002b53 100644 --- a/docs/output.md +++ b/docs/output.md @@ -12,7 +12,9 @@ The directories listed below will be created in the results directory after the - references: Indices for various tools and intermediate reference genome files - preprocessing: Per-sample concatenated FASTQ files -- quality_control: FastQC reports and TrimGalore reports +- quality_control + - fastqc: FastQC reports for raw reads + - trimgalore: Trim Galore! reports for trimmed reads - bsj_detection - combined: Combined BSJ calls across all samples - samples: Per sample BSJ calls @@ -45,7 +47,7 @@ The FastQC plots displayed in the MultiQC report show _untrimmed_ reads. They ma - `*_fastqc.html`: FastQC report containing quality metrics. - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. -> **NB:** The FastQC plots in this directory are generated relative to the raw, input reads. They may contain adapter sequence and regions of low quality. To see how your reads look after adapter and quality trimming please refer to the FastQC reports in the `trimgalore/fastqc/` directory. +> **NB:** The FastQC plots in this directory are generated relative to the raw, input reads. They may contain adapter sequence and regions of low quality. @@ -73,8 +75,6 @@ The FastQC plots displayed in the MultiQC report show _untrimmed_ reads. They ma [Trim Galore!](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) is a wrapper tool around Cutadapt and FastQC to peform quality and adapter trimming on FastQ files. By default, Trim Galore! will automatically detect and trim the appropriate adapter sequence. -> **NB:** TrimGalore! will only run using multiple cores if you are able to use more than > 5 and > 6 CPUs for single- and paired-end data, respectively. The total cores available to TrimGalore! will also be capped at 4 (7 and 8 CPUs in total for single- and paired-end data, respectively) because there is no longer a run-time benefit. See [release notes](https://github.com/FelixKrueger/TrimGalore/blob/master/Changelog.md#version-060-release-on-1-mar-2019) and [discussion whilst adding this logic to the nf-core/atacseq pipeline](https://github.com/nf-core/atacseq/pull/65). - ![MultiQC - cutadapt trimmed sequence length plot](images/mqc_cutadapt_trimmed.png) ### MultiQC @@ -90,29 +90,46 @@ The FastQC plots displayed in the MultiQC report show _untrimmed_ reads. They ma [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. `nf-core` outputs HTML reports for sequencing read quality control. -## Genome Index Files +## Reference files + +

      +Output files + +- `references` + - `index` + - `bowtie`: Directory containing `Bowtie` indices. + - `bowtie2`: Directory containing `Bowtie2` indices. + - `bwa`: Directory containing `BWA` indices. + - `fasta`: Directory containing FASTA index (`.fai`). + - `hisat2`: Directory containing `HISAT2` indices. + - `segemehl`: Directory containing `Segemehl` index file. + - `star`: Directory containing `STAR` indices. + - `genome` + - `clean_fasta`: Directory containing a FASTA file with reduced headers, since MapSplice has problems with multiple header fields. + - `filtered_gtf`: Directory containing a GTF file with only entries that reside on chromosomes present in the reference FASTA file. + - `chromosomes`: Directory containing individual FASTA files for each chromosome. + - `bsh_detection` + - `circexplorer2`: Directory containing the `CIRCexplorer2` annotation file. + - `mapsplice`: Directory containing the `MapSplice` annotation file. + - `mirna_prediction` + - `targetscan`: Directory containing the TargetScan miRNA database. + +
      + +`nf-core/circrna` will add the reference files to the output directory if `save_reference` is set to `true`. The resulting files, especially the aligner indices, can be used for speeding up future runs (if the `resume` option cannot be used). In order to achieve this, copy the indices to a location outside of the pipeline's output directory and provide the path to the indices via the corresponding aligner flags (check the [parameters documentation](https://nf-co.re/circrna/dev/parameters/#reference-genome-options) for more information). + +## Pipeline info
      Output files -- `reference_genome` - - `BowtieIndex/`: Directory containing `Bowtie` indices. - - `Bowtie2Index/`: Directory containing `Bowtie2` indices. - - `BWAIndex/`: Directory containing `BWA` indices. - - `Hisat2Index/`: Directory containing `HISAT2` indices. - - `SAMtoolsIndex`: Directory containing `SAMtools` index file. - - `STARIndex`: Directory containing `STAR` indices. - - `SegemehlIndex`: Directory containing `Segemehl` index file. -- `pipeline_info/` +- `pipeline_info` - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. - - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`. - Parameters used by the pipeline run: `params.json`.
      -`nf-core/circrna` will save genome indices when `--save_reference true`. This is highly encouraged to reduce runtimes on redeployment of the workflow, as you can supply them to aligner in question via the aligner flag (for example `--star '/path/to/STAR/'`. Available: `bowtie`, `bowtie2`, `bwa`, `hisat2`, `star`, `segemehl`). Make sure to move the saved genome indicies to a different location before doing so. - ## circRNA Quantification ## Common Outputs From bd08029ac7ac2f35b73ec02972b8f319cba4a30f Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 15:43:12 +0200 Subject: [PATCH 383/491] Improve STAR output documentation --- conf/modules.config | 6 +- docs/output.md | 145 +++++++++++++++++--------------------------- 2 files changed, 60 insertions(+), 91 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 4f959433..95fd32d9 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -237,7 +237,7 @@ process { "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/bsj_detection/tools/star/1st_pass" }, + path: { "${params.outdir}/bsj_detection/tools/star/1st_pass/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -245,7 +245,7 @@ process { withName: '.*:STAR2PASS:SJDB' { publishDir = [ - path: { "${params.outdir}/bsj_detection/tools/star/sjdb" }, + path: { "${params.outdir}/bsj_detection/tools/star/sjdb/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] @@ -265,7 +265,7 @@ process { "--chimSegmentMin ${params.chimSegmentMin}" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/bsj_detection/tools/star/2nd_pass" }, + path: { "${params.outdir}/bsj_detection/tools/star/2nd_pass/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] diff --git a/docs/output.md b/docs/output.md index cf002b53..aa706260 100644 --- a/docs/output.md +++ b/docs/output.md @@ -130,86 +130,46 @@ The FastQC plots displayed in the MultiQC report show _untrimmed_ reads. They ma -## circRNA Quantification +## BSJ detection -## Common Outputs +The rough workflow for the BSJ detection looks like this: +1. Each tools detects BSJs in each sample and quantifies how many reads support each BSJ. +2. Bring the tool outputs into a common format. +3. Apply a threshold (parameter `bsj_reads) to the BSJ reads to filter out lowly supported BSJs. +4. Combine all tool-specific BSJ calls per sample into a single file. +5. Filter out BSJs that are not supported by at least `tool_filter` tools. +6. Merge all samples into a single file. This now represents the "circular transcriptome" -The workflow is designed to output three files _per sample_, _per quantification tool_ in the `circrna_discovery` directory. Using the test dataset as an example, the directory structure for the `fust_1` sample is: +### Per tool -````console -|-- results/ - |-- circrna_discovery/ - |-- circexplorer2/ - | -- fust_1/ - | -- fust_1.bed - | -- fust_1.fasta - | -- fust_1.log - - -- `${sample_id}.bed`: A customised BED 12 file containing filtered, annotated circRNAs. Columns: chromosome, start, end, name, read counts, strand, start, end, RGB, number of exon blocks, size of exon blocks, start positions (within sequence) of exon blocks, parent gene ID(s), parent transcript ID(s), mature spliced length. -- `${sample_id}.log`: Script detailing the decisions made by `annotate_outputs.sh` when annotating each circRNA. -- `${sample_id}.fasta`: Mature spliced sequence of circRNA in FASTA format. Includes splice junction site (+-20bp). - -Sample outputs for the corresponding `.log`, `.bed` and `.fasta` entry are given below for a circRNA called by `CIRCexplorer2`: - -```console -[nf-core/circrna]: Starting analysis for: chrI:1140805-1147588:- -[nf-core/circrna]: chrI:1140805-1147588:- overlaps features in GTF file -[nf-core/circrna]: Inspecting Genes... -[nf-core/circrna]: Overlapping Gene IDs: Y48G8AL.10 -[nf-core/circrna]: Converting to BED12 -[nf-core/circrna]: Attempting to fit circRNA to gene exon boundaries -[nf-core/circrna]: chrI:1140805-1147588:- fits gene exons, is a circRNA -[nf-core/circrna]: cleaning up intermediate files -```` - -```console -chrI 1140805 1147588 chrI:1140805-1147588:- 2 - 1140805 1147588 0 5 229,214,191,141,499 0,1282,2546,4912,6284 circRNA Y48G8AL.10 NM_001306296,NM_001306297,NM_001306298,NM_001306299 1274 -``` +
      +Output files available for all tools -```console ->chrI:1087252-1088602:- -CATGAAGTCTCGAGATCTCGTTTATAAGCACCAATATCCACGTTCAGCATTATTGATTGataaaattaatttataaattcgaaaataaaatttaaatttttCTTTAGAAATTATCGATTTATCGACTTCCACGTAATTCCACACCACGCTAAAATTCCATATCAATCTCGCGTTGTTTGGCTTCTCGTTGGGTGTCCGCCGCGTGGGAGTAGTATCTGCAAAAAAAAATTTGAGAATAAAAAATGTAAAATTGtttttcctattttctattgccgaaatttgagatttccggcaaatcggcaaattgccggaattgaaatttgcggcaaatcggcaaactgccgcaattgaaatttcgggtaaatcggcaaatttccggcaaatcggcatattgccggaatttaaatttccggcaaggcggccaatcggaaaattggcaaattgccgcaattgaaatttgcggcaaatcggcaattgtcgactattttcgacaacttctcgctttgcacttttttgtacatttcagattttttttcaatttcaatcggcaaaaacatttccggcaaatcggtaaattgccagaattgaaatttccggcaaatcggcaaattgccggaattgaaatttcccgcaaatcggcaaatttctttaattgaaatttccggcaaatcggtaaattgccggaatttaaatttccggcaactcggcaaactgccccaattgaaatttccggtaaatcggtaaaatgccgaaatttaaatttccggcaaggtggcaaatcggaaaattggcaaattgccggaattcaaatatccggcaaatcggcaagttgctggaattgaaatttccggcaaggcggcaaatttccggcaaatcggcaattGTCTTATattttcgacaacttctcgttttgcacttttttttgtacatttcaggttttttttcaatttcaatcggcaaaaacatttccggcaaatctgatatccggcaaacggcaaatcggcaatttgccgaaaataaaaaattcaagcaactcggcaaaccggcaaattTTATAGAGCACATTTGACCCACCTATTGAGAATAAACAATTGCGAGATAAAAATCTTGATGTAAATTCCGGCGAATGCGATCAAAATTGCTTTTCGATCTGAAAAAAATCCAATTTTGCTCAGCCAATAAATGGACGGAGCTAAAAACAAGGCGCTACTCACGAGAAATCCACTCATACGGGTCTTCTGTCACATTTTCCTGCTCGGATTTCGATTTTGGCGTATCTTCGGTCGGATTTCCGTGGTAATCGGACAACCAGGCAATCACTACAATTATTGCGCAAATGAATCGGGCAAC -``` +- `unified`: Directory containing the BSJ calls in the BED6 format. +- `filtered`: Based on `unified`, but filtered for BSJs with at least `bsj_reads` supporting reads. +- `masked`: Based on `filtered`, but scores are replaced by a dot (.) +- `annotated`: Based on `masked`, but with additional columns for the circRNA type, the host gene(s), host transcript(s) and potential database hits. Contains a BED and a GTF file for each sample. +- `fasta`: Extracted sequences of the circRNAs in FASTA format. Based on `masked`. +- `intermediates`: Contains intermediate files generated by the BSJ detection tools, as explained below. -The workflow's manual annotation process is designed to mimick annotation performed by `CIRCexplorer2` to standardise the annotation process for all circRNA quantification tools. +
      -Intermediate files generated by each quantification tool are described in depth below. +An exemption of the above is `star`, which is not used as a standalone BSJ detection tool, but the output of a 2-pass STAR alignment is used by `CIRCexplorer2`, `circRNA finder` and `DCC`. -### CIRCexplorer2 +#### CIRCexplorer2
      Output files -- `circrna_discovery/circexplorer2/intermediates/${sample_id}/` - - - `*.bed`: Intermediate file generated by `CIRCexplorer2 parse` module, identifying STAR fusion junctions for downstream annotation. - - `*_circexplorer2_circs.bed`: Filtered BED6 file containing circRNA counts used for count matrix generation. - - `*.txt`: Output files generated by `CIRCexplorer2 annotate` module, based on BED 12 format containing circRNA genomic location information, exon cassette composition and an additional 6 columns specifying circRNA annotations. Full descriptions of the 18 columns can be found in the `CIRCexplorer2` [documentation](https://circexplorer2.readthedocs.io/en/latest/modules/annotate/#output). - -- `circrna_discovery/star` - - `1st_pass` - - `*.Aligned.out.bam`: Coordinate sorted bam file containing aligned reads and chimeric reads. - - `*.Chimeric.out.junction`: Each line contains the details of chimerically aligned reads. Full descriptions of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 5.4). - - `*.Log.final.out`: Summary mapping statistics after mapping job is complete, useful for quality control. The statistics are calculated for each read (single- or paired-end) and then summed or averaged over all reads. - - `*.Log.out`: Main log file with a lot of detailed information about the run. This file is most useful for troubleshooting and debugging. - - `*.Log.progress.out`: Reports job progress statistics, such as the number of processed reads, % of mapped reads etc. - - `*.SJ.out.tab`: High confidence collapsed splice junctions in tab-delimited form. Full description of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 4.4). - - `2nd_pass` - - `*.Aligned.out.bam`: Coordinate sorted bam file containing aligned reads and chimeric reads. - - `*.Chimeric.out.junction`: Each line contains the details of chimerically aligned reads. Full descriptions of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 5.4). - - `*.Log.final.out`: Summary mapping statistics after mapping job is complete, useful for quality control. The statistics are calculated for each read (single- or paired-end) and then summed or averaged over all reads. - - `*.Log.out`: Main log file with a lot of detailed information about the run. This file is most useful for troubleshooting and debugging. - - `*.Log.progress.out`: Reports job progress statistics, such as the number of processed reads, % of mapped reads etc. - - `*.SJ.out.tab`: High confidence collapsed splice junctions in tab-delimited form. Full description of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 4.4). - - `sjdb` - - `dataset.SJ.out.tab`: Chromosome, start, end & strand coordinates of novel splice junctions for **all samples** aligned using STAR 1st pass. +- `bsj_detection/tools/circexplorer2/intermediates/${sample_id}/` + - `${sample_id}.bed`: Intermediate file generated by `CIRCexplorer2 parse` module, identifying STAR fusion junctions for downstream annotation. + - `${sample_id}.txt`: Output files generated by `CIRCexplorer2 annotate` module, based on BED 12 format containing circRNA genomic location information, exon cassette composition and an additional 6 columns specifying circRNA annotations. Full descriptions of the 18 columns can be found in the `CIRCexplorer2` [documentation](https://circexplorer2.readthedocs.io/en/latest/modules/annotate/#output).
      [CIRCexplorer2](https://circexplorer2.readthedocs.io/en/latest/) uses `*.Chimeric.out.junction` files generated from `STAR` 2 pass mode to extract back-splice junction sites using the `CIRCexplorer2 parse` module. Following this, `CIRCexplorer2 annotate` performs re-alignment of reads to the back-splice junction sites to determine the precise positions of downstream donor and upstream acceptor splice sites. Back-splice junction sites are subsequently updated and annotated using the customised annotation text file. -### circRNA finder +#### circRNA finder
      Output files @@ -220,30 +180,11 @@ Intermediate files generated by each quantification tool are described in depth - `*.s_filteredJunctions.bed`: A bed file with those junctions in `*.filteredJunctions.bed` that are flanked by GT-AG splice sites. The score column indicates the number reads spanning each junction. - `*.s_filteredJunctions_fw.bed`: A bed file with the same circular junctions as in file (b), but here the score column gives the average number of forward spliced reads at both splice sites around each circular junction. -- `circrna_discovery/star` - - `1st_pass` - - `*.Aligned.out.bam`: Coordinate sorted bam file containing aligned reads and chimeric reads. - - `*.Chimeric.out.junction`: Each line contains the details of chimerically aligned reads. Full descriptions of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 5.4). - - `*.Log.final.out`: Summary mapping statistics after mapping job is complete, useful for quality control. The statistics are calculated for each read (single- or paired-end) and then summed or averaged over all reads. - - `*.Log.out`: Main log file with a lot of detailed information about the run. This file is most useful for troubleshooting and debugging. - - `*.Log.progress.out`: Reports job progress statistics, such as the number of processed reads, % of mapped reads etc. - - `*.SJ.out.tab`: High confidence collapsed splice junctions in tab-delimited form. Full description of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 4.4). - - `2nd_pass` - - `*.Aligned.out.bam`: Coordinate sorted bam file containing aligned reads and chimeric reads. - - `*.Chimeric.out.junction`: Each line contains the details of chimerically aligned reads. Full descriptions of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 5.4). - - `*.Chimeric.out.sam`: Chimeric alignments in SAM format. - - `*.Log.final.out`: Summary mapping statistics after mapping job is complete, useful for quality control. The statistics are calculated for each read (single- or paired-end) and then summed or averaged over all reads. - - `*.Log.out`: Main log file with a lot of detailed information about the run. This file is most useful for troubleshooting and debugging. - - `*.Log.progress.out`: Reports job progress statistics, such as the number of processed reads, % of mapped reads etc. - - `*.SJ.out.tab`: High confidence collapsed splice junctions in tab-delimited form. Full description of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 4.4). - - `sjdb` - - `dataset.SJ.out.tab`: Chromosome, start, end & strand coordinates of novel splice junctions for **all samples** aligned using STAR 1st pass. -
      [circRNA finder](https://github.com/orzechoj/circRNA_finder) uses `*.Chimeric.out.sam`, `*.Chimeric.out.junction` & `*.SJ.out.tab` from STAR 2nd pass files to identify circular RNAs in RNA-Seq data. -### CIRIquant +#### CIRIquant
      Output files @@ -264,7 +205,7 @@ Intermediate files generated by each quantification tool are described in depth [CIRIquant](https://github.com/Kevinzjy/CIRIquant) operates by aligning RNA-Seq reads using `HISAT2` and [CIRI2](https://sourceforge.net/projects/ciri/files/CIRI2/) to identify putative circRNAs. Next, a pseudo reference index is generated using `bwa index` by concatenating the two full-length sequences of the putative back-splice junction regions. Candidate circular reads are re-aligned against this pseudo reference using `bwa mem`, and back-splice junction reads are determined if they can be linearly and completely aligned to the putative back-splice junction regions. -### DCC +#### DCC
      Output files @@ -288,7 +229,7 @@ Intermediate files generated by each quantification tool are described in depth 4. Circular reads aligning to mitochondrial genome are removed. 5. Circular reads that lack a canonical (GT/AG) splicing signal at the circRNA junction borders are removed. -### Find circ +#### Find circ
      Output files @@ -310,7 +251,7 @@ Intermediate files generated by each quantification tool are described in depth 4. Breakpoint cannot reside more than 2nt inside a 20mer anchor. 5. 2 reads must support the junction. -### MapSplice +#### MapSplice
      Output files @@ -332,7 +273,7 @@ Intermediate files generated by each quantification tool are described in depth [MapSplice](http://www.netlab.uky.edu/p/bioinfo/MapSplice2) first splits reads into segments, and maps them to reference genome by using `Bowtie`. `MapSplice` attempts to fix unmapped segments as gapped alignments, with each gap corresponding to a splice junction. Finally a remapping step is used to identify back-spliced alignments that are in the presence of small exons. -### Segemehl +#### Segemehl
      Output files @@ -347,6 +288,34 @@ Intermediate files generated by each quantification tool are described in depth `Segemehl` implements split read alignment mode for reads that failed the attempt of collinear alignment. The algorithm will consider circular alignments. Circular splits are output to `${sample_id}.sngl.bed` and parsed using customised scripts to produce counts representative of `Segemehl` quantification. +#### STAR + +
      +Output files + +- `bsj_detection/tools/star` + - `1st_pass` + - `*.Aligned.out.bam`: Coordinate sorted bam file containing aligned reads and chimeric reads. + - `*.Chimeric.out.junction`: Each line contains the details of chimerically aligned reads. Full descriptions of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 5.4). + - `*.Log.final.out`: Summary mapping statistics after mapping job is complete, useful for quality control. The statistics are calculated for each read (single- or paired-end) and then summed or averaged over all reads. + - `*.Log.out`: Main log file with a lot of detailed information about the run. This file is most useful for troubleshooting and debugging. + - `*.Log.progress.out`: Reports job progress statistics, such as the number of processed reads, % of mapped reads etc. + - `*.SJ.out.tab`: High confidence collapsed splice junctions in tab-delimited form. Full description of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 4.4). + - `2nd_pass` + - `*.Aligned.out.bam`: Coordinate sorted bam file containing aligned reads and chimeric reads. + - `*.Chimeric.out.junction`: Each line contains the details of chimerically aligned reads. Full descriptions of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 5.4). + - `*.Chimeric.out.sam`: Chimeric alignments in SAM format. + - `*.Log.final.out`: Summary mapping statistics after mapping job is complete, useful for quality control. The statistics are calculated for each read (single- or paired-end) and then summed or averaged over all reads. + - `*.Log.out`: Main log file with a lot of detailed information about the run. This file is most useful for troubleshooting and debugging. + - `*.Log.progress.out`: Reports job progress statistics, such as the number of processed reads, % of mapped reads etc. + - `*.SJ.out.tab`: High confidence collapsed splice junctions in tab-delimited form. Full description of columns can be found in `STAR` [documentation](https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf) (section 4.4). + - `sjdb` + - `dataset.SJ.out.tab`: Chromosome, start, end & strand coordinates of novel splice junctions for **all samples** aligned using STAR 1st pass. + +
      + +STAR in 2-pass mode is used to identify novel splice junctions in RNA-Seq data. The first pass of STAR is used to generate a genome index and align reads to the reference genome. The second pass of STAR uses the splice junctions identified in the first pass to align reads to the reference genome. This does not increase the number of detected novel junctions, but allows for more sensitive detection of splice reads mapping to novel junctions. + ### Count Matrix
      From a311c4a24f565e78cd79e03831ec6cea819ab9b7 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 15:49:21 +0200 Subject: [PATCH 384/491] Improve output docs for various detection tools --- conf/modules.config | 2 +- docs/output.md | 22 +++++++++------------- 2 files changed, 10 insertions(+), 14 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 95fd32d9..fac43d45 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -173,7 +173,7 @@ process { "-S" ].join(' ').trim() publishDir = [ - path: { "${params.outdir}/bsj_detection/tools/segemehl/raw" }, + path: { "${params.outdir}/bsj_detection/tools/segemehl/intermediates" }, mode: params.publish_dir_mode, saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } ] diff --git a/docs/output.md b/docs/output.md index aa706260..a25daabb 100644 --- a/docs/output.md +++ b/docs/output.md @@ -162,8 +162,8 @@ An exemption of the above is `star`, which is not used as a standalone BSJ detec Output files - `bsj_detection/tools/circexplorer2/intermediates/${sample_id}/` - - `${sample_id}.bed`: Intermediate file generated by `CIRCexplorer2 parse` module, identifying STAR fusion junctions for downstream annotation. - - `${sample_id}.txt`: Output files generated by `CIRCexplorer2 annotate` module, based on BED 12 format containing circRNA genomic location information, exon cassette composition and an additional 6 columns specifying circRNA annotations. Full descriptions of the 18 columns can be found in the `CIRCexplorer2` [documentation](https://circexplorer2.readthedocs.io/en/latest/modules/annotate/#output). + - `*.bed`: Intermediate file generated by `CIRCexplorer2 parse` module, identifying STAR fusion junctions for downstream annotation. + - `*.txt`: Output files generated by `CIRCexplorer2 annotate` module, based on BED 12 format containing circRNA genomic location information, exon cassette composition and an additional 6 columns specifying circRNA annotations. Full descriptions of the 18 columns can be found in the `CIRCexplorer2` [documentation](https://circexplorer2.readthedocs.io/en/latest/modules/annotate/#output).
      @@ -174,7 +174,7 @@ An exemption of the above is `star`, which is not used as a standalone BSJ detec
      Output files -- `circrna_discovery/circrna_finder/intermediates/${sample_id}/` +- `bsj_detection/tools/circrna_finder/intermediates/${sample_id}/` - `*.filteredJunctions.bed`: A bed file with **all** circular junctions found by the pipeline. The score column indicates the number reads spanning each junction. - `*.s_filteredJunctions.bed`: A bed file with those junctions in `*.filteredJunctions.bed` that are flanked by GT-AG splice sites. The score column indicates the number reads spanning each junction. @@ -189,7 +189,7 @@ An exemption of the above is `star`, which is not used as a standalone BSJ detec
      Output files -- `circrna_discovery/ciriquant/intermediates/${sample_id}/` +- `bsj_detection/tools/ciriquant/intermediates/${sample_id}/` - `*.log`: A `CIRIerror.log` file which should be empty, and a `${sample_id}.log` file which contains the output log of `CIRIquant`. - `*.bed`: `CIRI2` output file in BED 6 format. - `*.gtf`: Output file from `CIRIquant` in GTF format. Full description of the columns available in the `CIRIquant` [documentation](https://ciriquant-cookbook.readthedocs.io/en/latest/quantification.html#output-format). @@ -210,12 +210,8 @@ An exemption of the above is `star`, which is not used as a standalone BSJ detec
      Output files -- `/circrna_discovery/DCC/intermediates/${sample_id}/` - - - `*CircCoordinates`: Circular RNA annotations in BED format. Full description of the columns are available in the `DCC` [documentation](https://github.com/dieterich-lab/DCC#output-files-generated-by-dcc). - - `*CircRNACount`: A table containing read counts for circRNAs detected. - - `mate1/`: Output directory of STAR 2nd pass alignment for R1. - - `mate2/`: Output directory of STAR 2nd pass alignment for R2. +- `/bsj_detection/tools/dcc/intermediates/${sample_id}/` + - `*.txt`: Output file from `DCC` containing position and BSJ read counts of circRNAs.
      @@ -234,7 +230,7 @@ An exemption of the above is `star`, which is not used as a standalone BSJ detec
      Output files -- `circrna_discovery/find_circ/intermediates/${sample_id}/` +- `bsj_detection/tools/find_circ/intermediates/${sample_id}/` - `*_anchors.qfa.gz`: 20mer anchors extracted from unmapped reads. - `*_unmapped.bam`: Unmapped RNA-Seq reads to reference genome. - `*.sites.bed`: Output from `find_circ`, first six columns are in standard BED format. A description of the remaining columns is available in the `find_circ` [documentation](https://github.com/marvin-jens/find_circ#output-format). @@ -256,7 +252,7 @@ An exemption of the above is `star`, which is not used as a standalone BSJ detec
      Output files -- `circrna_discovery/mapsplice/intermediates/${sample_id}/` +- `bsj_detection/tools/mapsplice/intermediates/${sample_id}/` - `alignments.bam`: Bam file containing aligned reads and fusion alignments. - `deletions.txt`: Report of deletions. - `Fusion output files`: @@ -278,7 +274,7 @@ An exemption of the above is `star`, which is not used as a standalone BSJ detec
      Output files -- `circrna_discovery/segemehl/intermediates/${sample_id}/` +- `bsj_detection/tools/segemehl/intermediates/${sample_id}/` - `*.bam`: Aligned reads in BAM format - `*.mult.bed`: Thus, this bed file contains all splice events of a read. The start and end positions indicate the nucleotide after the first split (i.e. the beginning of the first intron) and the nucleotide before the last split (i.e. the end of the last intron), respectively. The name and score are equivalent to the one in the \*.sngl file described above. The following fields 7 & 8 (thickStart and thickEnd) should be the identical to fields 2 & 3. Field 9 holds the color information for the item in RGB encoding (itemRGB). Field 10 (blockCount) indicates the number of splits represented by the BED item. Field 11 is a comma separated list of the intron sizes (blockSizes). Field 12 is the comma separated list of intron starts (blockStarts). - `*.sngl.bed`: The bed file contains all single splice events predicted in the split read alignments. From 7314a42a3057bde5518dc567c7d5545a68deb356 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 16:08:10 +0200 Subject: [PATCH 385/491] Finalize BSJ detection output docs --- docs/output.md | 33 +++++++++++++++++++++++++++++---- 1 file changed, 29 insertions(+), 4 deletions(-) diff --git a/docs/output.md b/docs/output.md index a25daabb..787a7a00 100644 --- a/docs/output.md +++ b/docs/output.md @@ -312,17 +312,42 @@ An exemption of the above is `star`, which is not used as a standalone BSJ detec STAR in 2-pass mode is used to identify novel splice junctions in RNA-Seq data. The first pass of STAR is used to generate a genome index and align reads to the reference genome. The second pass of STAR uses the splice junctions identified in the first pass to align reads to the reference genome. This does not increase the number of detected novel junctions, but allows for more sensitive detection of splice reads mapping to novel junctions. -### Count Matrix +### Per sample
      Output files -- `circrna_discovery/` - - `count_matrix.txt`: Raw circRNA read counts for all samples in matrix format. +- `bsj_detection/samples/${sample_id}/` + - `*.grouped.bed`: Grouped BSJ calls in BED format. Score column represents the number of tools that support the BSJ. + - `*.filtered.bed`: Based on `*.grouped.bed`, but filtered for BSJs with at least `tool_filter` supporting tools. + - `*.intersect_gtf.bed`: Intersection of `*.filtered.bed` with the reference GTF file. Intermediate file for annotation. + - `*.intersect_database.bed`: Intersection of `*.filtered.bed` with the database BED file. Intermediate file for annotation. + - `*.annotated.bed`: Annotated BSJ calls in BED format, based on `*.filtered.bed`. + - `*.annotated.gtf`: Annotated BSJ calls in GTF format, based on `*.filtered.bed`. + - `*.fa`: Extracted sequences of the circRNAs in FASTA format, based on `*.filtered.bed`. + - `*.upset.png`: Sample-specific upset plot of BSJ calls across tools.
      -`nf-core/circrna` produces a counts matrix of circRNA read counts for each sample. circRNAs with BSJ reads < `--bsj_reads ` have been removed during the quantification step, with a further filtering step included depending on the number of quantification tools selected. If the user has selected more than one circRNA quantification tool, `nf-core/circrna` will demand that a circRNA be called by at least two quantification tools or else it is removed. This approach is recommended to reduce the number of false positives. +`nf-core/circrna` produces a sample-specific set of BSJ calls. The BSJ calls are filtered for BSJs with at least `tool_filter` supporting tools. The filtered BSJ calls are then annotated with the reference GTF file and the database BED file. An upset plot is generated to visualise the overlap of BSJ calls across tools. + +### Combined + +
      +Output files + +- `bsj_detection/combined/` + - `*.combined.bed`: Unique BSJ calls across samples in BED format. + - `*.intersect_gtf.bed`: Intersection of `*.filtered.bed` with the reference GTF file. Intermediate file for annotation. + - `*.intersect_database.bed`: Intersection of `*.filtered.bed` with the database BED file. Intermediate file for annotation. + - `*.annotated.bed`: Annotated BSJ calls in BED format, based on `*.filtered.bed`. + - `*.annotated.gtf`: Annotated BSJ calls in GTF format, based on `*.filtered.bed`. + - `*.fa`: Extracted sequences of the circRNAs in FASTA format, based on `*.filtered.bed`. + - `*.upset.png`: Combined upset plot of BSJ calls across samples. + +
      + +`nf-core/circrna` combines the sample-specific BSJ calls into a single file. The filtered BSJ calls are then annotated with the reference GTF file and the database BED file. An upset plot is generated to visualise the overlap of BSJ calls across tools. ## miRNA Prediction From c38f066d0c119c1df0f7864d78dc930b19c98bca Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 16:41:06 +0200 Subject: [PATCH 386/491] Update output docs for mirna prediction and quantification --- docs/output.md | 71 +++++++++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 67 insertions(+), 4 deletions(-) diff --git a/docs/output.md b/docs/output.md index 787a7a00..3138f9ba 100644 --- a/docs/output.md +++ b/docs/output.md @@ -349,6 +349,69 @@ STAR in 2-pass mode is used to identify novel splice junctions in RNA-Seq data. `nf-core/circrna` combines the sample-specific BSJ calls into a single file. The filtered BSJ calls are then annotated with the reference GTF file and the database BED file. An upset plot is generated to visualise the overlap of BSJ calls across tools. +## Quantification + +Since we now know the BSJ locations, we can now quantify their expression by mapping the reads to the region between the BSJ start and end coordinates. As each read can potentially originate from both linear and circular transcripts, the pipeline performs a joint quantification of the linear and circular transcriptome. +The quantification is performed using psirc-quant, which is a wrapper around `kallisto`. It allows for inferential-uncertainty aware quantification of linear and circular transcripts. + +### Transcriptome + +
      +Output files + +- `quantification/transcriptome/` + - `*.combined.gtf`: Combined linear and circular transcriptome in GTF format. + - `*.filtered.gtf`: Filtered linear and circular transcriptome in GTF format, based on `*.combined.gtf`. + - `*.fasta`: Combined linear and circular transcriptome in FASTA format, based on `*.filtered.gtf`. + - `*.marked.fasta`: Transcript sequences in FASTA format with the circRNA sequences marked with a `C` field in the header. + - `*.tx2gene.tsv`: Transcript to gene mapping file. + +### Per sample + +
      +Output files + +- `quantification/samples/${sample_id}/` + - `psirc` + - `*.abundance.h5`: Abundance estimates in HDF5 format. + - `*.abundance.tsv`: Abundance estimates in TSV format. + - `*.run_info.json`: Run information in JSON format. + - `pseudoalignments.bam`: Pseudoalignments in BAM format. + - `pseudoalignments.bai`: Index file for pseudoalignments. + - `tximeta/` + - `*.rds`: RDS file containing the the sample-specific transcript quantification data. + - `tximport/` + - `*.gene_counts_length_scaled.tsv`: Gene counts scaled by transcript length. + - `*.gene_counts_scaled.tsv`: Gene counts scaled by library size. + - `*.gene_counts.tsv`: Gene counts. + - `*.gene_lengths.tsv`: Gene lengths. + - `*.gene_tpm.tsv`: Gene TPM values. + - `*.transcript_counts.tsv`: Transcript counts. + - `*.transcript_lengths.tsv`: Transcript lengths. + - `*.transcript_tpm.tsv`: Transcript TPM values. + +
      + +`nf-core/circrna` performs quantification of linear and circular transcripts using `psirc-quant`. The quantification results are stored in HDF5 and TSV format. The pipeline also generates a `tximeta` RDS file containing the sample-specific transcript quantification data. The `tximport` directory contains gene and transcript counts, lengths and TPM values. + +### Combined + +
      +Output files + +- `quantification/combined/` + - `gene_counts.csv`: Count matrix of genes across samples. + - `gene_tpm.csv`: TPM matrix of genes across samples. + - `tx_counts.csv`: Count matrix of transcripts across samples. + - `tx_tpm.csv`: TPM matrix of transcripts across samples. + - `linear.tsv`: Count matrix of linear transcripts across samples. + - `circular.tsv`: Count matrix of circular transcripts across samples. + - `experiments.merged.rds`: RDS file containing a SummarizedExperiment with the merged transcript quantification data. + +
      + +`nf-core/circrna` combines the sample-specific quantification results into proper count matrices. It also generates an RDS file containing a SummarizedExperiment with the merged transcript quantification data. + ## miRNA Prediction ### miRanda @@ -356,7 +419,7 @@ STAR in 2-pass mode is used to identify novel splice junctions in RNA-Seq data.
      Output files -- `mirna_prediction/miRanda/${sample_id}/` +- `mirna_prediction/miranda/` - `*.miRanda.txt`: Raw outputs from `miRanda`.
      @@ -371,19 +434,19 @@ STAR in 2-pass mode is used to identify novel splice junctions in RNA-Seq data.
      Output files -- `mirna_prediction/TargetScan/${sample_id}/` +- `mirna_prediction/targetscan/` - `*.targetscan.txt`: Raw outputs from `TargetScan`.
      [TargetScan](http://www.targetscan.org/vert_72/) predicts biological targets of miRNAs by searching for the presence of conserved 8mer, 7mer, and 6mer sites within the circRNA mature sequence that match the seed region of each miRNA. -### miRNA targets +### Combined
      Output files -- `mirna_prediction/${sample_id}/` +- `mirna_prediction/combined/` - `*_miRNA_targets.txt`: Filtered target miRNAs of circRNAs called by quantification tools. Columns are self explanatory: miRNA, Score, Energy_KcalMol, Start, End, Site_type.
      From cd5c1d466bb686804b05e523de2e29e7e18937c2 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 3 Aug 2024 16:44:16 +0200 Subject: [PATCH 387/491] Prettier --- README.md | 1 + docs/output.md | 1 + docs/usage.md | 15 +++++++++------ 3 files changed, 11 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 875ce95c..9006955a 100644 --- a/README.md +++ b/README.md @@ -25,6 +25,7 @@ **nf-core/circrna** is a bioinformatics pipeline that can be used to analyse total RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming, back-splice junction (BSJ) detection, annotation, quantification and miRNA target prediction of circular RNAs. The pipeline is still under development, but the BSJ detection and quantification steps are already implemented and functional. The following features are planned to be implemented soon: + - Isoform-level circRNA detection and quantification - circRNA-miRNA interaction analysis using [SPONGE](https://doi.org/10.1093/bioinformatics/btz314) and [spongEffects](https://doi.org/10.1093/bioinformatics/btad276) - Improved downstream analyses diff --git a/docs/output.md b/docs/output.md index 3138f9ba..2e1da196 100644 --- a/docs/output.md +++ b/docs/output.md @@ -133,6 +133,7 @@ The FastQC plots displayed in the MultiQC report show _untrimmed_ reads. They ma ## BSJ detection The rough workflow for the BSJ detection looks like this: + 1. Each tools detects BSJs in each sample and quantifies how many reads support each BSJ. 2. Bring the tool outputs into a common format. 3. Apply a threshold (parameter `bsj_reads) to the BSJ reads to filter out lowly supported BSJs. diff --git a/docs/usage.md b/docs/usage.md index 6f694f6e..d39eb853 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -56,11 +56,12 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p ## BSJ detection This part of the pipeline is responsible for the detection of back-splice junctions (BSJs) in the input data. The following tools are currently supported: + - `CIRCexplorer2` - `circRNA finder` - `CIRIquant` - `DCC` -- `find circ` +- `find circ` - `MapSplice` - `Segemehl` @@ -76,23 +77,25 @@ The annotation is generally based on the reference GTF file. It can also utilize The GTF-based annotation allows setting the parameter `exon_boundary` to specify a window around exons. If the BSJ is within this window, it will be annotated as a circRNA - otherwise, it will be annotated as an exon-intron circRNA (EI-circRNA). The default value is 0. For the database-based annotation, an additional sample sheet is required: + ```csv title="annotation.csv" name,file,min_overlap db1,db1.bed,0.9 db2,db2.bed,0.8 ``` -| Column | Description | -| ------------ | --------------------------------------------------------------------------------------------- | -| `name` | Name of the database. This will be used as a prefix for the region names in the output files. | -| `file` | Path to the BED file. The file has to be a valid BED6 file. | -| `min_overlap`| Minimum bidirectional overlap required between the BSJ and the region in the BED file. | +| Column | Description | +| ------------- | --------------------------------------------------------------------------------------------- | +| `name` | Name of the database. This will be used as a prefix for the region names in the output files. | +| `file` | Path to the BED file. The file has to be a valid BED6 file. | +| `min_overlap` | Minimum bidirectional overlap required between the BSJ and the region in the BED file. | The output of the annotation step will be bundled with the outputs of the BSJ detection step. ## miRNA prediction This section allows looking for miRNA binding sites in the circRNAs. The following tools are currently supported: + - `miRanda` - `TargetScan` From 3d25e2d65a5dd66607b55cc7dc29aabbfa13a3c1 Mon Sep 17 00:00:00 2001 From: Nico Trummer <52698566+nictru@users.noreply.github.com> Date: Tue, 6 Aug 2024 14:24:26 +0200 Subject: [PATCH 388/491] Update README.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 9006955a..a7feba50 100644 --- a/README.md +++ b/README.md @@ -22,7 +22,7 @@ ## Introduction -**nf-core/circrna** is a bioinformatics pipeline that can be used to analyse total RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming, back-splice junction (BSJ) detection, annotation, quantification and miRNA target prediction of circular RNAs. +**nf-core/circrna** is a bioinformatics pipeline to analyse total RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming, back-splice junction (BSJ) detection, annotation, quantification and miRNA target prediction of circular RNAs. The pipeline is still under development, but the BSJ detection and quantification steps are already implemented and functional. The following features are planned to be implemented soon: From ffd92e314bc05506a2cbd52b35281ba306c39e0a Mon Sep 17 00:00:00 2001 From: Nico Trummer <52698566+nictru@users.noreply.github.com> Date: Tue, 6 Aug 2024 14:24:43 +0200 Subject: [PATCH 389/491] Update README.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index a7feba50..6e8bb401 100644 --- a/README.md +++ b/README.md @@ -48,7 +48,7 @@ If you want to contribute, feel free to create an issue or pull request on the [ - [`MapSplice`](http://www.netlab.uky.edu/p/bioinfo/MapSplice2) - [`Segemehl`](https://www.bioinf.uni-leipzig.de/Software/segemehl/) - circRNA annotation - - Based on GTF file + - Based on a GTF file - Based on database files (if provided) - Extract circRNA sequences and build circular transcriptome - Merge circular transcriptome with linear transcriptome derived from provided GTF From fd16cccd851c6dd76efcaaa0e16920e337bbe254 Mon Sep 17 00:00:00 2001 From: Nico Trummer <52698566+nictru@users.noreply.github.com> Date: Tue, 6 Aug 2024 14:25:26 +0200 Subject: [PATCH 390/491] Update docs/output.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- docs/output.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index 2e1da196..5731110c 100644 --- a/docs/output.md +++ b/docs/output.md @@ -47,7 +47,9 @@ The FastQC plots displayed in the MultiQC report show _untrimmed_ reads. They ma - `*_fastqc.html`: FastQC report containing quality metrics. - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. -> **NB:** The FastQC plots in this directory are generated relative to the raw, input reads. They may contain adapter sequence and regions of low quality. +::: note +The FastQC plots in this directory are generated relative to the raw, input reads. They may contain adapter sequence and regions of low quality. +:::
      From 753517026c36fb524ffc0dd85a8c8d105364820d Mon Sep 17 00:00:00 2001 From: Nico Trummer <52698566+nictru@users.noreply.github.com> Date: Tue, 6 Aug 2024 14:25:51 +0200 Subject: [PATCH 391/491] Update docs/output.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index 5731110c..8f3686a5 100644 --- a/docs/output.md +++ b/docs/output.md @@ -118,7 +118,7 @@ The FastQC plots in this directory are generated relative to the raw, input read
      -`nf-core/circrna` will add the reference files to the output directory if `save_reference` is set to `true`. The resulting files, especially the aligner indices, can be used for speeding up future runs (if the `resume` option cannot be used). In order to achieve this, copy the indices to a location outside of the pipeline's output directory and provide the path to the indices via the corresponding aligner flags (check the [parameters documentation](https://nf-co.re/circrna/dev/parameters/#reference-genome-options) for more information). +`nf-core/circrna` will add the reference files to the output directory if `save_reference` is set to `true`. The resulting files, especially the aligner indices, can be used for speeding up future runs (if the `resume` option cannot be used). In order to achieve this, copy the indices to a location outside of the pipeline's output directory and provide the path to the indices via the corresponding aligner flags (check the [parameters documentation](https://nf-co.re/circrna/parameters/#reference-genome-options) for more information). ## Pipeline info From 0ffaf3068ffe9dca1f702ba5d6488ae71f0d03a8 Mon Sep 17 00:00:00 2001 From: Nico Trummer <52698566+nictru@users.noreply.github.com> Date: Tue, 6 Aug 2024 14:27:23 +0200 Subject: [PATCH 392/491] Update nextflow_schema.json MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index eb5452be..8217b765 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -95,7 +95,7 @@ "exon_boundary": { "type": "integer", "description": "Specify the distance at which the annotation script decides if a candidate is a circRNA or EI-circRNA.", - "help_text": "During annotation, if one of the start or end position of a circular candidate imperfectly overlaps an exon boundary, the script will consider positions within 'exon_boundary' (default 200bp) to be an exonic circRNA. If they fall outside of this range, the candidate is assumed to be an exonic-intronic circRNA, and the entire underlying sequence is taken for miRNA analysis, as opposed to just the exonic sequences for canonical exonic circRNAs. ", + "help_text": "During annotation, if one of the start or end position of a circular candidate imperfectly overlaps an exon boundary, the script will consider positions within 'exon_boundary' (default 0bp) to be an exonic circRNA. If they fall outside of this range, the candidate is assumed to be an exonic-intronic circRNA, and the entire underlying sequence is taken for miRNA analysis, as opposed to just the exonic sequences for canonical exonic circRNAs. ", "default": 0 } } From 65497575c89658ed1998759bbb546c767b047c8d Mon Sep 17 00:00:00 2001 From: Nico Trummer <52698566+nictru@users.noreply.github.com> Date: Tue, 6 Aug 2024 14:29:14 +0200 Subject: [PATCH 393/491] Update nextflow_schema.json MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nextflow_schema.json | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow_schema.json b/nextflow_schema.json index 8217b765..9c952c23 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -65,6 +65,7 @@ "type": "string", "fa_icon": "fas fa-wrench", "description": "Comma separated list of circRNA quantification tools to use. Supported tools: ciriquant, circexplorer2, find_circ, circrna_finder, mapsplice, dcc, segemehl", + "pattern": "^(ciriquant|circexplorer2|find_circ|circrna_finder|mapsplice|dcc|segemehl)(,(ciriquant|circexplorer2|find_circ|circrna_finder|mapsplice|dcc|segemehl))*$" "help_text": "Select one or a combination of circRNA quantification tools for the pipeline e.g:\n--tool 'circexplorer2, ciriquant, find_circ'\n\nN.B: Selecting more than one circRNA quantification tool will trigger the circRNA filtering parameter --tool_filter", "default": "circexplorer2", "pattern": "^((circexplorer2|circrna_finder|ciriquant|dcc|find_circ|mapsplice|segemehl)?,?)*[^,]+$" From 636330d58d7f269f0950eb455014c21ea45509ca Mon Sep 17 00:00:00 2001 From: Nico Trummer <52698566+nictru@users.noreply.github.com> Date: Tue, 6 Aug 2024 14:29:32 +0200 Subject: [PATCH 394/491] Update docs/output.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index 8f3686a5..dfaaf826 100644 --- a/docs/output.md +++ b/docs/output.md @@ -136,7 +136,7 @@ The FastQC plots in this directory are generated relative to the raw, input read The rough workflow for the BSJ detection looks like this: -1. Each tools detects BSJs in each sample and quantifies how many reads support each BSJ. +1. Each tool detects BSJs in each sample and quantifies how many reads support each BSJ. 2. Bring the tool outputs into a common format. 3. Apply a threshold (parameter `bsj_reads) to the BSJ reads to filter out lowly supported BSJs. 4. Combine all tool-specific BSJ calls per sample into a single file. From f3b98806de007fd72a870dda8468d01ef6acf3fb Mon Sep 17 00:00:00 2001 From: Nico Trummer <52698566+nictru@users.noreply.github.com> Date: Tue, 6 Aug 2024 14:29:46 +0200 Subject: [PATCH 395/491] Update docs/output.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index dfaaf826..a5249fbe 100644 --- a/docs/output.md +++ b/docs/output.md @@ -138,7 +138,7 @@ The rough workflow for the BSJ detection looks like this: 1. Each tool detects BSJs in each sample and quantifies how many reads support each BSJ. 2. Bring the tool outputs into a common format. -3. Apply a threshold (parameter `bsj_reads) to the BSJ reads to filter out lowly supported BSJs. +3. Apply a threshold (parameter `bsj_reads`) to the BSJ reads to filter out lowly supported BSJs. 4. Combine all tool-specific BSJ calls per sample into a single file. 5. Filter out BSJs that are not supported by at least `tool_filter` tools. 6. Merge all samples into a single file. This now represents the "circular transcriptome" From 96a20d50eb9b35e7b943a1d5c2206dc54c31006d Mon Sep 17 00:00:00 2001 From: Nico Trummer <52698566+nictru@users.noreply.github.com> Date: Tue, 6 Aug 2024 14:29:53 +0200 Subject: [PATCH 396/491] Update docs/usage.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index d39eb853..61fc076c 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -69,7 +69,7 @@ The tools to be used can be specified using the `tools` parameter. Each of the tools also quantifies how many reads support each BSJ. You can specify a cutoff for the minimum number of reads supporting a BSJ using the `bsj_reads` parameter. Additionally, the parameter `tool_filter` can be used to specify how many tools a BSJ has to be detected by to be considered as a valid hit. -For instructions on how to interpret the output of this section, please check out the [output documentation](https://nf-co.re/circrna/dev/output#bsj-detection). +For instructions on how to interpret the output of this section, please check out the [output documentation](https://nf-co.re/circrna/output#bsj-detection). ## Annotation From 6c45fa856a8ce6b5bec88b61b12c74183143c851 Mon Sep 17 00:00:00 2001 From: Nico Trummer <52698566+nictru@users.noreply.github.com> Date: Tue, 6 Aug 2024 14:30:06 +0200 Subject: [PATCH 397/491] Update docs/usage.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index 61fc076c..13a1b410 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -74,7 +74,7 @@ For instructions on how to interpret the output of this section, please check ou ## Annotation The annotation is generally based on the reference GTF file. It can also utilize BED files that are provided by the various circRNA databases. -The GTF-based annotation allows setting the parameter `exon_boundary` to specify a window around exons. If the BSJ is within this window, it will be annotated as a circRNA - otherwise, it will be annotated as an exon-intron circRNA (EI-circRNA). The default value is 0. +The GTF-based annotation allows setting the parameter `exon_boundary` to specify a window around exons. If the BSJ is within this window, it will be annotated as a circRNA - otherwise, it will be annotated as an exon-intron circRNA (EI-circRNA). The default value is `0`. For the database-based annotation, an additional sample sheet is required: From 2209284d5db8a907bb4c50d6cab97ea1c4bd245d Mon Sep 17 00:00:00 2001 From: Nico Trummer <52698566+nictru@users.noreply.github.com> Date: Tue, 6 Aug 2024 14:30:32 +0200 Subject: [PATCH 398/491] Update docs/output.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index a5249fbe..1c9e2dbf 100644 --- a/docs/output.md +++ b/docs/output.md @@ -140,7 +140,7 @@ The rough workflow for the BSJ detection looks like this: 2. Bring the tool outputs into a common format. 3. Apply a threshold (parameter `bsj_reads`) to the BSJ reads to filter out lowly supported BSJs. 4. Combine all tool-specific BSJ calls per sample into a single file. -5. Filter out BSJs that are not supported by at least `tool_filter` tools. +5. Filter out BSJs that are not supported by at least as many tools as specified by`tool_filter`. 6. Merge all samples into a single file. This now represents the "circular transcriptome" ### Per tool From ff1d11a9bb760f97e2f26dd8c7b823d4acd489ad Mon Sep 17 00:00:00 2001 From: Nico Trummer <52698566+nictru@users.noreply.github.com> Date: Tue, 6 Aug 2024 14:30:45 +0200 Subject: [PATCH 399/491] Update docs/output.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index 1c9e2dbf..4f751c34 100644 --- a/docs/output.md +++ b/docs/output.md @@ -332,7 +332,7 @@ STAR in 2-pass mode is used to identify novel splice junctions in RNA-Seq data.
      -`nf-core/circrna` produces a sample-specific set of BSJ calls. The BSJ calls are filtered for BSJs with at least `tool_filter` supporting tools. The filtered BSJ calls are then annotated with the reference GTF file and the database BED file. An upset plot is generated to visualise the overlap of BSJ calls across tools. +nf-core/circrna produces a sample-specific set of BSJ calls. The BSJ calls are filtered for BSJs with at least `tool_filter` supporting tools. The filtered BSJ calls are then annotated with the reference GTF file and the database BED file. An upset plot is generated to visualise the overlap of BSJ calls across tools. ### Combined From e3844bb4e85764ced9a22e922509131ba7187fdc Mon Sep 17 00:00:00 2001 From: Nico Trummer <52698566+nictru@users.noreply.github.com> Date: Tue, 6 Aug 2024 14:31:01 +0200 Subject: [PATCH 400/491] Update docs/output.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index 4f751c34..d31355ff 100644 --- a/docs/output.md +++ b/docs/output.md @@ -350,7 +350,7 @@ nf-core/circrna produces a sample-specific set of BSJ calls. The BSJ calls are f
      -`nf-core/circrna` combines the sample-specific BSJ calls into a single file. The filtered BSJ calls are then annotated with the reference GTF file and the database BED file. An upset plot is generated to visualise the overlap of BSJ calls across tools. +nf-core/circrna combines the sample-specific BSJ calls into a single file. The filtered BSJ calls are then annotated with the reference GTF file and the database BED file. An upset plot is generated to visualise the overlap of BSJ calls across tools. ## Quantification From cce50cb6457fb3a8dbbd1035061bbda57f5b7bab Mon Sep 17 00:00:00 2001 From: Nico Trummer <52698566+nictru@users.noreply.github.com> Date: Tue, 6 Aug 2024 14:31:15 +0200 Subject: [PATCH 401/491] Update docs/output.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index d31355ff..e4e8c323 100644 --- a/docs/output.md +++ b/docs/output.md @@ -395,7 +395,7 @@ The quantification is performed using psirc-quant, which is a wrapper around `ka
      -`nf-core/circrna` performs quantification of linear and circular transcripts using `psirc-quant`. The quantification results are stored in HDF5 and TSV format. The pipeline also generates a `tximeta` RDS file containing the sample-specific transcript quantification data. The `tximport` directory contains gene and transcript counts, lengths and TPM values. +nf-core/circrna performs quantification of linear and circular transcripts using `psirc-quant`. The quantification results are stored in HDF5 and TSV format. The pipeline also generates a `tximeta` RDS file containing the sample-specific transcript quantification data. The `tximport` directory contains gene and transcript counts, lengths and TPM values. ### Combined From af15e96bfda741aaa8556fe586da81dd70da23c4 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 6 Aug 2024 14:34:24 +0200 Subject: [PATCH 402/491] Fix syntax error in nextflow_schema.json --- nextflow_schema.json | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 9c952c23..69d123e6 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -65,10 +65,9 @@ "type": "string", "fa_icon": "fas fa-wrench", "description": "Comma separated list of circRNA quantification tools to use. Supported tools: ciriquant, circexplorer2, find_circ, circrna_finder, mapsplice, dcc, segemehl", - "pattern": "^(ciriquant|circexplorer2|find_circ|circrna_finder|mapsplice|dcc|segemehl)(,(ciriquant|circexplorer2|find_circ|circrna_finder|mapsplice|dcc|segemehl))*$" + "pattern": "^(ciriquant|circexplorer2|find_circ|circrna_finder|mapsplice|dcc|segemehl)(,(ciriquant|circexplorer2|find_circ|circrna_finder|mapsplice|dcc|segemehl))*$", "help_text": "Select one or a combination of circRNA quantification tools for the pipeline e.g:\n--tool 'circexplorer2, ciriquant, find_circ'\n\nN.B: Selecting more than one circRNA quantification tool will trigger the circRNA filtering parameter --tool_filter", - "default": "circexplorer2", - "pattern": "^((circexplorer2|circrna_finder|ciriquant|dcc|find_circ|mapsplice|segemehl)?,?)*[^,]+$" + "default": "circexplorer2" }, "bsj_reads": { "type": "integer", From 237bf49b7a639758b4dadfb7e24940c36c1aa6c3 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 6 Aug 2024 14:37:16 +0200 Subject: [PATCH 403/491] Write pipeline name in standard formatting in output docs --- docs/output.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/output.md b/docs/output.md index e4e8c323..7c00df20 100644 --- a/docs/output.md +++ b/docs/output.md @@ -118,7 +118,7 @@ The FastQC plots in this directory are generated relative to the raw, input read
      -`nf-core/circrna` will add the reference files to the output directory if `save_reference` is set to `true`. The resulting files, especially the aligner indices, can be used for speeding up future runs (if the `resume` option cannot be used). In order to achieve this, copy the indices to a location outside of the pipeline's output directory and provide the path to the indices via the corresponding aligner flags (check the [parameters documentation](https://nf-co.re/circrna/parameters/#reference-genome-options) for more information). +nf-core/circrna will add the reference files to the output directory if `save_reference` is set to `true`. The resulting files, especially the aligner indices, can be used for speeding up future runs (if the `resume` option cannot be used). In order to achieve this, copy the indices to a location outside of the pipeline's output directory and provide the path to the indices via the corresponding aligner flags (check the [parameters documentation](https://nf-co.re/circrna/parameters/#reference-genome-options) for more information). ## Pipeline info @@ -223,7 +223,7 @@ An exemption of the above is `star`, which is not used as a standalone BSJ detec `DCC` then performs a series of filtering steps on candidate circular reads: 1. Mapping of mates must be consistent with a circular RNA template i.e align to the back-splice junction. -2. Filtering by a minimum number of junction reads per replicate (`nf-core/circrna` has set this parameter to`-Nr 1 1` allowing all reads). +2. Filtering by a minimum number of junction reads per replicate (nf-core/circrna has set this parameter to`-Nr 1 1` allowing all reads). 3. Circular reads are not allowed span more than one gene. 4. Circular reads aligning to mitochondrial genome are removed. 5. Circular reads that lack a canonical (GT/AG) splicing signal at the circRNA junction borders are removed. @@ -413,7 +413,7 @@ nf-core/circrna performs quantification of linear and circular transcripts using
      -`nf-core/circrna` combines the sample-specific quantification results into proper count matrices. It also generates an RDS file containing a SummarizedExperiment with the merged transcript quantification data. +nf-core/circrna combines the sample-specific quantification results into proper count matrices. It also generates an RDS file containing a SummarizedExperiment with the merged transcript quantification data. ## miRNA Prediction @@ -454,7 +454,7 @@ nf-core/circrna performs quantification of linear and circular transcripts using
      -`nf-core/circrna` performs miRNA target filtering on `miRanda` and `TargetScan` predictions: +nf-core/circrna performs miRNA target filtering on `miRanda` and `TargetScan` predictions: 1. miRNA must be called by both `miRanda` and `TargetScan`. 2. If a site within the circRNA mature sequence shares duplicate miRNA ID's overlapping the same coordinates, the miRNA with the highest score is kept. From 90172a00bd369bf3f90f65e3f829d2a641f49c62 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Tue, 6 Aug 2024 14:38:32 +0200 Subject: [PATCH 404/491] Update bsj_reads help text --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 69d123e6..f881e277 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -73,7 +73,7 @@ "type": "integer", "fa_icon": "fas fa-circle-notch", "description": "Minimum number of reads spanning circRNA back-splice junction required for circRNA to be output by workflow.", - "help_text": "Filter low confidence circRNAs by removing circRNAs with read counts below a specified value. To disable, set the value to 0 (default).", + "help_text": "Filter low confidence circRNAs by removing circRNAs with read counts below a specified value. To disable, set the value to 1 (default).", "default": 1, "minimum": 1 }, From 9a4ece6f3e7d458b306ecc4fceb606b0eb198e1b Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Fri, 26 Apr 2024 10:17:56 +0200 Subject: [PATCH 405/491] Adding mirna_expression param to subworkflow mirna_prediction --- main.nf | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/main.nf b/main.nf index 23b4c9c0..192ac42e 100644 --- a/main.nf +++ b/main.nf @@ -57,8 +57,10 @@ workflow NFCORE_CIRCRNA { ch_samplesheet = Channel.fromSamplesheet("input") ch_fasta = Channel.value([[id: "fasta"], file(params.fasta, checkIfExists:true)]) ch_gtf = Channel.value([[id: "gtf"], file(params.gtf, checkIfExists:true)]) - ch_mature = params.mature ? Channel.value([[id: "mature"], file(params.mature, checkIfExists:true)]) : Channel.empty() + ch_mature = params.module.split(',').contains('mirna_prediction') ? Channel.value([[id: "mature"], file(params.mature, checkIfExists:true)]) : Channel.empty() ch_phenotype = params.phenotype ? Channel.value([[id: "phenotype"], file(params.phenotype, checkIfExists:true)]) : Channel.empty() + ch_species = params.phenotype ? Channel.value(params.species_id) : Channel.empty() + ch_mirna = params.module.split(',').contains('mirna_prediction') ? Channel.value(params.mirna_expression) : Channel.empty() ch_annotation = params.annotation ? Channel.fromSamplesheet("annotation") : Channel.empty() CIRCRNA ( From ea567a3f58f99db60d8a824b763fd7dad3fedbac Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Fri, 26 Apr 2024 10:18:22 +0200 Subject: [PATCH 406/491] Adding mirna_expression param to config --- nextflow.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow.config b/nextflow.config index d693ca69..ec8da623 100644 --- a/nextflow.config +++ b/nextflow.config @@ -14,6 +14,7 @@ params { outdir = null phenotype = null annotation = null + mirna_expression = null // workflow options tools = 'circexplorer2' From b800bdb7c254acc31bfaaf4aecd8e4696395f447 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Fri, 26 Apr 2024 10:18:51 +0200 Subject: [PATCH 407/491] Adding mirna_expression param to nextflow_schema.json --- nextflow_schema.json | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/nextflow_schema.json b/nextflow_schema.json index f881e277..b884688e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -51,6 +51,16 @@ "description": "Path to a CSV file containing BED files that should be used for annotation.", "help_text": "The annotation file should be a CSV file with the following columns: `name`, `file` and `min_overlap`. The `name` column should contain a unique identifier for the annotation, the `file` column should contain the path to the BED file and the `min_overlap` column should contain the minimum overlap required for a circRNA to be considered as overlapping with the annotation. The `min_overlap` column is optional and defaults to 0.9 if not provided.", "fa_icon": "fas fa-file-csv" + }, + "mirna_expression": { + "type": "string", + "format": "file-path", + "exists": true, + "schema": "assets/schema_input.json", + "mimetype": "text/tsv", + "pattern": "^\\S+\\.tsv$", + "description": "Path to tab-separated file providing the expression counts of miRNAs, which are created in pipeline 'smrnaseq'. \n\n\t sample1 \t sample2 \t sample3 \t\nid1\t count_sample1 \t count_sample2 \t count_sample3 \t\nid2 \t ... \t ... \t ... \t \n", + "fa_icon": "fas fa-file-tsv" } } }, From 0aa5c0f3de69cd633847319f50a02dd5363b185e Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Mon, 29 Apr 2024 22:04:17 +0200 Subject: [PATCH 408/491] adding process DESEQ2_NORMALIZATION --- main.nf | 6 +- .../deseq2/normalization/environment.yml | 8 +++ modules/local/deseq2/normalization/main.nf | 32 ++++++++++ .../templates/deseq_normalization.R | 58 +++++++++++++++++++ nextflow_schema.json | 3 +- subworkflows/local/mirna_prediction.nf | 19 ++++-- workflows/circrna/main.nf | 3 + 7 files changed, 120 insertions(+), 9 deletions(-) create mode 100644 modules/local/deseq2/normalization/environment.yml create mode 100644 modules/local/deseq2/normalization/main.nf create mode 100644 modules/local/deseq2/normalization/templates/deseq_normalization.R diff --git a/main.nf b/main.nf index 192ac42e..94437354 100644 --- a/main.nf +++ b/main.nf @@ -60,8 +60,8 @@ workflow NFCORE_CIRCRNA { ch_mature = params.module.split(',').contains('mirna_prediction') ? Channel.value([[id: "mature"], file(params.mature, checkIfExists:true)]) : Channel.empty() ch_phenotype = params.phenotype ? Channel.value([[id: "phenotype"], file(params.phenotype, checkIfExists:true)]) : Channel.empty() ch_species = params.phenotype ? Channel.value(params.species_id) : Channel.empty() - ch_mirna = params.module.split(',').contains('mirna_prediction') ? Channel.value(params.mirna_expression) : Channel.empty() ch_annotation = params.annotation ? Channel.fromSamplesheet("annotation") : Channel.empty() + ch_mirna = params.mature ? Channel.value([[id: "mirna"], file(params.mirna_expression, checkIfExists:true)]) : Channel.empty() CIRCRNA ( ch_samplesheet, @@ -70,7 +70,9 @@ workflow NFCORE_CIRCRNA { ch_gtf, ch_mature, ch_annotation, - ch_versions + ch_species, + ch_versions, + ch_mirna ) emit: diff --git a/modules/local/deseq2/normalization/environment.yml b/modules/local/deseq2/normalization/environment.yml new file mode 100644 index 00000000..8bd70ac0 --- /dev/null +++ b/modules/local/deseq2/normalization/environment.yml @@ -0,0 +1,8 @@ +name: deseq2_normalization +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bioconductor-deseq2=1.34.0 + - conda-forge::r-data.table=1.15.2 diff --git a/modules/local/deseq2/normalization/main.nf b/modules/local/deseq2/normalization/main.nf new file mode 100644 index 00000000..97b13efa --- /dev/null +++ b/modules/local/deseq2/normalization/main.nf @@ -0,0 +1,32 @@ +process DESEQ2_NORMALIZATION { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bioconductor-deseq2:1.34.0--r41hc247a5b_3' : + 'biocontainers/bioconductor-deseq2:1.34.0--r41hc247a5b_3' }" + + input: + tuple val(meta), path(counts) + + output: + tuple val(meta), path("${meta.id}.normalized_counts.tsv"), emit: normalized + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + template 'deseq_normalization.R' + + stub: + """ + touch ${meta.id}.normalized_counts.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bioconductor-deseq2: \$(Rscript -e "library(DESeq2); cat(as.character(packageVersion('DESeq2')))") + END_VERSIONS + """ +} diff --git a/modules/local/deseq2/normalization/templates/deseq_normalization.R b/modules/local/deseq2/normalization/templates/deseq_normalization.R new file mode 100644 index 00000000..daada9f6 --- /dev/null +++ b/modules/local/deseq2/normalization/templates/deseq_normalization.R @@ -0,0 +1,58 @@ +#!/usr/bin/env Rscript + +library(DESeq2) + +raw_counts <- read.table("$counts", sep = "\\t", + header = TRUE, + stringsAsFactors = FALSE, + check.names = FALSE) +samples <- colnames(raw_counts)[-c(1)] + +row.names(raw_counts) <- raw_counts\$miRNA +data <- raw_counts[, -1] +mirna_names <- data.frame(miRNA = raw_counts\$miRNA, + order = seq_len(nrow(raw_counts))) + +# normalize using DeSeq2, Library Size Estimation +meta_data <- data.frame(samples) +row.names(meta_data) <- meta_data\$samples +all(colnames(data) %in% rownames(meta_data)) +all(colnames(data) == rownames(meta_data)) + +dds <- DESeqDataSetFromMatrix(countData = data, + colData = meta_data, + design = ~ 1) +dds <- estimateSizeFactors(dds) +sizeFactors(dds) +normalized_counts <- DESeq2::counts(dds, normalized = TRUE) + +# add miRNA IDs back to counts table +merged_data <- merge(mirna_names, normalized_counts, + by.x = "miRNA", by.y = "row.names") +merged_data <- merged_data[order(merged_data\$order), ] + +norm_data <- subset(merged_data, select = -c(order)) + +write.table(norm_data, paste0("${meta.id}.normalized_counts.tsv"), + quote = FALSE, sep = "\\t", row.names = FALSE) + +# TODO: Perform normalization and save as "${meta.id}.normalized_counts.tsv" +# TODO: (Can be done later) Add support for Samplesheet so that we can eliminate batch effects + + +################################################ +################################################ +## VERSIONS FILE ## +################################################ +################################################ + +r.version <- strsplit(version[['version.string']], ' ')[[1]][3] +deseq2.version <- as.character(packageVersion('DESeq2')) + +writeLines( + c( + '"${task.process}":', + paste(' r-base:', r.version), + paste(' bioconductor-deseq2:', deseq2.version) + ), +'versions.yml') diff --git a/nextflow_schema.json b/nextflow_schema.json index b884688e..7397a535 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -56,10 +56,9 @@ "type": "string", "format": "file-path", "exists": true, - "schema": "assets/schema_input.json", "mimetype": "text/tsv", "pattern": "^\\S+\\.tsv$", - "description": "Path to tab-separated file providing the expression counts of miRNAs, which are created in pipeline 'smrnaseq'. \n\n\t sample1 \t sample2 \t sample3 \t\nid1\t count_sample1 \t count_sample2 \t count_sample3 \t\nid2 \t ... \t ... \t ... \t \n", + "description": "Path to tab-separated file providing the expression counts of miRNAs, which are created in pipeline 'smrnaseq'. \n\nmirna \t sample1 \t sample2 \t sample3 \t\nid1\t count_sample1 \t count_sample2 \t count_sample3 \t\nid2 \t ... \t ... \t ... \t \n", "fa_icon": "fas fa-file-tsv" } } diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index 1bf7623f..b58b14fe 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -1,8 +1,8 @@ -include { GAWK as ADD_BACKSPLICE } from '../../modules/nf-core/gawk' -include { TARGETSCAN_DATABASE } from '../../modules/local/targetscan/database/main' -include { TARGETSCAN } from '../../modules/local/targetscan/predict/main' -include { MIRANDA } from '../../modules/nf-core/miranda/main' -include { MIRNA_TARGETS } from '../../modules/local/mirna_targets/main' +include { TARGETSCAN_DATABASE } from '../../modules/local/targetscan/database' +include { TARGETSCAN } from '../../modules/local/targetscan/predict' +include { MIRANDA } from '../../modules/nf-core/miranda' +include { MIRNA_TARGETS } from '../../modules/local/mirna_targets' +include { DESEQ2_NORMALIZATION } from '../../modules/local/deseq2/normalization' workflow MIRNA_PREDICTION{ @@ -10,6 +10,7 @@ workflow MIRNA_PREDICTION{ circrna_fasta circrna_bed12 ch_mature + ch_mirna main: ch_versions = Channel.empty() @@ -17,6 +18,14 @@ workflow MIRNA_PREDICTION{ ADD_BACKSPLICE( circrna_fasta, [] ) ch_versions = ch_versions.mix(ADD_BACKSPLICE.out.versions) + // + // MIRNA QUANTIFICATION WORKFLOW: + // + + ch_mirna_normalized = DESEQ2_NORMALIZATION( ch_mirna ).normalized + + ch_versions = ch_versions.mix(DESEQ2_NORMALIZATION.out.versions) + // // TARGETSCAN WORKFLOW: // diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 4c1e76ea..b82646f7 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -61,6 +61,7 @@ workflow CIRCRNA { ch_mature ch_annotation ch_versions + ch_mirna main: @@ -173,11 +174,13 @@ workflow CIRCRNA { // // 4. miRNA prediction // + if (params.mature) { MIRNA_PREDICTION( BSJ_DETECTION.out.fasta, BSJ_DETECTION.out.bed, ch_mature + ch_mirna ) ch_versions = ch_versions.mix(MIRNA_PREDICTION.out.versions) } From 4a90115a73393d6a21d850b5bcb8a8746f950ef2 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Fri, 10 May 2024 12:13:24 +0200 Subject: [PATCH 409/491] Adding deseq2 module and mirna normalization module (including params) --- .../deseq2/normalization/environment.yml | 1 - modules/local/deseq2/normalization/main.nf | 2 +- modules/local/mirna_filtering/environment.yml | 4 ++ modules/local/mirna_filtering/main.nf | 24 +++++++++ .../templates/mirna_filtering.R | 51 +++++++++++++++++++ nextflow.config | 7 +++ nextflow_schema.json | 44 +++++++++++++++- 7 files changed, 130 insertions(+), 3 deletions(-) create mode 100644 modules/local/mirna_filtering/environment.yml create mode 100644 modules/local/mirna_filtering/main.nf create mode 100644 modules/local/mirna_filtering/templates/mirna_filtering.R diff --git a/modules/local/deseq2/normalization/environment.yml b/modules/local/deseq2/normalization/environment.yml index 8bd70ac0..8eb117c3 100644 --- a/modules/local/deseq2/normalization/environment.yml +++ b/modules/local/deseq2/normalization/environment.yml @@ -5,4 +5,3 @@ channels: - defaults dependencies: - bioconda::bioconductor-deseq2=1.34.0 - - conda-forge::r-data.table=1.15.2 diff --git a/modules/local/deseq2/normalization/main.nf b/modules/local/deseq2/normalization/main.nf index 97b13efa..74cb8b5a 100644 --- a/modules/local/deseq2/normalization/main.nf +++ b/modules/local/deseq2/normalization/main.nf @@ -12,7 +12,7 @@ process DESEQ2_NORMALIZATION { output: tuple val(meta), path("${meta.id}.normalized_counts.tsv"), emit: normalized - path "versions.yml" , emit: versions + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/mirna_filtering/environment.yml b/modules/local/mirna_filtering/environment.yml new file mode 100644 index 00000000..1aa60c3d --- /dev/null +++ b/modules/local/mirna_filtering/environment.yml @@ -0,0 +1,4 @@ +name: mirna_filtering +channels: + - conda-forge + - defaults diff --git a/modules/local/mirna_filtering/main.nf b/modules/local/mirna_filtering/main.nf new file mode 100644 index 00000000..035354d1 --- /dev/null +++ b/modules/local/mirna_filtering/main.nf @@ -0,0 +1,24 @@ +process MIRNA_FILTERING { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/r-base:4.2.1' : + 'biocontainers/r-base:4.2.1' }" + + input: + tuple val(meta), path(normalized_counts) + val(mirna_min_sample_percentage) + val(mirna_min_reads) + + output: + tuple val(meta), path("${meta.id}.normalized_counts_filtered.tsv"), emit: filtered + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + template 'mirna_filtering.R' +} diff --git a/modules/local/mirna_filtering/templates/mirna_filtering.R b/modules/local/mirna_filtering/templates/mirna_filtering.R new file mode 100644 index 00000000..32521c8e --- /dev/null +++ b/modules/local/mirna_filtering/templates/mirna_filtering.R @@ -0,0 +1,51 @@ +#!/usr/bin/env Rscript + +expression_norm <- read.table("$normalized_counts", + sep = "\\t", + header = TRUE, + stringsAsFactors = FALSE, + check.names = FALSE +) + +samples <- colnames(expression_norm)[-c(1)] + +# filter data: counts > 5 in at least 20% of samples +if (length(samples) < 5) { + stop("Cannot perform filtering on less than 5 samples") +} + +sample_nr_cutoff <- ceiling($mirna_min_sample_percentage * length(samples)) +rows_to_keep <- c() + +for (i in seq_len(nrow(expression_norm))) { + mirna_per_sample <- 0 + for (j in 5:ncol(expression_norm)) { + if (expression_norm[i, j] >= $mirna_min_reads) { + mirna_per_sample <- mirna_per_sample + 1 + } + } + if (mirna_per_sample >= sample_nr_cutoff) { + rows_to_keep <- append(rows_to_keep, i) + } +} + +filtered_data <- expression_norm[rows_to_keep, ] + +write.table(filtered_data, paste0("${meta.id}.normalized_counts_filtered.tsv"), + quote = FALSE, sep = "\\t", + row.names = FALSE) + +################################################ +################################################ +## VERSIONS FILE ## +################################################ +################################################ + +r.version <- strsplit(version[['version.string']], ' ')[[1]][3] + +writeLines( + c( + '"${task.process}":', + paste(' r-base:', r.version) + ), +'versions.yml') diff --git a/nextflow.config b/nextflow.config index ec8da623..3790a3bb 100644 --- a/nextflow.config +++ b/nextflow.config @@ -65,6 +65,13 @@ params { //> Quantification bootstrap_samples = 30 + //> MIRNA processing + mirna_expression = null + mirna_min_reads = 5 + mirna_min_sample_percentage = 0.2 + mirna_tools = 'miranda, targetscan' + mirna_vote = 1 + //> MISC save_unaligned = false seq_center = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 7397a535..e266c70a 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -51,7 +51,16 @@ "description": "Path to a CSV file containing BED files that should be used for annotation.", "help_text": "The annotation file should be a CSV file with the following columns: `name`, `file` and `min_overlap`. The `name` column should contain a unique identifier for the annotation, the `file` column should contain the path to the BED file and the `min_overlap` column should contain the minimum overlap required for a circRNA to be considered as overlapping with the annotation. The `min_overlap` column is optional and defaults to 0.9 if not provided.", "fa_icon": "fas fa-file-csv" - }, + } + } + }, + "mirna_processing_options": { + "title": "miRNA options", + "type": "object", + "fa_icon": "fas fa-terminal", + "description": "Define paths and threasholds for miRNA analysis.", + "required": ["mirna_expression"], + "properties": { "mirna_expression": { "type": "string", "format": "file-path", @@ -60,6 +69,22 @@ "pattern": "^\\S+\\.tsv$", "description": "Path to tab-separated file providing the expression counts of miRNAs, which are created in pipeline 'smrnaseq'. \n\nmirna \t sample1 \t sample2 \t sample3 \t\nid1\t count_sample1 \t count_sample2 \t count_sample3 \t\nid2 \t ... \t ... \t ... \t \n", "fa_icon": "fas fa-file-tsv" + }, + "mirna_min_sample_percentage": { + "type": "number", + "fa_icon": "fas fa-circle-notch", + "description": "Minimum percentage of samples, a miRNA has to be expressed in to pass filtering.", + "help_text": "The mirna_min_percentage parameter sets the minimum percentage of samples in which a miRNA must be expressed to pass filtering. The default value is 0.2, which means a miRNA must be detected in at least 20% of the samples to be included in the analysis.", + "default": 0.2, + "minimum": 0 + }, + "mirna_min_reads": { + "type": "integer", + "fa_icon": "fas fa-circle-notch", + "description": "Minimum number of reads, a miRNA is required to have to pass filtering.", + "help_text": "This parameter determines the minimum number of reads that a miRNA must have to pass filtering. The default is 5, meaning a miRNA must have at least 5 reads across the samples to be considered for analysis.", + "default": 5, + "minimum": 0 } } }, @@ -106,6 +131,23 @@ "description": "Specify the distance at which the annotation script decides if a candidate is a circRNA or EI-circRNA.", "help_text": "During annotation, if one of the start or end position of a circular candidate imperfectly overlaps an exon boundary, the script will consider positions within 'exon_boundary' (default 0bp) to be an exonic circRNA. If they fall outside of this range, the candidate is assumed to be an exonic-intronic circRNA, and the entire underlying sequence is taken for miRNA analysis, as opposed to just the exonic sequences for canonical exonic circRNAs. ", "default": 0 + }, + "mirna_tools": { + "type": "string", + "fa_icon": "fas fa-wrench", + "description": "Comma separated list of miRNA bindingsite prediction tools to use. Supported tools: miranda, targetscan.", + "help_text": "Select one or a combination of miRNA bindingsite prediction tools for the pipeline e.g:\n--tool 'miranda, targetscan'", + "default": "miranda, targetscan", + "pattern": "^((miranda|targetscan|pita|tarpmir)?,?)*[^,]+$" + }, + "mirna_vote": { + "type": "integer", + "fa_icon": "fas fa-intersection", + "description": "Specify the number of votes required for a miRNA to be further considered in downstream analysis.'", + "help_text": "Controls the number of votes required for a binding site prediction to be considered valid. If a miRNA binding site was predicted by two different tools (e.g., miRanda and TargetScan), it receives two votes. By specifying additional tools for miRNA binding site prediction (using the 'mirna_tools' parameter), you can adjust the number of votes required for a binding site to be considered valid.", + "default": 1, + "minimum": 1, + "maximum": 4 } } }, From 3617290865b07035dc44841c0ae44d4b4305e56f Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Fri, 10 May 2024 12:14:25 +0200 Subject: [PATCH 410/491] Adding formatting of mirna prediction output --- conf/modules.config | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index fac43d45..722660a3 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -804,6 +804,30 @@ process { ] } + withName: COUNTS_COMBINED { + ext.when = { params.module.split(',').contains('circrna_discovery') } + } + + withName: COUNTS_TO_BED { + ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3, \".\", \".\" }'" + ext.suffix = "bed" + } + + withName: MIRANDA_TO_MAJORITY { + ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { print \$1, \$2, \$7, \$8, \"miranda\" }'" + ext.suffix = "tsv" + } + + withName: TARGETSCAN_TO_MAJORITY { + ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { print \$2, \$1, \$6, \$7, \"targetscan\" }'" + ext.suffix = "tsv" + } + + withName: UNIQUE_REGIONS { + ext.args = "-k 1,1 -k2,2n -k3,3n -u" + ext.suffix = "unique.bed" + } + withName: COMBINE_TRANSCRIPTOME_GTFS { ext.args = "-k 1,1 -k4,4n -k5,5n" ext.suffix = "combined.gtf" From e7a8f73575ea3313473ac44a15a15e9c55e817ab Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Fri, 10 May 2024 12:17:10 +0200 Subject: [PATCH 411/491] embedding mirna filtering and output formatting in mirna_prediction subworkflow --- subworkflows/local/mirna_prediction.nf | 22 ++++++++++++++++------ 1 file changed, 16 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index b58b14fe..3a0eb0ab 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -1,8 +1,11 @@ -include { TARGETSCAN_DATABASE } from '../../modules/local/targetscan/database' -include { TARGETSCAN } from '../../modules/local/targetscan/predict' -include { MIRANDA } from '../../modules/nf-core/miranda' -include { MIRNA_TARGETS } from '../../modules/local/mirna_targets' -include { DESEQ2_NORMALIZATION } from '../../modules/local/deseq2/normalization' +include { TARGETSCAN_DATABASE } from '../../modules/local/targetscan/database' +include { TARGETSCAN } from '../../modules/local/targetscan/predict' +include { MIRANDA } from '../../modules/nf-core/miranda' +include { MIRNA_TARGETS } from '../../modules/local/mirna_targets' +include { DESEQ2_NORMALIZATION } from '../../modules/local/deseq2/normalization' +include { MIRNA_FILTERING } from '../../modules/local/mirna_filtering' +include { GAWK as MIRANDA_TO_MAJORITY } from '../../modules/nf-core/gawk' +include { GAWK as TARGETSCAN_TO_MAJORITY } from '../../modules/nf-core/gawk' workflow MIRNA_PREDICTION{ @@ -26,12 +29,18 @@ workflow MIRNA_PREDICTION{ ch_versions = ch_versions.mix(DESEQ2_NORMALIZATION.out.versions) + ch_mirna_filtered = MIRNA_FILTERING( ch_mirna_normalized, + params.mirna_min_sample_percentage, + params.mirna_min_reads + ).filtered + ch_versions = ch_versions.mix(MIRNA_FILTERING.out.versions) // // TARGETSCAN WORKFLOW: // TARGETSCAN_DATABASE( ch_mature ) TARGETSCAN( circrna_fasta, TARGETSCAN_DATABASE.out.mature_txt ) + TARGETSCAN_TO_MAJORITY( TARGETSCAN.out.txt, [] ) ch_versions = ch_versions.mix(TARGETSCAN_DATABASE.out.versions) ch_versions = ch_versions.mix(TARGETSCAN.out.versions) @@ -41,8 +50,9 @@ workflow MIRNA_PREDICTION{ // MIRANDA( circrna_fasta, ch_mature.map{meta, mature -> mature} ) + MIRANDA_TO_MAJORITY( MIRANDA.out.txt, [] ) + ch_versions = ch_versions.mix(MIRANDA.out.versions) - ch_versions = ch_versions.mix(MIRANDA.out.versions) // // CONSOLIDATE PREDICTIONS WORKFLOW: From 3596c5f41ee190a8608614579c941ad57d97b4f0 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Sat, 11 May 2024 17:30:07 +0200 Subject: [PATCH 412/491] extending miranda output formatting to ignore unwanted prefix --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 722660a3..90211131 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -814,7 +814,7 @@ process { } withName: MIRANDA_TO_MAJORITY { - ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { print \$1, \$2, \$7, \$8, \"miranda\" }'" + ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { sub(/^${params.species_id}-/, \"\", \$1); print \$1, \$2, \$7, \$8, \"miranda\" }'" ext.suffix = "tsv" } From 2715dfa40fd2956ffa6cbefc7135986cbaafb492 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Wed, 15 May 2024 19:28:55 +0200 Subject: [PATCH 413/491] implementing concatenation of mirna predictions, work in progress --- conf/modules.config | 10 +++++-- subworkflows/local/mirna_prediction.nf | 39 ++++++++++++++++++++------ 2 files changed, 38 insertions(+), 11 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 90211131..50a4553d 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -815,12 +815,16 @@ process { withName: MIRANDA_TO_MAJORITY { ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { sub(/^${params.species_id}-/, \"\", \$1); print \$1, \$2, \$7, \$8, \"miranda\" }'" - ext.suffix = "tsv" + ext.suffix = "miranda.tsv" } - + withName: TARGETSCAN_TO_MAJORITY { ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { print \$2, \$1, \$6, \$7, \"targetscan\" }'" - ext.suffix = "tsv" + ext.suffix = "targetscan.tsv" + } + + withName: COMBINE_BINDINGSITES { + ext.prefix = "bindingsites.tsv" } withName: UNIQUE_REGIONS { diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index 3a0eb0ab..ce1e1b3d 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -1,11 +1,14 @@ -include { TARGETSCAN_DATABASE } from '../../modules/local/targetscan/database' -include { TARGETSCAN } from '../../modules/local/targetscan/predict' -include { MIRANDA } from '../../modules/nf-core/miranda' -include { MIRNA_TARGETS } from '../../modules/local/mirna_targets' -include { DESEQ2_NORMALIZATION } from '../../modules/local/deseq2/normalization' -include { MIRNA_FILTERING } from '../../modules/local/mirna_filtering' -include { GAWK as MIRANDA_TO_MAJORITY } from '../../modules/nf-core/gawk' -include { GAWK as TARGETSCAN_TO_MAJORITY } from '../../modules/nf-core/gawk' +include { TARGETSCAN_DATABASE } from '../../modules/local/targetscan/database' +include { TARGETSCAN } from '../../modules/local/targetscan/predict' +include { MIRANDA } from '../../modules/nf-core/miranda' +include { MIRNA_TARGETS } from '../../modules/local/mirna_targets' +include { DESEQ2_NORMALIZATION } from '../../modules/local/deseq2/normalization' +include { MIRNA_FILTERING } from '../../modules/local/mirna_filtering' +include { GAWK as MIRANDA_TO_MAJORITY } from '../../modules/nf-core/gawk' +include { GAWK as TARGETSCAN_TO_MAJORITY } from '../../modules/nf-core/gawk' +include { CAT_CAT as COMBINE_BINDINGSITES } from '../../modules/nf-core/cat/cat' + +// include { MAJORITY_VOTE } from '../../modules/local/majority_vote' workflow MIRNA_PREDICTION{ @@ -17,6 +20,7 @@ workflow MIRNA_PREDICTION{ main: ch_versions = Channel.empty() + ch_predictions = Channel.empty() ADD_BACKSPLICE( circrna_fasta, [] ) ch_versions = ch_versions.mix(ADD_BACKSPLICE.out.versions) @@ -33,7 +37,9 @@ workflow MIRNA_PREDICTION{ params.mirna_min_sample_percentage, params.mirna_min_reads ).filtered + ch_versions = ch_versions.mix(MIRNA_FILTERING.out.versions) + // // TARGETSCAN WORKFLOW: // @@ -44,6 +50,8 @@ workflow MIRNA_PREDICTION{ ch_versions = ch_versions.mix(TARGETSCAN_DATABASE.out.versions) ch_versions = ch_versions.mix(TARGETSCAN.out.versions) + + ch_predictions = ch_predictions.mix(TARGETSCAN_TO_MAJORITY.out.output) // // MIRANDA WORKFLOW: @@ -51,7 +59,9 @@ workflow MIRNA_PREDICTION{ MIRANDA( circrna_fasta, ch_mature.map{meta, mature -> mature} ) MIRANDA_TO_MAJORITY( MIRANDA.out.txt, [] ) + ch_versions = ch_versions.mix(MIRANDA.out.versions) + ch_predictions = ch_predictions.mix(MIRANDA_TO_MAJORITY.out.output) // @@ -63,6 +73,19 @@ workflow MIRNA_PREDICTION{ ch_versions = ch_versions.mix(MIRNA_TARGETS.out.versions) + + // + // UNIFICATION OF PREDICTIONS + // + + ch_predictions.map{meta, file -> file}.collect().map{[[id: "mirna"], it]} + + COMBINE_BINDINGSITES ( ch_predictions ) + + // + // MAJORITY VOTE: TODO + // + emit: versions = ch_versions } From 60fe2a8b34113e8d6538d371da3c48bb15e8f43b Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Fri, 17 May 2024 16:50:05 +0200 Subject: [PATCH 414/491] preparing majority vote --- modules/local/majority_vote/main.nf | 23 +++++++++++++++++ .../local/majority_vote/templates/majority.py | 25 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 modules/local/majority_vote/main.nf create mode 100644 modules/local/majority_vote/templates/majority.py diff --git a/modules/local/majority_vote/main.nf b/modules/local/majority_vote/main.nf new file mode 100644 index 00000000..76442d1f --- /dev/null +++ b/modules/local/majority_vote/main.nf @@ -0,0 +1,23 @@ +process MAJORITY_VOTE { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/r-base:4.2.1' : + 'biocontainers/r-base:4.2.1' }" + + input: + tuple val(meta), path(miranda_data) + path(targetscan_data) + + output: + tuple val(meta), path("${meta.id}.majority.tsv.gz") , emit: tsv + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + template 'majority.R' +} diff --git a/modules/local/majority_vote/templates/majority.py b/modules/local/majority_vote/templates/majority.py new file mode 100644 index 00000000..58a356fc --- /dev/null +++ b/modules/local/majority_vote/templates/majority.py @@ -0,0 +1,25 @@ +import pandas as pd + + +if __name__ == "__main__": + predictions = pd.read_csv("/home/malte/projects/refactorring/majority_test/main.tsv", + sep="\\t", header=0, names=['mirna', 'target', 'start', 'end', 'tool' ]) + + start = False + end = True + complete = False # TODO: Ask if this means an exact match or an "either ..., or ..." + majority = 2 + + if start: # group by start indices + predictions = predictions.groupby(['mirna', 'target', 'start'])['tool'].apply(set).reset_index() + elif end: # group by end indices + predictions = predictions.groupby(['mirna', 'target', 'end'])['tool'].apply(set).reset_index() + elif complete: # group by both indices + predictions = predictions.groupby(['mirna', 'target', 'start', 'end'])['tool'].apply(set).reset_index() + + # performing majority vote keeping only mirna binding sites that meet the required number of votes + post_vote_predictions = predictions[predictions['tool'].apply(len) >= majority].copy() + post_vote_predictions = post_vote_predictions.drop('tool', axis=1) + + + predictions_out.to_csv('filtered_bindingsites.tsv', sep='\\t', index=False) From 8a7772dce85501116fc3f486dfca19b2bc4d8354 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Fri, 17 May 2024 16:51:49 +0200 Subject: [PATCH 415/491] fixing channel structure of predictions for cat cat --- subworkflows/local/mirna_prediction.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index ce1e1b3d..160e569f 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -8,7 +8,7 @@ include { GAWK as MIRANDA_TO_MAJORITY } from '../../modules/nf-core/gawk' include { GAWK as TARGETSCAN_TO_MAJORITY } from '../../modules/nf-core/gawk' include { CAT_CAT as COMBINE_BINDINGSITES } from '../../modules/nf-core/cat/cat' -// include { MAJORITY_VOTE } from '../../modules/local/majority_vote' +// include { MAJORITY_VOTE } from '../../modules/local/majority_vote' workflow MIRNA_PREDICTION{ @@ -78,9 +78,9 @@ workflow MIRNA_PREDICTION{ // UNIFICATION OF PREDICTIONS // - ch_predictions.map{meta, file -> file}.collect().map{[[id: "mirna"], it]} + ch_combined = ch_predictions.map{meta, file -> file}.collect().map{[[id: "mirna"], it]} - COMBINE_BINDINGSITES ( ch_predictions ) + COMBINE_BINDINGSITES ( ch_combined ) // // MAJORITY VOTE: TODO From c7a82da25a8e1ae5611924d711d1fc7e9dd55752 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Sat, 18 May 2024 18:00:58 +0200 Subject: [PATCH 416/491] Embedding majority vote for mirna predictions --- modules/local/majority_vote/main.nf | 29 +++++--- .../local/majority_vote/templates/majority.py | 68 ++++++++++++++----- subworkflows/local/mirna_prediction.nf | 11 ++- 3 files changed, 79 insertions(+), 29 deletions(-) diff --git a/modules/local/majority_vote/main.nf b/modules/local/majority_vote/main.nf index 76442d1f..5cd86ae3 100644 --- a/modules/local/majority_vote/main.nf +++ b/modules/local/majority_vote/main.nf @@ -2,22 +2,33 @@ process MAJORITY_VOTE { tag "$meta.id" label 'process_single' - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-base:4.2.1' : - 'biocontainers/r-base:4.2.1' }" + conda "bioconda::pandas=1.5.2" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : + 'biocontainers/pandas:1.5.2' }" input: - tuple val(meta), path(miranda_data) - path(targetscan_data) + tuple val(meta), path(bindingsites) + output: - tuple val(meta), path("${meta.id}.majority.tsv.gz") , emit: tsv - path "versions.yml" , emit: versions + tuple val(meta), path("${meta.id}.majority.tsv") , emit: tsv + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - template 'majority.R' + template 'majority.py' + + stub: + """ + touch ${meta.id}.majority.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //g') + pandas: \$(python -c "import pandas; print(pandas.__version__)") + END_VERSIONS + """ } diff --git a/modules/local/majority_vote/templates/majority.py b/modules/local/majority_vote/templates/majority.py index 58a356fc..6c362dc4 100644 --- a/modules/local/majority_vote/templates/majority.py +++ b/modules/local/majority_vote/templates/majority.py @@ -1,25 +1,59 @@ +#!/usr/bin/env python3 import pandas as pd +import platform -if __name__ == "__main__": - predictions = pd.read_csv("/home/malte/projects/refactorring/majority_test/main.tsv", - sep="\\t", header=0, names=['mirna', 'target', 'start', 'end', 'tool' ]) +def format_yaml_like(data: dict, indent: int = 0) -> str: + """Formats a dictionary to a YAML-like string. - start = False - end = True - complete = False # TODO: Ask if this means an exact match or an "either ..., or ..." - majority = 2 + Args: + data (dict): The dictionary to format. + indent (int): The current indentation level. - if start: # group by start indices - predictions = predictions.groupby(['mirna', 'target', 'start'])['tool'].apply(set).reset_index() - elif end: # group by end indices - predictions = predictions.groupby(['mirna', 'target', 'end'])['tool'].apply(set).reset_index() - elif complete: # group by both indices - predictions = predictions.groupby(['mirna', 'target', 'start', 'end'])['tool'].apply(set).reset_index() + Returns: + str: A string formatted as YAML. + """ + yaml_str = "" + for key, value in data.items(): + spaces = " " * indent + if isinstance(value, dict): + yaml_str += f"{spaces}{key}:\\n{format_yaml_like(value, indent + 1)}" + else: + yaml_str += f"{spaces}{key}: {value}\\n" + return yaml_str - # performing majority vote keeping only mirna binding sites that meet the required number of votes - post_vote_predictions = predictions[predictions['tool'].apply(len) >= majority].copy() - post_vote_predictions = post_vote_predictions.drop('tool', axis=1) +predictions = pd.read_csv("$bindingsites", + sep="\\t", header=0, names=['mirna', 'target', 'start', 'end', 'tool' ]) - predictions_out.to_csv('filtered_bindingsites.tsv', sep='\\t', index=False) +# start = False # TODO: Probably needs to be removed +# end = False +complete = True # TODO: Ask if this means an exact match or an "either ..., or ..." +majority = ${params.mirna_vote} + +# if start: # group by start indices +# predictions = predictions.groupby(['mirna', 'target', 'start'])['tool'].apply(set).reset_index() +# elif end: # group by end indices +# predictions = predictions.groupby(['mirna', 'target', 'end'])['tool'].apply(set).reset_index() +# elif complete: # group by both indices +# predictions = predictions.groupby(['mirna', 'target', 'start', 'end'])['tool'].apply(set).reset_index() + +predictions = predictions.groupby(['mirna', 'target', 'start', 'end'])['tool'].apply(set).reset_index() + +# performing majority vote keeping only mirna binding sites that meet the required number of votes +post_vote_predictions = predictions[predictions['tool'].apply(len) >= majority].copy() +post_vote_predictions = post_vote_predictions.drop('tool', axis=1) + + +post_vote_predictions.to_csv('${meta.id}.majority.tsv', sep='\\t', index=False) + +# Create version file +versions = { + "${task.process}" : { + "python": platform.python_version(), + "pandas": pd.__version__, + } +} + +with open("versions.yml", "w") as f: + f.write(format_yaml_like(versions)) diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index 160e569f..d5529933 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -8,7 +8,7 @@ include { GAWK as MIRANDA_TO_MAJORITY } from '../../modules/nf-core/gawk' include { GAWK as TARGETSCAN_TO_MAJORITY } from '../../modules/nf-core/gawk' include { CAT_CAT as COMBINE_BINDINGSITES } from '../../modules/nf-core/cat/cat' -// include { MAJORITY_VOTE } from '../../modules/local/majority_vote' +include { MAJORITY_VOTE } from '../../modules/local/majority_vote' workflow MIRNA_PREDICTION{ @@ -21,6 +21,7 @@ workflow MIRNA_PREDICTION{ main: ch_versions = Channel.empty() ch_predictions = Channel.empty() + ch_votings = Channel.empty() ADD_BACKSPLICE( circrna_fasta, [] ) ch_versions = ch_versions.mix(ADD_BACKSPLICE.out.versions) @@ -81,11 +82,15 @@ workflow MIRNA_PREDICTION{ ch_combined = ch_predictions.map{meta, file -> file}.collect().map{[[id: "mirna"], it]} COMBINE_BINDINGSITES ( ch_combined ) - + ch_votings = ch_votings.mix(COMBINE_BINDINGSITES.out.file_out) + ch_votings.view() + // - // MAJORITY VOTE: TODO + // MAJORITY VOTE: // + MAJORITY_VOTE( ch_votings ) + emit: versions = ch_versions } From bb5d520bfb00296e6500553cb5e48ee36f14acd3 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Sat, 1 Jun 2024 11:07:48 +0200 Subject: [PATCH 417/491] updating miranda to majority gawk --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 50a4553d..42e5a0f9 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -814,7 +814,7 @@ process { } withName: MIRANDA_TO_MAJORITY { - ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { sub(/^${params.species_id}-/, \"\", \$1); print \$1, \$2, \$7, \$8, \"miranda\" }'" + ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { print \$1, \$2, \$7, \$8, \"miranda\" }'" ext.suffix = "miranda.tsv" } From d9dea25c721f4a533ddcb914c98ed1868d154fd5 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Sat, 1 Jun 2024 11:10:14 +0200 Subject: [PATCH 418/491] adding compute correlations module --- .../compute_correlations/environment.yml | 4 + modules/local/compute_correlations/main.nf | 30 ++++ .../templates/compute_correlations.R | 142 ++++++++++++++++++ subworkflows/local/mirna_prediction.nf | 68 ++++++++- workflows/circrna/main.nf | 1 + 5 files changed, 237 insertions(+), 8 deletions(-) create mode 100644 modules/local/compute_correlations/environment.yml create mode 100644 modules/local/compute_correlations/main.nf create mode 100644 modules/local/compute_correlations/templates/compute_correlations.R diff --git a/modules/local/compute_correlations/environment.yml b/modules/local/compute_correlations/environment.yml new file mode 100644 index 00000000..d0903bfd --- /dev/null +++ b/modules/local/compute_correlations/environment.yml @@ -0,0 +1,4 @@ +name: compute_correlations +channels: + - conda-forge + - defaults diff --git a/modules/local/compute_correlations/main.nf b/modules/local/compute_correlations/main.nf new file mode 100644 index 00000000..eae4add2 --- /dev/null +++ b/modules/local/compute_correlations/main.nf @@ -0,0 +1,30 @@ +process COMPUTE_CORRELATIONS { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/r-base:4.2.1' : + 'biocontainers/r-base:4.2.1' }" + + input: + tuple val(meta), path(bindingsites) + path(filtered_mirnas) + path(filtered_circrnas) + + + output: + tuple val(meta), path("${meta.id}.circrna_correlation.tsv") , emit: correlation + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + template 'compute_correlations.R' + + stub: + """ + touch ${meta.id}.circrna_correlation.tsv + """ +} diff --git a/modules/local/compute_correlations/templates/compute_correlations.R b/modules/local/compute_correlations/templates/compute_correlations.R new file mode 100644 index 00000000..add9a221 --- /dev/null +++ b/modules/local/compute_correlations/templates/compute_correlations.R @@ -0,0 +1,142 @@ +#!/usr/bin/env Rscript + +dataset <- read.table('${params.input}', sep = ",", header=T, stringsAsFactors = F, check.names = F) +samples <- dataset\$sample + +pairBindSites <- read.table('$bindingsites', header = F, sep = "\\t", stringsAsFactors = F, check.names = F) +pairBindSites <- as.data.frame.matrix(table(pairBindSites[,2], pairBindSites[,1])) + +if (!nrow(pairBindSites) > 1) { # check if there are samples that survived majority vote + stop("\\nMajority vote resulted in no bindingsites! Check majority.tsv and adjust the parameter 'mirn_vote' in your nextflow.config to a lower number.") +} + +miRNA_expression <- read.table('$filtered_mirnas', header = T, stringsAsFactors = F, check.names = F, sep = "\\t") + + +if(length(samples) < 5){ + stop("Cannot perform correlation on less than 5 samples") +} + +circRNA_expression <- read.table('$filtered_circrnas', header = T, stringsAsFactors = F, check.names = F, sep="\\t") + +circRNA_expression\$tx <- sub("^circ_", "", circRNA_expression\$tx) +rownames(circRNA_expression) <- circRNA_expression\$tx + + +# filter expression for miRNA binding pairs +valid_circRNAs <- intersect(circRNA_expression\$tx, rownames(pairBindSites)) +valid_miRNAs <- intersect(miRNA_expression\$miRNA, colnames(pairBindSites)) + +circRNA_expression <- circRNA_expression[valid_circRNAs,] +miRNA_expression <- miRNA_expression[miRNA_expression\$miRNA %in% valid_miRNAs,] + +# check for annotation +annotation <- "circBaseID" %in% colnames(circRNA_expression) #TODO Do we need this? + +header <- "circRNA\\tmiRNA\\tcircRNA_miRNA_ratio\\tmiRNA_binding_sites\\tpearson_R\\tcorr_pval\\tRSS_norm\\tintercept\\tintercept_pval\\tslope\\tslope_pval\\tadj_r_squared" +#write(header, file=paste0("filtered_circRNA_miRNA_correlation_libSizeEstNorm_directwritten.tsv"), append = F) + +miRNA_for_row <- function(miRNA_expr_line, circRNA, circRNA_counts){ + + mirna <- as.character(miRNA_expr_line[1]) + # get sample counts for current miRNA + miRNA_counts <- miRNA_expr_line[-1] + + miRNA_counts <- data.frame(sample = as.character(names(miRNA_counts)), "miRNA_counts" = as.numeric(unname(miRNA_counts))) + # compute circRNA expression vs. miRNA expression + joined_counts <- merge(miRNA_counts, circRNA_counts, by="sample") + + # analyse circRNA/miRNA ratio + mean_circRNA_counts <- mean(joined_counts\$circRNA_counts) + mean_miRNA_counts <- mean(joined_counts\$miRNA_counts) + circRNA_miRNA_ratio <- mean_circRNA_counts/mean_miRNA_counts + + binding_sites <- pairBindSites[circRNA, mirna] + + # compute circRNA-miRNA correlation for all samples + cor_res <- cor.test(joined_counts\$miRNA_counts, joined_counts\$circRNA_counts, method = "pearson", use = "complete.obs") + corr_R <- as.numeric(as.character(cor_res\$estimate)) + corr_pval <- as.numeric(as.character(cor_res\$p.value)) + + # compute linear regression + regression_model <- lm(miRNA_counts~circRNA_counts, data = joined_counts) + intercept <- summary(regression_model)\$coefficients[1,1] + intercept_pval <- summary(regression_model)\$coefficients[1,4] + slope <- summary(regression_model)\$coefficients[2,1] + slope_pval <- summary(regression_model)\$coefficients[2,4] + adj_r_squared <- summary(regression_model)\$adj.r.squared + + # compute residuals sum of squares + # normalize counts for residuals sum of squares + normalized_counts <- joined_counts[,c("circRNA_counts", "miRNA_counts")] + min_circRNA_counts <- min(normalized_counts\$circRNA_counts) + max_circRNA_counts <- max(normalized_counts\$circRNA_counts) + normalized_counts[,"circRNA_counts"] <- (normalized_counts[,"circRNA_counts"] - min_circRNA_counts)/(max_circRNA_counts - min_circRNA_counts) + min_miRNA_counts <- min(normalized_counts\$miRNA_counts) + max_miRNA_counts <- max(normalized_counts\$miRNA_counts) + normalized_counts[,"miRNA_counts"] <- (normalized_counts[,"miRNA_counts"] - min_miRNA_counts)/(max_miRNA_counts - min_miRNA_counts) + norm_reg_model <- lm(miRNA_counts~circRNA_counts, data = normalized_counts) + RSS_norm <- sum(norm_reg_model\$residuals^2) + + res <- data.frame(circRNA = as.character(circRNA), miRNA = as.character(mirna), + circRNA_miRNA_ratio = as.numeric(circRNA_miRNA_ratio), + miRNA_binding_sites = as.numeric(binding_sites), + pearson_R = as.numeric(corr_R), corr_pval = as.numeric(corr_pval), + RSS_norm = RSS_norm, intercept = intercept, + intercept_pval = intercept_pval, slope = slope, + slope_pval = slope_pval, adj_r_squared = adj_r_squared) + + return(res) +} + +circRNA_for_row <- function(circRNA_expr_line){ + # get coordinations of current circRNA + circRNA <- as.character(circRNA_expr_line[1]) + + # annotate if possible + if (annotation){ + an = circRNA_expression[circRNA,"circBaseID"] + if (an != "None") { + message("processing: ", circRNA, " (", an, ")") + circRNA = an + } + + } else { + message("processing: ", circRNA) + } + + # extract pure counts only + circRNA_counts <- circRNA_expr_line[samples] # passt + + # get sample counts for current circRNA + circRNA_counts <- data.frame(sample = as.character(names(circRNA_counts)), "circRNA_counts" = as.numeric(unname(circRNA_counts))) + + if (all(circRNA_counts\$circRNA_counts != 0)) { + res_list <- apply(miRNA_expression, 1, FUN = miRNA_for_row, circRNA, circRNA_counts) + res_df <- do.call(rbind, res_list) + return(res_df) + } + +} + +correlations_list <- apply(circRNA_expression, MARGIN = 1, circRNA_for_row) +correlations_df <- do.call(rbind, correlations_list) +correlations_df\$adj_pval <- p.adjust(correlations_df\$corr_pval, method = "BH") + +write.table(correlations_df, file=paste0("${meta.id}.circrna_correlation.tsv"), sep = "\\t", quote = F, row.names = F, col.names = T) + + +################################################ +################################################ +## VERSIONS FILE ## +################################################ +################################################ + +r.version <- strsplit(version[['version.string']], ' ')[[1]][3] + +writeLines( + c( + '"${task.process}":', + paste(' r-base:', r.version) + ), +'versions.yml') diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index d5529933..0dd3e01a 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -7,8 +7,8 @@ include { MIRNA_FILTERING } from '../../modules/local/mirna_filt include { GAWK as MIRANDA_TO_MAJORITY } from '../../modules/nf-core/gawk' include { GAWK as TARGETSCAN_TO_MAJORITY } from '../../modules/nf-core/gawk' include { CAT_CAT as COMBINE_BINDINGSITES } from '../../modules/nf-core/cat/cat' - include { MAJORITY_VOTE } from '../../modules/local/majority_vote' +include { COMPUTE_CORRELATIONS } from '../../modules/local/compute_correlations' workflow MIRNA_PREDICTION{ @@ -17,11 +17,13 @@ workflow MIRNA_PREDICTION{ circrna_bed12 ch_mature ch_mirna + circrna_counts main: ch_versions = Channel.empty() ch_predictions = Channel.empty() ch_votings = Channel.empty() + ch_targetscan_meta_formatted = Channel.empty() ADD_BACKSPLICE( circrna_fasta, [] ) ch_versions = ch_versions.mix(ADD_BACKSPLICE.out.versions) @@ -45,13 +47,12 @@ workflow MIRNA_PREDICTION{ // TARGETSCAN WORKFLOW: // - TARGETSCAN_DATABASE( ch_mature ) - TARGETSCAN( circrna_fasta, TARGETSCAN_DATABASE.out.mature_txt ) + ch_targetscan_meta_formatted = ch_targetscan_meta_formatted.mix(formatMiRNAForTargetScan( ch_mature )).collect() + + TARGETSCAN( circrna_fasta, ch_targetscan_meta_formatted ) TARGETSCAN_TO_MAJORITY( TARGETSCAN.out.txt, [] ) - ch_versions = ch_versions.mix(TARGETSCAN_DATABASE.out.versions) ch_versions = ch_versions.mix(TARGETSCAN.out.versions) - ch_predictions = ch_predictions.mix(TARGETSCAN_TO_MAJORITY.out.output) // @@ -82,15 +83,66 @@ workflow MIRNA_PREDICTION{ ch_combined = ch_predictions.map{meta, file -> file}.collect().map{[[id: "mirna"], it]} COMBINE_BINDINGSITES ( ch_combined ) - ch_votings = ch_votings.mix(COMBINE_BINDINGSITES.out.file_out) - ch_votings.view() + + ch_votings = ch_votings.mix(COMBINE_BINDINGSITES.out.file_out) + ch_versions.mix(COMBINE_BINDINGSITES.out.versions) // // MAJORITY VOTE: // - MAJORITY_VOTE( ch_votings ) + ch_bindingsites = Channel.empty() + MAJORITY_VOTE( ch_votings ) + + ch_bindingsites = ch_bindingsites.mix(MAJORITY_VOTE.output.tsv) + ch_versions = ch_versions.mix(MAJORITY_VOTE.output.versions) + + // + // COMPUTE CORREALTION: + // + + COMPUTE_CORRELATIONS( ch_bindingsites, + ch_mirna_filtered.map{meta, file -> file}.collect(), + circrna_counts.map{meta, file -> file}.collect() + ) + + ch_versions = ch_versions.mix(COMPUTE_CORRELATIONS.out.versions) + emit: versions = ch_versions } + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ +// Fromatting miRNA input for taretscan +// takes mature.fa, iterates over entries (id, seq) and generates a new file +// writing: +// 1. miR ID +// 2. miR (7bp) seed sequence from mature seq +// 3. Species ID (set to 0000, not important for output). +// to new file +def formatMiRNAForTargetScan(ch_mature) { + + def ch_targetscan_meta_formatted = ch_mature + .map { meta, mature -> mature } + .splitFasta(by: 1) + .map { entry -> + def lines = entry.readLines() + def id = lines[0] + def seq = lines[1..-1].join() + return [id, seq] + } + .map { id, seq -> + def newSeq = seq[1..7] // Extract sub-sequence (2) + return [id, newSeq, '0000'] // Add species ID (3) + } + .map { id, newSeq, s_id -> "$id\t$newSeq\t$s_id\n" } + .collectFile(name: 'mature.txt') + + ch_targetscan_meta_formatted = ch_targetscan_meta_formatted.map { [[id: "mature_targetscan"], it] } + return ch_targetscan_meta_formatted +} diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index b82646f7..47642d7b 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -181,6 +181,7 @@ workflow CIRCRNA { BSJ_DETECTION.out.bed, ch_mature ch_mirna + QUANTIFICATION.out.circular_tx_counts ) ch_versions = ch_versions.mix(MIRNA_PREDICTION.out.versions) } From f51de26fea4e4d4401e95f02cca990ddcf939723 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Sat, 1 Jun 2024 11:10:31 +0200 Subject: [PATCH 419/491] todos --- .../deseq2/normalization/templates/deseq_normalization.R | 1 - modules/local/majority_vote/templates/majority.py | 9 +++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/modules/local/deseq2/normalization/templates/deseq_normalization.R b/modules/local/deseq2/normalization/templates/deseq_normalization.R index daada9f6..131bfd54 100644 --- a/modules/local/deseq2/normalization/templates/deseq_normalization.R +++ b/modules/local/deseq2/normalization/templates/deseq_normalization.R @@ -36,7 +36,6 @@ norm_data <- subset(merged_data, select = -c(order)) write.table(norm_data, paste0("${meta.id}.normalized_counts.tsv"), quote = FALSE, sep = "\\t", row.names = FALSE) -# TODO: Perform normalization and save as "${meta.id}.normalized_counts.tsv" # TODO: (Can be done later) Add support for Samplesheet so that we can eliminate batch effects diff --git a/modules/local/majority_vote/templates/majority.py b/modules/local/majority_vote/templates/majority.py index 6c362dc4..b172591d 100644 --- a/modules/local/majority_vote/templates/majority.py +++ b/modules/local/majority_vote/templates/majority.py @@ -26,9 +26,10 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: predictions = pd.read_csv("$bindingsites", sep="\\t", header=0, names=['mirna', 'target', 'start', 'end', 'tool' ]) -# start = False # TODO: Probably needs to be removed +# start = False # end = False -complete = True # TODO: Ask if this means an exact match or an "either ..., or ..." +# TODO: Ask if this means an exact match or an "either ..., or ..." +complete = True majority = ${params.mirna_vote} # if start: # group by start indices @@ -42,10 +43,10 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: # performing majority vote keeping only mirna binding sites that meet the required number of votes post_vote_predictions = predictions[predictions['tool'].apply(len) >= majority].copy() -post_vote_predictions = post_vote_predictions.drop('tool', axis=1) +out = post_vote_predictions.drop('tool', axis=1) -post_vote_predictions.to_csv('${meta.id}.majority.tsv', sep='\\t', index=False) +out.to_csv('${meta.id}.majority.tsv', sep='\\t', index=False) # Create version file versions = { From c31d3d9efa4624462d0c73e67b1a4ccfb376bdaa Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 1 Jun 2024 11:21:28 +0200 Subject: [PATCH 420/491] Replace tabs with spaces --- subworkflows/local/mirna_prediction.nf | 104 ++++++++++++------------- 1 file changed, 52 insertions(+), 52 deletions(-) diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index 0dd3e01a..ed7f3ebc 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -17,13 +17,13 @@ workflow MIRNA_PREDICTION{ circrna_bed12 ch_mature ch_mirna - circrna_counts + circrna_counts main: ch_versions = Channel.empty() ch_predictions = Channel.empty() - ch_votings = Channel.empty() - ch_targetscan_meta_formatted = Channel.empty() + ch_votings = Channel.empty() + ch_targetscan_meta_formatted = Channel.empty() ADD_BACKSPLICE( circrna_fasta, [] ) ch_versions = ch_versions.mix(ADD_BACKSPLICE.out.versions) @@ -37,11 +37,11 @@ workflow MIRNA_PREDICTION{ ch_versions = ch_versions.mix(DESEQ2_NORMALIZATION.out.versions) ch_mirna_filtered = MIRNA_FILTERING( ch_mirna_normalized, - params.mirna_min_sample_percentage, - params.mirna_min_reads - ).filtered + params.mirna_min_sample_percentage, + params.mirna_min_reads + ).filtered - ch_versions = ch_versions.mix(MIRNA_FILTERING.out.versions) + ch_versions = ch_versions.mix(MIRNA_FILTERING.out.versions) // // TARGETSCAN WORKFLOW: @@ -50,20 +50,20 @@ workflow MIRNA_PREDICTION{ ch_targetscan_meta_formatted = ch_targetscan_meta_formatted.mix(formatMiRNAForTargetScan( ch_mature )).collect() TARGETSCAN( circrna_fasta, ch_targetscan_meta_formatted ) - TARGETSCAN_TO_MAJORITY( TARGETSCAN.out.txt, [] ) + TARGETSCAN_TO_MAJORITY( TARGETSCAN.out.txt, [] ) ch_versions = ch_versions.mix(TARGETSCAN.out.versions) - ch_predictions = ch_predictions.mix(TARGETSCAN_TO_MAJORITY.out.output) + ch_predictions = ch_predictions.mix(TARGETSCAN_TO_MAJORITY.out.output) // // MIRANDA WORKFLOW: // MIRANDA( circrna_fasta, ch_mature.map{meta, mature -> mature} ) - MIRANDA_TO_MAJORITY( MIRANDA.out.txt, [] ) + MIRANDA_TO_MAJORITY( MIRANDA.out.txt, [] ) - ch_versions = ch_versions.mix(MIRANDA.out.versions) - ch_predictions = ch_predictions.mix(MIRANDA_TO_MAJORITY.out.output) + ch_versions = ch_versions.mix(MIRANDA.out.versions) + ch_predictions = ch_predictions.mix(MIRANDA_TO_MAJORITY.out.output) // @@ -76,39 +76,39 @@ workflow MIRNA_PREDICTION{ ch_versions = ch_versions.mix(MIRNA_TARGETS.out.versions) - // - // UNIFICATION OF PREDICTIONS - // + // + // UNIFICATION OF PREDICTIONS + // ch_combined = ch_predictions.map{meta, file -> file}.collect().map{[[id: "mirna"], it]} - - COMBINE_BINDINGSITES ( ch_combined ) - ch_votings = ch_votings.mix(COMBINE_BINDINGSITES.out.file_out) - ch_versions.mix(COMBINE_BINDINGSITES.out.versions) + COMBINE_BINDINGSITES ( ch_combined ) + + ch_votings = ch_votings.mix(COMBINE_BINDINGSITES.out.file_out) + ch_versions.mix(COMBINE_BINDINGSITES.out.versions) - // - // MAJORITY VOTE: - // + // + // MAJORITY VOTE: + // - ch_bindingsites = Channel.empty() + ch_bindingsites = Channel.empty() MAJORITY_VOTE( ch_votings ) - ch_bindingsites = ch_bindingsites.mix(MAJORITY_VOTE.output.tsv) - ch_versions = ch_versions.mix(MAJORITY_VOTE.output.versions) + ch_bindingsites = ch_bindingsites.mix(MAJORITY_VOTE.output.tsv) + ch_versions = ch_versions.mix(MAJORITY_VOTE.output.versions) - // - // COMPUTE CORREALTION: - // + // + // COMPUTE CORREALTION: + // - COMPUTE_CORRELATIONS( ch_bindingsites, - ch_mirna_filtered.map{meta, file -> file}.collect(), - circrna_counts.map{meta, file -> file}.collect() - ) + COMPUTE_CORRELATIONS( ch_bindingsites, + ch_mirna_filtered.map{meta, file -> file}.collect(), + circrna_counts.map{meta, file -> file}.collect() + ) - ch_versions = ch_versions.mix(COMPUTE_CORRELATIONS.out.versions) - + ch_versions = ch_versions.mix(COMPUTE_CORRELATIONS.out.versions) + emit: versions = ch_versions } @@ -127,22 +127,22 @@ workflow MIRNA_PREDICTION{ // to new file def formatMiRNAForTargetScan(ch_mature) { - def ch_targetscan_meta_formatted = ch_mature - .map { meta, mature -> mature } - .splitFasta(by: 1) - .map { entry -> - def lines = entry.readLines() - def id = lines[0] - def seq = lines[1..-1].join() - return [id, seq] - } - .map { id, seq -> - def newSeq = seq[1..7] // Extract sub-sequence (2) - return [id, newSeq, '0000'] // Add species ID (3) - } - .map { id, newSeq, s_id -> "$id\t$newSeq\t$s_id\n" } - .collectFile(name: 'mature.txt') - - ch_targetscan_meta_formatted = ch_targetscan_meta_formatted.map { [[id: "mature_targetscan"], it] } - return ch_targetscan_meta_formatted + def ch_targetscan_meta_formatted = ch_mature + .map { meta, mature -> mature } + .splitFasta(by: 1) + .map { entry -> + def lines = entry.readLines() + def id = lines[0] + def seq = lines[1..-1].join() + return [id, seq] + } + .map { id, seq -> + def newSeq = seq[1..7] // Extract sub-sequence (2) + return [id, newSeq, '0000'] // Add species ID (3) + } + .map { id, newSeq, s_id -> "$id\t$newSeq\t$s_id\n" } + .collectFile(name: 'mature.txt') + + ch_targetscan_meta_formatted = ch_targetscan_meta_formatted.map { [[id: "mature_targetscan"], it] } + return ch_targetscan_meta_formatted } From eb03b026cc3e4a2ffac88b6f4c7a29020e5d7f8e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 1 Jun 2024 11:49:33 +0200 Subject: [PATCH 421/491] Implement MIRNA_BINDINGSITES subworkflow --- conf/modules.config | 4 +- .../local/mirna/mirna_bindingsites.nf | 97 +++++++++++++++ subworkflows/local/mirna_prediction.nf | 116 ++---------------- 3 files changed, 110 insertions(+), 107 deletions(-) create mode 100644 subworkflows/local/mirna/mirna_bindingsites.nf diff --git a/conf/modules.config b/conf/modules.config index 42e5a0f9..6126cc11 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -813,12 +813,12 @@ process { ext.suffix = "bed" } - withName: MIRANDA_TO_MAJORITY { + withName: UNIFY_MIRANDA { ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { print \$1, \$2, \$7, \$8, \"miranda\" }'" ext.suffix = "miranda.tsv" } - withName: TARGETSCAN_TO_MAJORITY { + withName: UNIFY_TARGETSCAN { ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { print \$2, \$1, \$6, \$7, \"targetscan\" }'" ext.suffix = "targetscan.tsv" } diff --git a/subworkflows/local/mirna/mirna_bindingsites.nf b/subworkflows/local/mirna/mirna_bindingsites.nf new file mode 100644 index 00000000..780bde22 --- /dev/null +++ b/subworkflows/local/mirna/mirna_bindingsites.nf @@ -0,0 +1,97 @@ +include { MIRANDA } from '../../../modules/nf-core/miranda' +include { GAWK as UNIFY_MIRANDA } from '../../../modules/nf-core/gawk' +include { TARGETSCAN } from '../../../modules/local/targetscan/predict' +include { GAWK as UNIFY_TARGETSCAN } from '../../../modules/nf-core/gawk' +include { MIRNA_TARGETS } from '../../../modules/local/mirna_targets' +include { CAT_CAT as COMBINE_BINDINGSITES } from '../../../modules/nf-core/cat/cat' +include { MAJORITY_VOTE } from '../../../modules/local/majority_vote' + +workflow MIRNA_BINDINGSITES { + take: + circrna_fasta + circrna_bed12 + mirna_fasta + + main: + ch_versions = Channel.empty() + ch_predictions = Channel.empty() + + // + // TARGETSCAN WORKFLOW: + // + TARGETSCAN( circrna_fasta, formatMiRNAForTargetScan( mirna_fasta ).collect() ) + UNIFY_TARGETSCAN( TARGETSCAN.out.txt, [] ) + + ch_versions = ch_versions.mix(TARGETSCAN.out.versions) + ch_versions = ch_versions.mix(UNIFY_TARGETSCAN.out.versions) + ch_predictions = ch_predictions.mix(UNIFY_TARGETSCAN.out.output) + + // + // MIRANDA WORKFLOW: + // + + MIRANDA( circrna_fasta, mirna_fasta.map{meta, mature -> mature} ) + UNIFY_MIRANDA( MIRANDA.out.txt, [] ) + + ch_versions = ch_versions.mix(MIRANDA.out.versions) + ch_versions = ch_versions.mix(UNIFY_MIRANDA.out.versions) + ch_predictions = ch_predictions.mix(UNIFY_MIRANDA.out.output) + + // + // CONSOLIDATE PREDICTIONS WORKFLOW: + // + // TODO: This is an artifact and should be removed if we have a replacement + + consolidate_targets = TARGETSCAN.out.txt.join(MIRANDA.out.txt).join(circrna_bed12) + MIRNA_TARGETS( consolidate_targets ) + + ch_versions = ch_versions.mix(MIRNA_TARGETS.out.versions) + + // + // MAJORITY VOTING: + // + COMBINE_BINDINGSITES ( ch_predictions.map{meta, file -> file}.collect().map{[[id: "mirna"], it]} ) + MAJORITY_VOTE( COMBINE_BINDINGSITES.out.file_out ) + + ch_versions = ch_versions.mix(COMBINE_BINDINGSITES.out.versions) + ch_versions = ch_versions.mix(MAJORITY_VOTE.out.versions) + + emit: + binding_sites = MAJORITY_VOTE.out.tsv + + versions = ch_versions +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ +// Formatting miRNA input for targetscan +// takes mature.fa, iterates over entries (id, seq) and generates a new file +// writing: +// 1. miR ID +// 2. miR (7bp) seed sequence from mature seq +// 3. Species ID (set to 0000, not important for output). +// to new file +def formatMiRNAForTargetScan(ch_mature) { + + def ch_targetscan_meta_formatted = ch_mature + .map { meta, mature -> mature } + .splitFasta(by: 1) + .map { entry -> + def lines = entry.readLines() + def id = lines[0] + def seq = lines[1..-1].join() + return [id, seq] + } + .map { id, seq -> + def newSeq = seq[1..7] // Extract sub-sequence (2) + return [id, newSeq, '0000'] // Add species ID (3) + } + .map { id, newSeq, s_id -> "$id\t$newSeq\t$s_id\n" } + .collectFile(name: 'mature.txt') + + ch_targetscan_meta_formatted = ch_targetscan_meta_formatted.map { [[id: "mature_targetscan"], it] } + return ch_targetscan_meta_formatted +} diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index ed7f3ebc..45ee0a1d 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -1,16 +1,12 @@ -include { TARGETSCAN_DATABASE } from '../../modules/local/targetscan/database' -include { TARGETSCAN } from '../../modules/local/targetscan/predict' -include { MIRANDA } from '../../modules/nf-core/miranda' -include { MIRNA_TARGETS } from '../../modules/local/mirna_targets' +// MODULES include { DESEQ2_NORMALIZATION } from '../../modules/local/deseq2/normalization' include { MIRNA_FILTERING } from '../../modules/local/mirna_filtering' -include { GAWK as MIRANDA_TO_MAJORITY } from '../../modules/nf-core/gawk' -include { GAWK as TARGETSCAN_TO_MAJORITY } from '../../modules/nf-core/gawk' -include { CAT_CAT as COMBINE_BINDINGSITES } from '../../modules/nf-core/cat/cat' -include { MAJORITY_VOTE } from '../../modules/local/majority_vote' -include { COMPUTE_CORRELATIONS } from '../../modules/local/compute_correlations' +include { COMPUTE_CORRELATIONS } from '../../modules/local/compute_correlations' -workflow MIRNA_PREDICTION{ +// SUBWORKFLOWS +include { MIRNA_BINDINGSITES } from './mirna/mirna_bindingsites' + +workflow MIRNA_PREDICTION { take: circrna_fasta @@ -21,15 +17,14 @@ workflow MIRNA_PREDICTION{ main: ch_versions = Channel.empty() - ch_predictions = Channel.empty() - ch_votings = Channel.empty() - ch_targetscan_meta_formatted = Channel.empty() + + MIRNA_BINDINGSITES( circrna_fasta, circrna_bed12, ch_mature ) ADD_BACKSPLICE( circrna_fasta, [] ) ch_versions = ch_versions.mix(ADD_BACKSPLICE.out.versions) // - // MIRNA QUANTIFICATION WORKFLOW: + // MIRNA NORMALIZATION WORKFLOW: // ch_mirna_normalized = DESEQ2_NORMALIZATION( ch_mirna ).normalized @@ -43,106 +38,17 @@ workflow MIRNA_PREDICTION{ ch_versions = ch_versions.mix(MIRNA_FILTERING.out.versions) - // - // TARGETSCAN WORKFLOW: - // - - ch_targetscan_meta_formatted = ch_targetscan_meta_formatted.mix(formatMiRNAForTargetScan( ch_mature )).collect() - - TARGETSCAN( circrna_fasta, ch_targetscan_meta_formatted ) - TARGETSCAN_TO_MAJORITY( TARGETSCAN.out.txt, [] ) - - ch_versions = ch_versions.mix(TARGETSCAN.out.versions) - ch_predictions = ch_predictions.mix(TARGETSCAN_TO_MAJORITY.out.output) - - // - // MIRANDA WORKFLOW: - // - - MIRANDA( circrna_fasta, ch_mature.map{meta, mature -> mature} ) - MIRANDA_TO_MAJORITY( MIRANDA.out.txt, [] ) - - ch_versions = ch_versions.mix(MIRANDA.out.versions) - ch_predictions = ch_predictions.mix(MIRANDA_TO_MAJORITY.out.output) - - - // - // CONSOLIDATE PREDICTIONS WORKFLOW: - // - - consolidate_targets = TARGETSCAN.out.txt.join(MIRANDA.out.txt).join(circrna_bed12) - MIRNA_TARGETS( consolidate_targets ) - - ch_versions = ch_versions.mix(MIRNA_TARGETS.out.versions) - - - // - // UNIFICATION OF PREDICTIONS - // - - ch_combined = ch_predictions.map{meta, file -> file}.collect().map{[[id: "mirna"], it]} - - COMBINE_BINDINGSITES ( ch_combined ) - - ch_votings = ch_votings.mix(COMBINE_BINDINGSITES.out.file_out) - ch_versions.mix(COMBINE_BINDINGSITES.out.versions) - - // - // MAJORITY VOTE: - // - - ch_bindingsites = Channel.empty() - - MAJORITY_VOTE( ch_votings ) - - ch_bindingsites = ch_bindingsites.mix(MAJORITY_VOTE.output.tsv) - ch_versions = ch_versions.mix(MAJORITY_VOTE.output.versions) - // // COMPUTE CORREALTION: // - COMPUTE_CORRELATIONS( ch_bindingsites, + COMPUTE_CORRELATIONS( MIRNA_BINDINGSITES.out.binding_sites, ch_mirna_filtered.map{meta, file -> file}.collect(), circrna_counts.map{meta, file -> file}.collect() ) - ch_versions = ch_versions.mix(COMPUTE_CORRELATIONS.out.versions) + ch_versions = ch_versions.mix(COMPUTE_CORRELATIONS.out.versions) emit: versions = ch_versions } - -/* -======================================================================================== - FUNCTIONS -======================================================================================== -*/ -// Fromatting miRNA input for taretscan -// takes mature.fa, iterates over entries (id, seq) and generates a new file -// writing: -// 1. miR ID -// 2. miR (7bp) seed sequence from mature seq -// 3. Species ID (set to 0000, not important for output). -// to new file -def formatMiRNAForTargetScan(ch_mature) { - - def ch_targetscan_meta_formatted = ch_mature - .map { meta, mature -> mature } - .splitFasta(by: 1) - .map { entry -> - def lines = entry.readLines() - def id = lines[0] - def seq = lines[1..-1].join() - return [id, seq] - } - .map { id, seq -> - def newSeq = seq[1..7] // Extract sub-sequence (2) - return [id, newSeq, '0000'] // Add species ID (3) - } - .map { id, newSeq, s_id -> "$id\t$newSeq\t$s_id\n" } - .collectFile(name: 'mature.txt') - - ch_targetscan_meta_formatted = ch_targetscan_meta_formatted.map { [[id: "mature_targetscan"], it] } - return ch_targetscan_meta_formatted -} From a8128573893d497bf4e8c3179cf48851712d89a7 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 1 Jun 2024 11:49:58 +0200 Subject: [PATCH 422/491] Add versions capture for MIRNA_BINDINGSITES --- subworkflows/local/mirna_prediction.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index 45ee0a1d..d0c1b929 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -19,6 +19,7 @@ workflow MIRNA_PREDICTION { ch_versions = Channel.empty() MIRNA_BINDINGSITES( circrna_fasta, circrna_bed12, ch_mature ) + ch_versions = ch_versions.mix(MIRNA_BINDINGSITES.out.versions) ADD_BACKSPLICE( circrna_fasta, [] ) ch_versions = ch_versions.mix(ADD_BACKSPLICE.out.versions) From d0360e21f5245cb19b2d3b820736921d4dfc1f63 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 1 Jun 2024 12:09:53 +0200 Subject: [PATCH 423/491] Use full transcriptome in miRNA binding site detection --- subworkflows/local/mirna/mirna_bindingsites.nf | 13 ++++++++++--- subworkflows/local/mirna_prediction.nf | 14 +++++++------- subworkflows/local/quantification.nf | 1 + 3 files changed, 18 insertions(+), 10 deletions(-) diff --git a/subworkflows/local/mirna/mirna_bindingsites.nf b/subworkflows/local/mirna/mirna_bindingsites.nf index 780bde22..34cb1a48 100644 --- a/subworkflows/local/mirna/mirna_bindingsites.nf +++ b/subworkflows/local/mirna/mirna_bindingsites.nf @@ -1,3 +1,4 @@ +include { GAWK as ADD_BACKSPLICE } from '../../../modules/nf-core/gawk' include { MIRANDA } from '../../../modules/nf-core/miranda' include { GAWK as UNIFY_MIRANDA } from '../../../modules/nf-core/gawk' include { TARGETSCAN } from '../../../modules/local/targetscan/predict' @@ -8,7 +9,7 @@ include { MAJORITY_VOTE } from '../../../modules/local/majorit workflow MIRNA_BINDINGSITES { take: - circrna_fasta + transcriptome_fasta circrna_bed12 mirna_fasta @@ -16,10 +17,16 @@ workflow MIRNA_BINDINGSITES { ch_versions = Channel.empty() ch_predictions = Channel.empty() + // miRNAs can potentially bind to circRNAs right at the backsplice site + // In this case, the miRNA binding sequence would partially overlap with start and end of the circRNA + // To account for this, the first 25bp of the circRNA are added to the end of the circRNA sequence + ADD_BACKSPLICE( transcriptome_fasta, []) + ch_versions = ch_versions.mix(ADD_BACKSPLICE.out.versions) + // // TARGETSCAN WORKFLOW: // - TARGETSCAN( circrna_fasta, formatMiRNAForTargetScan( mirna_fasta ).collect() ) + TARGETSCAN( transcriptome_fasta, formatMiRNAForTargetScan( mirna_fasta ).collect() ) UNIFY_TARGETSCAN( TARGETSCAN.out.txt, [] ) ch_versions = ch_versions.mix(TARGETSCAN.out.versions) @@ -30,7 +37,7 @@ workflow MIRNA_BINDINGSITES { // MIRANDA WORKFLOW: // - MIRANDA( circrna_fasta, mirna_fasta.map{meta, mature -> mature} ) + MIRANDA( transcriptome_fasta, mirna_fasta.map{meta, mature -> mature} ) UNIFY_MIRANDA( MIRANDA.out.txt, [] ) ch_versions = ch_versions.mix(MIRANDA.out.versions) diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index d0c1b929..e59adac8 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -9,7 +9,7 @@ include { MIRNA_BINDINGSITES } from './mirna/mirna_bindingsites' workflow MIRNA_PREDICTION { take: - circrna_fasta + transcriptome_fasta circrna_bed12 ch_mature ch_mirna @@ -18,7 +18,7 @@ workflow MIRNA_PREDICTION { main: ch_versions = Channel.empty() - MIRNA_BINDINGSITES( circrna_fasta, circrna_bed12, ch_mature ) + MIRNA_BINDINGSITES( transcriptome_fasta, circrna_bed12, ch_mature ) ch_versions = ch_versions.mix(MIRNA_BINDINGSITES.out.versions) ADD_BACKSPLICE( circrna_fasta, [] ) @@ -43,12 +43,12 @@ workflow MIRNA_PREDICTION { // COMPUTE CORREALTION: // - COMPUTE_CORRELATIONS( MIRNA_BINDINGSITES.out.binding_sites, - ch_mirna_filtered.map{meta, file -> file}.collect(), - circrna_counts.map{meta, file -> file}.collect() - ) + //COMPUTE_CORRELATIONS( MIRNA_BINDINGSITES.out.binding_sites, + // ch_mirna_filtered.map{meta, file -> file}.collect(), + // circrna_counts.map{meta, file -> file}.collect() + // ) - ch_versions = ch_versions.mix(COMPUTE_CORRELATIONS.out.versions) + //ch_versions = ch_versions.mix(COMPUTE_CORRELATIONS.out.versions) emit: versions = ch_versions diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index 695fd524..5c5bf48e 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -121,6 +121,7 @@ workflow QUANTIFICATION { emit: se = MERGE_EXPERIMENTS.out.merged + transcriptome = TRANSCRIPTOME.out.transcriptome gene_counts = JOIN_GENE_COUNTS.out.csv gene_tpm = JOIN_GENE_TPM.out.csv tx_counts = JOIN_TX_COUNTS.out.csv From 282ddc61b14ff40c7a6d2925c6ea6cb81cdf95f9 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 1 Jun 2024 12:56:14 +0200 Subject: [PATCH 424/491] Use BIOAWK for ADD_BACKSPLICE --- conf/modules.config | 2 +- modules.json | 205 +++++++++++++----- modules/nf-core/bioawk/bioawk.diff | 24 ++ modules/nf-core/bioawk/environment.yml | 7 + modules/nf-core/bioawk/main.nf | 37 ++++ modules/nf-core/bioawk/meta.yml | 46 ++++ .../local/mirna/mirna_bindingsites.nf | 8 +- 7 files changed, 270 insertions(+), 59 deletions(-) create mode 100644 modules/nf-core/bioawk/bioawk.diff create mode 100644 modules/nf-core/bioawk/environment.yml create mode 100644 modules/nf-core/bioawk/main.nf create mode 100644 modules/nf-core/bioawk/meta.yml diff --git a/conf/modules.config b/conf/modules.config index 6126cc11..61492e6a 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -795,7 +795,7 @@ process { } withName: ADD_BACKSPLICE { - ext.args = "'{ if (/^>/) { print \$0 } else { start = substr(\$0, 1, 25); print \$0 start } }'" + ext.args = "-c fastx '{ if (\$name ~ /^circ_/) { \$seq = \$seq substr(\$seq, 1, 25) } print \">\" \$name; print \$seq }'" ext.suffix = "backspliced.fa" publishDir = [ path: { "${params.outdir}/mirna_prediction" }, diff --git a/modules.json b/modules.json index 36315754..b0cd0057 100644 --- a/modules.json +++ b/modules.json @@ -8,7 +8,9 @@ "bedtools/getfasta": { "branch": "master", "git_sha": "cdcdd5e3d806f0ff3983c40c69e0b07bb44ec299", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/groupby": { "branch": "master", @@ -18,72 +20,108 @@ "bedtools/intersect": { "branch": "master", "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/sort": { "branch": "master", "git_sha": "571a5feac4c9ce0a8df0bc15b94230e7f3e8db47", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] + }, + "bioawk": { + "branch": "master", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "modules" + ], + "patch": "modules/nf-core/bioawk/bioawk.diff" }, "bowtie/align": { "branch": "master", "git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bowtie/build": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bowtie2/align": { "branch": "master", "git_sha": "e4bad511789f16d0df39ee306b2cd50418365048", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bowtie2/build": { "branch": "master", "git_sha": "1fea64f5132a813ec97c1c6d3a74e0aee7142b6d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bwa/index": { "branch": "master", - "git_sha": "e0ff65e1fb313677de09f5f477ae3da30ce19b7b", - "installed_by": ["modules"] + "git_sha": "086fa66260595e123b0ea47a6512539b72a9afa3", + "installed_by": [ + "modules" + ] }, "cat/cat": { "branch": "master", "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cat/fastq": { "branch": "master", "git_sha": "4fc983ad0b30e6e32696fa7d980c76c7bfe1c03e", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "circexplorer2/annotate": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "circexplorer2/parse": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "csvtk/join": { "branch": "master", "git_sha": "614abbf126f287a3068dc86997b2e1b6a93abe20", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "csvtk/split": { "branch": "master", "git_sha": "614abbf126f287a3068dc86997b2e1b6a93abe20", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "de45447d060b8c8b98575bc637a4a575fd0638e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/gtffilter": { "branch": "master", @@ -93,117 +131,165 @@ "custom/tx2gene": { "branch": "master", "git_sha": "ec155021a9104441bf6a9bae3b55d1b5b0bfdb3a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "fastqc": { "branch": "master", "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gawk": { "branch": "master", "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gnu/sort": { "branch": "master", - "git_sha": "a3cc42943548378b726610f45bb5a79ab3f0b633", - "installed_by": ["modules"] + "git_sha": "ca199cfe5aa4f1ea3c41302158f0af2cfaa58957", + "installed_by": [ + "modules" + ] }, "hisat2/align": { "branch": "master", "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "hisat2/build": { "branch": "master", "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "hisat2/extractsplicesites": { "branch": "master", "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "miranda": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/faidx": { "branch": "master", - "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": ["modules"] + "git_sha": "f153f1f10e1083c49935565844cccb7453021682", + "installed_by": [ + "modules" + ] }, "samtools/flagstat": { "branch": "master", - "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": ["bam_stats_samtools"] + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "installed_by": [ + "bam_stats_samtools" + ] }, "samtools/idxstats": { "branch": "master", - "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": ["bam_stats_samtools"] + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "installed_by": [ + "bam_stats_samtools" + ] }, "samtools/index": { "branch": "master", - "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": ["bam_sort_stats_samtools", "modules"] + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "installed_by": [ + "bam_sort_stats_samtools", + "modules" + ] }, "samtools/sort": { "branch": "master", - "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": ["bam_sort_stats_samtools", "modules"] + "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", + "installed_by": [ + "bam_sort_stats_samtools", + "modules" + ] }, "samtools/stats": { "branch": "master", - "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": ["bam_stats_samtools"] + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "installed_by": [ + "bam_stats_samtools" + ] }, "samtools/view": { "branch": "master", - "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": ["modules"] + "git_sha": "0bd7d2333a88483aa0476acea172e9f5f6dd83bb", + "installed_by": [ + "modules" + ] }, "segemehl/align": { "branch": "master", "git_sha": "9a6b0745dbb5359286d36dee2183ffab240abba0", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "segemehl/index": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "star/align": { "branch": "master", "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "star/genomegenerate": { "branch": "master", "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "stringtie/stringtie": { "branch": "master", "git_sha": "b1b959609bda44341120aed1766329909f54b8d0", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "trimgalore": { "branch": "master", "git_sha": "a98418419ae6c9df3cf6cf108d1e1aba71037d5a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tximeta/tximport": { "branch": "master", "git_sha": "5d095e8413da1f4c72b7d07ce87f75c09482486f", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -211,28 +297,39 @@ "nf-core": { "bam_sort_stats_samtools": { "branch": "master", - "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": ["subworkflows"] + "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", + "installed_by": [ + "subworkflows" + ] }, "bam_stats_samtools": { "branch": "master", - "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": ["bam_sort_stats_samtools", "subworkflows"] + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "installed_by": [ + "bam_sort_stats_samtools", + "subworkflows" + ] }, "utils_nextflow_pipeline": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfvalidation_plugin": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } diff --git a/modules/nf-core/bioawk/bioawk.diff b/modules/nf-core/bioawk/bioawk.diff new file mode 100644 index 00000000..1303738f --- /dev/null +++ b/modules/nf-core/bioawk/bioawk.diff @@ -0,0 +1,24 @@ +Changes in module 'nf-core/bioawk' +--- modules/nf-core/bioawk/main.nf ++++ modules/nf-core/bioawk/main.nf +@@ -20,15 +20,15 @@ + script: + def args = task.ext.args ?: '' // args is used for the main arguments of the tool + prefix = task.ext.prefix ?: "${meta.id}" ++ suffix = task.ext.suffix ?: input.extension ++ file_name = "${prefix}.${suffix}" + + def VERSION = '1.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + """ + bioawk \\ + $args \\ + $input \\ +- > ${prefix} +- +- gzip ${prefix} ++ > ${file_name} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + +************************************************************ diff --git a/modules/nf-core/bioawk/environment.yml b/modules/nf-core/bioawk/environment.yml new file mode 100644 index 00000000..5fdfd417 --- /dev/null +++ b/modules/nf-core/bioawk/environment.yml @@ -0,0 +1,7 @@ +name: bioawk +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bioawk=1.0 diff --git a/modules/nf-core/bioawk/main.nf b/modules/nf-core/bioawk/main.nf new file mode 100644 index 00000000..0fded517 --- /dev/null +++ b/modules/nf-core/bioawk/main.nf @@ -0,0 +1,37 @@ +process BIOAWK { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bioawk:1.0--h5bf99c6_6': + 'biocontainers/bioawk:1.0--h5bf99c6_6' }" + + input: + tuple val(meta), path(input) + + output: + tuple val(meta), path("${prefix}.${suffix}"), emit: output + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' // args is used for the main arguments of the tool + prefix = task.ext.prefix ?: "${meta.id}" + suffix = task.ext.suffix ?: input.extension + + def VERSION = '1.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + """ + bioawk \\ + $args \\ + $input \\ + > ${prefix}.${suffix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bioawk: $VERSION + END_VERSIONS + """ +} diff --git a/modules/nf-core/bioawk/meta.yml b/modules/nf-core/bioawk/meta.yml new file mode 100644 index 00000000..c9d00111 --- /dev/null +++ b/modules/nf-core/bioawk/meta.yml @@ -0,0 +1,46 @@ +name: "bioawk" +description: Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats. +keywords: + - bioawk + - fastq + - fasta + - sam + - file manipulation + - awk +tools: + - "bioawk": + description: "BWK awk modified for biological data" + homepage: "https://github.com/lh3/bioawk" + documentation: "https://github.com/lh3/bioawk" + tool_dev_url: "https://github.com/lh3/bioawk" + licence: "['Free software license (https://github.com/lh3/bioawk/blob/master/README.awk#L1)']" +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Input sequence biological sequence file (optionally gzipped) to be manipulated via program specified in `$args`. + pattern: "*.{bed,gff,sam,vcf,fastq,fasta,tab,bed.gz,gff.gz,sam.gz,vcf.gz,fastq.gz,fasta.gz,tab.gz}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - output: + type: file + description: | + Manipulated and gzipped version of input sequence file following program specified in `args`. + File name will be what is specified in `$prefix`. Do not include `.gz` suffix in `$prefix`! Output files` will be gzipped for you! + pattern: "*.gz" +authors: + - "@jfy133" +maintainers: + - "@jfy133" diff --git a/subworkflows/local/mirna/mirna_bindingsites.nf b/subworkflows/local/mirna/mirna_bindingsites.nf index 34cb1a48..4c68c800 100644 --- a/subworkflows/local/mirna/mirna_bindingsites.nf +++ b/subworkflows/local/mirna/mirna_bindingsites.nf @@ -1,4 +1,4 @@ -include { GAWK as ADD_BACKSPLICE } from '../../../modules/nf-core/gawk' +include { BIOAWK as ADD_BACKSPLICE } from '../../../modules/nf-core/bioawk' include { MIRANDA } from '../../../modules/nf-core/miranda' include { GAWK as UNIFY_MIRANDA } from '../../../modules/nf-core/gawk' include { TARGETSCAN } from '../../../modules/local/targetscan/predict' @@ -20,13 +20,13 @@ workflow MIRNA_BINDINGSITES { // miRNAs can potentially bind to circRNAs right at the backsplice site // In this case, the miRNA binding sequence would partially overlap with start and end of the circRNA // To account for this, the first 25bp of the circRNA are added to the end of the circRNA sequence - ADD_BACKSPLICE( transcriptome_fasta, []) + ADD_BACKSPLICE( transcriptome_fasta) ch_versions = ch_versions.mix(ADD_BACKSPLICE.out.versions) // // TARGETSCAN WORKFLOW: // - TARGETSCAN( transcriptome_fasta, formatMiRNAForTargetScan( mirna_fasta ).collect() ) + TARGETSCAN( ADD_BACKSPLICE.out.output, formatMiRNAForTargetScan( mirna_fasta ).collect() ) UNIFY_TARGETSCAN( TARGETSCAN.out.txt, [] ) ch_versions = ch_versions.mix(TARGETSCAN.out.versions) @@ -37,7 +37,7 @@ workflow MIRNA_BINDINGSITES { // MIRANDA WORKFLOW: // - MIRANDA( transcriptome_fasta, mirna_fasta.map{meta, mature -> mature} ) + MIRANDA( ADD_BACKSPLICE.out.output, mirna_fasta.map{meta, mature -> mature} ) UNIFY_MIRANDA( MIRANDA.out.txt, [] ) ch_versions = ch_versions.mix(MIRANDA.out.versions) From 91436e32403350ba4a7626177a3a41e2cca8e998 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 1 Jun 2024 13:13:09 +0200 Subject: [PATCH 425/491] Pass correct count info to mirna_prediction --- subworkflows/local/mirna_prediction.nf | 5 +++-- subworkflows/local/quantification.nf | 1 + workflows/circrna/main.nf | 1 + 3 files changed, 5 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index e59adac8..3428df6a 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -13,7 +13,8 @@ workflow MIRNA_PREDICTION { circrna_bed12 ch_mature ch_mirna - circrna_counts + transcript_counts + quantification_rds main: ch_versions = Channel.empty() @@ -45,7 +46,7 @@ workflow MIRNA_PREDICTION { //COMPUTE_CORRELATIONS( MIRNA_BINDINGSITES.out.binding_sites, // ch_mirna_filtered.map{meta, file -> file}.collect(), - // circrna_counts.map{meta, file -> file}.collect() + // transcript_counts.map{meta, file -> file}.collect() // ) //ch_versions = ch_versions.mix(COMPUTE_CORRELATIONS.out.versions) diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf index 5c5bf48e..62abc16a 100644 --- a/subworkflows/local/quantification.nf +++ b/subworkflows/local/quantification.nf @@ -122,6 +122,7 @@ workflow QUANTIFICATION { emit: se = MERGE_EXPERIMENTS.out.merged transcriptome = TRANSCRIPTOME.out.transcriptome + rds = MERGE_EXPERIMENTS.out.merged gene_counts = JOIN_GENE_COUNTS.out.csv gene_tpm = JOIN_GENE_TPM.out.csv tx_counts = JOIN_TX_COUNTS.out.csv diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index 47642d7b..cf2abf1e 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -182,6 +182,7 @@ workflow CIRCRNA { ch_mature ch_mirna QUANTIFICATION.out.circular_tx_counts + QUANTIFICATION.out.rds ) ch_versions = ch_versions.mix(MIRNA_PREDICTION.out.versions) } From 05f588fb8b61e856cd5e6ca8b387f6d409ae0b11 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 1 Jun 2024 13:38:56 +0200 Subject: [PATCH 426/491] Implement transcriptome batch splitting in MIRNA_BINDINGSITES --- subworkflows/local/mirna/mirna_bindingsites.nf | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/mirna/mirna_bindingsites.nf b/subworkflows/local/mirna/mirna_bindingsites.nf index 4c68c800..61bd0964 100644 --- a/subworkflows/local/mirna/mirna_bindingsites.nf +++ b/subworkflows/local/mirna/mirna_bindingsites.nf @@ -23,10 +23,14 @@ workflow MIRNA_BINDINGSITES { ADD_BACKSPLICE( transcriptome_fasta) ch_versions = ch_versions.mix(ADD_BACKSPLICE.out.versions) + ch_transcriptome_batches = ADD_BACKSPLICE.out.output + .splitFasta(by: 100, file: true) + .map{ meta, file -> [[id: "batch_" + file.baseName.split("\\.").last()], file]} + // // TARGETSCAN WORKFLOW: // - TARGETSCAN( ADD_BACKSPLICE.out.output, formatMiRNAForTargetScan( mirna_fasta ).collect() ) + TARGETSCAN( ch_transcriptome_batches, formatMiRNAForTargetScan( mirna_fasta ).collect() ) UNIFY_TARGETSCAN( TARGETSCAN.out.txt, [] ) ch_versions = ch_versions.mix(TARGETSCAN.out.versions) @@ -37,7 +41,7 @@ workflow MIRNA_BINDINGSITES { // MIRANDA WORKFLOW: // - MIRANDA( ADD_BACKSPLICE.out.output, mirna_fasta.map{meta, mature -> mature} ) + MIRANDA( ch_transcriptome_batches, mirna_fasta.map{meta, mature -> mature} ) UNIFY_MIRANDA( MIRANDA.out.txt, [] ) ch_versions = ch_versions.mix(MIRANDA.out.versions) From 7a097fea4f562ed521a42e23e976eb74965df9f2 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 1 Jun 2024 14:16:04 +0200 Subject: [PATCH 427/491] Improve targetscan input preparation --- subworkflows/local/mirna/mirna_bindingsites.nf | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/subworkflows/local/mirna/mirna_bindingsites.nf b/subworkflows/local/mirna/mirna_bindingsites.nf index 61bd0964..ba204bf3 100644 --- a/subworkflows/local/mirna/mirna_bindingsites.nf +++ b/subworkflows/local/mirna/mirna_bindingsites.nf @@ -89,18 +89,10 @@ def formatMiRNAForTargetScan(ch_mature) { def ch_targetscan_meta_formatted = ch_mature .map { meta, mature -> mature } - .splitFasta(by: 1) - .map { entry -> - def lines = entry.readLines() - def id = lines[0] - def seq = lines[1..-1].join() - return [id, seq] + .splitFasta(record: [id: true, seqString: true]) + .map { record -> + return "${record.id}\t${record.seqString[1..7]}\t0000\n" } - .map { id, seq -> - def newSeq = seq[1..7] // Extract sub-sequence (2) - return [id, newSeq, '0000'] // Add species ID (3) - } - .map { id, newSeq, s_id -> "$id\t$newSeq\t$s_id\n" } .collectFile(name: 'mature.txt') ch_targetscan_meta_formatted = ch_targetscan_meta_formatted.map { [[id: "mature_targetscan"], it] } From 4683f79b5a7012fa2f54ffdc0482a44f0a953a1c Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 1 Jun 2024 14:37:37 +0200 Subject: [PATCH 428/491] Improve majority vote script --- .../local/majority_vote/templates/majority.py | 26 +++++-------------- 1 file changed, 6 insertions(+), 20 deletions(-) diff --git a/modules/local/majority_vote/templates/majority.py b/modules/local/majority_vote/templates/majority.py index b172591d..3c60dc2f 100644 --- a/modules/local/majority_vote/templates/majority.py +++ b/modules/local/majority_vote/templates/majority.py @@ -23,30 +23,16 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: return yaml_str -predictions = pd.read_csv("$bindingsites", +df = pd.read_csv("$bindingsites", sep="\\t", header=0, names=['mirna', 'target', 'start', 'end', 'tool' ]) - -# start = False -# end = False -# TODO: Ask if this means an exact match or an "either ..., or ..." -complete = True -majority = ${params.mirna_vote} - -# if start: # group by start indices -# predictions = predictions.groupby(['mirna', 'target', 'start'])['tool'].apply(set).reset_index() -# elif end: # group by end indices -# predictions = predictions.groupby(['mirna', 'target', 'end'])['tool'].apply(set).reset_index() -# elif complete: # group by both indices -# predictions = predictions.groupby(['mirna', 'target', 'start', 'end'])['tool'].apply(set).reset_index() - -predictions = predictions.groupby(['mirna', 'target', 'start', 'end'])['tool'].apply(set).reset_index() +df = df.groupby(['mirna', 'target'])['tool'].apply(set).reset_index() # performing majority vote keeping only mirna binding sites that meet the required number of votes -post_vote_predictions = predictions[predictions['tool'].apply(len) >= majority].copy() -out = post_vote_predictions.drop('tool', axis=1) - +min_tools = int("${params.mirna_vote}") +df = df[df['tool'].apply(len) >= min_tools].copy() +df = df.drop('tool', axis=1) -out.to_csv('${meta.id}.majority.tsv', sep='\\t', index=False) +df.to_csv('${meta.id}.majority.tsv', sep='\\t', index=False) # Create version file versions = { From 5852fe94283fa2bc5ba5b427ddfaf1b104173b7e Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 1 Jun 2024 14:50:32 +0200 Subject: [PATCH 429/491] Improve styling --- modules/local/compute_correlations/main.nf | 23 +++++++++++----------- subworkflows/local/mirna_prediction.nf | 16 +++++++-------- 2 files changed, 19 insertions(+), 20 deletions(-) diff --git a/modules/local/compute_correlations/main.nf b/modules/local/compute_correlations/main.nf index eae4add2..df6e7823 100644 --- a/modules/local/compute_correlations/main.nf +++ b/modules/local/compute_correlations/main.nf @@ -5,26 +5,25 @@ process COMPUTE_CORRELATIONS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-base:4.2.1' : - 'biocontainers/r-base:4.2.1' }" + 'biocontainers/r-base:4.2.1' }" input: - tuple val(meta), path(bindingsites) - path(filtered_mirnas) - path(filtered_circrnas) - + tuple val(meta), path(bindingsites) + tuple val(meta2), path(mirna_expression) + tuple val(meta3), path(transcript_rds) output: - tuple val(meta), path("${meta.id}.circrna_correlation.tsv") , emit: correlation - path "versions.yml" , emit: versions + tuple val(meta), path("${meta.id}.circrna_correlation.tsv"), emit: correlation + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: template 'compute_correlations.R' - - stub: - """ - touch ${meta.id}.circrna_correlation.tsv - """ + + stub: + """ + touch ${meta.id}.circrna_correlation.tsv + """ } diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index 3428df6a..86858033 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -33,10 +33,10 @@ workflow MIRNA_PREDICTION { ch_versions = ch_versions.mix(DESEQ2_NORMALIZATION.out.versions) - ch_mirna_filtered = MIRNA_FILTERING( ch_mirna_normalized, - params.mirna_min_sample_percentage, - params.mirna_min_reads - ).filtered + ch_mirna_filtered = MIRNA_FILTERING(ch_mirna_normalized, + params.mirna_min_sample_percentage, + params.mirna_min_reads + ).filtered ch_versions = ch_versions.mix(MIRNA_FILTERING.out.versions) @@ -44,10 +44,10 @@ workflow MIRNA_PREDICTION { // COMPUTE CORREALTION: // - //COMPUTE_CORRELATIONS( MIRNA_BINDINGSITES.out.binding_sites, - // ch_mirna_filtered.map{meta, file -> file}.collect(), - // transcript_counts.map{meta, file -> file}.collect() - // ) + COMPUTE_CORRELATIONS( MIRNA_BINDINGSITES.out.binding_sites, + ch_mirna_filtered, + quantification_rds + ) //ch_versions = ch_versions.mix(COMPUTE_CORRELATIONS.out.versions) From 8d2c151cdcb0fac8d437cba044c742d654b03145 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 1 Jun 2024 14:52:57 +0200 Subject: [PATCH 430/491] Add majority targets output --- modules/local/majority_vote/main.nf | 5 +++-- modules/local/majority_vote/templates/majority.py | 3 +++ 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/modules/local/majority_vote/main.nf b/modules/local/majority_vote/main.nf index 5cd86ae3..6f965262 100644 --- a/modules/local/majority_vote/main.nf +++ b/modules/local/majority_vote/main.nf @@ -12,8 +12,9 @@ process MAJORITY_VOTE { output: - tuple val(meta), path("${meta.id}.majority.tsv") , emit: tsv - path "versions.yml" , emit: versions + tuple val(meta), path("${meta.id}.majority.tsv"), emit: tsv + tuple val(meta), path("${meta.id}.targets.tsv") , emit: targets + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/majority_vote/templates/majority.py b/modules/local/majority_vote/templates/majority.py index 3c60dc2f..786fdb8c 100644 --- a/modules/local/majority_vote/templates/majority.py +++ b/modules/local/majority_vote/templates/majority.py @@ -34,6 +34,9 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: df.to_csv('${meta.id}.majority.tsv', sep='\\t', index=False) +df = df.groupby('target')['mirna'].apply(lambda x: ','.join(x)).reset_index() +df.to_csv('${meta.id}.targets.tsv', sep='\\t', index=False, header=False) + # Create version file versions = { "${task.process}" : { From 56007a751c6c9fa35aa4fee5f0aadd0f080a9283 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 1 Jun 2024 15:03:33 +0200 Subject: [PATCH 431/491] Transpose binding site output --- modules/local/majority_vote/main.nf | 20 +++++++++---------- .../local/majority_vote/templates/majority.py | 2 +- .../local/mirna/mirna_bindingsites.nf | 2 +- subworkflows/local/mirna_prediction.nf | 12 +++++++---- 4 files changed, 20 insertions(+), 16 deletions(-) diff --git a/modules/local/majority_vote/main.nf b/modules/local/majority_vote/main.nf index 6f965262..8ed51f0a 100644 --- a/modules/local/majority_vote/main.nf +++ b/modules/local/majority_vote/main.nf @@ -2,14 +2,14 @@ process MAJORITY_VOTE { tag "$meta.id" label 'process_single' - conda "bioconda::pandas=1.5.2" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : - 'biocontainers/pandas:1.5.2' }" + conda "bioconda::pandas=1.5.2" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : + 'biocontainers/pandas:1.5.2' }" input: tuple val(meta), path(bindingsites) - + output: tuple val(meta), path("${meta.id}.majority.tsv"), emit: tsv @@ -21,15 +21,15 @@ process MAJORITY_VOTE { script: template 'majority.py' - - stub: - """ - touch ${meta.id}.majority.tsv + + stub: + """ + touch ${meta.id}.majority.tsv cat <<-END_VERSIONS > versions.yml "${task.process}": python: \$(python --version | sed 's/Python //g') pandas: \$(python -c "import pandas; print(pandas.__version__)") END_VERSIONS - """ + """ } diff --git a/modules/local/majority_vote/templates/majority.py b/modules/local/majority_vote/templates/majority.py index 786fdb8c..2969ce54 100644 --- a/modules/local/majority_vote/templates/majority.py +++ b/modules/local/majority_vote/templates/majority.py @@ -34,7 +34,7 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: df.to_csv('${meta.id}.majority.tsv', sep='\\t', index=False) -df = df.groupby('target')['mirna'].apply(lambda x: ','.join(x)).reset_index() +df = df.groupby('mirna')['target'].apply(lambda x: ','.join(x)).reset_index() df.to_csv('${meta.id}.targets.tsv', sep='\\t', index=False, header=False) # Create version file diff --git a/subworkflows/local/mirna/mirna_bindingsites.nf b/subworkflows/local/mirna/mirna_bindingsites.nf index ba204bf3..e46233f4 100644 --- a/subworkflows/local/mirna/mirna_bindingsites.nf +++ b/subworkflows/local/mirna/mirna_bindingsites.nf @@ -68,7 +68,7 @@ workflow MIRNA_BINDINGSITES { ch_versions = ch_versions.mix(MAJORITY_VOTE.out.versions) emit: - binding_sites = MAJORITY_VOTE.out.tsv + binding_sites = MAJORITY_VOTE.out.targets versions = ch_versions } diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index 86858033..ff75a8fe 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -44,10 +44,14 @@ workflow MIRNA_PREDICTION { // COMPUTE CORREALTION: // - COMPUTE_CORRELATIONS( MIRNA_BINDINGSITES.out.binding_sites, - ch_mirna_filtered, - quantification_rds - ) + ch_binding_site_batches = MIRNA_BINDINGSITES.out.binding_sites + .splitText(by: 100, file: true) + .map{ meta, file -> [[id: "batch_" + file.baseName.split("\\.").last()], file]} + .view() + + // COMPUTE_CORRELATIONS( ch_binding_site_batches, + // ch_mirna_filtered, + // quantification_rds) //ch_versions = ch_versions.mix(COMPUTE_CORRELATIONS.out.versions) From 825f0d1bb85efc30893efd2885e41d56615054f3 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 1 Jun 2024 15:16:01 +0200 Subject: [PATCH 432/491] Start refactoring correlation --- .../compute_correlations/environment.yml | 5 +- modules/local/compute_correlations/main.nf | 6 +- .../templates/compute_correlations.R | 128 +----------------- subworkflows/local/mirna_prediction.nf | 7 +- 4 files changed, 14 insertions(+), 132 deletions(-) diff --git a/modules/local/compute_correlations/environment.yml b/modules/local/compute_correlations/environment.yml index d0903bfd..efe72834 100644 --- a/modules/local/compute_correlations/environment.yml +++ b/modules/local/compute_correlations/environment.yml @@ -1,4 +1,7 @@ -name: compute_correlations +name: "compute_correlations" channels: - conda-forge - defaults + - bioconda +dependencies: + - "bioconda::bioconductor-fishpond=2.8.0--r43hdfd78af_0" diff --git a/modules/local/compute_correlations/main.nf b/modules/local/compute_correlations/main.nf index df6e7823..dd8d48b3 100644 --- a/modules/local/compute_correlations/main.nf +++ b/modules/local/compute_correlations/main.nf @@ -4,8 +4,8 @@ process COMPUTE_CORRELATIONS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/r-base:4.2.1' : - 'biocontainers/r-base:4.2.1' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-fishpond:2.8.0--r43hdfd78af_0' : + 'biocontainers/bioconductor-fishpond:2.8.0--r43hdfd78af_0' }" input: tuple val(meta), path(bindingsites) @@ -13,7 +13,7 @@ process COMPUTE_CORRELATIONS { tuple val(meta3), path(transcript_rds) output: - tuple val(meta), path("${meta.id}.circrna_correlation.tsv"), emit: correlation + //tuple val(meta), path("${meta.id}.circrna_correlation.tsv"), emit: correlation path "versions.yml" , emit: versions when: diff --git a/modules/local/compute_correlations/templates/compute_correlations.R b/modules/local/compute_correlations/templates/compute_correlations.R index add9a221..4640b0a0 100644 --- a/modules/local/compute_correlations/templates/compute_correlations.R +++ b/modules/local/compute_correlations/templates/compute_correlations.R @@ -1,130 +1,10 @@ #!/usr/bin/env Rscript -dataset <- read.table('${params.input}', sep = ",", header=T, stringsAsFactors = F, check.names = F) -samples <- dataset\$sample - -pairBindSites <- read.table('$bindingsites', header = F, sep = "\\t", stringsAsFactors = F, check.names = F) -pairBindSites <- as.data.frame.matrix(table(pairBindSites[,2], pairBindSites[,1])) - -if (!nrow(pairBindSites) > 1) { # check if there are samples that survived majority vote - stop("\\nMajority vote resulted in no bindingsites! Check majority.tsv and adjust the parameter 'mirn_vote' in your nextflow.config to a lower number.") -} - -miRNA_expression <- read.table('$filtered_mirnas', header = T, stringsAsFactors = F, check.names = F, sep = "\\t") - - -if(length(samples) < 5){ - stop("Cannot perform correlation on less than 5 samples") -} - -circRNA_expression <- read.table('$filtered_circrnas', header = T, stringsAsFactors = F, check.names = F, sep="\\t") - -circRNA_expression\$tx <- sub("^circ_", "", circRNA_expression\$tx) -rownames(circRNA_expression) <- circRNA_expression\$tx - - -# filter expression for miRNA binding pairs -valid_circRNAs <- intersect(circRNA_expression\$tx, rownames(pairBindSites)) -valid_miRNAs <- intersect(miRNA_expression\$miRNA, colnames(pairBindSites)) - -circRNA_expression <- circRNA_expression[valid_circRNAs,] -miRNA_expression <- miRNA_expression[miRNA_expression\$miRNA %in% valid_miRNAs,] - -# check for annotation -annotation <- "circBaseID" %in% colnames(circRNA_expression) #TODO Do we need this? - -header <- "circRNA\\tmiRNA\\tcircRNA_miRNA_ratio\\tmiRNA_binding_sites\\tpearson_R\\tcorr_pval\\tRSS_norm\\tintercept\\tintercept_pval\\tslope\\tslope_pval\\tadj_r_squared" -#write(header, file=paste0("filtered_circRNA_miRNA_correlation_libSizeEstNorm_directwritten.tsv"), append = F) - -miRNA_for_row <- function(miRNA_expr_line, circRNA, circRNA_counts){ - - mirna <- as.character(miRNA_expr_line[1]) - # get sample counts for current miRNA - miRNA_counts <- miRNA_expr_line[-1] - - miRNA_counts <- data.frame(sample = as.character(names(miRNA_counts)), "miRNA_counts" = as.numeric(unname(miRNA_counts))) - # compute circRNA expression vs. miRNA expression - joined_counts <- merge(miRNA_counts, circRNA_counts, by="sample") - - # analyse circRNA/miRNA ratio - mean_circRNA_counts <- mean(joined_counts\$circRNA_counts) - mean_miRNA_counts <- mean(joined_counts\$miRNA_counts) - circRNA_miRNA_ratio <- mean_circRNA_counts/mean_miRNA_counts - - binding_sites <- pairBindSites[circRNA, mirna] - - # compute circRNA-miRNA correlation for all samples - cor_res <- cor.test(joined_counts\$miRNA_counts, joined_counts\$circRNA_counts, method = "pearson", use = "complete.obs") - corr_R <- as.numeric(as.character(cor_res\$estimate)) - corr_pval <- as.numeric(as.character(cor_res\$p.value)) - - # compute linear regression - regression_model <- lm(miRNA_counts~circRNA_counts, data = joined_counts) - intercept <- summary(regression_model)\$coefficients[1,1] - intercept_pval <- summary(regression_model)\$coefficients[1,4] - slope <- summary(regression_model)\$coefficients[2,1] - slope_pval <- summary(regression_model)\$coefficients[2,4] - adj_r_squared <- summary(regression_model)\$adj.r.squared - - # compute residuals sum of squares - # normalize counts for residuals sum of squares - normalized_counts <- joined_counts[,c("circRNA_counts", "miRNA_counts")] - min_circRNA_counts <- min(normalized_counts\$circRNA_counts) - max_circRNA_counts <- max(normalized_counts\$circRNA_counts) - normalized_counts[,"circRNA_counts"] <- (normalized_counts[,"circRNA_counts"] - min_circRNA_counts)/(max_circRNA_counts - min_circRNA_counts) - min_miRNA_counts <- min(normalized_counts\$miRNA_counts) - max_miRNA_counts <- max(normalized_counts\$miRNA_counts) - normalized_counts[,"miRNA_counts"] <- (normalized_counts[,"miRNA_counts"] - min_miRNA_counts)/(max_miRNA_counts - min_miRNA_counts) - norm_reg_model <- lm(miRNA_counts~circRNA_counts, data = normalized_counts) - RSS_norm <- sum(norm_reg_model\$residuals^2) - - res <- data.frame(circRNA = as.character(circRNA), miRNA = as.character(mirna), - circRNA_miRNA_ratio = as.numeric(circRNA_miRNA_ratio), - miRNA_binding_sites = as.numeric(binding_sites), - pearson_R = as.numeric(corr_R), corr_pval = as.numeric(corr_pval), - RSS_norm = RSS_norm, intercept = intercept, - intercept_pval = intercept_pval, slope = slope, - slope_pval = slope_pval, adj_r_squared = adj_r_squared) - - return(res) -} - -circRNA_for_row <- function(circRNA_expr_line){ - # get coordinations of current circRNA - circRNA <- as.character(circRNA_expr_line[1]) - - # annotate if possible - if (annotation){ - an = circRNA_expression[circRNA,"circBaseID"] - if (an != "None") { - message("processing: ", circRNA, " (", an, ")") - circRNA = an - } - - } else { - message("processing: ", circRNA) - } - - # extract pure counts only - circRNA_counts <- circRNA_expr_line[samples] # passt - - # get sample counts for current circRNA - circRNA_counts <- data.frame(sample = as.character(names(circRNA_counts)), "circRNA_counts" = as.numeric(unname(circRNA_counts))) - - if (all(circRNA_counts\$circRNA_counts != 0)) { - res_list <- apply(miRNA_expression, 1, FUN = miRNA_for_row, circRNA, circRNA_counts) - res_df <- do.call(rbind, res_list) - return(res_df) - } - -} - -correlations_list <- apply(circRNA_expression, MARGIN = 1, circRNA_for_row) -correlations_df <- do.call(rbind, correlations_list) -correlations_df\$adj_pval <- p.adjust(correlations_df\$corr_pval, method = "BH") - -write.table(correlations_df, file=paste0("${meta.id}.circrna_correlation.tsv"), sep = "\\t", quote = F, row.names = F, col.names = T) +library(fishpond) +tx_expression <- readRDS('${transcript_rds}') +mi_expression <- read.table('${mirna_expression}', header=TRUE, row.names=1, sep='\\t') +interactions <- read.table('${bindingsites}', sep='\\t') ################################################ ################################################ diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index ff75a8fe..88aa08e8 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -47,11 +47,10 @@ workflow MIRNA_PREDICTION { ch_binding_site_batches = MIRNA_BINDINGSITES.out.binding_sites .splitText(by: 100, file: true) .map{ meta, file -> [[id: "batch_" + file.baseName.split("\\.").last()], file]} - .view() - // COMPUTE_CORRELATIONS( ch_binding_site_batches, - // ch_mirna_filtered, - // quantification_rds) + COMPUTE_CORRELATIONS( ch_binding_site_batches, + ch_mirna_filtered, + quantification_rds) //ch_versions = ch_versions.mix(COMPUTE_CORRELATIONS.out.versions) From 4317c98a72089b9ff4e45f4c7f04c9b73861d068 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 1 Jun 2024 15:55:50 +0200 Subject: [PATCH 433/491] Implement first draft of correlation analysis --- .../templates/compute_correlations.R | 27 +++++++++++++++++++ .../templates/merge_experiments.r | 5 +++- subworkflows/local/mirna_prediction.nf | 9 ++++++- 3 files changed, 39 insertions(+), 2 deletions(-) diff --git a/modules/local/compute_correlations/templates/compute_correlations.R b/modules/local/compute_correlations/templates/compute_correlations.R index 4640b0a0..57837c40 100644 --- a/modules/local/compute_correlations/templates/compute_correlations.R +++ b/modules/local/compute_correlations/templates/compute_correlations.R @@ -1,11 +1,38 @@ #!/usr/bin/env Rscript library(fishpond) +suppressMessages(library(SummarizedExperiment)) tx_expression <- readRDS('${transcript_rds}') mi_expression <- read.table('${mirna_expression}', header=TRUE, row.names=1, sep='\\t') interactions <- read.table('${bindingsites}', sep='\\t') +# Iterate rows of interactions +for (i in 1:nrow(interactions)) { + # Get miRNA and target gene + miRNA <- interactions[i, 1] + targets <- unlist(strsplit(interactions[i, 2], ',')) + + # TODO: Remove this check after making sure that lowly expressed miRNAs + # are filtered out before binding site detection + if (!miRNA %in% rownames(mi_expression)) { + print(paste('miRNA', miRNA, 'not found')) + next + } + + mirna_expression <- mi_expression[miRNA,] + transcript_expression <- tx_expression[targets,] + + # Add miRNA expression to colData so that it can be used for correlation + colData(transcript_expression) <- cbind( + colData(transcript_expression), + t(mirna_expression[, rownames(colData(transcript_expression))]) + ) + + result <- rowData(swish(transcript_expression, miRNA, cor = "pearson")) + print(colnames(result)) +} + ################################################ ################################################ ## VERSIONS FILE ## diff --git a/modules/local/quantification/merge_experiments/templates/merge_experiments.r b/modules/local/quantification/merge_experiments/templates/merge_experiments.r index 12d1f6b5..4e82e57d 100644 --- a/modules/local/quantification/merge_experiments/templates/merge_experiments.r +++ b/modules/local/quantification/merge_experiments/templates/merge_experiments.r @@ -42,12 +42,15 @@ for (col in colnames(colData(se))) { } } +rownames(colData(se)) <- colData(se)\$names +colData(se)\$names <- NULL + # Add transcript annotation annotation <- annotation[match(rownames(se), annotation\$transcript_id),] rowData(se) <- annotation # Add TPM -assay(se, "tpm", withDimnames = FALSE) <- tpm[rownames(se), colData(se)\$names] +assay(se, "tpm", withDimnames = FALSE) <- tpm[rownames(se), rownames(colData(se))] saveRDS(se, '${meta.id}.merged.rds') diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index 88aa08e8..b176aacc 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -41,7 +41,14 @@ workflow MIRNA_PREDICTION { ch_versions = ch_versions.mix(MIRNA_FILTERING.out.versions) // - // COMPUTE CORREALTION: + // MIRNA BINDING SITES: + // + // TODO: Implement filtering of miRNAs from ch_mature if they are not present in ch_mirna_filtered + MIRNA_BINDINGSITES( transcriptome_fasta, circrna_bed12, ch_mature ) + ch_versions = ch_versions.mix(MIRNA_BINDINGSITES.out.versions) + + // + // COMPUTE CORRELATION: // ch_binding_site_batches = MIRNA_BINDINGSITES.out.binding_sites From 2bdabcc675aa9d2fc708edfae3056fbe3131f113 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 1 Jun 2024 16:02:43 +0200 Subject: [PATCH 434/491] Save correlation results --- modules/local/compute_correlations/main.nf | 4 ++-- .../compute_correlations/templates/compute_correlations.R | 7 +++++-- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/modules/local/compute_correlations/main.nf b/modules/local/compute_correlations/main.nf index dd8d48b3..25172c7a 100644 --- a/modules/local/compute_correlations/main.nf +++ b/modules/local/compute_correlations/main.nf @@ -13,8 +13,8 @@ process COMPUTE_CORRELATIONS { tuple val(meta3), path(transcript_rds) output: - //tuple val(meta), path("${meta.id}.circrna_correlation.tsv"), emit: correlation - path "versions.yml" , emit: versions + tuple val(meta), path("*.tsv"), emit: correlations + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/local/compute_correlations/templates/compute_correlations.R b/modules/local/compute_correlations/templates/compute_correlations.R index 57837c40..b4f0d02a 100644 --- a/modules/local/compute_correlations/templates/compute_correlations.R +++ b/modules/local/compute_correlations/templates/compute_correlations.R @@ -7,6 +7,8 @@ tx_expression <- readRDS('${transcript_rds}') mi_expression <- read.table('${mirna_expression}', header=TRUE, row.names=1, sep='\\t') interactions <- read.table('${bindingsites}', sep='\\t') +result_cols <- c('stat', 'log2FC', 'pvalue', 'locfdr', 'qvalue') + # Iterate rows of interactions for (i in 1:nrow(interactions)) { # Get miRNA and target gene @@ -29,8 +31,9 @@ for (i in 1:nrow(interactions)) { t(mirna_expression[, rownames(colData(transcript_expression))]) ) - result <- rowData(swish(transcript_expression, miRNA, cor = "pearson")) - print(colnames(result)) + # TODO: Allow setting "spearman" + result <- rowData(swish(transcript_expression, miRNA, cor = "pearson"))[, result_cols] + write.table(result, paste0(miRNA, '.tsv')) } ################################################ From bb0a858066fde0747ee9ad1bdab568547a3c5fed Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 1 Jun 2024 16:09:21 +0200 Subject: [PATCH 435/491] Switch correlation output to TSV --- .../compute_correlations/templates/compute_correlations.R | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/modules/local/compute_correlations/templates/compute_correlations.R b/modules/local/compute_correlations/templates/compute_correlations.R index b4f0d02a..5f0d8db0 100644 --- a/modules/local/compute_correlations/templates/compute_correlations.R +++ b/modules/local/compute_correlations/templates/compute_correlations.R @@ -33,7 +33,9 @@ for (i in 1:nrow(interactions)) { # TODO: Allow setting "spearman" result <- rowData(swish(transcript_expression, miRNA, cor = "pearson"))[, result_cols] - write.table(result, paste0(miRNA, '.tsv')) + # TODO: Find out why NaN rows occur + result <- result[complete.cases(result), ] + write.table(result, paste0(miRNA, '.tsv'), sep = '\\t') } ################################################ From 8c2ae5560b348f644fc4597a51f46c7c32361b1f Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sat, 1 Jun 2024 16:16:21 +0200 Subject: [PATCH 436/491] Handle correlation output channels --- subworkflows/local/mirna_prediction.nf | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index b176aacc..d8ffb157 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -58,8 +58,13 @@ workflow MIRNA_PREDICTION { COMPUTE_CORRELATIONS( ch_binding_site_batches, ch_mirna_filtered, quantification_rds) + + ch_correlation_results = COMPUTE_CORRELATIONS.out.correlations + .map{meta, results -> results} + .flatten().collect() + .map{results -> [[id: 'correlation'], results]} - //ch_versions = ch_versions.mix(COMPUTE_CORRELATIONS.out.versions) + ch_versions = ch_versions.mix(COMPUTE_CORRELATIONS.out.versions) emit: versions = ch_versions From 9e97abb9cc2956f5aad015dd5ffcee1a5ed9f8e7 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Fri, 7 Jun 2024 17:28:09 +0200 Subject: [PATCH 437/491] fixing MIRNA_TARGETS --- modules/local/mirna_targets/main.nf | 8 +-- .../local/mirna/mirna_bindingsites.nf | 56 ++++++++++++------- 2 files changed, 39 insertions(+), 25 deletions(-) diff --git a/modules/local/mirna_targets/main.nf b/modules/local/mirna_targets/main.nf index 94b31eeb..e525a9f5 100644 --- a/modules/local/mirna_targets/main.nf +++ b/modules/local/mirna_targets/main.nf @@ -8,7 +8,7 @@ process MIRNA_TARGETS { 'biocontainers/bedtools:2.30.0--h7d7f7ad_2' }" input: - tuple val(meta), path(targetscan), path(miranda), path(bed12) + tuple val(meta), path(targetscan), path(miranda) output: tuple val(meta), path("${prefix}.mirna_targets.txt"), emit: results @@ -22,8 +22,8 @@ process MIRNA_TARGETS { prefix = task.ext.prefix ?: "${meta.id}" """ ## reformat and sort miRanda, TargetScan outputs, convert to BED for overlaps. - tail -n +2 $targetscan | sort -k1,1 -k4n | awk -v OFS="\\t" '{print \$1, \$2, \$4, \$5, \$9}' | awk -v OFS="\t" '{print \$2, \$3, \$4, \$1, "0", \$5}' > targetscan.bed - tail -n +2 $miranda | sort -k2,2 -k7n | awk -v OFS="\\t" '{print \$2, \$1, \$3, \$4, \$7, \$8}' | awk -v OFS="\t" '{print \$2, \$5, \$6, \$1, \$3, \$4}' | sed 's/^[^-]*-//g' > miranda.bed + tail -n +2 $targetscan | sort -k1,1 -k4n | awk -v OFS="\\t" '{print \$1, \$2, \$4, \$5, \$9}' | awk -v OFS="\\t" '{print \$2, \$3, \$4, \$1, "0", \$5}' > targetscan.bed + tail -n +2 $miranda | sort -k2,2 -k7n | awk -v OFS="\\t" '{print \$2, \$1, \$3, \$4, \$7, \$8}' | awk -v OFS="\\t" '{print \$2, \$5, \$6, \$1, \$3, \$4}' > miranda.bed ## intersect, consolidate miRanda, TargetScan information about miRs. ## -wa to output miRanda hits - targetscan makes it difficult to resolve duplicate miRNAs at MRE sites. @@ -32,7 +32,7 @@ process MIRNA_TARGETS { ## remove duplicate miRNA entries at MRE sites. ## strategy: sory by circs, sort by start position, sort by site type - the goal is to take the best site type (i.e rank site type found at MRE site). - paste ${prefix}.mirnas.tmp mirna_type | sort -k3,3 -k2n -k7r | awk -v OFS="\\t" '{print \$4,\$1,\$2,\$3,\$5,\$6,\$7}' | awk -F "\\t" '{if (!seen[\$1,\$2,\$3,\$4,\$5,\$6]++)print}' | sort -k1,1 -k3n > ${prefix}.mirna_targets.tmp + paste ${prefix}.mirnas.tmp mirna_type | sort -k3n -k2n -k7r | awk -v OFS="\\t" '{print \$4,\$1,\$2,\$3,\$5,\$6,\$7}' | awk -F "\\t" '{if (!seen[\$1,\$2,\$3,\$4,\$5,\$6]++)print}' | sort -k1,1 -k3n > ${prefix}.mirna_targets.tmp echo -e "circRNA\\tmiRNA\\tStart\\tEnd\\tScore\\tEnergy_KcalMol\\tSite_type" | cat - ${prefix}.mirna_targets.tmp > ${prefix}.mirna_targets.txt cat <<-END_VERSIONS > versions.yml diff --git a/subworkflows/local/mirna/mirna_bindingsites.nf b/subworkflows/local/mirna/mirna_bindingsites.nf index e46233f4..e0755b5e 100644 --- a/subworkflows/local/mirna/mirna_bindingsites.nf +++ b/subworkflows/local/mirna/mirna_bindingsites.nf @@ -7,7 +7,7 @@ include { MIRNA_TARGETS } from '../../../modules/local/mirna_t include { CAT_CAT as COMBINE_BINDINGSITES } from '../../../modules/nf-core/cat/cat' include { MAJORITY_VOTE } from '../../../modules/local/majority_vote' -workflow MIRNA_BINDINGSITES { +workflow MIRNA_BINDINGSITES { take: transcriptome_fasta circrna_bed12 @@ -20,7 +20,7 @@ workflow MIRNA_BINDINGSITES { // miRNAs can potentially bind to circRNAs right at the backsplice site // In this case, the miRNA binding sequence would partially overlap with start and end of the circRNA // To account for this, the first 25bp of the circRNA are added to the end of the circRNA sequence - ADD_BACKSPLICE( transcriptome_fasta) + ADD_BACKSPLICE( transcriptome_fasta ) ch_versions = ch_versions.mix(ADD_BACKSPLICE.out.versions) ch_transcriptome_batches = ADD_BACKSPLICE.out.output @@ -28,32 +28,46 @@ workflow MIRNA_BINDINGSITES { .map{ meta, file -> [[id: "batch_" + file.baseName.split("\\.").last()], file]} // - // TARGETSCAN WORKFLOW: + // MIRNA PREDICTION TOOLS: // - TARGETSCAN( ch_transcriptome_batches, formatMiRNAForTargetScan( mirna_fasta ).collect() ) - UNIFY_TARGETSCAN( TARGETSCAN.out.txt, [] ) - - ch_versions = ch_versions.mix(TARGETSCAN.out.versions) - ch_versions = ch_versions.mix(UNIFY_TARGETSCAN.out.versions) - ch_predictions = ch_predictions.mix(UNIFY_TARGETSCAN.out.output) - - // - // MIRANDA WORKFLOW: - // - - MIRANDA( ch_transcriptome_batches, mirna_fasta.map{meta, mature -> mature} ) - UNIFY_MIRANDA( MIRANDA.out.txt, [] ) - - ch_versions = ch_versions.mix(MIRANDA.out.versions) - ch_versions = ch_versions.mix(UNIFY_MIRANDA.out.versions) - ch_predictions = ch_predictions.mix(UNIFY_MIRANDA.out.output) + tools_selected = params.mirna_tools.split(',').collect{it.trim().toLowerCase()} + + if (tools_selected.size() == 0) { + error 'No tools selected for miRNA discovery.' + } + + if (tools_selected.contains('targetscan')) { + // + // TARGETSCAN WORKFLOW: + // + TARGETSCAN( ch_transcriptome_batches, formatMiRNAForTargetScan( mirna_fasta ).collect() ) + UNIFY_TARGETSCAN( TARGETSCAN.out.txt, [] ) + + ch_versions = ch_versions.mix(TARGETSCAN.out.versions) + ch_versions = ch_versions.mix(UNIFY_TARGETSCAN.out.versions) + ch_predictions = ch_predictions.mix(UNIFY_TARGETSCAN.out.output) + } + + if (tools_selected.contains('miranda')) { + // + // MIRANDA WORKFLOW: + // + MIRANDA( ch_transcriptome_batches, mirna_fasta.map{meta, mature -> mature} ) + UNIFY_MIRANDA( MIRANDA.out.txt, [] ) + + ch_versions = ch_versions.mix(MIRANDA.out.versions) + ch_versions = ch_versions.mix(UNIFY_MIRANDA.out.versions) + ch_predictions = ch_predictions.mix(UNIFY_MIRANDA.out.output) + } // // CONSOLIDATE PREDICTIONS WORKFLOW: // // TODO: This is an artifact and should be removed if we have a replacement - consolidate_targets = TARGETSCAN.out.txt.join(MIRANDA.out.txt).join(circrna_bed12) + // consolidate_targets = TARGETSCAN.out.txt.join(MIRANDA.out.txt).join(circrna_bed12) + consolidate_targets = TARGETSCAN.out.txt.join(MIRANDA.out.txt) + MIRNA_TARGETS( consolidate_targets ) ch_versions = ch_versions.mix(MIRNA_TARGETS.out.versions) From 2be8d5efd8db56fa0bc5491e7357819c6dd2bbbf Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Mon, 17 Jun 2024 16:37:24 +0200 Subject: [PATCH 438/491] Filtering mature based on filtered mirnas --- subworkflows/local/mirna_prediction.nf | 28 ++++++++++++++++++++------ 1 file changed, 22 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index d8ffb157..1121bb26 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -8,7 +8,7 @@ include { MIRNA_BINDINGSITES } from './mirna/mirna_bindingsites' workflow MIRNA_PREDICTION { - take: + take: transcriptome_fasta circrna_bed12 ch_mature @@ -43,8 +43,24 @@ workflow MIRNA_PREDICTION { // // MIRNA BINDING SITES: // - // TODO: Implement filtering of miRNAs from ch_mature if they are not present in ch_mirna_filtered - MIRNA_BINDINGSITES( transcriptome_fasta, circrna_bed12, ch_mature ) + + // Filtering miRNAs from ch_mature if they are not in ch_mirna_filtered. + ch_uniq_mirnas = ch_mirna_filtered.map{ meta, path -> path }.splitCsv( sep: '\t' ).map{ it[0] }.unique().collect() + ch_mature_filtered = ch_mature + .map{ meta, path -> + path + } + .splitFasta( record: [id:true, seqString:true] ) + .combine(ch_uniq_mirnas.map{ it -> [it]}) // Not sure why this mapping is necessary but I think it is + .filter{ record, mirnas -> + ch_uniq_mirnas.contains(record.id) + }.map{ record, mirnas -> + ">${record.id}\n${record.seqString}" + } + .collectFile( name: 'mature_filtered.fa', newLine: true) + ch_mature_filtered = ch_mature_filtered.map{ it -> [[id: 'mature_filtered'], it]} + + MIRNA_BINDINGSITES( transcriptome_fasta, circrna_bed12, ch_mature_filtered ) ch_versions = ch_versions.mix(MIRNA_BINDINGSITES.out.versions) // @@ -55,9 +71,9 @@ workflow MIRNA_PREDICTION { .splitText(by: 100, file: true) .map{ meta, file -> [[id: "batch_" + file.baseName.split("\\.").last()], file]} - COMPUTE_CORRELATIONS( ch_binding_site_batches, - ch_mirna_filtered, - quantification_rds) + COMPUTE_CORRELATIONS( ch_binding_site_batches, + ch_mirna_filtered, + quantification_rds ) ch_correlation_results = COMPUTE_CORRELATIONS.out.correlations .map{meta, results -> results} From 0f6313d11ea939beddb6ec4709be3a27eb22a4a4 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Fri, 21 Jun 2024 23:12:27 +0200 Subject: [PATCH 439/491] Adding missing .collect() to MIRANDA process --- subworkflows/local/mirna/mirna_bindingsites.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/mirna/mirna_bindingsites.nf b/subworkflows/local/mirna/mirna_bindingsites.nf index e0755b5e..7683524f 100644 --- a/subworkflows/local/mirna/mirna_bindingsites.nf +++ b/subworkflows/local/mirna/mirna_bindingsites.nf @@ -52,7 +52,7 @@ workflow MIRNA_BINDINGSITES { // // MIRANDA WORKFLOW: // - MIRANDA( ch_transcriptome_batches, mirna_fasta.map{meta, mature -> mature} ) + MIRANDA( ch_transcriptome_batches, mirna_fasta.map{meta, mature -> mature}.collect() ) UNIFY_MIRANDA( MIRANDA.out.txt, [] ) ch_versions = ch_versions.mix(MIRANDA.out.versions) From 3d8b9eff13ea544ea3450089e30dcbc315c33285 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Sat, 22 Jun 2024 20:39:22 +0200 Subject: [PATCH 440/491] fixing filtering of mature --- subworkflows/local/mirna_prediction.nf | 101 +++++++++++++------------ 1 file changed, 54 insertions(+), 47 deletions(-) diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index 1121bb26..0ca665ac 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -29,58 +29,65 @@ workflow MIRNA_PREDICTION { // MIRNA NORMALIZATION WORKFLOW: // - ch_mirna_normalized = DESEQ2_NORMALIZATION( ch_mirna ).normalized + if (params.mirna_expression) { + + ch_mirna_normalized = DESEQ2_NORMALIZATION( ch_mirna ).normalized + + ch_versions = ch_versions.mix(DESEQ2_NORMALIZATION.out.versions) + + ch_mirna_filtered = MIRNA_FILTERING(ch_mirna_normalized, + params.mirna_min_sample_percentage, + params.mirna_min_reads + ).filtered + + ch_versions = ch_versions.mix(MIRNA_FILTERING.out.versions) + + // + // MIRNA BINDING SITES: + // + + // Filtering miRNAs from ch_mature if they are not in ch_mirna_filtered. + ch_uniq_mirnas = ch_mirna_filtered.map{ meta, path -> path }.splitCsv( sep: '\t' ).map{ it[0] }.unique().collect() + + ch_mature = ch_mature + .map{ meta, path -> + path + } + .splitFasta( record: [id:true, seqString:true] ) + .combine(ch_uniq_mirnas.map{ it -> [it]}) // Not sure why this mapping is necessary but I think it is + .filter{ record, mirnas -> + ch_uniq_mirnas.contains(record.id).value + }.map{ record, mirnas -> + ">${record.id}\n${record.seqString}" + } + .collectFile( name: 'mature_filtered.fa', newLine: true) + ch_mature = ch_mature.map{ it -> [[id: 'mature_filtered'], it]} + } - ch_versions = ch_versions.mix(DESEQ2_NORMALIZATION.out.versions) - ch_mirna_filtered = MIRNA_FILTERING(ch_mirna_normalized, - params.mirna_min_sample_percentage, - params.mirna_min_reads - ).filtered - - ch_versions = ch_versions.mix(MIRNA_FILTERING.out.versions) - - // - // MIRNA BINDING SITES: - // - - // Filtering miRNAs from ch_mature if they are not in ch_mirna_filtered. - ch_uniq_mirnas = ch_mirna_filtered.map{ meta, path -> path }.splitCsv( sep: '\t' ).map{ it[0] }.unique().collect() - ch_mature_filtered = ch_mature - .map{ meta, path -> - path - } - .splitFasta( record: [id:true, seqString:true] ) - .combine(ch_uniq_mirnas.map{ it -> [it]}) // Not sure why this mapping is necessary but I think it is - .filter{ record, mirnas -> - ch_uniq_mirnas.contains(record.id) - }.map{ record, mirnas -> - ">${record.id}\n${record.seqString}" - } - .collectFile( name: 'mature_filtered.fa', newLine: true) - ch_mature_filtered = ch_mature_filtered.map{ it -> [[id: 'mature_filtered'], it]} - - MIRNA_BINDINGSITES( transcriptome_fasta, circrna_bed12, ch_mature_filtered ) + MIRNA_BINDINGSITES( transcriptome_fasta, circrna_bed12, ch_mature ) ch_versions = ch_versions.mix(MIRNA_BINDINGSITES.out.versions) - // - // COMPUTE CORRELATION: - // - - ch_binding_site_batches = MIRNA_BINDINGSITES.out.binding_sites - .splitText(by: 100, file: true) - .map{ meta, file -> [[id: "batch_" + file.baseName.split("\\.").last()], file]} - - COMPUTE_CORRELATIONS( ch_binding_site_batches, - ch_mirna_filtered, - quantification_rds ) - - ch_correlation_results = COMPUTE_CORRELATIONS.out.correlations - .map{meta, results -> results} - .flatten().collect() - .map{results -> [[id: 'correlation'], results]} + if (params.mirna_expression) { + // + // COMPUTE CORRELATION: + // + ch_binding_site_batches = MIRNA_BINDINGSITES.out.binding_sites + .splitText(by: 100, file: true) + .map{ meta, file -> [[id: "batch_" + file.baseName.split("\\.").last()], file]} + + COMPUTE_CORRELATIONS( ch_binding_site_batches, + ch_mirna_filtered, + quantification_rds ) + + ch_correlation_results = COMPUTE_CORRELATIONS.out.correlations + .map{meta, results -> results} + .flatten().collect() + .map{results -> [[id: 'correlation'], results]} + + ch_versions = ch_versions.mix(COMPUTE_CORRELATIONS.out.versions) + } - ch_versions = ch_versions.mix(COMPUTE_CORRELATIONS.out.versions) emit: versions = ch_versions From d9619dc27ae942aede7a4114cfa692d129f7c4db Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Sat, 22 Jun 2024 20:39:54 +0200 Subject: [PATCH 441/491] Cleaning up --- nextflow.config | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nextflow.config b/nextflow.config index 3790a3bb..152873f7 100644 --- a/nextflow.config +++ b/nextflow.config @@ -65,12 +65,12 @@ params { //> Quantification bootstrap_samples = 30 - //> MIRNA processing + //> MIRNA processing mirna_expression = null - mirna_min_reads = 5 + mirna_min_reads = 1 mirna_min_sample_percentage = 0.2 - mirna_tools = 'miranda, targetscan' - mirna_vote = 1 + mirna_tools = 'miranda, targetscan' + mirna_vote = 1 //> MISC save_unaligned = false From d87def8a6eb099b548308576cbae47a66df4f01d Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Sat, 22 Jun 2024 21:12:21 +0200 Subject: [PATCH 442/491] Adding param to switch between spearman and pearson correlation --- .../templates/compute_correlations.R | 23 ++++++++++++------- nextflow.config | 2 ++ nextflow_schema.json | 12 ++++++++-- 3 files changed, 27 insertions(+), 10 deletions(-) diff --git a/modules/local/compute_correlations/templates/compute_correlations.R b/modules/local/compute_correlations/templates/compute_correlations.R index 5f0d8db0..78c05e53 100644 --- a/modules/local/compute_correlations/templates/compute_correlations.R +++ b/modules/local/compute_correlations/templates/compute_correlations.R @@ -7,6 +7,13 @@ tx_expression <- readRDS('${transcript_rds}') mi_expression <- read.table('${mirna_expression}', header=TRUE, row.names=1, sep='\\t') interactions <- read.table('${bindingsites}', sep='\\t') +tx_expression <- scaleInfReps(tx_expression) +tx_expression <- labelKeep(tx_expression) # Here one can perform custom filtering + +if (!any(mcols(tx_expression)\$keep)) { + stop('No transcripts left after filtering') +} + result_cols <- c('stat', 'log2FC', 'pvalue', 'locfdr', 'qvalue') # Iterate rows of interactions @@ -15,16 +22,14 @@ for (i in 1:nrow(interactions)) { miRNA <- interactions[i, 1] targets <- unlist(strsplit(interactions[i, 2], ',')) - # TODO: Remove this check after making sure that lowly expressed miRNAs - # are filtered out before binding site detection - if (!miRNA %in% rownames(mi_expression)) { - print(paste('miRNA', miRNA, 'not found')) - next - } - mirna_expression <- mi_expression[miRNA,] transcript_expression <- tx_expression[targets,] + if (!any(mcols(transcript_expression)\$keep)) { + print(paste('No transcripts left after filtering for miRNA', miRNA)) + next + } + # Add miRNA expression to colData so that it can be used for correlation colData(transcript_expression) <- cbind( colData(transcript_expression), @@ -32,8 +37,10 @@ for (i in 1:nrow(interactions)) { ) # TODO: Allow setting "spearman" - result <- rowData(swish(transcript_expression, miRNA, cor = "pearson"))[, result_cols] + result <- rowData(swish(transcript_expression, miRNA, cor = "${params.mirna_correlation}"))[, result_cols] # TODO: Find out why NaN rows occur + # NaNs occur whenever mcols(transcript_expression)\$keep is false + # Because in this case the corresponding entry is ignored result <- result[complete.cases(result), ] write.table(result, paste0(miRNA, '.tsv'), sep = '\\t') } diff --git a/nextflow.config b/nextflow.config index 152873f7..d4062a9e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -71,6 +71,8 @@ params { mirna_min_sample_percentage = 0.2 mirna_tools = 'miranda, targetscan' mirna_vote = 1 + mirna_correlation = 'pearson' + //> MISC save_unaligned = false diff --git a/nextflow_schema.json b/nextflow_schema.json index e266c70a..10d9ca4e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -66,8 +66,8 @@ "format": "file-path", "exists": true, "mimetype": "text/tsv", - "pattern": "^\\S+\\.tsv$", - "description": "Path to tab-separated file providing the expression counts of miRNAs, which are created in pipeline 'smrnaseq'. \n\nmirna \t sample1 \t sample2 \t sample3 \t\nid1\t count_sample1 \t count_sample2 \t count_sample3 \t\nid2 \t ... \t ... \t ... \t \n", + "pattern": "^\\s+\\.tsv$", + "description": "path to tab-separated file providing the expression counts of mirnas, which are created in pipeline 'smrnaseq'. \n\nmirna \t sample1 \t sample2 \t sample3 \t\nid1\t count_sample1 \t count_sample2 \t count_sample3 \t\nid2 \t ... \t ... \t ... \t \n", "fa_icon": "fas fa-file-tsv" }, "mirna_min_sample_percentage": { @@ -85,6 +85,14 @@ "help_text": "This parameter determines the minimum number of reads that a miRNA must have to pass filtering. The default is 5, meaning a miRNA must have at least 5 reads across the samples to be considered for analysis.", "default": 5, "minimum": 0 + }, + "mirna_correlation": { + "type": "string", + "fa_icon": "fas fa-wrench", + "description": "Specifies the type of correlation to be used when analyzing the relationship between miRNA and transcript expression levels. Valid options are 'pearson' or 'spearman'.", + "help_text": "Select the correlation method to be applied in the correlation analysis of miRNAs.", + "default": "pearson", + "pattern": "^(pearson|spearman)$" } } }, From bd5345ecefb27a26e9099575b1edfbc03a1e7175 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Sun, 23 Jun 2024 18:22:42 +0200 Subject: [PATCH 443/491] More resources for MAJORITY_VOTE --- modules/local/majority_vote/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/majority_vote/main.nf b/modules/local/majority_vote/main.nf index 8ed51f0a..7b58a67f 100644 --- a/modules/local/majority_vote/main.nf +++ b/modules/local/majority_vote/main.nf @@ -1,6 +1,6 @@ process MAJORITY_VOTE { tag "$meta.id" - label 'process_single' + label 'process_medium' conda "bioconda::pandas=1.5.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? From fbc094a40ac69839c7396caae8ba2d34f5bb8ecd Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Sun, 23 Jun 2024 18:23:12 +0200 Subject: [PATCH 444/491] removing todo comment --- .../local/compute_correlations/templates/compute_correlations.R | 1 - 1 file changed, 1 deletion(-) diff --git a/modules/local/compute_correlations/templates/compute_correlations.R b/modules/local/compute_correlations/templates/compute_correlations.R index 78c05e53..c3cb8ec6 100644 --- a/modules/local/compute_correlations/templates/compute_correlations.R +++ b/modules/local/compute_correlations/templates/compute_correlations.R @@ -36,7 +36,6 @@ for (i in 1:nrow(interactions)) { t(mirna_expression[, rownames(colData(transcript_expression))]) ) - # TODO: Allow setting "spearman" result <- rowData(swish(transcript_expression, miRNA, cor = "${params.mirna_correlation}"))[, result_cols] # TODO: Find out why NaN rows occur # NaNs occur whenever mcols(transcript_expression)\$keep is false From b5adea20851c3dffc190a136729ee65ec5cd5203 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Tue, 25 Jun 2024 22:44:00 +0200 Subject: [PATCH 445/491] removing TODO comment --- .../compute_correlations/templates/compute_correlations.R | 3 --- 1 file changed, 3 deletions(-) diff --git a/modules/local/compute_correlations/templates/compute_correlations.R b/modules/local/compute_correlations/templates/compute_correlations.R index c3cb8ec6..e60ccc73 100644 --- a/modules/local/compute_correlations/templates/compute_correlations.R +++ b/modules/local/compute_correlations/templates/compute_correlations.R @@ -37,9 +37,6 @@ for (i in 1:nrow(interactions)) { ) result <- rowData(swish(transcript_expression, miRNA, cor = "${params.mirna_correlation}"))[, result_cols] - # TODO: Find out why NaN rows occur - # NaNs occur whenever mcols(transcript_expression)\$keep is false - # Because in this case the corresponding entry is ignored result <- result[complete.cases(result), ] write.table(result, paste0(miRNA, '.tsv'), sep = '\\t') } From ff1edcfffc1762c3ecc5d2f45e5fa8c0a5a29a4f Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Tue, 25 Jun 2024 22:44:37 +0200 Subject: [PATCH 446/491] correlations output set to optional --- modules/local/compute_correlations/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/compute_correlations/main.nf b/modules/local/compute_correlations/main.nf index 25172c7a..773fddae 100644 --- a/modules/local/compute_correlations/main.nf +++ b/modules/local/compute_correlations/main.nf @@ -13,7 +13,7 @@ process COMPUTE_CORRELATIONS { tuple val(meta3), path(transcript_rds) output: - tuple val(meta), path("*.tsv"), emit: correlations + tuple val(meta), path("*.tsv"), emit: correlations, optional: true path "versions.yml" , emit: versions when: From 1e8b04f9f9bf44be8fc7ad4502063b994d92b567 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sun, 4 Aug 2024 22:43:46 +0200 Subject: [PATCH 447/491] Fix major rebase problems --- main.nf | 4 +--- subworkflows/local/mirna_prediction.nf | 10 ++++------ workflows/circrna/main.nf | 10 +++++----- 3 files changed, 10 insertions(+), 14 deletions(-) diff --git a/main.nf b/main.nf index 94437354..b5a47b01 100644 --- a/main.nf +++ b/main.nf @@ -57,9 +57,8 @@ workflow NFCORE_CIRCRNA { ch_samplesheet = Channel.fromSamplesheet("input") ch_fasta = Channel.value([[id: "fasta"], file(params.fasta, checkIfExists:true)]) ch_gtf = Channel.value([[id: "gtf"], file(params.gtf, checkIfExists:true)]) - ch_mature = params.module.split(',').contains('mirna_prediction') ? Channel.value([[id: "mature"], file(params.mature, checkIfExists:true)]) : Channel.empty() + ch_mature = params.mature ? Channel.value([[id: "mature"], file(params.mature, checkIfExists:true)]) : Channel.empty() ch_phenotype = params.phenotype ? Channel.value([[id: "phenotype"], file(params.phenotype, checkIfExists:true)]) : Channel.empty() - ch_species = params.phenotype ? Channel.value(params.species_id) : Channel.empty() ch_annotation = params.annotation ? Channel.fromSamplesheet("annotation") : Channel.empty() ch_mirna = params.mature ? Channel.value([[id: "mirna"], file(params.mirna_expression, checkIfExists:true)]) : Channel.empty() @@ -70,7 +69,6 @@ workflow NFCORE_CIRCRNA { ch_gtf, ch_mature, ch_annotation, - ch_species, ch_versions, ch_mirna ) diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index 0ca665ac..9f8425d1 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -1,4 +1,5 @@ // MODULES +include { BIOAWK as ADD_BACKSPLICE } from '../../modules/nf-core/bioawk' include { DESEQ2_NORMALIZATION } from '../../modules/local/deseq2/normalization' include { MIRNA_FILTERING } from '../../modules/local/mirna_filtering' include { COMPUTE_CORRELATIONS } from '../../modules/local/compute_correlations' @@ -10,7 +11,7 @@ workflow MIRNA_PREDICTION { take: transcriptome_fasta - circrna_bed12 + circrna_annotation ch_mature ch_mirna transcript_counts @@ -19,10 +20,7 @@ workflow MIRNA_PREDICTION { main: ch_versions = Channel.empty() - MIRNA_BINDINGSITES( transcriptome_fasta, circrna_bed12, ch_mature ) - ch_versions = ch_versions.mix(MIRNA_BINDINGSITES.out.versions) - - ADD_BACKSPLICE( circrna_fasta, [] ) + ADD_BACKSPLICE( transcriptome_fasta, [] ) ch_versions = ch_versions.mix(ADD_BACKSPLICE.out.versions) // @@ -65,7 +63,7 @@ workflow MIRNA_PREDICTION { } - MIRNA_BINDINGSITES( transcriptome_fasta, circrna_bed12, ch_mature ) + MIRNA_BINDINGSITES( transcriptome_fasta, circrna_annotation, ch_mature ) ch_versions = ch_versions.mix(MIRNA_BINDINGSITES.out.versions) if (params.mirna_expression) { diff --git a/workflows/circrna/main.nf b/workflows/circrna/main.nf index cf2abf1e..048b4da3 100644 --- a/workflows/circrna/main.nf +++ b/workflows/circrna/main.nf @@ -177,11 +177,11 @@ workflow CIRCRNA { if (params.mature) { MIRNA_PREDICTION( - BSJ_DETECTION.out.fasta, - BSJ_DETECTION.out.bed, - ch_mature - ch_mirna - QUANTIFICATION.out.circular_tx_counts + QUANTIFICATION.out.transcriptome, + BSJ_DETECTION.out.bed12, + ch_mature, + ch_mirna, + QUANTIFICATION.out.circular_tx_counts, QUANTIFICATION.out.rds ) ch_versions = ch_versions.mix(MIRNA_PREDICTION.out.versions) From cdb265ef5b5dc67890f054a820a3a307f2e387f8 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sun, 4 Aug 2024 22:57:19 +0200 Subject: [PATCH 448/491] Fix small bug with backsplice junction adding --- subworkflows/local/mirna_prediction.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index 9f8425d1..be598045 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -20,7 +20,7 @@ workflow MIRNA_PREDICTION { main: ch_versions = Channel.empty() - ADD_BACKSPLICE( transcriptome_fasta, [] ) + ADD_BACKSPLICE( transcriptome_fasta ) ch_versions = ch_versions.mix(ADD_BACKSPLICE.out.versions) // From abac8e292a2e6ef2c2b13982e0c9cc3ddfe8c059 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sun, 4 Aug 2024 23:17:57 +0200 Subject: [PATCH 449/491] Improve mirna prediction formatting --- subworkflows/local/mirna_prediction.nf | 28 +++++++++++--------------- 1 file changed, 12 insertions(+), 16 deletions(-) diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index be598045..117701c8 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -20,9 +20,6 @@ workflow MIRNA_PREDICTION { main: ch_versions = Channel.empty() - ADD_BACKSPLICE( transcriptome_fasta ) - ch_versions = ch_versions.mix(ADD_BACKSPLICE.out.versions) - // // MIRNA NORMALIZATION WORKFLOW: // @@ -48,21 +45,20 @@ workflow MIRNA_PREDICTION { ch_uniq_mirnas = ch_mirna_filtered.map{ meta, path -> path }.splitCsv( sep: '\t' ).map{ it[0] }.unique().collect() ch_mature = ch_mature - .map{ meta, path -> - path - } - .splitFasta( record: [id:true, seqString:true] ) - .combine(ch_uniq_mirnas.map{ it -> [it]}) // Not sure why this mapping is necessary but I think it is - .filter{ record, mirnas -> - ch_uniq_mirnas.contains(record.id).value - }.map{ record, mirnas -> - ">${record.id}\n${record.seqString}" - } - .collectFile( name: 'mature_filtered.fa', newLine: true) - ch_mature = ch_mature.map{ it -> [[id: 'mature_filtered'], it]} + .map{ meta, path -> + path + } + .splitFasta( record: [id:true, seqString:true] ) + .combine(ch_uniq_mirnas.map{ it -> [it]}) // Not sure why this mapping is necessary but I think it is + .filter{ record, mirnas -> + ch_uniq_mirnas.contains(record.id).value + }.map{ record, mirnas -> + ">${record.id}\n${record.seqString}" + } + .collectFile( name: 'mature_filtered.fa', newLine: true) + .map{ it -> [[id: 'mature_filtered'], it]} } - MIRNA_BINDINGSITES( transcriptome_fasta, circrna_annotation, ch_mature ) ch_versions = ch_versions.mix(MIRNA_BINDINGSITES.out.versions) From f3a6233cb93b33da62e39076b90276e89451d9b1 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Sun, 4 Aug 2024 23:58:38 +0200 Subject: [PATCH 450/491] Improve output structure for mirna prediction --- conf/modules.config | 56 ++++++++++++++++++++++++-- subworkflows/local/mirna_prediction.nf | 1 - 2 files changed, 53 insertions(+), 4 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 61492e6a..9f09196f 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -816,11 +816,21 @@ process { withName: UNIFY_MIRANDA { ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { print \$1, \$2, \$7, \$8, \"miranda\" }'" ext.suffix = "miranda.tsv" + publishDir = [ + path: { "${params.outdir}/mirna_prediction/binding_sites/tools/miranda/unified" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + ] } withName: UNIFY_TARGETSCAN { ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { print \$2, \$1, \$6, \$7, \"targetscan\" }'" ext.suffix = "targetscan.tsv" + publishDir = [ + path: { "${params.outdir}/mirna_prediction/binding_sites/tools/targetscan/unified" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + ] } withName: COMBINE_BINDINGSITES { @@ -940,6 +950,22 @@ process { ] } + withName: '.*:MIRNA_PREDICTION:DESEQ2_NORMALIZATION' { + publishDir = [ + path: { "${params.outdir}/mirna_prediction/mirna_expression" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + ] + } + + withName: '.*:MIRNA_PREDICTION:MIRNA_FILTERING' { + publishDir = [ + path: { "${params.outdir}/mirna_prediction/mirna_expression" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + ] + } + withName: TARGETSCAN_DATABASE { publishDir = [ path: { "${params.outdir}/references/mirna_prediction/targetscan" }, @@ -952,7 +978,7 @@ process { withName: TARGETSCAN { ext.prefix = { "${meta.id}.targetscan" } publishDir = [ - path: { "${params.outdir}/mirna_prediction/targetscan" }, + path: { "${params.outdir}/mirna_prediction/binding_sites/tools/targetscan/output" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.txt" @@ -963,7 +989,7 @@ process { ext.prefix = { "${meta.id}.miranda" } ext.args = "-strict" publishDir = [ - path: { "${params.outdir}/mirna_prediction/miranda" }, + path: { "${params.outdir}/mirna_prediction/binding_sites/tools/miranda/output" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.txt" @@ -972,13 +998,37 @@ process { withName: MIRNA_TARGETS { publishDir = [ - path: { "${params.outdir}/mirna_prediction/combined" }, + path: { "${params.outdir}/mirna_prediction/binding_sites/targets" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, pattern: "*.txt" ] } + withName: COMBINE_BINDINGSITES { + publishDir = [ + path: { "${params.outdir}/mirna_prediction/binding_sites/majority_vote" }, + mode: params.publish_dir_mode, + saveAs: { filename -> ( filename != 'versions.yml' && params.save_intermediates ) ? filename : null } + ] + } + + withName: MAJORITY_VOTE { + publishDir = [ + path: { "${params.outdir}/mirna_prediction/binding_sites/majority_vote" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + ] + } + + withName: '.*:MIRNA_PREDICTION:COMPUTE_CORRELATIONS' { + publishDir = [ + path: { "${params.outdir}/mirna_prediction/correlation" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + ] + } + withName: CIRCTEST_PREPARE { publishDir = [ path: { "${params.outdir}/statistical_tests/circtest" }, diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index 117701c8..48c64fbe 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -82,7 +82,6 @@ workflow MIRNA_PREDICTION { ch_versions = ch_versions.mix(COMPUTE_CORRELATIONS.out.versions) } - emit: versions = ch_versions } From 2b28c808ab864165cd6d0b93e48bdfb18b0b850d Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Tue, 6 Aug 2024 16:41:36 +0200 Subject: [PATCH 451/491] fixing formatting in modules --- modules.json | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/modules.json b/modules.json index b0cd0057..35714771 100644 --- a/modules.json +++ b/modules.json @@ -15,7 +15,9 @@ "bedtools/groupby": { "branch": "master", "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/intersect": { "branch": "master", @@ -126,7 +128,9 @@ "custom/gtffilter": { "branch": "master", "git_sha": "a0aee18374b7f072aa0f89f4d66f5a3a9f8176d2", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/tx2gene": { "branch": "master", @@ -335,4 +339,4 @@ } } } -} +} \ No newline at end of file From 86c7958a30da3ac08b09bb0d330230c124935bc9 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Tue, 6 Aug 2024 16:41:54 +0200 Subject: [PATCH 452/491] adjusting mirna_min_reads to match nextflow_schema --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index d4062a9e..21270121 100644 --- a/nextflow.config +++ b/nextflow.config @@ -67,7 +67,7 @@ params { //> MIRNA processing mirna_expression = null - mirna_min_reads = 1 + mirna_min_reads = 5 mirna_min_sample_percentage = 0.2 mirna_tools = 'miranda, targetscan' mirna_vote = 1 From 3ddfe3e56c1e3924111bc5a8330714679ca89080 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Tue, 6 Aug 2024 16:45:00 +0200 Subject: [PATCH 453/491] fixing formatting and adding missing allOf field for mirna_processing_options --- nextflow_schema.json | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 10d9ca4e..21f3dfb1 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -151,7 +151,7 @@ "mirna_vote": { "type": "integer", "fa_icon": "fas fa-intersection", - "description": "Specify the number of votes required for a miRNA to be further considered in downstream analysis.'", + "description": "Specify the number of votes required for a miRNA to be further considered in downstream analysis.'", "help_text": "Controls the number of votes required for a binding site prediction to be considered valid. If a miRNA binding site was predicted by two different tools (e.g., miRanda and TargetScan), it receives two votes. By specifying additional tools for miRNA binding site prediction (using the 'mirna_tools' parameter), you can adjust the number of votes required for a binding site to be considered valid.", "default": 1, "minimum": 1, @@ -614,6 +614,9 @@ { "$ref": "#/definitions/discovery_options" }, + { + "$ref": "#/definitions/mirna_processing_options" + }, { "$ref": "#/definitions/institutional_config_options" }, From 45dd40741c855e53259ef4397d85feb7673c2242 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Tue, 6 Aug 2024 17:03:55 +0200 Subject: [PATCH 454/491] removing non used configs in modules.config --- conf/modules.config | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 9f09196f..4f6fea71 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -804,15 +804,6 @@ process { ] } - withName: COUNTS_COMBINED { - ext.when = { params.module.split(',').contains('circrna_discovery') } - } - - withName: COUNTS_TO_BED { - ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { print \$1, \$2, \$3, \$1 \":\" \$2 \"-\" \$3, \".\", \".\" }'" - ext.suffix = "bed" - } - withName: UNIFY_MIRANDA { ext.args = "-v FS='\\t' -v OFS='\\t' 'NR>1 { print \$1, \$2, \$7, \$8, \"miranda\" }'" ext.suffix = "miranda.tsv" @@ -837,11 +828,6 @@ process { ext.prefix = "bindingsites.tsv" } - withName: UNIQUE_REGIONS { - ext.args = "-k 1,1 -k2,2n -k3,3n -u" - ext.suffix = "unique.bed" - } - withName: COMBINE_TRANSCRIPTOME_GTFS { ext.args = "-k 1,1 -k4,4n -k5,5n" ext.suffix = "combined.gtf" From 4cbb345872ab8777f5b26f351f6982a201b680ed Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Tue, 6 Aug 2024 17:16:28 +0200 Subject: [PATCH 455/491] updating nf-core modules --- modules.json | 56 +- modules/nf-core/bioawk/main.nf | 11 +- modules/nf-core/bowtie/align/environment.yml | 1 + modules/nf-core/bowtie/align/main.nf | 35 +- modules/nf-core/bowtie/align/meta.yml | 21 +- .../nf-core/bowtie/align/tests/main.nf.test | 129 + .../bowtie/align/tests/main.nf.test.snap | 192 ++ modules/nf-core/bowtie/align/tests/tags.yml | 2 + modules/nf-core/bowtie/build/main.nf | 32 +- modules/nf-core/bowtie/build/meta.yml | 12 +- .../nf-core/bowtie/build/tests/main.nf.test | 57 + .../bowtie/build/tests/main.nf.test.snap | 96 + modules/nf-core/bowtie/build/tests/tags.yml | 2 + .../nf-core/bowtie2/align/tests/main.nf.test | 90 +- modules/nf-core/cat/cat/main.nf | 1 - modules/nf-core/cat/cat/tests/main.nf.test | 27 +- .../nf-core/cat/cat/tests/main.nf.test.snap | 74 +- modules/nf-core/cat/fastq/main.nf | 10 +- modules/nf-core/cat/fastq/tests/main.nf.test | 136 +- .../nf-core/cat/fastq/tests/main.nf.test.snap | 207 ++ .../templates/dumpsoftwareversions.py | 1 - .../custom/tx2gene/templates/tx2gene.py | 24 +- .../nf-core/custom/tx2gene/tests/main.nf.test | 45 +- .../custom/tx2gene/tests/main.nf.test.snap | 96 +- modules/nf-core/fastqc/tests/main.nf.test | 225 +- .../nf-core/fastqc/tests/main.nf.test.snap | 370 ++- modules/nf-core/hisat2/align/main.nf | 19 + .../nf-core/hisat2/align/tests/main.nf.test | 202 ++ .../hisat2/align/tests/main.nf.test.snap | 338 ++- modules/nf-core/hisat2/build/main.nf | 11 + .../nf-core/hisat2/build/tests/main.nf.test | 47 +- .../hisat2/build/tests/main.nf.test.snap | 66 +- .../nf-core/hisat2/extractsplicesites/main.nf | 11 + .../extractsplicesites/tests/main.nf.test | 26 + .../tests/main.nf.test.snap | 37 + modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 10 +- modules/nf-core/multiqc/meta.yml | 13 + modules/nf-core/multiqc/tests/main.nf.test | 6 + .../nf-core/multiqc/tests/main.nf.test.snap | 18 +- .../samtools/flagstat/tests/main.nf.test | 28 +- .../samtools/flagstat/tests/main.nf.test.snap | 78 +- .../samtools/idxstats/tests/main.nf.test | 29 +- .../samtools/idxstats/tests/main.nf.test.snap | 78 +- modules/nf-core/samtools/index/main.nf | 7 +- .../nf-core/samtools/index/tests/main.nf.test | 87 +- .../samtools/index/tests/main.nf.test.snap | 264 +- modules/nf-core/samtools/sort/main.nf | 14 +- .../nf-core/samtools/sort/tests/main.nf.test | 54 +- .../samtools/sort/tests/main.nf.test.snap | 202 +- .../samtools/sort/tests/nextflow_cram.config | 8 + .../nf-core/samtools/stats/tests/main.nf.test | 57 +- .../samtools/stats/tests/main.nf.test.snap | 82 +- modules/nf-core/samtools/view/main.nf | 40 +- modules/nf-core/samtools/view/meta.yml | 9 + .../nf-core/samtools/view/tests/main.nf.test | 2 + .../samtools/view/tests/main.nf.test.snap | 22 +- modules/nf-core/star/align/main.nf | 4 +- modules/nf-core/star/align/tests/main.nf.test | 523 +++- .../star/align/tests/main.nf.test.snap | 2288 +++++++++++++---- .../star/genomegenerate/tests/main.nf.test | 39 +- .../genomegenerate/tests/main.nf.test.snap | 182 +- .../stringtie/stringtie/tests/main.nf.test | 139 +- .../stringtie/tests/main.nf.test.snap | 504 +++- modules/nf-core/trimgalore/main.nf | 21 + modules/nf-core/trimgalore/tests/main.nf.test | 47 + .../trimgalore/tests/main.nf.test.snap | 154 ++ 67 files changed, 6315 insertions(+), 1405 deletions(-) create mode 100644 modules/nf-core/bowtie/align/tests/main.nf.test create mode 100644 modules/nf-core/bowtie/align/tests/main.nf.test.snap create mode 100644 modules/nf-core/bowtie/align/tests/tags.yml create mode 100644 modules/nf-core/bowtie/build/tests/main.nf.test create mode 100644 modules/nf-core/bowtie/build/tests/main.nf.test.snap create mode 100644 modules/nf-core/bowtie/build/tests/tags.yml create mode 100644 modules/nf-core/samtools/sort/tests/nextflow_cram.config diff --git a/modules.json b/modules.json index 35714771..6b2ae568 100644 --- a/modules.json +++ b/modules.json @@ -35,7 +35,7 @@ }, "bioawk": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "dee3479f3b4a828df6052d318403d2b6a87b2d2e", "installed_by": [ "modules" ], @@ -43,21 +43,21 @@ }, "bowtie/align": { "branch": "master", - "git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde", + "git_sha": "54381508775905f1ecd4fc0dea3fc2f07c78d1c6", "installed_by": [ "modules" ] }, "bowtie/build": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "54381508775905f1ecd4fc0dea3fc2f07c78d1c6", "installed_by": [ "modules" ] }, "bowtie2/align": { "branch": "master", - "git_sha": "e4bad511789f16d0df39ee306b2cd50418365048", + "git_sha": "9bfc81874554e87740bcb3e5e07acf0a153c9ecb", "installed_by": [ "modules" ] @@ -71,21 +71,21 @@ }, "bwa/index": { "branch": "master", - "git_sha": "086fa66260595e123b0ea47a6512539b72a9afa3", + "git_sha": "e0ff65e1fb313677de09f5f477ae3da30ce19b7b", "installed_by": [ "modules" ] }, "cat/cat": { "branch": "master", - "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8", + "git_sha": "5bb8ca085e17549e185e1823495ab8d20727a805", "installed_by": [ "modules" ] }, "cat/fastq": { "branch": "master", - "git_sha": "4fc983ad0b30e6e32696fa7d980c76c7bfe1c03e", + "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7", "installed_by": [ "modules" ] @@ -120,7 +120,7 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "de45447d060b8c8b98575bc637a4a575fd0638e1", + "git_sha": "82024cf6325d2ee194e7f056d841ecad2f6856e9", "installed_by": [ "modules" ] @@ -134,14 +134,14 @@ }, "custom/tx2gene": { "branch": "master", - "git_sha": "ec155021a9104441bf6a9bae3b55d1b5b0bfdb3a", + "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", "installed_by": [ "modules" ] }, "fastqc": { "branch": "master", - "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", + "git_sha": "46eca555142d6e597729fcb682adcc791796f514", "installed_by": [ "modules" ] @@ -155,28 +155,28 @@ }, "gnu/sort": { "branch": "master", - "git_sha": "ca199cfe5aa4f1ea3c41302158f0af2cfaa58957", + "git_sha": "a3cc42943548378b726610f45bb5a79ab3f0b633", "installed_by": [ "modules" ] }, "hisat2/align": { "branch": "master", - "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", + "git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f", "installed_by": [ "modules" ] }, "hisat2/build": { "branch": "master", - "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", + "git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f", "installed_by": [ "modules" ] }, "hisat2/extractsplicesites": { "branch": "master", - "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", + "git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f", "installed_by": [ "modules" ] @@ -190,35 +190,35 @@ }, "multiqc": { "branch": "master", - "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", + "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396", "installed_by": [ "modules" ] }, "samtools/faidx": { "branch": "master", - "git_sha": "f153f1f10e1083c49935565844cccb7453021682", + "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", "installed_by": [ "modules" ] }, "samtools/flagstat": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "46eca555142d6e597729fcb682adcc791796f514", "installed_by": [ "bam_stats_samtools" ] }, "samtools/idxstats": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "46eca555142d6e597729fcb682adcc791796f514", "installed_by": [ "bam_stats_samtools" ] }, "samtools/index": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "46eca555142d6e597729fcb682adcc791796f514", "installed_by": [ "bam_sort_stats_samtools", "modules" @@ -226,7 +226,7 @@ }, "samtools/sort": { "branch": "master", - "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", + "git_sha": "46eca555142d6e597729fcb682adcc791796f514", "installed_by": [ "bam_sort_stats_samtools", "modules" @@ -234,14 +234,14 @@ }, "samtools/stats": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "46eca555142d6e597729fcb682adcc791796f514", "installed_by": [ "bam_stats_samtools" ] }, "samtools/view": { "branch": "master", - "git_sha": "0bd7d2333a88483aa0476acea172e9f5f6dd83bb", + "git_sha": "6c2309aaec566c0d44a6cf14d4b2d0c51afe2e91", "installed_by": [ "modules" ] @@ -262,28 +262,28 @@ }, "star/align": { "branch": "master", - "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", + "git_sha": "46eca555142d6e597729fcb682adcc791796f514", "installed_by": [ "modules" ] }, "star/genomegenerate": { "branch": "master", - "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", + "git_sha": "46eca555142d6e597729fcb682adcc791796f514", "installed_by": [ "modules" ] }, "stringtie/stringtie": { "branch": "master", - "git_sha": "b1b959609bda44341120aed1766329909f54b8d0", + "git_sha": "c789476080a150f87066ca3ed42a622339a26c0b", "installed_by": [ "modules" ] }, "trimgalore": { "branch": "master", - "git_sha": "a98418419ae6c9df3cf6cf108d1e1aba71037d5a", + "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1", "installed_by": [ "modules" ] @@ -301,14 +301,14 @@ "nf-core": { "bam_sort_stats_samtools": { "branch": "master", - "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", + "git_sha": "46eca555142d6e597729fcb682adcc791796f514", "installed_by": [ "subworkflows" ] }, "bam_stats_samtools": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab", "installed_by": [ "bam_sort_stats_samtools", "subworkflows" diff --git a/modules/nf-core/bioawk/main.nf b/modules/nf-core/bioawk/main.nf index 0fded517..a537dcf4 100644 --- a/modules/nf-core/bioawk/main.nf +++ b/modules/nf-core/bioawk/main.nf @@ -11,8 +11,8 @@ process BIOAWK { tuple val(meta), path(input) output: - tuple val(meta), path("${prefix}.${suffix}"), emit: output - path "versions.yml" , emit: versions + tuple val(meta), path("*.gz"), emit: output + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -20,14 +20,15 @@ process BIOAWK { script: def args = task.ext.args ?: '' // args is used for the main arguments of the tool prefix = task.ext.prefix ?: "${meta.id}" - suffix = task.ext.suffix ?: input.extension - + if ("${input}" == "${prefix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" def VERSION = '1.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ bioawk \\ $args \\ $input \\ - > ${prefix}.${suffix} + > ${prefix} + + gzip ${prefix} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bowtie/align/environment.yml b/modules/nf-core/bowtie/align/environment.yml index 2617e6f0..fb5d7c1e 100644 --- a/modules/nf-core/bowtie/align/environment.yml +++ b/modules/nf-core/bowtie/align/environment.yml @@ -5,3 +5,4 @@ channels: - defaults dependencies: - bioconda::bowtie=1.3.0 + - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index 29e9cd53..5e72b02a 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -9,13 +9,14 @@ process BOWTIE_ALIGN { input: tuple val(meta), path(reads) - path index + tuple val(meta2), path(index) + val (save_unaligned) output: - tuple val(meta), path('*.bam'), emit: bam - tuple val(meta), path('*.out'), emit: log - path "versions.yml" , emit: versions - tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq + tuple val(meta), path('*.bam') , emit: bam + tuple val(meta), path('*.out') , emit: log + tuple val(meta), path('*fastq.gz') , emit: fastq, optional : true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -24,10 +25,10 @@ process BOWTIE_ALIGN { def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped.fastq" : '' + def unaligned = save_unaligned ? "--un ${prefix}.unmapped.fastq" : '' def endedness = meta.single_end ? "$reads" : "-1 ${reads[0]} -2 ${reads[1]}" """ - INDEX=`find -L ./ -name "*.3.ebwt" | sed 's/\\.3.ebwt\$//'` + INDEX=\$(find -L ./ -name "*.3.ebwt" | sed 's/\\.3.ebwt\$//') bowtie \\ --threads $task.cpus \\ --sam \\ @@ -53,4 +54,24 @@ process BOWTIE_ALIGN { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def unaligned = save_unaligned ? + meta.single_end ? "echo '' | gzip > ${prefix}.unmapped.fastq.gz" : + "echo '' | gzip > ${prefix}.unmapped_1.fastq.gz; echo '' | gzip > ${prefix}.unmapped_2.fastq.gz" + : '' + """ + touch ${prefix}.bam + touch ${prefix}.out + $unaligned + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bowtie: \$(echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//') + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ + + } diff --git a/modules/nf-core/bowtie/align/meta.yml b/modules/nf-core/bowtie/align/meta.yml index 89eaedd6..7c7e8237 100644 --- a/modules/nf-core/bowtie/align/meta.yml +++ b/modules/nf-core/bowtie/align/meta.yml @@ -27,23 +27,36 @@ input: description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. + - meta2: + type: map + description: | + Groovy Map containing genome information + e.g. [ id:'sarscov2' ] - index: type: file description: Bowtie genome index files pattern: "*.ebwt" + - save_unaligned: + type: boolean + description: Whether to save fastq files containing the reads which did not align. output: - bam: type: file description: Output BAM file containing read alignments pattern: "*.{bam}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: type: file description: Unaligned FastQ files pattern: "*.fastq.gz" + - log: + type: file + description: Log file + pattern: "*.log" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + authors: - "@kevinmenden" maintainers: diff --git a/modules/nf-core/bowtie/align/tests/main.nf.test b/modules/nf-core/bowtie/align/tests/main.nf.test new file mode 100644 index 00000000..3403ae22 --- /dev/null +++ b/modules/nf-core/bowtie/align/tests/main.nf.test @@ -0,0 +1,129 @@ +nextflow_process { + + name "Test Process BOWTIE_ALIGN" + script "../main.nf" + process "BOWTIE_ALIGN" + + tag "modules" + tag "modules_nfcore" + tag "bowtie" + tag "bowtie/align" + tag "bowtie/build" + + + setup { + run("BOWTIE_BUILD") { + script "../../../bowtie/build/main.nf" + process { + """ + input[0] = [[ id:'sarscov2' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + """ + } + } + } + + test("sarscov2 - single_end") { + + when { + process { + """ + input[0] = [ [id:"test", single_end:true], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + input[1] = BOWTIE_BUILD.out.index + input[2] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions, + process.out.bam.collect { bam(it[1]).getReadsMD5() }, + process.out.fastq, + process.out.log + ).match() } + ) + } + + } + + test("sarscov2 - single_end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [id:"test", single_end:true], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + input[1] = BOWTIE_BUILD.out.index + input[2] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - paired_end") { + + when { + process { + """ + input[0] = [ [id:"test", single_end:false], + [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ] + input[1] = BOWTIE_BUILD.out.index + input[2] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions, + process.out.bam.collect { bam(it[1]).getReads(2) }, + process.out.log + ).match() } + ) + } + + } + + test("sarscov2 - paired_end - stub") { + + options "-stub" + when { + process { + """ + input[0] = [ [id:"test", single_end:false], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + input[1] = BOWTIE_BUILD.out.index + input[2] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/bowtie/align/tests/main.nf.test.snap b/modules/nf-core/bowtie/align/tests/main.nf.test.snap new file mode 100644 index 00000000..de95bb81 --- /dev/null +++ b/modules/nf-core/bowtie/align/tests/main.nf.test.snap @@ -0,0 +1,192 @@ +{ + "sarscov2 - single_end": { + "content": [ + [ + "versions.yml:md5,96e36b0b99c80da0be8239d03db30ecc" + ], + [ + "7bdcfc6f54ae6e8f4570395cc85db9a3" + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.unmapped.fastq.gz:md5,5729a694abd09657da3b9101861090c4" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.out:md5,4b9140ceadb8a18ae9330885370f8a0b" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-26T09:25:24.60746041" + }, + "sarscov2 - single_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": true + }, + "test.unmapped.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "3": [ + "versions.yml:md5,96e36b0b99c80da0be8239d03db30ecc" + ], + "bam": [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fastq": [ + [ + { + "id": "test", + "single_end": true + }, + "test.unmapped.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "log": [ + [ + { + "id": "test", + "single_end": true + }, + "test.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,96e36b0b99c80da0be8239d03db30ecc" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T10:00:28.666281812" + }, + "sarscov2 - paired_end": { + "content": [ + [ + "versions.yml:md5,96e36b0b99c80da0be8239d03db30ecc" + ], + [ + [ + "ATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTG", + "ACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGA" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.out:md5,5e13272d112cef8faeedcdbd7c602de0" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-26T11:57:56.604464368" + }, + "sarscov2 - paired_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,96e36b0b99c80da0be8239d03db30ecc" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fastq": [ + + ], + "log": [ + [ + { + "id": "test", + "single_end": false + }, + "test.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,96e36b0b99c80da0be8239d03db30ecc" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T10:01:02.043164876" + } +} \ No newline at end of file diff --git a/modules/nf-core/bowtie/align/tests/tags.yml b/modules/nf-core/bowtie/align/tests/tags.yml new file mode 100644 index 00000000..a5753d58 --- /dev/null +++ b/modules/nf-core/bowtie/align/tests/tags.yml @@ -0,0 +1,2 @@ +bowtie/align: + - "modules/nf-core/bowtie/align/**" diff --git a/modules/nf-core/bowtie/build/main.nf b/modules/nf-core/bowtie/build/main.nf index 05e22fe8..d5b4c690 100644 --- a/modules/nf-core/bowtie/build/main.nf +++ b/modules/nf-core/bowtie/build/main.nf @@ -1,5 +1,5 @@ process BOWTIE_BUILD { - tag "$fasta" + tag "${meta.id}" label 'process_high' conda "${moduleDir}/environment.yml" @@ -8,23 +8,43 @@ process BOWTIE_BUILD { 'biocontainers/bowtie:1.3.0--py38hed8969a_1' }" input: - path fasta + tuple val(meta), path(fasta) output: - path 'bowtie' , emit: index - path "versions.yml" , emit: versions + tuple val(meta), path('bowtie') , emit: index + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" """ - mkdir bowtie - bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName} + mkdir -p bowtie + bowtie-build --threads $task.cpus $fasta bowtie/${prefix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bowtie: \$(echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + mkdir -p bowtie + touch bowtie/${prefix}.1.ebwt + touch bowtie/${prefix}.2.ebwt + touch bowtie/${prefix}.3.ebwt + touch bowtie/${prefix}.4.ebwt + touch bowtie/${prefix}.rev.1.ebwt + touch bowtie/${prefix}.rev.2.ebwt + cat <<-END_VERSIONS > versions.yml "${task.process}": bowtie: \$(echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//') END_VERSIONS """ + } diff --git a/modules/nf-core/bowtie/build/meta.yml b/modules/nf-core/bowtie/build/meta.yml index 262855f4..dd48004f 100644 --- a/modules/nf-core/bowtie/build/meta.yml +++ b/modules/nf-core/bowtie/build/meta.yml @@ -15,13 +15,23 @@ tools: arxiv: arXiv:1303.3997 licence: ["Artistic-2.0"] input: + - meta: + type: map + description: | + Groovy Map containing information about the genome fasta + e.g. [ id:'test' ] - fasta: type: file description: Input genome fasta file output: + - meta: + type: map + description: | + Groovy Map containing nformation about the genome fasta + e.g. [ id:'test' ] - index: type: file - description: Bowtie genome index files + description: Folder containing bowtie genome index files pattern: "*.ebwt" - versions: type: file diff --git a/modules/nf-core/bowtie/build/tests/main.nf.test b/modules/nf-core/bowtie/build/tests/main.nf.test new file mode 100644 index 00000000..2a1e0dc0 --- /dev/null +++ b/modules/nf-core/bowtie/build/tests/main.nf.test @@ -0,0 +1,57 @@ +nextflow_process { + + name "Test Process BOWTIE_BUILD" + script "../main.nf" + process "BOWTIE_BUILD" + + tag "modules" + tag "modules_nfcore" + tag "bowtie" + tag "bowtie/build" + + test("sarscov2 - fasta") { + + when { + process { + """ + input[0] = [ + [id: 'sarscov2'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - fasta - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [[id: 'sarscov2'], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/bowtie/build/tests/main.nf.test.snap b/modules/nf-core/bowtie/build/tests/main.nf.test.snap new file mode 100644 index 00000000..e8061756 --- /dev/null +++ b/modules/nf-core/bowtie/build/tests/main.nf.test.snap @@ -0,0 +1,96 @@ +{ + "sarscov2 - fasta - stub": { + "content": [ + { + "0": [ + [ + { + "id": "sarscov2" + }, + [ + "sarscov2.1.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sarscov2.2.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sarscov2.3.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sarscov2.4.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sarscov2.rev.1.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sarscov2.rev.2.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,afbd066e1dd5ae4a30b21c49149ea09a" + ], + "index": [ + [ + { + "id": "sarscov2" + }, + [ + "sarscov2.1.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sarscov2.2.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sarscov2.3.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sarscov2.4.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sarscov2.rev.1.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sarscov2.rev.2.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,afbd066e1dd5ae4a30b21c49149ea09a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-18T08:38:14.852528155" + }, + "sarscov2 - fasta": { + "content": [ + { + "0": [ + [ + { + "id": "sarscov2" + }, + [ + "sarscov2.1.ebwt:md5,d9b76ecf9fd0413240173273b38d8199", + "sarscov2.2.ebwt:md5,02b44af9f94c62ecd3c583048e25d4cf", + "sarscov2.3.ebwt:md5,4ed93abba181d8dfab2e303e33114777", + "sarscov2.4.ebwt:md5,c25be5f8b0378abf7a58c8a880b87626", + "sarscov2.rev.1.ebwt:md5,b37aaf11853e65a3b13561f27a912b06", + "sarscov2.rev.2.ebwt:md5,9e6b0c4c1ddb99ae71ff8a4fe5ec6459" + ] + ] + ], + "1": [ + "versions.yml:md5,afbd066e1dd5ae4a30b21c49149ea09a" + ], + "index": [ + [ + { + "id": "sarscov2" + }, + [ + "sarscov2.1.ebwt:md5,d9b76ecf9fd0413240173273b38d8199", + "sarscov2.2.ebwt:md5,02b44af9f94c62ecd3c583048e25d4cf", + "sarscov2.3.ebwt:md5,4ed93abba181d8dfab2e303e33114777", + "sarscov2.4.ebwt:md5,c25be5f8b0378abf7a58c8a880b87626", + "sarscov2.rev.1.ebwt:md5,b37aaf11853e65a3b13561f27a912b06", + "sarscov2.rev.2.ebwt:md5,9e6b0c4c1ddb99ae71ff8a4fe5ec6459" + ] + ] + ], + "versions": [ + "versions.yml:md5,afbd066e1dd5ae4a30b21c49149ea09a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-18T08:37:53.65689025" + } +} \ No newline at end of file diff --git a/modules/nf-core/bowtie/build/tests/tags.yml b/modules/nf-core/bowtie/build/tests/tags.yml new file mode 100644 index 00000000..1ccfa30c --- /dev/null +++ b/modules/nf-core/bowtie/build/tests/tags.yml @@ -0,0 +1,2 @@ +bowtie/build: + - "modules/nf-core/bowtie/build/**" diff --git a/modules/nf-core/bowtie2/align/tests/main.nf.test b/modules/nf-core/bowtie2/align/tests/main.nf.test index 03aeaf9e..0de5950f 100644 --- a/modules/nf-core/bowtie2/align/tests/main.nf.test +++ b/modules/nf-core/bowtie2/align/tests/main.nf.test @@ -18,7 +18,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -30,10 +30,10 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -64,7 +64,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -76,10 +76,10 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -110,7 +110,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -122,10 +122,10 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -155,7 +155,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -167,10 +167,10 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -200,7 +200,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -213,12 +213,12 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -248,7 +248,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -261,12 +261,12 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -297,7 +297,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -309,10 +309,10 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -343,7 +343,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -356,12 +356,12 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -391,7 +391,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -404,12 +404,12 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -439,7 +439,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -451,10 +451,10 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -486,7 +486,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -499,12 +499,12 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[3] = false //save_unaligned input[4] = true //sort """ @@ -533,7 +533,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -546,12 +546,12 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -583,7 +583,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] """ } @@ -595,10 +595,10 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index adbdbd7b..2862c64c 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -76,4 +76,3 @@ def getFileSuffix(filename) { def match = filename =~ /^.*?((\.\w{1,5})?(\.\w{1,5}\.gz$))/ return match ? match[0][1] : filename.substring(filename.lastIndexOf('.')) } - diff --git a/modules/nf-core/cat/cat/tests/main.nf.test b/modules/nf-core/cat/cat/tests/main.nf.test index fcee2d19..9cb16178 100644 --- a/modules/nf-core/cat/cat/tests/main.nf.test +++ b/modules/nf-core/cat/cat/tests/main.nf.test @@ -29,7 +29,8 @@ nextflow_process { then { assertAll( { assert !process.success }, - { assert process.stdout.toString().contains("The name of the input file can't be the same as for the output prefix") } + { assert process.stdout.toString().contains("The name of the input file can't be the same as for the output prefix") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -83,8 +84,12 @@ nextflow_process { def lines = path(process.out.file_out.get(0).get(1)).linesGzip assertAll( { assert process.success }, - { assert snapshot(lines[0..5]).match("test_cat_zipped_zipped_lines") }, - { assert snapshot(lines.size()).match("test_cat_zipped_zipped_size")} + { assert snapshot( + lines[0..5], + lines.size(), + process.out.versions + ).match() + } ) } } @@ -142,8 +147,12 @@ nextflow_process { def lines = path(process.out.file_out.get(0).get(1)).linesGzip assertAll( { assert process.success }, - { assert snapshot(lines[0..5]).match("test_cat_unzipped_zipped_lines") }, - { assert snapshot(lines.size()).match("test_cat_unzipped_zipped_size")} + { assert snapshot( + lines[0..5], + lines.size(), + process.out.versions + ).match() + } ) } } @@ -170,8 +179,12 @@ nextflow_process { def lines = path(process.out.file_out.get(0).get(1)).linesGzip assertAll( { assert process.success }, - { assert snapshot(lines[0..5]).match("test_cat_one_file_unzipped_zipped_lines") }, - { assert snapshot(lines.size()).match("test_cat_one_file_unzipped_zipped_size")} + { assert snapshot( + lines[0..5], + lines.size(), + process.out.versions + ).match() + } ) } } diff --git a/modules/nf-core/cat/cat/tests/main.nf.test.snap b/modules/nf-core/cat/cat/tests/main.nf.test.snap index 423571ba..b7623ee6 100644 --- a/modules/nf-core/cat/cat/tests/main.nf.test.snap +++ b/modules/nf-core/cat/cat/tests/main.nf.test.snap @@ -1,10 +1,4 @@ { - "test_cat_unzipped_zipped_size": { - "content": [ - 375 - ], - "timestamp": "2023-10-16T14:33:08.049445686" - }, "test_cat_unzipped_unzipped": { "content": [ { @@ -34,6 +28,10 @@ ] } ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, "timestamp": "2023-10-16T14:32:18.500464399" }, "test_cat_zipped_unzipped": { @@ -65,9 +63,13 @@ ] } ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, "timestamp": "2023-10-16T14:32:49.642741302" }, - "test_cat_zipped_zipped_lines": { + "test_cat_zipped_zipped": { "content": [ [ "MT192765.1\tGenbank\ttranscript\t259\t29667\t.\t+\t.\tID=unknown_transcript_1;geneID=orf1ab;gene_name=orf1ab", @@ -76,11 +78,31 @@ "MT192765.1\tGenbank\tCDS\t13461\t21548\t.\t+\t0\tParent=unknown_transcript_1;exception=\"ribosomal slippage\";gbkey=CDS;gene=orf1ab;note=\"pp1ab;translated=by -1 ribosomal frameshift\";product=\"orf1ab polyprotein\";protein_id=QIK50426.1", "MT192765.1\tGenbank\tCDS\t21556\t25377\t.\t+\t0\tParent=unknown_transcript_1;gbkey=CDS;gene=S;note=\"structural protein\";product=\"surface glycoprotein\";protein_id=QIK50427.1", "MT192765.1\tGenbank\tgene\t21556\t25377\t.\t+\t.\tParent=unknown_transcript_1" + ], + 78, + [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:51:46.802978" + }, + "test_cat_name_conflict": { + "content": [ + [ + ] ], - "timestamp": "2023-10-16T14:32:33.629048645" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:51:29.45394" }, - "test_cat_unzipped_zipped_lines": { + "test_cat_one_file_unzipped_zipped": { "content": [ [ ">MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome", @@ -89,11 +111,19 @@ "TAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGG", "GTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTT", "ACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAG" + ], + 374, + [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" ] ], - "timestamp": "2023-10-16T14:33:08.038830506" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:52:02.774016" }, - "test_cat_one_file_unzipped_zipped_lines": { + "test_cat_unzipped_zipped": { "content": [ [ ">MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome", @@ -102,20 +132,16 @@ "TAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGG", "GTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTT", "ACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAG" + ], + 375, + [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" ] ], - "timestamp": "2023-10-16T14:33:21.39642399" - }, - "test_cat_zipped_zipped_size": { - "content": [ - 78 - ], - "timestamp": "2023-10-16T14:32:33.641869244" - }, - "test_cat_one_file_unzipped_zipped_size": { - "content": [ - 374 - ], - "timestamp": "2023-10-16T14:33:21.4094373" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:51:57.581523" } } \ No newline at end of file diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index f132b2ad..b68e5f91 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -53,9 +53,9 @@ process CAT_FASTQ { def prefix = task.ext.prefix ?: "${meta.id}" def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()] if (meta.single_end) { - if (readList.size > 1) { + if (readList.size >= 1) { """ - touch ${prefix}.merged.fastq.gz + echo '' | gzip > ${prefix}.merged.fastq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -64,10 +64,10 @@ process CAT_FASTQ { """ } } else { - if (readList.size > 2) { + if (readList.size >= 2) { """ - touch ${prefix}_1.merged.fastq.gz - touch ${prefix}_2.merged.fastq.gz + echo '' | gzip > ${prefix}_1.merged.fastq.gz + echo '' | gzip > ${prefix}_2.merged.fastq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test index a71dcb8d..f88a78b6 100644 --- a/modules/nf-core/cat/fastq/tests/main.nf.test +++ b/modules/nf-core/cat/fastq/tests/main.nf.test @@ -13,9 +13,6 @@ nextflow_process { test("test_cat_fastq_single_end") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -38,9 +35,6 @@ nextflow_process { test("test_cat_fastq_paired_end") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -65,9 +59,6 @@ nextflow_process { test("test_cat_fastq_single_end_same_name") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -90,9 +81,6 @@ nextflow_process { test("test_cat_fastq_paired_end_same_name") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -117,9 +105,129 @@ nextflow_process { test("test_cat_fastq_single_end_single_file") { when { - params { - outdir = "$outputDir" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_same_name - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end_same_name - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) + """ } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_single_file - stub") { + + options "-stub" + + when { process { """ input[0] = Channel.of([ diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test.snap b/modules/nf-core/cat/fastq/tests/main.nf.test.snap index 43dfe28f..aec119a9 100644 --- a/modules/nf-core/cat/fastq/tests/main.nf.test.snap +++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap @@ -28,6 +28,10 @@ ] } ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-01-17T17:30:39.816981" }, "test_cat_fastq_single_end_same_name": { @@ -59,6 +63,10 @@ ] } ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-01-17T17:32:35.229332" }, "test_cat_fastq_single_end_single_file": { @@ -90,6 +98,10 @@ ] } ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-01-17T17:34:00.058829" }, "test_cat_fastq_paired_end_same_name": { @@ -127,8 +139,123 @@ ] } ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-01-17T17:33:33.031555" }, + "test_cat_fastq_single_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-05T12:07:28.244999" + }, + "test_cat_fastq_paired_end_same_name - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-05T12:07:57.070911" + }, + "test_cat_fastq_single_end_same_name - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-05T12:07:46.796254" + }, "test_cat_fastq_paired_end": { "content": [ { @@ -164,6 +291,86 @@ ] } ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-01-17T17:32:02.270935" + }, + "test_cat_fastq_paired_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-05T12:07:37.807553" + }, + "test_cat_fastq_single_end_single_file - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-05T12:14:51.861264" } } \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py index da033408..9a493ace 100755 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -3,7 +3,6 @@ """Provide functions to merge multiple versions.yml files.""" - import yaml import platform from textwrap import dedent diff --git a/modules/nf-core/custom/tx2gene/templates/tx2gene.py b/modules/nf-core/custom/tx2gene/templates/tx2gene.py index 7fd0de64..8c2e3b1f 100755 --- a/modules/nf-core/custom/tx2gene/templates/tx2gene.py +++ b/modules/nf-core/custom/tx2gene/templates/tx2gene.py @@ -17,6 +17,7 @@ logger = logging.getLogger(__name__) logger.setLevel(logging.INFO) + def format_yaml_like(data: dict, indent: int = 0) -> str: """Formats a dictionary to a YAML-like string. @@ -36,6 +37,7 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: yaml_str += f"{spaces}{key}: {value}\\n" return yaml_str + def read_top_transcripts(quant_dir: str, file_pattern: str) -> Set[str]: """ Read the top 100 transcripts from the quantification file. @@ -123,7 +125,12 @@ def parse_attributes(attributes_text: str) -> Dict[str, str]: def map_transcripts_to_gene( - quant_type: str, gtf_file: str, quant_dir: str, gene_id: str, extra_id_field: str, output_file: str + quant_type: str, + gtf_file: str, + quant_dir: str, + gene_id: str, + extra_id_field: str, + output_file: str, ) -> bool: """ Map transcripts to gene names and write the output to a file. @@ -156,7 +163,10 @@ def map_transcripts_to_gene( attr_dict = parse_attributes(cols[8]) if gene_id in attr_dict and transcript_attribute in attr_dict: # Create a unique identifier for the transcript-gene combination - transcript_gene_pair = (attr_dict[transcript_attribute], attr_dict[gene_id]) + transcript_gene_pair = ( + attr_dict[transcript_attribute], + attr_dict[gene_id], + ) # Check if the combination has already been seen if transcript_gene_pair not in seen: @@ -170,14 +180,14 @@ def map_transcripts_to_gene( # Main function to parse arguments and call the mapping function if __name__ == "__main__": - if '${task.ext.prefix}' != "null": + if "${task.ext.prefix}" != "null": prefix = "${task.ext.prefix}." - elif '$meta.id' != "null": - prefix = '${meta.id}.' + elif "$meta.id" != "null": + prefix = "${meta.id}." else: - prefix = '' + prefix = "" - if not map_transcripts_to_gene('$quant_type', '$gtf', 'quants', '$id', '$extra', f"{prefix}tx2gene.tsv"): + if not map_transcripts_to_gene("$quant_type", "$gtf", "quants", "$id", "$extra", f"{prefix}tx2gene.tsv"): logger.error("Failed to map transcripts to genes.") # Write the versions diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test b/modules/nf-core/custom/tx2gene/tests/main.nf.test index b1559279..4cbb8d4e 100644 --- a/modules/nf-core/custom/tx2gene/tests/main.nf.test +++ b/modules/nf-core/custom/tx2gene/tests/main.nf.test @@ -10,22 +10,21 @@ nextflow_process { tag "custom/tx2gene" tag "untar" - setup { + test("saccharomyces_cerevisiae - gtf") { - run("UNTAR") { - script "../../../untar/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test'], // meta map - file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz', checkIfExists: true) - ]) - """ + setup { + run("UNTAR") { + script "../../../untar/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz', checkIfExists: true) + ]) + """ + } } } - } - - test("saccharomyces_cerevisiae - gtf") { when { process { @@ -45,8 +44,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.tx2gene).match('tx2gene') }, - { assert snapshot(process.out.versions).match('versions') } + { assert snapshot(process.out).match() } ) } } @@ -55,6 +53,20 @@ nextflow_process { options "-stub" + setup { + run("UNTAR") { + script "../../../untar/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz', checkIfExists: true) + ]) + """ + } + } + } + when { process { """ @@ -73,8 +85,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.tx2gene).match('tx2gene - stub') }, - { assert snapshot(process.out.versions).match('versions - stub') } + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap index 1e76e10d..c19f10f7 100644 --- a/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap +++ b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap @@ -1,60 +1,68 @@ { - "versions": { + "saccharomyces_cerevisiae - gtf": { "content": [ - [ - "versions.yml:md5,fb8145d7fbc6043ba031249b23ecda50" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" - }, - "timestamp": "2024-02-26T13:14:18.218251" - }, - "tx2gene": { - "content": [ - [ - [ - { - "id": "test" - }, - "test.tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" + { + "0": [ + [ + { + "id": "test" + }, + "test.tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" + ] + ], + "1": [ + "versions.yml:md5,fb8145d7fbc6043ba031249b23ecda50" + ], + "tx2gene": [ + [ + { + "id": "test" + }, + "test.tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" + ] + ], + "versions": [ + "versions.yml:md5,fb8145d7fbc6043ba031249b23ecda50" ] - ] + } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-26T13:14:18.21054" + "timestamp": "2024-07-05T13:13:11.305047" }, - "tx2gene - stub": { + "saccharomyces_cerevisiae - gtf - stub": { "content": [ - [ - [ - { - "id": "test" - }, - "test.tx2gene.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + { + "0": [ + [ + { + "id": "test" + }, + "test.tx2gene.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60" + ], + "tx2gene": [ + [ + { + "id": "test" + }, + "test.tx2gene.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" - }, - "timestamp": "2024-02-26T13:14:25.915434" - }, - "versions - stub": { - "content": [ - [ - "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60" - ] + } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "24.04.3" }, - "timestamp": "2024-02-26T13:14:25.919243" + "timestamp": "2024-07-10T15:15:34.064489" } } \ No newline at end of file diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 70edae4d..e9d79a07 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -23,17 +23,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
      Mon 2 Oct 2023
      test.gz
      - // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("
    ") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_single") } + { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
    Mon 2 Oct 2023
    test.gz
    + // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("    ") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -54,16 +51,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("") }, - { assert path(process.out.html[0][1][1]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_paired") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("") }, + { assert path(process.out.html[0][1][1]).text.contains("") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -83,13 +78,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -109,13 +102,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_bam") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -138,22 +129,20 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("") }, - { assert path(process.out.html[0][1][1]).text.contains("") }, - { assert path(process.out.html[0][1][2]).text.contains("") }, - { assert path(process.out.html[0][1][3]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, + { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, + { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("") }, + { assert path(process.out.html[0][1][1]).text.contains("") }, + { assert path(process.out.html[0][1][2]).text.contains("") }, + { assert path(process.out.html[0][1][3]).text.contains("") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -173,21 +162,18 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + { assert snapshot(process.out.versions).match() } ) } } test("sarscov2 single-end [fastq] - stub") { - options "-stub" - + options "-stub" when { process { """ @@ -201,12 +187,123 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert snapshot(process.out.html.collect { file(it[1]).getName() } + - process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match("fastqc_stub") } + { assert process.success }, + { assert snapshot(process.out).match() } ) } } + test("sarscov2 paired-end [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 interleaved [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 paired-end [bam] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 multiple [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 custom_prefix - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'mysample', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 86f7c311..d5db3092 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,88 +1,392 @@ { - "fastqc_versions_interleaved": { + "sarscov2 custom_prefix": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:07.293713" + "timestamp": "2024-07-22T11:02:16.374038" }, - "fastqc_stub": { + "sarscov2 single-end [fastq] - stub": { "content": [ - [ - "test.html", - "test.zip", - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:24.993809" + }, + "sarscov2 custom_prefix - stub": { + "content": [ + { + "0": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:31:01.425198" + "timestamp": "2024-07-22T11:03:10.93942" }, - "fastqc_versions_multiple": { + "sarscov2 interleaved [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:55.797907" + "timestamp": "2024-07-22T11:01:42.355718" }, - "fastqc_versions_bam": { + "sarscov2 paired-end [bam]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:26.795862" + "timestamp": "2024-07-22T11:01:53.276274" }, - "fastqc_versions_single": { + "sarscov2 multiple [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:27.043675" + "timestamp": "2024-07-22T11:02:05.527626" }, - "fastqc_versions_paired": { + "sarscov2 paired-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:31.188871" + }, + "sarscov2 paired-end [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:34.273566" + }, + "sarscov2 multiple [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:47.584191" + "timestamp": "2024-07-22T11:03:02.304411" }, - "fastqc_versions_custom_prefix": { + "sarscov2 single-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:19.095607" + }, + "sarscov2 interleaved [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:44.640184" + }, + "sarscov2 paired-end [bam] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:41:14.576531" + "timestamp": "2024-07-22T11:02:53.550742" } } \ No newline at end of file diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf index 2289a9fc..ea186f62 100644 --- a/modules/nf-core/hisat2/align/main.nf +++ b/modules/nf-core/hisat2/align/main.nf @@ -90,4 +90,23 @@ process HISAT2_ALIGN { END_VERSIONS """ } + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def unaligned = params.save_unaligned ? "echo '' | gzip > ${prefix}.unmapped_1.fastq.gz \n echo '' | gzip > ${prefix}.unmapped_2.fastq.gz" : '' + def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + """ + ${unaligned} + + touch ${prefix}.hisat2.summary.log + touch ${prefix}.bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + hisat2: $VERSION + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ + + } diff --git a/modules/nf-core/hisat2/align/tests/main.nf.test b/modules/nf-core/hisat2/align/tests/main.nf.test index 3a520e9a..396757d7 100644 --- a/modules/nf-core/hisat2/align/tests/main.nf.test +++ b/modules/nf-core/hisat2/align/tests/main.nf.test @@ -68,6 +68,63 @@ nextflow_process { } } + test("Single-End - stub") { + options "-stub" + + setup { + run("HISAT2_EXTRACTSPLICESITES") { + script "../../extractsplicesites/main.nf" + process { + """ + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ]) + """ + } + } + + run("HISAT2_BUILD") { + script "../../build/main.nf" + process { + """ + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[1] = Channel.of([ [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ]) + input[2] = HISAT2_EXTRACTSPLICESITES.out.txt + """ + } + } + } + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + input[1] = HISAT2_BUILD.out.index + input[2] = HISAT2_EXTRACTSPLICESITES.out.txt + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + test("Paired-End") { setup { @@ -127,6 +184,64 @@ nextflow_process { } } + test("Paired-End - stub") { + options "-stub" + + setup { + run("HISAT2_EXTRACTSPLICESITES") { + script "../../extractsplicesites/main.nf" + process { + """ + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ]) + """ + } + } + + run("HISAT2_BUILD") { + script "../../build/main.nf" + process { + """ + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[1] = Channel.of([ [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ]) + input[2] = HISAT2_EXTRACTSPLICESITES.out.txt + """ + } + } + } + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) + input[1] = HISAT2_BUILD.out.index + input[2] = HISAT2_EXTRACTSPLICESITES.out.txt + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + test("Single-End No Splice Sites") { setup { @@ -171,6 +286,49 @@ nextflow_process { } } + test("Single-End No Splice Sites - stub") { + options "-stub" + + setup { + run("HISAT2_BUILD") { + script "../../build/main.nf" + process { + """ + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[1] = [[:],[]] + input[2] = [[:],[]] + """ + } + } + } + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + ]) + input[1] = HISAT2_BUILD.out.index + input[2] = [[:],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + test("Paired-End No Splice Sites") { setup { @@ -215,4 +373,48 @@ nextflow_process { ) } } + + test("Paired-End No Splice Sites - stub") { + options "-stub" + + setup { + run("HISAT2_BUILD") { + script "../../build/main.nf" + process { + """ + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[1] = [[:],[]] + input[2] = [[:],[]] + """ + } + } + } + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) + input[1] = HISAT2_BUILD.out.index + input[2] = [[:],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } diff --git a/modules/nf-core/hisat2/align/tests/main.nf.test.snap b/modules/nf-core/hisat2/align/tests/main.nf.test.snap index a80fa3c5..ff670d45 100644 --- a/modules/nf-core/hisat2/align/tests/main.nf.test.snap +++ b/modules/nf-core/hisat2/align/tests/main.nf.test.snap @@ -5,21 +5,129 @@ "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" ] ], - "timestamp": "2023-10-16T15:14:50.269895296" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-21T09:08:33.735489" }, - "se_no_ss_summary": { + "Paired-End - stub": { "content": [ - [ - [ - { - "id": "test", - "single_end": true - }, - "test.hisat2.summary.log:md5,7b8a9e61b7646da1089b041333c41a87" + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fastq": [ + + ], + "summary": [ + [ + { + "id": "test", + "single_end": false + }, + "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" ] - ] + } ], - "timestamp": "2023-10-16T15:15:22.897386626" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-21T09:09:14.35626" + }, + "Single-End - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" + ], + "bam": [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fastq": [ + + ], + "summary": [ + [ + { + "id": "test", + "single_end": true + }, + "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-21T09:08:47.404885" }, "pe_no_ss_versions": { "content": [ @@ -27,15 +135,70 @@ "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" ] ], - "timestamp": "2023-10-16T15:15:42.583699978" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-21T09:09:52.076955" }, - "se_no_ss_versions": { + "Paired-End No Splice Sites - stub": { "content": [ - [ - "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fastq": [ + + ], + "summary": [ + [ + { + "id": "test", + "single_end": false + }, + "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" + ] + } ], - "timestamp": "2023-10-16T15:15:22.909407356" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-21T09:10:03.739697" }, "pe_no_ss_summary": { "content": [ @@ -49,7 +212,11 @@ ] ] ], - "timestamp": "2023-10-16T15:15:42.569775538" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-21T09:09:52.068244" }, "pe_no_ss_fastq": { "content": [ @@ -57,7 +224,11 @@ ] ], - "timestamp": "2023-10-16T15:15:42.576881608" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-21T09:09:52.072985" }, "se_summary": { "content": [ @@ -71,7 +242,11 @@ ] ] ], - "timestamp": "2023-10-16T15:14:50.252466896" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-21T09:08:33.727355" }, "pe_summary": { "content": [ @@ -85,7 +260,11 @@ ] ] ], - "timestamp": "2023-10-16T15:15:09.881690889" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-21T09:09:01.495439" }, "pe_fastq": { "content": [ @@ -93,23 +272,124 @@ ] ], - "timestamp": "2023-10-16T15:15:09.888696129" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-21T09:09:01.500755" }, - "se_no_ss_fastq": { + "se_fastq": { "content": [ [ ] ], - "timestamp": "2023-10-16T15:15:22.904010016" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-21T09:08:33.732523" }, - "se_fastq": { + "se_no_ss_summary": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.hisat2.summary.log:md5,7b8a9e61b7646da1089b041333c41a87" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-21T09:09:26.851884" + }, + "se_no_ss_versions": { + "content": [ + [ + "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-21T09:09:26.89234" + }, + "se_no_ss_fastq": { "content": [ [ ] ], - "timestamp": "2023-10-16T15:14:50.264366105" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-21T09:09:26.871369" + }, + "Single-End No Splice Sites - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" + ], + "bam": [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fastq": [ + + ], + "summary": [ + [ + { + "id": "test", + "single_end": true + }, + "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-21T09:09:39.544807" }, "pe_versions": { "content": [ @@ -117,6 +397,10 @@ "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" ] ], - "timestamp": "2023-10-16T15:15:09.894683308" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-21T09:09:01.506346" } } \ No newline at end of file diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf index 766e8731..17d8fdd5 100644 --- a/modules/nf-core/hisat2/build/main.nf +++ b/modules/nf-core/hisat2/build/main.nf @@ -61,4 +61,15 @@ process HISAT2_BUILD { hisat2: $VERSION END_VERSIONS """ + + stub: + def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + """ + mkdir hisat2 + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + hisat2: $VERSION + END_VERSIONS + """ } diff --git a/modules/nf-core/hisat2/build/tests/main.nf.test b/modules/nf-core/hisat2/build/tests/main.nf.test index 5b31debc..e19692c4 100644 --- a/modules/nf-core/hisat2/build/tests/main.nf.test +++ b/modules/nf-core/hisat2/build/tests/main.nf.test @@ -50,4 +50,49 @@ nextflow_process { ) } } -} + + test("Should run without failures - stub") { + + options "-stub" + + setup { + run("HISAT2_EXTRACTSPLICESITES") { + script "../../extractsplicesites/main.nf" + process { + """ + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ]) + """ + } + } + } + + when { + params { + outdir = "$outputDir" + } + + process { + """ + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[1] = Channel.of([ [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ]) + input[2] = HISAT2_EXTRACTSPLICESITES.out.txt + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/hisat2/build/tests/main.nf.test.snap b/modules/nf-core/hisat2/build/tests/main.nf.test.snap index c7d364db..0e3b5c57 100644 --- a/modules/nf-core/hisat2/build/tests/main.nf.test.snap +++ b/modules/nf-core/hisat2/build/tests/main.nf.test.snap @@ -1,4 +1,64 @@ { + "test - stub": { + "content": [ + { + "0": [ + + ], + "1": [ + + ], + "index": [ + + ], + "versions": [ + + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-20T17:29:31.567024" + }, + "Should run without failures - stub": { + "content": [ + { + "0": [ + [ + { + "id": "genome" + }, + [ + + ] + ] + ], + "1": [ + "versions.yml:md5,e36ef3cd73d19ccf2378c9358fe942c0" + ], + "index": [ + [ + { + "id": "genome" + }, + [ + + ] + ] + ], + "versions": [ + "versions.yml:md5,e36ef3cd73d19ccf2378c9358fe942c0" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-20T18:18:08.896422" + }, "Should run without failures": { "content": [ { @@ -44,6 +104,10 @@ ] } ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2023-10-16T14:42:22.381609786" } -} \ No newline at end of file +} diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf index b0c8513a..588a9947 100644 --- a/modules/nf-core/hisat2/extractsplicesites/main.nf +++ b/modules/nf-core/hisat2/extractsplicesites/main.nf @@ -28,4 +28,15 @@ process HISAT2_EXTRACTSPLICESITES { hisat2: $VERSION END_VERSIONS """ + + stub: + def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + """ + touch ${gtf.baseName}.splice_sites.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + hisat2: $VERSION + END_VERSIONS + """ } diff --git a/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test b/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test index 72eb6d53..14129cff 100644 --- a/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test +++ b/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test @@ -32,4 +32,30 @@ nextflow_process { ) } } + + test("test - stub") { + + options "-stub" + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } diff --git a/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test.snap b/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test.snap index 17f1c8eb..1dcd8af2 100644 --- a/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test.snap +++ b/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test.snap @@ -1,10 +1,47 @@ { + "test - stub": { + "content": [ + { + "0": [ + [ + { + "id": "genome" + }, + "genome.splice_sites.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,eeea7231fe197810659b8bad4133aff2" + ], + "txt": [ + [ + { + "id": "genome" + }, + "genome.splice_sites.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,eeea7231fe197810659b8bad4133aff2" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-20T17:34:13.229903" + }, "Should run without failures": { "content": [ [ "versions.yml:md5,eeea7231fe197810659b8bad4133aff2" ] ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-01-18T20:56:30.71763" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index ca39fb67..2121492d 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.21 + - bioconda::multiqc=1.23 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 47ac352f..459dfea5 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,14 +3,16 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : - 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.23--pyhdfd78af_0' : + 'biocontainers/multiqc:1.23--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" path(multiqc_config) path(extra_multiqc_config) path(multiqc_logo) + path(replace_names) + path(sample_names) output: path "*multiqc_report.html", emit: report @@ -26,6 +28,8 @@ process MULTIQC { def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' + def replace = replace_names ? "--replace-names ${replace_names}" : '' + def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ @@ -33,6 +37,8 @@ process MULTIQC { $config \\ $extra_config \\ $logo \\ + $replace \\ + $samples \\ . cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 45a9bc35..382c08cb 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -29,6 +29,19 @@ input: type: file description: Optional logo file for MultiQC pattern: "*.{png}" + - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" output: - report: type: file diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index f1c4242e..6aa27f4c 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -17,6 +17,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -41,6 +43,8 @@ nextflow_process { input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -66,6 +70,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index bfebd802..45e95e5d 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:48:55.657331" + "timestamp": "2024-07-10T12:41:34.562023" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:49.071937" + "timestamp": "2024-07-10T11:27:11.933869532" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:25.457567" + "timestamp": "2024-07-10T11:26:56.709849369" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test b/modules/nf-core/samtools/flagstat/tests/main.nf.test index 24c3c04b..3b648a37 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test @@ -11,9 +11,30 @@ nextflow_process { test("BAM") { when { - params { - outdir = "$outputDir" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + """ } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("BAM - stub") { + + options "-stub" + + when { process { """ input[0] = Channel.of([ @@ -28,8 +49,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.flagstat).match("flagstat") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap index e9f85efa..23989c61 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap @@ -1,32 +1,72 @@ { - "flagstat": { + "BAM - stub": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + ], + "flagstat": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" ] - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-12T18:31:37.783927" + "timestamp": "2024-07-22T14:17:28.002887" }, - "versions": { + "BAM": { "content": [ - [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + ] + ], + "1": [ + "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + ], + "flagstat": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + ] + ], + "versions": [ + "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-28T15:41:52.516253882" + "timestamp": "2024-07-22T14:17:13.330971" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test b/modules/nf-core/samtools/idxstats/tests/main.nf.test index a2dcb27c..5fd1fc78 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test @@ -11,9 +11,6 @@ nextflow_process { test("bam") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -28,9 +25,29 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.idxstats).match("idxstats") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out).match() } ) } } -} + + test("bam - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + }} diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap index 4eacdb90..a5ac8104 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap @@ -1,32 +1,72 @@ { - "versions": { + "bam - stub": { "content": [ - [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + ], + "idxstats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-28T15:46:46.617989517" + "timestamp": "2024-07-22T14:17:56.180093" }, - "idxstats": { + "bam": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + ] + ], + "1": [ + "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + ], + "idxstats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + ] + ], + "versions": [ + "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" ] - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-12T18:36:41.561026" + "timestamp": "2024-07-22T14:17:41.408704" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index b523c21b..e002585b 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -35,10 +35,11 @@ process SAMTOOLS_INDEX { """ stub: + def args = task.ext.args ?: '' + def extension = file(input).getExtension() == 'cram' ? + "crai" : args.contains("-c") ? "csi" : "bai" """ - touch ${input}.bai - touch ${input}.crai - touch ${input}.csi + touch ${input}.${extension} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test index bb7756d1..ca34fb5c 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -9,11 +9,7 @@ nextflow_process { tag "samtools/index" test("bai") { - when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -27,18 +23,13 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.bai).match("bai") }, - { assert snapshot(process.out.versions).match("bai_versions") } + { assert snapshot(process.out).match() } ) } } test("crai") { - when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -52,20 +43,83 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.crai).match("crai") }, - { assert snapshot(process.out.versions).match("crai_versions") } + { assert snapshot(process.out).match() } ) } } test("csi") { - config "./csi.nextflow.config" when { - params { - outdir = "$outputDir" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.csi[0][1]).name, + process.out.versions + ).match() } + ) + } + } + + test("bai - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("crai - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true) + ]) + """ } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("csi - stub") { + options "-stub" + config "./csi.nextflow.config" + + when { process { """ input[0] = Channel.of([ @@ -79,8 +133,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert path(process.out.csi.get(0).get(1)).exists() }, - { assert snapshot(process.out.versions).match("csi_versions") } + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 52756e85..799d199c 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -1,74 +1,250 @@ { - "crai_versions": { + "csi - stub": { "content": [ - [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" - ] + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ], + "bai": [ + + ], + "crai": [ + + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-28T15:42:04.203740976" + "timestamp": "2024-07-22T16:51:53.9057" }, - "csi_versions": { + "crai - stub": { "content": [ - [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" - ] + { + "0": [ + + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ], + "bai": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-28T15:42:09.57475878" + "timestamp": "2024-07-22T16:51:45.931558" }, - "crai": { + "bai - stub": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ], + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "crai": [ + + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" ] - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-12T18:41:38.446424" + "timestamp": "2024-07-22T16:51:34.807525" }, - "bai": { + "csi": { "content": [ + "test.paired_end.sorted.bam.csi", [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" - ] + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-12T18:40:46.579747" + "timestamp": "2024-07-22T16:52:55.688799" }, - "bai_versions": { + "crai": { "content": [ - [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" - ] + { + "0": [ + + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ], + "3": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ], + "bai": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T16:51:17.609533" + }, + "bai": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ], + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ], + "crai": [ + + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-28T15:41:57.929287369" + "timestamp": "2024-07-22T16:51:04.16585" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 596c6f7e..8e019099 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -50,10 +50,20 @@ process SAMTOOLS_SORT { """ stub: + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + def extension = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt cram") ? "cram" : + "bam" """ - touch ${prefix}.bam - touch ${prefix}.bam.csi + touch ${prefix}.${extension} + if [ "${extension}" == "bam" ]; + then + touch ${prefix}.${extension}.csi + elif [ "${extension}" == "cram" ]; + then + touch ${prefix}.${extension}.crai + fi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index fb38ed9b..c2ea9c72 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -32,16 +32,16 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.bam, - process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } } - ).match("test_bam") - } + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match()} ) } } test("cram") { - config "./nextflow.config" + config "./nextflow_cram.config" when { process { @@ -62,23 +62,20 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - process.out.bam, - process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } } - ).match("test_cram") - } + process.out.cram.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.crai.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match()} ) } } - test("bam_stub") { + test("bam - stub") { - config "./nextflow.config" options "-stub" + config "./nextflow.config" when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -96,8 +93,35 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(file(process.out.bam[0][1]).name).match("bam_stub_bam") }, - { assert snapshot(process.out.versions).match("bam_stub_versions") } + { assert snapshot(process.out).match() } + ) + } + } + + test("cram - stub") { + + options "-stub" + config "./nextflow_cram.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index 5a27de1d..da38d5d1 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -7,54 +7,159 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,21c992d59615936b99f2ad008aa54400" + "test.sorted.cram" ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram.crai" + ] + ], + [ + "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-31T08:13:54.512837189" + "timestamp": "2024-07-22T17:19:37.196205" }, - "bam_stub_bam": { + "bam - stub": { "content": [ - "test.sorted.bam" + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-31T07:29:00.761845507" + "timestamp": "2024-07-22T15:54:46.580756" }, - "test_cram": { + "cram - stub": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,22b2093be34a7637f5fbc84272b89d06" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.csi" + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + + ], + "4": [ + "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + ], + "bam": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cram": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" ] - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-31T09:16:51.924951855" + "timestamp": "2024-07-22T15:57:30.505698" }, - "test_bam": { + "bam": { "content": [ [ [ @@ -73,42 +178,15 @@ }, "test.sorted.bam.csi" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-05-31T08:28:12.15952312" - }, - "bam_stub_versions": { - "content": [ + ], [ "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-05-31T07:29:00.765038811" - }, - "bam": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,21c992d59615936b99f2ad008aa54400" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-31T08:13:48.538030517" + "timestamp": "2024-07-22T15:54:25.872954" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/tests/nextflow_cram.config b/modules/nf-core/samtools/sort/tests/nextflow_cram.config new file mode 100644 index 00000000..3a8c0188 --- /dev/null +++ b/modules/nf-core/samtools/sort/tests/nextflow_cram.config @@ -0,0 +1,8 @@ +process { + + withName: SAMTOOLS_SORT { + ext.prefix = { "${meta.id}.sorted" } + ext.args = "--write-index --output-fmt cram" + } + +} diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test b/modules/nf-core/samtools/stats/tests/main.nf.test index e3d5cb14..28a77db2 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test +++ b/modules/nf-core/samtools/stats/tests/main.nf.test @@ -11,9 +11,6 @@ nextflow_process { test("bam") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -37,9 +34,59 @@ nextflow_process { test("cram") { when { - params { - outdir = "$outputDir" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ } + } + + then { + assertAll( + {assert process.success}, + {assert snapshot(process.out).match()} + ) + } + } + + test("bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + {assert process.success}, + {assert snapshot(process.out).match()} + ) + } + } + + test("cram - stub") { + + options "-stub" + + when { process { """ input[0] = Channel.of([ diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap index 2747fd6c..3828f378 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -29,10 +29,80 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-28T15:45:24.403941966" + "timestamp": "2024-07-22T14:20:24.885816" + }, + "bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T14:20:39.310713" + }, + "cram - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T14:21:04.771199" }, "bam": { "content": [ @@ -64,9 +134,9 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-28T15:45:06.711251947" + "timestamp": "2024-07-22T14:19:06.645466" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index 38df8576..dc611448 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -13,13 +13,15 @@ process SAMTOOLS_VIEW { path qname output: - tuple val(meta), path("*.bam"), emit: bam, optional: true - tuple val(meta), path("*.cram"), emit: cram, optional: true - tuple val(meta), path("*.sam"), emit: sam, optional: true - tuple val(meta), path("*.bai"), emit: bai, optional: true - tuple val(meta), path("*.csi"), emit: csi, optional: true - tuple val(meta), path("*.crai"), emit: crai, optional: true - path "versions.yml", emit: versions + tuple val(meta), path("${prefix}.bam"), emit: bam, optional: true + tuple val(meta), path("${prefix}.cram"), emit: cram, optional: true + tuple val(meta), path("${prefix}.sam"), emit: sam, optional: true + tuple val(meta), path("${prefix}.${file_type}.bai"), emit: bai, optional: true + tuple val(meta), path("${prefix}.${file_type}.csi"), emit: csi, optional: true + tuple val(meta), path("${prefix}.${file_type}.crai"), emit: crai, optional: true + tuple val(meta), path("${prefix}.unselected.${file_type}"), emit: unselected, optional: true + tuple val(meta), path("${prefix}.unselected.${file_type}.{bai,csi,crsi}"), emit: unselected_index, optional: true + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -27,13 +29,13 @@ process SAMTOOLS_VIEW { script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" def reference = fasta ? "--reference ${fasta}" : "" - def readnames = qname ? "--qname-file ${qname}": "" - def file_type = args.contains("--output-fmt sam") ? "sam" : - args.contains("--output-fmt bam") ? "bam" : - args.contains("--output-fmt cram") ? "cram" : - input.getExtension() + file_type = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt bam") ? "bam" : + args.contains("--output-fmt cram") ? "cram" : + input.getExtension() + readnames = qname ? "--qname-file ${qname} --output-unselected ${prefix}.unselected.${file_type}": "" if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ samtools \\ @@ -54,14 +56,14 @@ process SAMTOOLS_VIEW { stub: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def file_type = args.contains("--output-fmt sam") ? "sam" : - args.contains("--output-fmt bam") ? "bam" : - args.contains("--output-fmt cram") ? "cram" : - input.getExtension() + prefix = task.ext.prefix ?: "${meta.id}" + file_type = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt bam") ? "bam" : + args.contains("--output-fmt cram") ? "cram" : + input.getExtension() if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" - def index = args.contains("--write-index") ? "touch ${prefix}.csi" : "" + def index = args.contains("--write-index") ? "touch ${prefix}.${file_type}.csi" : "" """ touch ${prefix}.${file_type} diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml index 3dadafae..27be60d0 100644 --- a/modules/nf-core/samtools/view/meta.yml +++ b/modules/nf-core/samtools/view/meta.yml @@ -73,6 +73,15 @@ output: type: file description: optional CRAM file index pattern: "*.{crai}" + # unselected and unselected_index are created when passing a qname + - unselected: + type: file + description: optional file with unselected alignments + pattern: "*.unselected.{bam,cram,sam}" + - unselected_index: + type: file + description: index for the "unselected" file + pattern: "*.unselected.{bai,csi,crai}" - versions: type: file description: File containing software versions diff --git a/modules/nf-core/samtools/view/tests/main.nf.test b/modules/nf-core/samtools/view/tests/main.nf.test index 45a0defb..37b81a91 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test +++ b/modules/nf-core/samtools/view/tests/main.nf.test @@ -172,6 +172,8 @@ nextflow_process { { assert snapshot(process.out.crai).match("cram_to_bam_index_qname_crai") }, { assert snapshot(process.out.cram).match("cram_to_bam_index_qname_cram") }, { assert snapshot(process.out.sam).match("cram_to_bam_index_qname_sam") }, + { assert snapshot(file(process.out.unselected[0][1]).name).match("cram_to_bam_index_qname_unselected") }, + { assert snapshot(file(process.out.unselected_index[0][1]).name).match("cram_to_bam_index_qname_unselected_csi") }, { assert snapshot(process.out.versions).match("cram_to_bam_index_qname_versions") } ) } diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap index eb0c577c..6bcce9fe 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap @@ -355,6 +355,26 @@ }, "timestamp": "2024-02-12T19:38:23.322874" }, + "cram_to_bam_index_qname_unselected": { + "content": [ + "test.unselected.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.322874" + }, + "cram_to_bam_index_qname_unselected_csi": { + "content": [ + "test.unselected.bam.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.328458" + }, "bam_versions": { "content": [ [ @@ -477,7 +497,7 @@ }, "bam_stub_csi": { "content": [ - "test.csi" + "test.bam.csi" ], "meta": { "nf-test": "0.8.4", diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index 8e9c48b1..ae67e004 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -81,6 +81,8 @@ process STAR_ALIGN { stub: def prefix = task.ext.prefix ?: "${meta.id}" """ + echo "" | gzip > ${prefix}.unmapped_1.fastq.gz + echo "" | gzip > ${prefix}.unmapped_2.fastq.gz touch ${prefix}Xd.out.bam touch ${prefix}.Log.final.out touch ${prefix}.Log.out @@ -89,8 +91,6 @@ process STAR_ALIGN { touch ${prefix}.toTranscriptome.out.bam touch ${prefix}.Aligned.unsort.out.bam touch ${prefix}.Aligned.sortedByCoord.out.bam - touch ${prefix}.unmapped_1.fastq.gz - touch ${prefix}.unmapped_2.fastq.gz touch ${prefix}.tab touch ${prefix}.SJ.out.tab touch ${prefix}.ReadsPerGene.out.tab diff --git a/modules/nf-core/star/align/tests/main.nf.test b/modules/nf-core/star/align/tests/main.nf.test index 6ecd7786..2d9f72dd 100644 --- a/modules/nf-core/star/align/tests/main.nf.test +++ b/modules/nf-core/star/align/tests/main.nf.test @@ -9,27 +9,367 @@ nextflow_process { tag "star/align" tag "star/genomegenerate" - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" + test("homo_sapiens - single_end") { + config "./nextflow.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + + when { process { """ input[0] = Channel.of([ - [ id:'test_fasta' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ] ]) - input[1] = Channel.of([ + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ [ id:'test_gtf' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] ]) + input[3] = false + input[4] = 'illumina' + input[5] = false """ } } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.log_final[0][1]).name, + file(process.out.log_out[0][1]).name, + file(process.out.log_progress[0][1]).name, + process.out.bam, + process.out.bam_sorted, + process.out.bam_transcript, + process.out.bam_unsorted, + process.out.bedgraph, + process.out.fastq, + process.out.junction, + process.out.read_per_gene_tab, + process.out.sam, + process.out.spl_junc_tab, + process.out.tab, + process.out.wig, + process.out.versions + ).match() } + ) + } } - test("homo_sapiens - single_end") { + test("homo_sapiens - paired_end") { + config "./nextflow.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.log_final[0][1]).name, + file(process.out.log_out[0][1]).name, + file(process.out.log_progress[0][1]).name, + process.out.bam, + process.out.bam_sorted, + process.out.bam_transcript, + process.out.bam_unsorted, + process.out.bedgraph, + process.out.fastq, + process.out.junction, + process.out.read_per_gene_tab, + process.out.sam, + process.out.spl_junc_tab, + process.out.tab, + process.out.wig, + process.out.versions + ).match() } + ) + } + } + + test("homo_sapiens - paired_end - arriba") { + config "./nextflow.arriba.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.log_final[0][1]).name, + file(process.out.log_out[0][1]).name, + file(process.out.log_progress[0][1]).name, + process.out.bam, + process.out.bam_sorted, + process.out.bam_transcript, + process.out.bam_unsorted, + process.out.bedgraph, + process.out.fastq, + process.out.junction, + process.out.read_per_gene_tab, + process.out.sam, + process.out.spl_junc_tab, + process.out.tab, + process.out.wig, + process.out.versions + ).match() } + ) + } + } + + test("homo_sapiens - paired_end - starfusion") { + config "./nextflow.starfusion.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.log_final[0][1]).name, + file(process.out.log_out[0][1]).name, + file(process.out.log_progress[0][1]).name, + process.out.bam, + process.out.bam_sorted, + process.out.bam_transcript, + process.out.bam_unsorted, + process.out.bedgraph, + process.out.fastq, + process.out.junction, + process.out.read_per_gene_tab, + process.out.sam, + process.out.spl_junc_tab, + process.out.tab, + process.out.wig, + process.out.versions + ).match() } + ) + } + } + + test("homo_sapiens - paired_end - multiple") { config "./nextflow.config" + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.log_final[0][1]).name, + file(process.out.log_out[0][1]).name, + file(process.out.log_progress[0][1]).name, + process.out.bam, + process.out.bam_sorted, + process.out.bam_transcript, + process.out.bam_unsorted, + process.out.bedgraph, + process.out.fastq, + process.out.junction, + process.out.read_per_gene_tab, + process.out.sam, + process.out.spl_junc_tab, + process.out.tab, + process.out.wig, + process.out.versions + ).match() } + ) + } + } + + test("homo_sapiens - single_end - stub") { + options "-stub" + config "./nextflow.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + when { process { """ @@ -52,29 +392,33 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - single_end - log_final") }, - { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - single_end - log_out") }, - { assert snapshot(process.out.bam).match("homo_sapiens - single_end - bam") }, - { assert snapshot(process.out.bam_sorted).match("homo_sapiens - single_end - bam_sorted") }, - { assert snapshot(process.out.bam_transcript).match("homo_sapiens - single_end - bam_transcript") }, - { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - single_end - bam_unsorted") }, - { assert snapshot(process.out.bedgraph).match("homo_sapiens - single_end - bedgraph") }, - { assert snapshot(process.out.fastq).match("homo_sapiens - single_end - fastq") }, - { assert snapshot(process.out.junction).match("homo_sapiens - single_end - junction") }, - { assert snapshot(process.out.log_progress).match("homo_sapiens - single_end - log_progress") }, - { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - single_end - read_per_gene_tab") }, - { assert snapshot(process.out.sam).match("homo_sapiens - single_end - sam") }, - { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - single_end - spl_junc_tab") }, - { assert snapshot(process.out.tab).match("homo_sapiens - single_end - tab") }, - { assert snapshot(process.out.wig).match("homo_sapiens - single_end - wig") }, - { assert snapshot(process.out.versions).match("homo_sapiens - single_end - versions") } + { assert snapshot(process.out).match() } ) } } - test("homo_sapiens - paired_end") { + test("homo_sapiens - paired_end - stub") { + options "-stub" config "./nextflow.config" + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + when { process { """ @@ -100,29 +444,33 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - log_final") }, - { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - log_out") }, - { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - bam") }, - { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - bam_sorted") }, - { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - bam_transcript") }, - { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - bam_unsorted") }, - { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - bedgraph") }, - { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - fastq") }, - { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - junction") }, - { assert snapshot(process.out.log_progress).match("homo_sapiens - paired_end - log_progress") }, - { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - read_per_gene_tab") }, - { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - sam") }, - { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - spl_junc_tab") }, - { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - tab") }, - { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - wig") }, - { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - versions") } + { assert snapshot(process.out).match() } ) } } - test("homo_sapiens - paired_end - arriba") { + test("homo_sapiens - paired_end - arriba - stub") { + options "-stub" config "./nextflow.arriba.config" + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + when { process { """ @@ -148,29 +496,33 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - arriba - log_final") }, - { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - arriba - log_out") }, - { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - arriba - log_progress") }, - { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - arriba - bam") }, - { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - arriba - bam_sorted") }, - { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - arriba - bam_transcript") }, - { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - arriba - bam_unsorted") }, - { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - arriba - bedgraph") }, - { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - arriba - fastq") }, - { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - arriba - junction") }, - { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - arriba - read_per_gene_tab") }, - { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - arriba - sam") }, - { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - arriba - spl_junc_tab") }, - { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - arriba - tab") }, - { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - arriba - wig") }, - { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - arriba - versions") } + { assert snapshot(process.out).match() } ) } } - test("homo_sapiens - paired_end - starfusion") { + test("homo_sapiens - paired_end - starfusion - stub") { + options "-stub" config "./nextflow.starfusion.config" + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + when { process { """ @@ -196,29 +548,33 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_final") }, - { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_out") }, - { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_progress") }, - { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - starfusion - bam") }, - { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - starfusion - bam_sorted") }, - { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - starfusion - bam_transcript") }, - { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - starfusion - bam_unsorted") }, - { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - starfusion - bedgraph") }, - { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - starfusion - fastq") }, - { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - starfusion - junction") }, - { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - starfusion - read_per_gene_tab") }, - { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - starfusion - sam") }, - { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - starfusion - spl_junc_tab") }, - { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - starfusion - tab") }, - { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - starfusion - wig") }, - { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - starfusion - versions") } + { assert snapshot(process.out).match() } ) } } - test("homo_sapiens - paired_end - multiple") { + test("homo_sapiens - paired_end - multiple - stub") { + options "-stub" config "./nextflow.config" + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + when { process { """ @@ -246,22 +602,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - multiple - log_final") }, - { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - multiple - log_out") }, - { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - multiple - log_progress") }, - { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - multiple - bam") }, - { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - multiple - bam_sorted") }, - { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - multiple - bam_transcript") }, - { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - multiple - bam_unsorted") }, - { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - multiple - bedgraph") }, - { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - multiple - fastq") }, - { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - multiple - junction") }, - { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - multiple - read_per_gene_tab") }, - { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - multiple - sam") }, - { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - multiple - spl_junc_tab") }, - { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - multiple - tab") }, - { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - multiple - wig") }, - { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - multiple - versions") } + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/star/align/tests/main.nf.test.snap b/modules/nf-core/star/align/tests/main.nf.test.snap index 08edb914..c814eb56 100644 --- a/modules/nf-core/star/align/tests/main.nf.test.snap +++ b/modules/nf-core/star/align/tests/main.nf.test.snap @@ -1,382 +1,1170 @@ { - "homo_sapiens - paired_end - multiple - bam_sorted": { + "homo_sapiens - single_end - stub": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.sortedByCoord.out.bam:md5,ab07c21d63ab0a6c07d171d213c81d5a" + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "10": [ + [ + { + "id": "test", + "single_end": true + }, + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "11": [ + [ + { + "id": "test", + "single_end": true + }, + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "12": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "13": [ + [ + { + "id": 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read_per_gene_tab": { - "content": [ + ], [ - ] - ], - "timestamp": "2023-11-23T13:29:01.596406" - }, - "homo_sapiens - single_end - read_per_gene_tab": { - "content": [ + ], [ - ] - ], - "timestamp": "2023-11-23T13:22:55.205936" - }, - "homo_sapiens - paired_end - junction": { - "content": [ + ], [ - ] - ], - "timestamp": "2023-11-23T13:23:33.340653" - }, - "homo_sapiens - paired_end - spl_junc_tab": { - "content": [ + ], [ - [ - { - "id": "test", - "single_end": false - }, - "test.SJ.out.tab:md5,844af19ab0fc8cd9a3f75228445aca0d" - ] - ] - ], - "timestamp": "2023-12-04T17:54:12.185730856" - }, - "homo_sapiens - paired_end - starfusion - sam": { - "content": [ + + ], [ - ] - ], - "timestamp": "2023-11-23T13:27:56.300637" - }, - "homo_sapiens - paired_end - arriba - bam": { - "content": [ + ], + [ + + ], [ [ { "id": "test", "single_end": false }, - "test.Aligned.out.bam:md5,c1b1747f5873f2d17762725636e891d5" + "test.SJ.out.tab:md5,5155c9fd1f787ad6d7d80987fb06219c" ] - ] - ], - 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"test.Signal.UniqueMultiple.str1.out.bg:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + ], + "4": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "5": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "6": [ + [ + { + "id": "test", + "single_end": false + }, + "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "7": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "9": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "bam_sorted": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "bam_transcript": [ + [ + { + "id": "test", + "single_end": false + }, + "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_unsorted": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bedgraph": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Signal.UniqueMultiple.str1.out.bg:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fastq": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "junction": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "log_final": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "log_out": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "log_progress": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "read_per_gene_tab": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "sam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "spl_junc_tab": [ + [ + { + "id": "test", + "single_end": false + }, + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tab": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" + ], + "wig": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } ], - "timestamp": "2023-11-23T13:27:55.93945" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T15:16:40.64399" } } \ No newline at end of file diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test b/modules/nf-core/star/genomegenerate/tests/main.nf.test index c17c8ba4..4d619c47 100644 --- a/modules/nf-core/star/genomegenerate/tests/main.nf.test +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test @@ -28,15 +28,15 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_gtf_index") }, - { assert snapshot(process.out.versions).match("fasta_gtf_versions") } + { assert snapshot( + file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString(), + process.out.versions) + .match() } ) } } - test("fasta_gtf_stub") { - - options '-stub' + test("fasta") { when { process { @@ -45,10 +45,7 @@ nextflow_process { [ id:'test_fasta' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] - ]) + input[1] = Channel.of([ [], [] ]) """ } } @@ -56,13 +53,17 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_gtf_stub_index") }, - { assert snapshot(process.out.versions).match("fasta_gtf_stub_versions") } + { assert snapshot( + file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString(), + process.out.versions + ).match() } ) } } - test("fasta") { + test("fasta_gtf_stub") { + + options '-stub' when { process { @@ -71,7 +72,10 @@ nextflow_process { [ id:'test_fasta' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] ]) - input[1] = Channel.of([ [], [] ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) """ } } @@ -79,11 +83,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_index") }, - { assert snapshot(process.out.versions).match("fasta_versions") } + { assert snapshot(process.out).match() } ) } - } test("fasta_stub") { @@ -105,11 +107,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_stub_index") }, - { assert snapshot(process.out.versions).match("fasta_stub_versions") } + { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap index 5653d6e6..207f4b4f 100644 --- a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap @@ -1,90 +1,148 @@ { - "fasta_gtf_versions": { + "fasta_gtf": { "content": [ + "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]", [ "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-01T15:54:31.798555" + "timestamp": "2024-07-22T14:55:35.478401" }, - "fasta_stub_versions": { + "fasta_gtf_stub": { "content": [ - [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-01T15:55:07.521209" - }, - "fasta_gtf_stub_index": { - "content": [ - "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-01T15:54:46.478098" - }, - "fasta_gtf_stub_versions": { - "content": [ - [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" - ] + { + "0": [ + [ + { + "id": "test_fasta" + }, + [ + "Genome:md5,d41d8cd98f00b204e9800998ecf8427e", + "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "SA:md5,d41d8cd98f00b204e9800998ecf8427e", + "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "exonGeTrInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "exonInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "geneInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sjdbInfo.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sjdbList.fromGTF.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "sjdbList.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + ], + "index": [ + [ + { + "id": "test_fasta" + }, + [ + "Genome:md5,d41d8cd98f00b204e9800998ecf8427e", + "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "SA:md5,d41d8cd98f00b204e9800998ecf8427e", + "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "exonGeTrInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "exonInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "geneInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sjdbInfo.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sjdbList.fromGTF.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "sjdbList.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-01T15:54:46.491657" + "timestamp": "2024-07-22T14:55:57.247585" }, - "fasta_index": { + "fasta_stub": { "content": [ - "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]" + { + "0": [ + [ + { + "id": "test_fasta" + }, + [ + "Genome:md5,d41d8cd98f00b204e9800998ecf8427e", + "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "SA:md5,d41d8cd98f00b204e9800998ecf8427e", + "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + ], + "index": [ + [ + { + "id": "test_fasta" + }, + [ + "Genome:md5,d41d8cd98f00b204e9800998ecf8427e", + "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "SA:md5,d41d8cd98f00b204e9800998ecf8427e", + "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-01T15:54:57.552329" + "timestamp": "2024-07-22T14:56:07.01742" }, - "fasta_versions": { + "fasta": { "content": [ + "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]", [ "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-01T15:54:57.560541" - }, - "fasta_gtf_index": { - "content": [ - "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-01T15:54:31.786814" - }, - "fasta_stub_index": { - "content": [ - "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-01T15:55:07.517472" + "timestamp": "2024-07-22T14:55:45.48784" } } \ No newline at end of file diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test b/modules/nf-core/stringtie/stringtie/tests/main.nf.test index 00efe8f1..2204e849 100644 --- a/modules/nf-core/stringtie/stringtie/tests/main.nf.test +++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test @@ -3,6 +3,7 @@ nextflow_process { name "Test Process STRINGTIE_STRINGTIE" script "../main.nf" process "STRINGTIE_STRINGTIE" + config "./nextflow.config" tag "modules" tag "modules_nfcore" tag "stringtie" @@ -10,8 +11,6 @@ nextflow_process { test("sarscov2 [bam] - forward strandedness") { - config "./nextflow.config" - when { process { """ @@ -27,17 +26,17 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.transcript_gtf).match("fs_transcript_gtf") }, - { assert snapshot(process.out.abundance).match("fs_abundance") }, - { assert snapshot(process.out.versions).match("fs_versions") } + { assert snapshot( + process.out.abundance, + process.out.transcript_gtf, + process.out.versions + ).match() } ) } } test("sarscov2 [bam] - forward strandedness + reference annotation") { - config "./nextflow.config" - when { process { """ @@ -53,18 +52,18 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.transcript_gtf).match("fs_gtf_transcript_gtf") }, - { assert snapshot(process.out.abundance).match("fs_gtf_abundance") }, - { assert snapshot(process.out.ballgown).match("fs_gtf_ballgown") }, - { assert snapshot(process.out.versions).match("fs_gtf_versions") } + { assert snapshot( + process.out.abundance, + process.out.ballgown, + process.out.transcript_gtf, + process.out.versions + ).match() } ) } } test("sarscov2 [bam] - reverse strandedness") { - config "./nextflow.config" - when { process { """ @@ -80,16 +79,117 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.transcript_gtf).match("rs_transcript_gtf") }, - { assert snapshot(process.out.abundance).match("rs_abundance") }, - { assert snapshot(process.out.versions).match("rs_versions") } + { assert snapshot( + process.out.abundance, + process.out.transcript_gtf, + process.out.versions + ).match() } ) } } test("sarscov2 [bam] - reverse strandedness + reference annotation") { - config "./nextflow.config" + when { + process { + """ + input[0] = [ + [ id:'test', strandedness:'reverse' ], // meta map + [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ] + ] + input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.abundance, + process.out.ballgown, + process.out.transcript_gtf, + process.out.versions + ).match() } + ) + } + } + + test("sarscov2 [bam] - forward strandedness - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', strandedness:'forward' ], // meta map + [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ] + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 [bam] - forward strandedness + reference annotation - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', strandedness:'forward' ], // meta map + [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ] + ] + input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 [bam] - reverse strandedness - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', strandedness:'reverse' ], // meta map + [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ] + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 [bam] - reverse strandedness + reference annotation - stub") { + + options "-stub" when { process { @@ -106,10 +206,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.transcript_gtf).match("rs_gtf_transcript_gtf") }, - { assert snapshot(process.out.abundance).match("rs_gtf_abundance") }, - { assert snapshot(process.out.ballgown).match("rs_gtf_ballgown") }, - { assert snapshot(process.out.versions).match("rs_gtf_versions") } + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap index bf751636..124dd4cb 100644 --- a/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap +++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "fs_abundance": { + "sarscov2 [bam] - forward strandedness + reference annotation": { "content": [ [ [ @@ -7,49 +7,44 @@ "id": "test", "strandedness": "forward" }, - "test.gene.abundance.txt:md5,d6f5c8cadb8458f1df0427cf790246e3" + "test.gene.abundance.txt:md5,7d8bce7f2a922e367cedccae7267c22e" ] - ] - ], - "timestamp": "2023-11-23T13:55:41.032044613" - }, - "fs_transcript_gtf": { - "content": [ + ], [ [ { "id": "test", "strandedness": "forward" }, - "test.transcripts.gtf:md5,569137af5be452413086b50653a97203" + [ + "e2t.ctab:md5,e981c0038295ae54b63cedb1083f1540", + "e_data.ctab:md5,6b4cf69bc03f3f69890f972a0e8b7471", + "i2t.ctab:md5,8a117c8aa4334b4c2d4711932b006fb4", + "i_data.ctab:md5,be3abe09740603213f83d50dcf81427f", + "t_data.ctab:md5,3b66c065da73ae0dd41cc332eff6a818" + ] ] - ] - ], - "timestamp": "2023-11-23T13:55:41.017978904" - }, - "rs_abundance": { - "content": [ + ], [ [ { "id": "test", - "strandedness": "reverse" + "strandedness": "forward" }, - "test.gene.abundance.txt:md5,d6f5c8cadb8458f1df0427cf790246e3" + "test.transcripts.gtf:md5,f56cf8aba2c4a5673bc7963ba5f12d04" ] - ] - ], - "timestamp": "2023-11-23T13:56:13.601112933" - }, - "fs_gtf_versions": { - "content": [ + ], [ "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" ] ], - "timestamp": "2023-11-23T13:56:00.523797974" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T12:33:44.299962" }, - "fs_gtf_transcript_gtf": { + "sarscov2 [bam] - forward strandedness": { "content": [ [ [ @@ -57,50 +52,395 @@ "id": "test", "strandedness": "forward" }, - "test.transcripts.gtf:md5,f56cf8aba2c4a5673bc7963ba5f12d04" + "test.gene.abundance.txt:md5,d6f5c8cadb8458f1df0427cf790246e3" + ] + ], + [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.transcripts.gtf:md5,569137af5be452413086b50653a97203" ] + ], + [ + "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" ] ], - "timestamp": "2023-11-23T13:56:00.475164879" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T12:33:35.177738" }, - "rs_versions": { + "sarscov2 [bam] - forward strandedness - stub": { "content": [ - [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" - ] + { + "0": [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + ], + "abundance": [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "ballgown": [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "coverage_gtf": [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "transcript_gtf": [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + ] + } ], - "timestamp": "2023-11-23T13:56:13.623892691" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T12:36:32.885078" }, - "rs_gtf_transcript_gtf": { + "sarscov2 [bam] - forward strandedness + reference annotation - stub": { "content": [ - [ - [ - { - "id": "test", - "strandedness": "reverse" - }, - "test.transcripts.gtf:md5,bb346053a8c156b803b055133376c7fa" + { + "0": [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + ], + "abundance": [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "ballgown": [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "coverage_gtf": [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "transcript_gtf": [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" ] - ] + } ], - "timestamp": "2023-11-23T13:56:22.693599559" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T12:36:43.325777" }, - "fs_gtf_abundance": { + "sarscov2 [bam] - reverse strandedness + reference annotation - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + ], + "abundance": [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "ballgown": [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "coverage_gtf": [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "transcript_gtf": [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T12:37:06.085936" + }, + "sarscov2 [bam] - reverse strandedness - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + ], + "abundance": [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "ballgown": [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "coverage_gtf": [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "transcript_gtf": [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T12:36:53.837578" + }, + "sarscov2 [bam] - reverse strandedness + reference annotation": { "content": [ [ [ { "id": "test", - "strandedness": "forward" + "strandedness": "reverse" }, - "test.gene.abundance.txt:md5,7d8bce7f2a922e367cedccae7267c22e" + "test.gene.abundance.txt:md5,7385b870b955dae2c2ab78a70cf05cce" ] - ] - ], - "timestamp": "2023-11-23T13:56:00.482135418" - }, - "rs_gtf_ballgown": { - "content": [ + ], [ [ { @@ -115,72 +455,54 @@ "t_data.ctab:md5,3b66c065da73ae0dd41cc332eff6a818" ] ] - ] - ], - "timestamp": "2023-11-23T13:56:22.715698347" - }, - "rs_transcript_gtf": { - "content": [ + ], [ [ { "id": "test", "strandedness": "reverse" }, - "test.transcripts.gtf:md5,31c34aec2bf36bb0ea3c16c2afeeeb1f" + "test.transcripts.gtf:md5,bb346053a8c156b803b055133376c7fa" ] - ] - ], - "timestamp": "2023-11-23T13:56:13.590054035" - }, - "rs_gtf_versions": { - "content": [ + ], [ "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" ] ], - "timestamp": "2023-11-23T13:56:22.725513476" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T12:34:03.114695" }, - "fs_gtf_ballgown": { + "sarscov2 [bam] - reverse strandedness": { "content": [ [ [ { "id": "test", - "strandedness": "forward" + "strandedness": "reverse" }, - [ - "e2t.ctab:md5,e981c0038295ae54b63cedb1083f1540", - "e_data.ctab:md5,6b4cf69bc03f3f69890f972a0e8b7471", - "i2t.ctab:md5,8a117c8aa4334b4c2d4711932b006fb4", - "i_data.ctab:md5,be3abe09740603213f83d50dcf81427f", - "t_data.ctab:md5,3b66c065da73ae0dd41cc332eff6a818" - ] + "test.gene.abundance.txt:md5,d6f5c8cadb8458f1df0427cf790246e3" ] - ] - ], - "timestamp": "2023-11-23T13:56:00.494299817" - }, - "fs_versions": { - "content": [ - [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" - ] - ], - "timestamp": "2023-11-23T13:55:41.049417582" - }, - "rs_gtf_abundance": { - "content": [ + ], [ [ { "id": "test", "strandedness": "reverse" }, - "test.gene.abundance.txt:md5,7385b870b955dae2c2ab78a70cf05cce" + "test.transcripts.gtf:md5,31c34aec2bf36bb0ea3c16c2afeeeb1f" ] + ], + [ + "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" ] ], - "timestamp": "2023-11-23T13:56:22.701059059" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T12:33:52.874479" } -} +} \ No newline at end of file diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 24ead871..0e2f3290 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -72,4 +72,25 @@ process TRIMGALORE { END_VERSIONS """ } + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + if (meta.single_end) { + output_command = "echo '' | gzip > ${prefix}_trimmed.fq.gz ;" + output_command += "touch ${prefix}.fastq.gz_trimming_report.txt" + } else { + output_command = "echo '' | gzip > ${prefix}_1_trimmed.fq.gz ;" + output_command += "touch ${prefix}_1.fastq.gz_trimming_report.txt ;" + output_command += "echo '' | gzip > ${prefix}_2_trimmed.fq.gz ;" + output_command += "touch ${prefix}_2.fastq.gz_trimming_report.txt" + } + """ + ${output_command} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//') + cutadapt: \$(cutadapt --version) + END_VERSIONS + """ } diff --git a/modules/nf-core/trimgalore/tests/main.nf.test b/modules/nf-core/trimgalore/tests/main.nf.test index 43904ac3..2a3dbbb0 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test +++ b/modules/nf-core/trimgalore/tests/main.nf.test @@ -44,6 +44,28 @@ nextflow_process { } } + test("test_trimgalore_single_end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + test("test_trimgalore_paired_end") { when { @@ -100,4 +122,29 @@ nextflow_process { ) } } + + test("test_trimgalore_paired_end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap index 082c5500..6cb31c9f 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test.snap +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -11,6 +11,160 @@ }, "timestamp": "2024-02-29T16:33:20.401347" }, + "test_trimgalore_single_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + + ], + "4": [ + + ], + "5": [ + "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + ], + "html": [ + + ], + "log": [ + [ + { + "id": "test", + "single_end": true + }, + "test.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "unpaired": [ + + ], + "versions": [ + "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + ], + "zip": [ + + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-21T10:27:44.964166" + }, + "test_trimgalore_paired_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "2": [ + + ], + "3": [ + + ], + "4": [ + + ], + "5": [ + "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + ], + "html": [ + + ], + "log": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "unpaired": [ + + ], + "versions": [ + "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + ], + "zip": [ + + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-21T10:28:07.611496" + }, "test_trimgalore_paired_end": { "content": [ [ From 802768638db5ea81aec179a46d35fff17f8dd9a8 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Tue, 6 Aug 2024 17:43:44 +0200 Subject: [PATCH 456/491] Revert "updating nf-core modules" This reverts commit 4cbb345872ab8777f5b26f351f6982a201b680ed. --- modules.json | 56 +- modules/nf-core/bioawk/main.nf | 11 +- modules/nf-core/bowtie/align/environment.yml | 1 - modules/nf-core/bowtie/align/main.nf | 35 +- modules/nf-core/bowtie/align/meta.yml | 21 +- .../nf-core/bowtie/align/tests/main.nf.test | 129 - .../bowtie/align/tests/main.nf.test.snap | 192 -- modules/nf-core/bowtie/align/tests/tags.yml | 2 - modules/nf-core/bowtie/build/main.nf | 32 +- modules/nf-core/bowtie/build/meta.yml | 12 +- .../nf-core/bowtie/build/tests/main.nf.test | 57 - .../bowtie/build/tests/main.nf.test.snap | 96 - modules/nf-core/bowtie/build/tests/tags.yml | 2 - .../nf-core/bowtie2/align/tests/main.nf.test | 90 +- modules/nf-core/cat/cat/main.nf | 1 + modules/nf-core/cat/cat/tests/main.nf.test | 27 +- .../nf-core/cat/cat/tests/main.nf.test.snap | 74 +- modules/nf-core/cat/fastq/main.nf | 10 +- modules/nf-core/cat/fastq/tests/main.nf.test | 136 +- .../nf-core/cat/fastq/tests/main.nf.test.snap | 207 -- .../templates/dumpsoftwareversions.py | 1 + .../custom/tx2gene/templates/tx2gene.py | 24 +- .../nf-core/custom/tx2gene/tests/main.nf.test | 45 +- .../custom/tx2gene/tests/main.nf.test.snap | 96 +- modules/nf-core/fastqc/tests/main.nf.test | 225 +- .../nf-core/fastqc/tests/main.nf.test.snap | 370 +-- modules/nf-core/hisat2/align/main.nf | 19 - .../nf-core/hisat2/align/tests/main.nf.test | 202 -- .../hisat2/align/tests/main.nf.test.snap | 338 +-- modules/nf-core/hisat2/build/main.nf | 11 - .../nf-core/hisat2/build/tests/main.nf.test | 47 +- .../hisat2/build/tests/main.nf.test.snap | 66 +- .../nf-core/hisat2/extractsplicesites/main.nf | 11 - .../extractsplicesites/tests/main.nf.test | 26 - .../tests/main.nf.test.snap | 37 - modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 10 +- modules/nf-core/multiqc/meta.yml | 13 - modules/nf-core/multiqc/tests/main.nf.test | 6 - .../nf-core/multiqc/tests/main.nf.test.snap | 18 +- .../samtools/flagstat/tests/main.nf.test | 28 +- .../samtools/flagstat/tests/main.nf.test.snap | 78 +- .../samtools/idxstats/tests/main.nf.test | 29 +- .../samtools/idxstats/tests/main.nf.test.snap | 78 +- modules/nf-core/samtools/index/main.nf | 7 +- .../nf-core/samtools/index/tests/main.nf.test | 87 +- .../samtools/index/tests/main.nf.test.snap | 264 +- modules/nf-core/samtools/sort/main.nf | 14 +- .../nf-core/samtools/sort/tests/main.nf.test | 54 +- .../samtools/sort/tests/main.nf.test.snap | 202 +- .../samtools/sort/tests/nextflow_cram.config | 8 - .../nf-core/samtools/stats/tests/main.nf.test | 57 +- .../samtools/stats/tests/main.nf.test.snap | 82 +- modules/nf-core/samtools/view/main.nf | 40 +- modules/nf-core/samtools/view/meta.yml | 9 - .../nf-core/samtools/view/tests/main.nf.test | 2 - .../samtools/view/tests/main.nf.test.snap | 22 +- modules/nf-core/star/align/main.nf | 4 +- modules/nf-core/star/align/tests/main.nf.test | 523 +--- .../star/align/tests/main.nf.test.snap | 2288 ++++------------- .../star/genomegenerate/tests/main.nf.test | 39 +- .../genomegenerate/tests/main.nf.test.snap | 182 +- .../stringtie/stringtie/tests/main.nf.test | 139 +- .../stringtie/tests/main.nf.test.snap | 504 +--- modules/nf-core/trimgalore/main.nf | 21 - modules/nf-core/trimgalore/tests/main.nf.test | 47 - .../trimgalore/tests/main.nf.test.snap | 154 -- 67 files changed, 1405 insertions(+), 6315 deletions(-) delete mode 100644 modules/nf-core/bowtie/align/tests/main.nf.test delete mode 100644 modules/nf-core/bowtie/align/tests/main.nf.test.snap delete mode 100644 modules/nf-core/bowtie/align/tests/tags.yml delete mode 100644 modules/nf-core/bowtie/build/tests/main.nf.test delete mode 100644 modules/nf-core/bowtie/build/tests/main.nf.test.snap delete mode 100644 modules/nf-core/bowtie/build/tests/tags.yml delete mode 100644 modules/nf-core/samtools/sort/tests/nextflow_cram.config diff --git a/modules.json b/modules.json index 6b2ae568..35714771 100644 --- a/modules.json +++ b/modules.json @@ -35,7 +35,7 @@ }, "bioawk": { "branch": "master", - "git_sha": "dee3479f3b4a828df6052d318403d2b6a87b2d2e", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": [ "modules" ], @@ -43,21 +43,21 @@ }, "bowtie/align": { "branch": "master", - "git_sha": "54381508775905f1ecd4fc0dea3fc2f07c78d1c6", + "git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde", "installed_by": [ "modules" ] }, "bowtie/build": { "branch": "master", - "git_sha": "54381508775905f1ecd4fc0dea3fc2f07c78d1c6", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": [ "modules" ] }, "bowtie2/align": { "branch": "master", - "git_sha": "9bfc81874554e87740bcb3e5e07acf0a153c9ecb", + "git_sha": "e4bad511789f16d0df39ee306b2cd50418365048", "installed_by": [ "modules" ] @@ -71,21 +71,21 @@ }, "bwa/index": { "branch": "master", - "git_sha": "e0ff65e1fb313677de09f5f477ae3da30ce19b7b", + "git_sha": "086fa66260595e123b0ea47a6512539b72a9afa3", "installed_by": [ "modules" ] }, "cat/cat": { "branch": "master", - "git_sha": "5bb8ca085e17549e185e1823495ab8d20727a805", + "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8", "installed_by": [ "modules" ] }, "cat/fastq": { "branch": "master", - "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7", + "git_sha": "4fc983ad0b30e6e32696fa7d980c76c7bfe1c03e", "installed_by": [ "modules" ] @@ -120,7 +120,7 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "82024cf6325d2ee194e7f056d841ecad2f6856e9", + "git_sha": "de45447d060b8c8b98575bc637a4a575fd0638e1", "installed_by": [ "modules" ] @@ -134,14 +134,14 @@ }, "custom/tx2gene": { "branch": "master", - "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", + "git_sha": "ec155021a9104441bf6a9bae3b55d1b5b0bfdb3a", "installed_by": [ "modules" ] }, "fastqc": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", "installed_by": [ "modules" ] @@ -155,28 +155,28 @@ }, "gnu/sort": { "branch": "master", - "git_sha": "a3cc42943548378b726610f45bb5a79ab3f0b633", + "git_sha": "ca199cfe5aa4f1ea3c41302158f0af2cfaa58957", "installed_by": [ "modules" ] }, "hisat2/align": { "branch": "master", - "git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f", + "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", "installed_by": [ "modules" ] }, "hisat2/build": { "branch": "master", - "git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f", + "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", "installed_by": [ "modules" ] }, "hisat2/extractsplicesites": { "branch": "master", - "git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f", + "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", "installed_by": [ "modules" ] @@ -190,35 +190,35 @@ }, "multiqc": { "branch": "master", - "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396", + "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", "installed_by": [ "modules" ] }, "samtools/faidx": { "branch": "master", - "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", + "git_sha": "f153f1f10e1083c49935565844cccb7453021682", "installed_by": [ "modules" ] }, "samtools/flagstat": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": [ "bam_stats_samtools" ] }, "samtools/idxstats": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": [ "bam_stats_samtools" ] }, "samtools/index": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": [ "bam_sort_stats_samtools", "modules" @@ -226,7 +226,7 @@ }, "samtools/sort": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", "installed_by": [ "bam_sort_stats_samtools", "modules" @@ -234,14 +234,14 @@ }, "samtools/stats": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": [ "bam_stats_samtools" ] }, "samtools/view": { "branch": "master", - "git_sha": "6c2309aaec566c0d44a6cf14d4b2d0c51afe2e91", + "git_sha": "0bd7d2333a88483aa0476acea172e9f5f6dd83bb", "installed_by": [ "modules" ] @@ -262,28 +262,28 @@ }, "star/align": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", "installed_by": [ "modules" ] }, "star/genomegenerate": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", "installed_by": [ "modules" ] }, "stringtie/stringtie": { "branch": "master", - "git_sha": "c789476080a150f87066ca3ed42a622339a26c0b", + "git_sha": "b1b959609bda44341120aed1766329909f54b8d0", "installed_by": [ "modules" ] }, "trimgalore": { "branch": "master", - "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1", + "git_sha": "a98418419ae6c9df3cf6cf108d1e1aba71037d5a", "installed_by": [ "modules" ] @@ -301,14 +301,14 @@ "nf-core": { "bam_sort_stats_samtools": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", "installed_by": [ "subworkflows" ] }, "bam_stats_samtools": { "branch": "master", - "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": [ "bam_sort_stats_samtools", "subworkflows" diff --git a/modules/nf-core/bioawk/main.nf b/modules/nf-core/bioawk/main.nf index a537dcf4..0fded517 100644 --- a/modules/nf-core/bioawk/main.nf +++ b/modules/nf-core/bioawk/main.nf @@ -11,8 +11,8 @@ process BIOAWK { tuple val(meta), path(input) output: - tuple val(meta), path("*.gz"), emit: output - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.${suffix}"), emit: output + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -20,15 +20,14 @@ process BIOAWK { script: def args = task.ext.args ?: '' // args is used for the main arguments of the tool prefix = task.ext.prefix ?: "${meta.id}" - if ("${input}" == "${prefix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + suffix = task.ext.suffix ?: input.extension + def VERSION = '1.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ bioawk \\ $args \\ $input \\ - > ${prefix} - - gzip ${prefix} + > ${prefix}.${suffix} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bowtie/align/environment.yml b/modules/nf-core/bowtie/align/environment.yml index fb5d7c1e..2617e6f0 100644 --- a/modules/nf-core/bowtie/align/environment.yml +++ b/modules/nf-core/bowtie/align/environment.yml @@ -5,4 +5,3 @@ channels: - defaults dependencies: - bioconda::bowtie=1.3.0 - - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf index 5e72b02a..29e9cd53 100644 --- a/modules/nf-core/bowtie/align/main.nf +++ b/modules/nf-core/bowtie/align/main.nf @@ -9,14 +9,13 @@ process BOWTIE_ALIGN { input: tuple val(meta), path(reads) - tuple val(meta2), path(index) - val (save_unaligned) + path index output: - tuple val(meta), path('*.bam') , emit: bam - tuple val(meta), path('*.out') , emit: log - tuple val(meta), path('*fastq.gz') , emit: fastq, optional : true - path "versions.yml" , emit: versions + tuple val(meta), path('*.bam'), emit: bam + tuple val(meta), path('*.out'), emit: log + path "versions.yml" , emit: versions + tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq when: task.ext.when == null || task.ext.when @@ -25,10 +24,10 @@ process BOWTIE_ALIGN { def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def unaligned = save_unaligned ? "--un ${prefix}.unmapped.fastq" : '' + def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped.fastq" : '' def endedness = meta.single_end ? "$reads" : "-1 ${reads[0]} -2 ${reads[1]}" """ - INDEX=\$(find -L ./ -name "*.3.ebwt" | sed 's/\\.3.ebwt\$//') + INDEX=`find -L ./ -name "*.3.ebwt" | sed 's/\\.3.ebwt\$//'` bowtie \\ --threads $task.cpus \\ --sam \\ @@ -54,24 +53,4 @@ process BOWTIE_ALIGN { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - def unaligned = save_unaligned ? - meta.single_end ? "echo '' | gzip > ${prefix}.unmapped.fastq.gz" : - "echo '' | gzip > ${prefix}.unmapped_1.fastq.gz; echo '' | gzip > ${prefix}.unmapped_2.fastq.gz" - : '' - """ - touch ${prefix}.bam - touch ${prefix}.out - $unaligned - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bowtie: \$(echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//') - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS - """ - - } diff --git a/modules/nf-core/bowtie/align/meta.yml b/modules/nf-core/bowtie/align/meta.yml index 7c7e8237..89eaedd6 100644 --- a/modules/nf-core/bowtie/align/meta.yml +++ b/modules/nf-core/bowtie/align/meta.yml @@ -27,36 +27,23 @@ input: description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. - - meta2: - type: map - description: | - Groovy Map containing genome information - e.g. [ id:'sarscov2' ] - index: type: file description: Bowtie genome index files pattern: "*.ebwt" - - save_unaligned: - type: boolean - description: Whether to save fastq files containing the reads which did not align. output: - bam: type: file description: Output BAM file containing read alignments pattern: "*.{bam}" - - fastq: - type: file - description: Unaligned FastQ files - pattern: "*.fastq.gz" - - log: - type: file - description: Log file - pattern: "*.log" - versions: type: file description: File containing software versions pattern: "versions.yml" - + - fastq: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" authors: - "@kevinmenden" maintainers: diff --git a/modules/nf-core/bowtie/align/tests/main.nf.test b/modules/nf-core/bowtie/align/tests/main.nf.test deleted file mode 100644 index 3403ae22..00000000 --- a/modules/nf-core/bowtie/align/tests/main.nf.test +++ /dev/null @@ -1,129 +0,0 @@ -nextflow_process { - - name "Test Process BOWTIE_ALIGN" - script "../main.nf" - process "BOWTIE_ALIGN" - - tag "modules" - tag "modules_nfcore" - tag "bowtie" - tag "bowtie/align" - tag "bowtie/build" - - - setup { - run("BOWTIE_BUILD") { - script "../../../bowtie/build/main.nf" - process { - """ - input[0] = [[ id:'sarscov2' ], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] - """ - } - } - } - - test("sarscov2 - single_end") { - - when { - process { - """ - input[0] = [ [id:"test", single_end:true], - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) - ] - input[1] = BOWTIE_BUILD.out.index - input[2] = true - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out.versions, - process.out.bam.collect { bam(it[1]).getReadsMD5() }, - process.out.fastq, - process.out.log - ).match() } - ) - } - - } - - test("sarscov2 - single_end - stub") { - - options "-stub" - - when { - process { - """ - input[0] = [ [id:"test", single_end:true], - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) - ] - input[1] = BOWTIE_BUILD.out.index - input[2] = true - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - - } - - test("sarscov2 - paired_end") { - - when { - process { - """ - input[0] = [ [id:"test", single_end:false], - [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] - ] - input[1] = BOWTIE_BUILD.out.index - input[2] = false - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out.versions, - process.out.bam.collect { bam(it[1]).getReads(2) }, - process.out.log - ).match() } - ) - } - - } - - test("sarscov2 - paired_end - stub") { - - options "-stub" - when { - process { - """ - input[0] = [ [id:"test", single_end:false], - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) - ] - input[1] = BOWTIE_BUILD.out.index - input[2] = false - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - - } - -} diff --git a/modules/nf-core/bowtie/align/tests/main.nf.test.snap b/modules/nf-core/bowtie/align/tests/main.nf.test.snap deleted file mode 100644 index de95bb81..00000000 --- a/modules/nf-core/bowtie/align/tests/main.nf.test.snap +++ /dev/null @@ -1,192 +0,0 @@ -{ - "sarscov2 - single_end": { - "content": [ - [ - "versions.yml:md5,96e36b0b99c80da0be8239d03db30ecc" - ], - [ - "7bdcfc6f54ae6e8f4570395cc85db9a3" - ], - [ - [ - { - "id": "test", - "single_end": true - }, - "test.unmapped.fastq.gz:md5,5729a694abd09657da3b9101861090c4" - ] - ], - [ - [ - { - "id": "test", - "single_end": true - }, - "test.out:md5,4b9140ceadb8a18ae9330885370f8a0b" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-26T09:25:24.60746041" - }, - "sarscov2 - single_end - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test.out:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": true - }, - "test.unmapped.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "3": [ - "versions.yml:md5,96e36b0b99c80da0be8239d03db30ecc" - ], - "bam": [ - [ - { - "id": "test", - "single_end": true - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "fastq": [ - [ - { - "id": "test", - "single_end": true - }, - "test.unmapped.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "log": [ - [ - { - "id": "test", - "single_end": true - }, - "test.out:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,96e36b0b99c80da0be8239d03db30ecc" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-25T10:00:28.666281812" - }, - "sarscov2 - paired_end": { - "content": [ - [ - "versions.yml:md5,96e36b0b99c80da0be8239d03db30ecc" - ], - [ - [ - "ATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTG", - "ACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGA" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.out:md5,5e13272d112cef8faeedcdbd7c602de0" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-26T11:57:56.604464368" - }, - "sarscov2 - paired_end - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.out:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,96e36b0b99c80da0be8239d03db30ecc" - ], - "bam": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "fastq": [ - - ], - "log": [ - [ - { - "id": "test", - "single_end": false - }, - "test.out:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,96e36b0b99c80da0be8239d03db30ecc" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-25T10:01:02.043164876" - } -} \ No newline at end of file diff --git a/modules/nf-core/bowtie/align/tests/tags.yml b/modules/nf-core/bowtie/align/tests/tags.yml deleted file mode 100644 index a5753d58..00000000 --- a/modules/nf-core/bowtie/align/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bowtie/align: - - "modules/nf-core/bowtie/align/**" diff --git a/modules/nf-core/bowtie/build/main.nf b/modules/nf-core/bowtie/build/main.nf index d5b4c690..05e22fe8 100644 --- a/modules/nf-core/bowtie/build/main.nf +++ b/modules/nf-core/bowtie/build/main.nf @@ -1,5 +1,5 @@ process BOWTIE_BUILD { - tag "${meta.id}" + tag "$fasta" label 'process_high' conda "${moduleDir}/environment.yml" @@ -8,43 +8,23 @@ process BOWTIE_BUILD { 'biocontainers/bowtie:1.3.0--py38hed8969a_1' }" input: - tuple val(meta), path(fasta) + path fasta output: - tuple val(meta), path('bowtie') , emit: index - path "versions.yml" , emit: versions + path 'bowtie' , emit: index + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" """ - mkdir -p bowtie - bowtie-build --threads $task.cpus $fasta bowtie/${prefix} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bowtie: \$(echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//') - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - mkdir -p bowtie - touch bowtie/${prefix}.1.ebwt - touch bowtie/${prefix}.2.ebwt - touch bowtie/${prefix}.3.ebwt - touch bowtie/${prefix}.4.ebwt - touch bowtie/${prefix}.rev.1.ebwt - touch bowtie/${prefix}.rev.2.ebwt - + mkdir bowtie + bowtie-build --threads $task.cpus $fasta bowtie/${fasta.baseName} cat <<-END_VERSIONS > versions.yml "${task.process}": bowtie: \$(echo \$(bowtie --version 2>&1) | sed 's/^.*bowtie-align-s version //; s/ .*\$//') END_VERSIONS """ - } diff --git a/modules/nf-core/bowtie/build/meta.yml b/modules/nf-core/bowtie/build/meta.yml index dd48004f..262855f4 100644 --- a/modules/nf-core/bowtie/build/meta.yml +++ b/modules/nf-core/bowtie/build/meta.yml @@ -15,23 +15,13 @@ tools: arxiv: arXiv:1303.3997 licence: ["Artistic-2.0"] input: - - meta: - type: map - description: | - Groovy Map containing information about the genome fasta - e.g. [ id:'test' ] - fasta: type: file description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing nformation about the genome fasta - e.g. [ id:'test' ] - index: type: file - description: Folder containing bowtie genome index files + description: Bowtie genome index files pattern: "*.ebwt" - versions: type: file diff --git a/modules/nf-core/bowtie/build/tests/main.nf.test b/modules/nf-core/bowtie/build/tests/main.nf.test deleted file mode 100644 index 2a1e0dc0..00000000 --- a/modules/nf-core/bowtie/build/tests/main.nf.test +++ /dev/null @@ -1,57 +0,0 @@ -nextflow_process { - - name "Test Process BOWTIE_BUILD" - script "../main.nf" - process "BOWTIE_BUILD" - - tag "modules" - tag "modules_nfcore" - tag "bowtie" - tag "bowtie/build" - - test("sarscov2 - fasta") { - - when { - process { - """ - input[0] = [ - [id: 'sarscov2'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - - } - - test("sarscov2 - fasta - stub") { - - options "-stub" - - when { - process { - """ - input[0] = [[id: 'sarscov2'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - - } - -} diff --git a/modules/nf-core/bowtie/build/tests/main.nf.test.snap b/modules/nf-core/bowtie/build/tests/main.nf.test.snap deleted file mode 100644 index e8061756..00000000 --- a/modules/nf-core/bowtie/build/tests/main.nf.test.snap +++ /dev/null @@ -1,96 +0,0 @@ -{ - "sarscov2 - fasta - stub": { - "content": [ - { - "0": [ - [ - { - "id": "sarscov2" - }, - [ - "sarscov2.1.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e", - "sarscov2.2.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e", - "sarscov2.3.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e", - "sarscov2.4.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e", - "sarscov2.rev.1.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e", - "sarscov2.rev.2.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "1": [ - "versions.yml:md5,afbd066e1dd5ae4a30b21c49149ea09a" - ], - "index": [ - [ - { - "id": "sarscov2" - }, - [ - "sarscov2.1.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e", - "sarscov2.2.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e", - "sarscov2.3.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e", - "sarscov2.4.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e", - "sarscov2.rev.1.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e", - "sarscov2.rev.2.ebwt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "versions": [ - "versions.yml:md5,afbd066e1dd5ae4a30b21c49149ea09a" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-18T08:38:14.852528155" - }, - "sarscov2 - fasta": { - "content": [ - { - "0": [ - [ - { - "id": "sarscov2" - }, - [ - "sarscov2.1.ebwt:md5,d9b76ecf9fd0413240173273b38d8199", - "sarscov2.2.ebwt:md5,02b44af9f94c62ecd3c583048e25d4cf", - "sarscov2.3.ebwt:md5,4ed93abba181d8dfab2e303e33114777", - "sarscov2.4.ebwt:md5,c25be5f8b0378abf7a58c8a880b87626", - "sarscov2.rev.1.ebwt:md5,b37aaf11853e65a3b13561f27a912b06", - "sarscov2.rev.2.ebwt:md5,9e6b0c4c1ddb99ae71ff8a4fe5ec6459" - ] - ] - ], - "1": [ - "versions.yml:md5,afbd066e1dd5ae4a30b21c49149ea09a" - ], - "index": [ - [ - { - "id": "sarscov2" - }, - [ - "sarscov2.1.ebwt:md5,d9b76ecf9fd0413240173273b38d8199", - "sarscov2.2.ebwt:md5,02b44af9f94c62ecd3c583048e25d4cf", - "sarscov2.3.ebwt:md5,4ed93abba181d8dfab2e303e33114777", - "sarscov2.4.ebwt:md5,c25be5f8b0378abf7a58c8a880b87626", - "sarscov2.rev.1.ebwt:md5,b37aaf11853e65a3b13561f27a912b06", - "sarscov2.rev.2.ebwt:md5,9e6b0c4c1ddb99ae71ff8a4fe5ec6459" - ] - ] - ], - "versions": [ - "versions.yml:md5,afbd066e1dd5ae4a30b21c49149ea09a" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-18T08:37:53.65689025" - } -} \ No newline at end of file diff --git a/modules/nf-core/bowtie/build/tests/tags.yml b/modules/nf-core/bowtie/build/tests/tags.yml deleted file mode 100644 index 1ccfa30c..00000000 --- a/modules/nf-core/bowtie/build/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bowtie/build: - - "modules/nf-core/bowtie/build/**" diff --git a/modules/nf-core/bowtie2/align/tests/main.nf.test b/modules/nf-core/bowtie2/align/tests/main.nf.test index 0de5950f..03aeaf9e 100644 --- a/modules/nf-core/bowtie2/align/tests/main.nf.test +++ b/modules/nf-core/bowtie2/align/tests/main.nf.test @@ -18,7 +18,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] """ } @@ -30,10 +30,10 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -64,7 +64,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] """ } @@ -76,10 +76,10 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -110,7 +110,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] """ } @@ -122,10 +122,10 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -155,7 +155,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] """ } @@ -167,10 +167,10 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -200,7 +200,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] """ } @@ -213,12 +213,12 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -248,7 +248,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] """ } @@ -261,12 +261,12 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -297,7 +297,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] """ } @@ -309,10 +309,10 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -343,7 +343,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] """ } @@ -356,12 +356,12 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -391,7 +391,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] """ } @@ -404,12 +404,12 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -439,7 +439,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] """ } @@ -451,10 +451,10 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -486,7 +486,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] """ } @@ -499,12 +499,12 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] input[3] = false //save_unaligned input[4] = true //sort """ @@ -533,7 +533,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] """ } @@ -546,12 +546,12 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ @@ -583,7 +583,7 @@ nextflow_process { """ input[0] = [ [ id:'test'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] """ } @@ -595,10 +595,10 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] input[1] = BOWTIE2_BUILD.out.index - input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)] + input[2] = [[ id:'test'], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] input[3] = false //save_unaligned input[4] = false //sort """ diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index 2862c64c..adbdbd7b 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -76,3 +76,4 @@ def getFileSuffix(filename) { def match = filename =~ /^.*?((\.\w{1,5})?(\.\w{1,5}\.gz$))/ return match ? match[0][1] : filename.substring(filename.lastIndexOf('.')) } + diff --git a/modules/nf-core/cat/cat/tests/main.nf.test b/modules/nf-core/cat/cat/tests/main.nf.test index 9cb16178..fcee2d19 100644 --- a/modules/nf-core/cat/cat/tests/main.nf.test +++ b/modules/nf-core/cat/cat/tests/main.nf.test @@ -29,8 +29,7 @@ nextflow_process { then { assertAll( { assert !process.success }, - { assert process.stdout.toString().contains("The name of the input file can't be the same as for the output prefix") }, - { assert snapshot(process.out.versions).match() } + { assert process.stdout.toString().contains("The name of the input file can't be the same as for the output prefix") } ) } } @@ -84,12 +83,8 @@ nextflow_process { def lines = path(process.out.file_out.get(0).get(1)).linesGzip assertAll( { assert process.success }, - { assert snapshot( - lines[0..5], - lines.size(), - process.out.versions - ).match() - } + { assert snapshot(lines[0..5]).match("test_cat_zipped_zipped_lines") }, + { assert snapshot(lines.size()).match("test_cat_zipped_zipped_size")} ) } } @@ -147,12 +142,8 @@ nextflow_process { def lines = path(process.out.file_out.get(0).get(1)).linesGzip assertAll( { assert process.success }, - { assert snapshot( - lines[0..5], - lines.size(), - process.out.versions - ).match() - } + { assert snapshot(lines[0..5]).match("test_cat_unzipped_zipped_lines") }, + { assert snapshot(lines.size()).match("test_cat_unzipped_zipped_size")} ) } } @@ -179,12 +170,8 @@ nextflow_process { def lines = path(process.out.file_out.get(0).get(1)).linesGzip assertAll( { assert process.success }, - { assert snapshot( - lines[0..5], - lines.size(), - process.out.versions - ).match() - } + { assert snapshot(lines[0..5]).match("test_cat_one_file_unzipped_zipped_lines") }, + { assert snapshot(lines.size()).match("test_cat_one_file_unzipped_zipped_size")} ) } } diff --git a/modules/nf-core/cat/cat/tests/main.nf.test.snap b/modules/nf-core/cat/cat/tests/main.nf.test.snap index b7623ee6..423571ba 100644 --- a/modules/nf-core/cat/cat/tests/main.nf.test.snap +++ b/modules/nf-core/cat/cat/tests/main.nf.test.snap @@ -1,4 +1,10 @@ { + "test_cat_unzipped_zipped_size": { + "content": [ + 375 + ], + "timestamp": "2023-10-16T14:33:08.049445686" + }, "test_cat_unzipped_unzipped": { "content": [ { @@ -28,10 +34,6 @@ ] } ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" - }, "timestamp": "2023-10-16T14:32:18.500464399" }, "test_cat_zipped_unzipped": { @@ -63,13 +65,9 @@ ] } ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" - }, "timestamp": "2023-10-16T14:32:49.642741302" }, - "test_cat_zipped_zipped": { + "test_cat_zipped_zipped_lines": { "content": [ [ "MT192765.1\tGenbank\ttranscript\t259\t29667\t.\t+\t.\tID=unknown_transcript_1;geneID=orf1ab;gene_name=orf1ab", @@ -78,31 +76,11 @@ "MT192765.1\tGenbank\tCDS\t13461\t21548\t.\t+\t0\tParent=unknown_transcript_1;exception=\"ribosomal slippage\";gbkey=CDS;gene=orf1ab;note=\"pp1ab;translated=by -1 ribosomal frameshift\";product=\"orf1ab polyprotein\";protein_id=QIK50426.1", "MT192765.1\tGenbank\tCDS\t21556\t25377\t.\t+\t0\tParent=unknown_transcript_1;gbkey=CDS;gene=S;note=\"structural protein\";product=\"surface glycoprotein\";protein_id=QIK50427.1", "MT192765.1\tGenbank\tgene\t21556\t25377\t.\t+\t.\tParent=unknown_transcript_1" - ], - 78, - [ - "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:51:46.802978" - }, - "test_cat_name_conflict": { - "content": [ - [ - ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:51:29.45394" + "timestamp": "2023-10-16T14:32:33.629048645" }, - "test_cat_one_file_unzipped_zipped": { + "test_cat_unzipped_zipped_lines": { "content": [ [ ">MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome", @@ -111,19 +89,11 @@ "TAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGG", "GTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTT", "ACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAG" - ], - 374, - [ - "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:52:02.774016" + "timestamp": "2023-10-16T14:33:08.038830506" }, - "test_cat_unzipped_zipped": { + "test_cat_one_file_unzipped_zipped_lines": { "content": [ [ ">MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome", @@ -132,16 +102,20 @@ "TAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGG", "GTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTT", "ACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAG" - ], - 375, - [ - "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:51:57.581523" + "timestamp": "2023-10-16T14:33:21.39642399" + }, + "test_cat_zipped_zipped_size": { + "content": [ + 78 + ], + "timestamp": "2023-10-16T14:32:33.641869244" + }, + "test_cat_one_file_unzipped_zipped_size": { + "content": [ + 374 + ], + "timestamp": "2023-10-16T14:33:21.4094373" } } \ No newline at end of file diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index b68e5f91..f132b2ad 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -53,9 +53,9 @@ process CAT_FASTQ { def prefix = task.ext.prefix ?: "${meta.id}" def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()] if (meta.single_end) { - if (readList.size >= 1) { + if (readList.size > 1) { """ - echo '' | gzip > ${prefix}.merged.fastq.gz + touch ${prefix}.merged.fastq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -64,10 +64,10 @@ process CAT_FASTQ { """ } } else { - if (readList.size >= 2) { + if (readList.size > 2) { """ - echo '' | gzip > ${prefix}_1.merged.fastq.gz - echo '' | gzip > ${prefix}_2.merged.fastq.gz + touch ${prefix}_1.merged.fastq.gz + touch ${prefix}_2.merged.fastq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test index f88a78b6..a71dcb8d 100644 --- a/modules/nf-core/cat/fastq/tests/main.nf.test +++ b/modules/nf-core/cat/fastq/tests/main.nf.test @@ -13,6 +13,9 @@ nextflow_process { test("test_cat_fastq_single_end") { when { + params { + outdir = "$outputDir" + } process { """ input[0] = Channel.of([ @@ -35,6 +38,9 @@ nextflow_process { test("test_cat_fastq_paired_end") { when { + params { + outdir = "$outputDir" + } process { """ input[0] = Channel.of([ @@ -59,6 +65,9 @@ nextflow_process { test("test_cat_fastq_single_end_same_name") { when { + params { + outdir = "$outputDir" + } process { """ input[0] = Channel.of([ @@ -81,6 +90,9 @@ nextflow_process { test("test_cat_fastq_paired_end_same_name") { when { + params { + outdir = "$outputDir" + } process { """ input[0] = Channel.of([ @@ -105,129 +117,9 @@ nextflow_process { test("test_cat_fastq_single_end_single_file") { when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:true ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] - ]) - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("test_cat_fastq_single_end - stub") { - - options "-stub" - - when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:true ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] - ]) - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("test_cat_fastq_paired_end - stub") { - - options "-stub" - - when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)] - ]) - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("test_cat_fastq_single_end_same_name - stub") { - - options "-stub" - - when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:true ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] - ]) - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("test_cat_fastq_paired_end_same_name - stub") { - - options "-stub" - - when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] - ]) - """ + params { + outdir = "$outputDir" } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("test_cat_fastq_single_end_single_file - stub") { - - options "-stub" - - when { process { """ input[0] = Channel.of([ diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test.snap b/modules/nf-core/cat/fastq/tests/main.nf.test.snap index aec119a9..43dfe28f 100644 --- a/modules/nf-core/cat/fastq/tests/main.nf.test.snap +++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap @@ -28,10 +28,6 @@ ] } ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, "timestamp": "2024-01-17T17:30:39.816981" }, "test_cat_fastq_single_end_same_name": { @@ -63,10 +59,6 @@ ] } ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, "timestamp": "2024-01-17T17:32:35.229332" }, "test_cat_fastq_single_end_single_file": { @@ -98,10 +90,6 @@ ] } ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, "timestamp": "2024-01-17T17:34:00.058829" }, "test_cat_fastq_paired_end_same_name": { @@ -139,123 +127,8 @@ ] } ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, "timestamp": "2024-01-17T17:33:33.031555" }, - "test_cat_fastq_single_end - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" - ], - "reads": [ - [ - { - "id": "test", - "single_end": true - }, - "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-05T12:07:28.244999" - }, - "test_cat_fastq_paired_end_same_name - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" - ], - "reads": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-05T12:07:57.070911" - }, - "test_cat_fastq_single_end_same_name - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" - ], - "reads": [ - [ - { - "id": "test", - "single_end": true - }, - "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-05T12:07:46.796254" - }, "test_cat_fastq_paired_end": { "content": [ { @@ -291,86 +164,6 @@ ] } ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, "timestamp": "2024-01-17T17:32:02.270935" - }, - "test_cat_fastq_paired_end - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" - ], - "reads": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-05T12:07:37.807553" - }, - "test_cat_fastq_single_end_single_file - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" - ], - "reads": [ - [ - { - "id": "test", - "single_end": true - }, - "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-07-05T12:14:51.861264" } } \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py index 9a493ace..da033408 100755 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -3,6 +3,7 @@ """Provide functions to merge multiple versions.yml files.""" + import yaml import platform from textwrap import dedent diff --git a/modules/nf-core/custom/tx2gene/templates/tx2gene.py b/modules/nf-core/custom/tx2gene/templates/tx2gene.py index 8c2e3b1f..7fd0de64 100755 --- a/modules/nf-core/custom/tx2gene/templates/tx2gene.py +++ b/modules/nf-core/custom/tx2gene/templates/tx2gene.py @@ -17,7 +17,6 @@ logger = logging.getLogger(__name__) logger.setLevel(logging.INFO) - def format_yaml_like(data: dict, indent: int = 0) -> str: """Formats a dictionary to a YAML-like string. @@ -37,7 +36,6 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: yaml_str += f"{spaces}{key}: {value}\\n" return yaml_str - def read_top_transcripts(quant_dir: str, file_pattern: str) -> Set[str]: """ Read the top 100 transcripts from the quantification file. @@ -125,12 +123,7 @@ def parse_attributes(attributes_text: str) -> Dict[str, str]: def map_transcripts_to_gene( - quant_type: str, - gtf_file: str, - quant_dir: str, - gene_id: str, - extra_id_field: str, - output_file: str, + quant_type: str, gtf_file: str, quant_dir: str, gene_id: str, extra_id_field: str, output_file: str ) -> bool: """ Map transcripts to gene names and write the output to a file. @@ -163,10 +156,7 @@ def map_transcripts_to_gene( attr_dict = parse_attributes(cols[8]) if gene_id in attr_dict and transcript_attribute in attr_dict: # Create a unique identifier for the transcript-gene combination - transcript_gene_pair = ( - attr_dict[transcript_attribute], - attr_dict[gene_id], - ) + transcript_gene_pair = (attr_dict[transcript_attribute], attr_dict[gene_id]) # Check if the combination has already been seen if transcript_gene_pair not in seen: @@ -180,14 +170,14 @@ def map_transcripts_to_gene( # Main function to parse arguments and call the mapping function if __name__ == "__main__": - if "${task.ext.prefix}" != "null": + if '${task.ext.prefix}' != "null": prefix = "${task.ext.prefix}." - elif "$meta.id" != "null": - prefix = "${meta.id}." + elif '$meta.id' != "null": + prefix = '${meta.id}.' else: - prefix = "" + prefix = '' - if not map_transcripts_to_gene("$quant_type", "$gtf", "quants", "$id", "$extra", f"{prefix}tx2gene.tsv"): + if not map_transcripts_to_gene('$quant_type', '$gtf', 'quants', '$id', '$extra', f"{prefix}tx2gene.tsv"): logger.error("Failed to map transcripts to genes.") # Write the versions diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test b/modules/nf-core/custom/tx2gene/tests/main.nf.test index 4cbb8d4e..b1559279 100644 --- a/modules/nf-core/custom/tx2gene/tests/main.nf.test +++ b/modules/nf-core/custom/tx2gene/tests/main.nf.test @@ -10,21 +10,22 @@ nextflow_process { tag "custom/tx2gene" tag "untar" - test("saccharomyces_cerevisiae - gtf") { + setup { - setup { - run("UNTAR") { - script "../../../untar/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test'], // meta map - file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz', checkIfExists: true) - ]) - """ - } + run("UNTAR") { + script "../../../untar/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz', checkIfExists: true) + ]) + """ } } + } + + test("saccharomyces_cerevisiae - gtf") { when { process { @@ -44,7 +45,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out.tx2gene).match('tx2gene') }, + { assert snapshot(process.out.versions).match('versions') } ) } } @@ -53,20 +55,6 @@ nextflow_process { options "-stub" - setup { - run("UNTAR") { - script "../../../untar/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test'], // meta map - file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz', checkIfExists: true) - ]) - """ - } - } - } - when { process { """ @@ -85,7 +73,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out.tx2gene).match('tx2gene - stub') }, + { assert snapshot(process.out.versions).match('versions - stub') } ) } } diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap index c19f10f7..1e76e10d 100644 --- a/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap +++ b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap @@ -1,68 +1,60 @@ { - "saccharomyces_cerevisiae - gtf": { + "versions": { "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" - ] - ], - "1": [ - "versions.yml:md5,fb8145d7fbc6043ba031249b23ecda50" - ], - "tx2gene": [ - [ - { - "id": "test" - }, - "test.tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" - ] - ], - "versions": [ - "versions.yml:md5,fb8145d7fbc6043ba031249b23ecda50" + [ + "versions.yml:md5,fb8145d7fbc6043ba031249b23ecda50" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-26T13:14:18.218251" + }, + "tx2gene": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe" ] - } + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.01.0" }, - "timestamp": "2024-07-05T13:13:11.305047" + "timestamp": "2024-02-26T13:14:18.21054" }, - "saccharomyces_cerevisiae - gtf - stub": { + "tx2gene - stub": { "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.tx2gene.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60" - ], - "tx2gene": [ - [ - { - "id": "test" - }, - "test.tx2gene.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60" + [ + [ + { + "id": "test" + }, + "test.tx2gene.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] - } + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-26T13:14:25.915434" + }, + "versions - stub": { + "content": [ + [ + "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nextflow": "24.01.0" }, - "timestamp": "2024-07-10T15:15:34.064489" + "timestamp": "2024-02-26T13:14:25.919243" } } \ No newline at end of file diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index e9d79a07..70edae4d 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -23,14 +23,17 @@ nextflow_process { then { assertAll ( - { assert process.success }, - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
    Mon 2 Oct 2023
    test.gz
    - // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("    ") }, - { assert snapshot(process.out.versions).match() } + { assert process.success }, + + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
    Mon 2 Oct 2023
    test.gz
    + // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("    ") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_single") } ) } } @@ -51,14 +54,16 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("") }, - { assert path(process.out.html[0][1][1]).text.contains("") }, - { assert snapshot(process.out.versions).match() } + { assert process.success }, + + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("") }, + { assert path(process.out.html[0][1][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_paired") } ) } } @@ -78,11 +83,13 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match() } + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } ) } } @@ -102,11 +109,13 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match() } + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_bam") } ) } } @@ -129,20 +138,22 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("") }, - { assert path(process.out.html[0][1][1]).text.contains("") }, - { assert path(process.out.html[0][1][2]).text.contains("") }, - { assert path(process.out.html[0][1][3]).text.contains("") }, - { assert snapshot(process.out.versions).match() } + { assert process.success }, + + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, + { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, + { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("") }, + { assert path(process.out.html[0][1][1]).text.contains("") }, + { assert path(process.out.html[0][1][2]).text.contains("") }, + { assert path(process.out.html[0][1][3]).text.contains("") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } ) } } @@ -162,116 +173,27 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match() } - ) - } - } + { assert process.success }, - test("sarscov2 single-end [fastq] - stub") { + { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [ id: 'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } ) } } - test("sarscov2 paired-end [fastq] - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("sarscov2 interleaved [fastq] - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("sarscov2 paired-end [bam] - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } + test("sarscov2 single-end [fastq] - stub") { - test("sarscov2 multiple [fastq] - stub") { + options "-stub" - options "-stub" when { process { """ input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] + [ id: 'test', single_end:true ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] ]) """ } @@ -279,31 +201,12 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert process.success }, + { assert snapshot(process.out.html.collect { file(it[1]).getName() } + + process.out.zip.collect { file(it[1]).getName() } + + process.out.versions ).match("fastqc_stub") } ) } } - test("sarscov2 custom_prefix - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [ id:'mysample', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index d5db3092..86f7c311 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,392 +1,88 @@ { - "sarscov2 custom_prefix": { + "fastqc_versions_interleaved": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:02:16.374038" + "timestamp": "2024-01-31T17:40:07.293713" }, - "sarscov2 single-end [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "test", - "single_end": true - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "test", - "single_end": true - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:02:24.993809" - }, - "sarscov2 custom_prefix - stub": { - "content": [ - { - "0": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:03:10.93942" - }, - "sarscov2 interleaved [fastq]": { + "fastqc_stub": { "content": [ [ + "test.html", + "test.zip", "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:01:42.355718" + "timestamp": "2024-01-31T17:31:01.425198" }, - "sarscov2 paired-end [bam]": { + "fastqc_versions_multiple": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:01:53.276274" + "timestamp": "2024-01-31T17:40:55.797907" }, - "sarscov2 multiple [fastq]": { + "fastqc_versions_bam": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:02:05.527626" + "timestamp": "2024-01-31T17:40:26.795862" }, - "sarscov2 paired-end [fastq]": { + "fastqc_versions_single": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:01:31.188871" - }, - "sarscov2 paired-end [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:02:34.273566" + "timestamp": "2024-01-31T17:39:27.043675" }, - "sarscov2 multiple [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:03:02.304411" - }, - "sarscov2 single-end [fastq]": { + "fastqc_versions_paired": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:01:19.095607" - }, - "sarscov2 interleaved [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:02:44.640184" + "timestamp": "2024-01-31T17:39:47.584191" }, - "sarscov2 paired-end [bam] - stub": { + "fastqc_versions_custom_prefix": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:02:53.550742" + "timestamp": "2024-01-31T17:41:14.576531" } } \ No newline at end of file diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf index ea186f62..2289a9fc 100644 --- a/modules/nf-core/hisat2/align/main.nf +++ b/modules/nf-core/hisat2/align/main.nf @@ -90,23 +90,4 @@ process HISAT2_ALIGN { END_VERSIONS """ } - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - def unaligned = params.save_unaligned ? "echo '' | gzip > ${prefix}.unmapped_1.fastq.gz \n echo '' | gzip > ${prefix}.unmapped_2.fastq.gz" : '' - def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - """ - ${unaligned} - - touch ${prefix}.hisat2.summary.log - touch ${prefix}.bam - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hisat2: $VERSION - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS - """ - - } diff --git a/modules/nf-core/hisat2/align/tests/main.nf.test b/modules/nf-core/hisat2/align/tests/main.nf.test index 396757d7..3a520e9a 100644 --- a/modules/nf-core/hisat2/align/tests/main.nf.test +++ b/modules/nf-core/hisat2/align/tests/main.nf.test @@ -68,63 +68,6 @@ nextflow_process { } } - test("Single-End - stub") { - options "-stub" - - setup { - run("HISAT2_EXTRACTSPLICESITES") { - script "../../extractsplicesites/main.nf" - process { - """ - input[0] = Channel.of([ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) - ]) - """ - } - } - - run("HISAT2_BUILD") { - script "../../build/main.nf" - process { - """ - input[0] = Channel.of([ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ]) - input[1] = Channel.of([ [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) - ]) - input[2] = HISAT2_EXTRACTSPLICESITES.out.txt - """ - } - } - } - - when { - params { - outdir = "$outputDir" - } - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:true ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] - ]) - input[1] = HISAT2_BUILD.out.index - input[2] = HISAT2_EXTRACTSPLICESITES.out.txt - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - test("Paired-End") { setup { @@ -184,64 +127,6 @@ nextflow_process { } } - test("Paired-End - stub") { - options "-stub" - - setup { - run("HISAT2_EXTRACTSPLICESITES") { - script "../../extractsplicesites/main.nf" - process { - """ - input[0] = Channel.of([ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) - ]) - """ - } - } - - run("HISAT2_BUILD") { - script "../../build/main.nf" - process { - """ - input[0] = Channel.of([ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ]) - input[1] = Channel.of([ [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) - ]) - input[2] = HISAT2_EXTRACTSPLICESITES.out.txt - """ - } - } - } - - when { - params { - outdir = "$outputDir" - } - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] - ]) - input[1] = HISAT2_BUILD.out.index - input[2] = HISAT2_EXTRACTSPLICESITES.out.txt - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - test("Single-End No Splice Sites") { setup { @@ -286,49 +171,6 @@ nextflow_process { } } - test("Single-End No Splice Sites - stub") { - options "-stub" - - setup { - run("HISAT2_BUILD") { - script "../../build/main.nf" - process { - """ - input[0] = Channel.of([ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ]) - input[1] = [[:],[]] - input[2] = [[:],[]] - """ - } - } - } - - when { - params { - outdir = "$outputDir" - } - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:true ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - input[1] = HISAT2_BUILD.out.index - input[2] = [[:],[]] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - test("Paired-End No Splice Sites") { setup { @@ -373,48 +215,4 @@ nextflow_process { ) } } - - test("Paired-End No Splice Sites - stub") { - options "-stub" - - setup { - run("HISAT2_BUILD") { - script "../../build/main.nf" - process { - """ - input[0] = Channel.of([ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ]) - input[1] = [[:],[]] - input[2] = [[:],[]] - """ - } - } - } - - when { - params { - outdir = "$outputDir" - } - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] - ]) - input[1] = HISAT2_BUILD.out.index - input[2] = [[:],[]] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } } diff --git a/modules/nf-core/hisat2/align/tests/main.nf.test.snap b/modules/nf-core/hisat2/align/tests/main.nf.test.snap index ff670d45..a80fa3c5 100644 --- a/modules/nf-core/hisat2/align/tests/main.nf.test.snap +++ b/modules/nf-core/hisat2/align/tests/main.nf.test.snap @@ -5,129 +5,21 @@ "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T09:08:33.735489" + "timestamp": "2023-10-16T15:14:50.269895296" }, - "Paired-End - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" - ], - "bam": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "fastq": [ - - ], - "summary": [ - [ - { - "id": "test", - "single_end": false - }, - "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T09:09:14.35626" - }, - "Single-End - stub": { + "se_no_ss_summary": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" - ], - "bam": [ - [ - { - "id": "test", - "single_end": true - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "fastq": [ - - ], - "summary": [ - [ - { - "id": "test", - "single_end": true - }, - "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" + [ + [ + { + "id": "test", + "single_end": true + }, + "test.hisat2.summary.log:md5,7b8a9e61b7646da1089b041333c41a87" ] - } + ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T09:08:47.404885" + "timestamp": "2023-10-16T15:15:22.897386626" }, "pe_no_ss_versions": { "content": [ @@ -135,70 +27,15 @@ "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T09:09:52.076955" + "timestamp": "2023-10-16T15:15:42.583699978" }, - "Paired-End No Splice Sites - stub": { + "se_no_ss_versions": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" - ], - "bam": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "fastq": [ - - ], - "summary": [ - [ - { - "id": "test", - "single_end": false - }, - "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" - ] - } + [ + "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" + ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T09:10:03.739697" + "timestamp": "2023-10-16T15:15:22.909407356" }, "pe_no_ss_summary": { "content": [ @@ -212,11 +49,7 @@ ] ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T09:09:52.068244" + "timestamp": "2023-10-16T15:15:42.569775538" }, "pe_no_ss_fastq": { "content": [ @@ -224,11 +57,7 @@ ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T09:09:52.072985" + "timestamp": "2023-10-16T15:15:42.576881608" }, "se_summary": { "content": [ @@ -242,11 +71,7 @@ ] ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T09:08:33.727355" + "timestamp": "2023-10-16T15:14:50.252466896" }, "pe_summary": { "content": [ @@ -260,11 +85,7 @@ ] ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T09:09:01.495439" + "timestamp": "2023-10-16T15:15:09.881690889" }, "pe_fastq": { "content": [ @@ -272,124 +93,23 @@ ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T09:09:01.500755" + "timestamp": "2023-10-16T15:15:09.888696129" }, - "se_fastq": { + "se_no_ss_fastq": { "content": [ [ ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T09:08:33.732523" - }, - "se_no_ss_summary": { - "content": [ - [ - [ - { - "id": "test", - "single_end": true - }, - "test.hisat2.summary.log:md5,7b8a9e61b7646da1089b041333c41a87" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T09:09:26.851884" + "timestamp": "2023-10-16T15:15:22.904010016" }, - "se_no_ss_versions": { - "content": [ - [ - "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T09:09:26.89234" - }, - "se_no_ss_fastq": { + "se_fastq": { "content": [ [ ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T09:09:26.871369" - }, - "Single-End No Splice Sites - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" - ], - "bam": [ - [ - { - "id": "test", - "single_end": true - }, - "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "fastq": [ - - ], - "summary": [ - [ - { - "id": "test", - "single_end": true - }, - "test.hisat2.summary.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T09:09:39.544807" + "timestamp": "2023-10-16T15:14:50.264366105" }, "pe_versions": { "content": [ @@ -397,10 +117,6 @@ "versions.yml:md5,ceb638f44ebdaf09ba1f5c5c409585e2" ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T09:09:01.506346" + "timestamp": "2023-10-16T15:15:09.894683308" } } \ No newline at end of file diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf index 17d8fdd5..766e8731 100644 --- a/modules/nf-core/hisat2/build/main.nf +++ b/modules/nf-core/hisat2/build/main.nf @@ -61,15 +61,4 @@ process HISAT2_BUILD { hisat2: $VERSION END_VERSIONS """ - - stub: - def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - """ - mkdir hisat2 - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hisat2: $VERSION - END_VERSIONS - """ } diff --git a/modules/nf-core/hisat2/build/tests/main.nf.test b/modules/nf-core/hisat2/build/tests/main.nf.test index e19692c4..5b31debc 100644 --- a/modules/nf-core/hisat2/build/tests/main.nf.test +++ b/modules/nf-core/hisat2/build/tests/main.nf.test @@ -50,49 +50,4 @@ nextflow_process { ) } } - - test("Should run without failures - stub") { - - options "-stub" - - setup { - run("HISAT2_EXTRACTSPLICESITES") { - script "../../extractsplicesites/main.nf" - process { - """ - input[0] = Channel.of([ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) - ]) - """ - } - } - } - - when { - params { - outdir = "$outputDir" - } - - process { - """ - input[0] = Channel.of([ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ]) - input[1] = Channel.of([ [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) - ]) - input[2] = HISAT2_EXTRACTSPLICESITES.out.txt - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } -} \ No newline at end of file +} diff --git a/modules/nf-core/hisat2/build/tests/main.nf.test.snap b/modules/nf-core/hisat2/build/tests/main.nf.test.snap index 0e3b5c57..c7d364db 100644 --- a/modules/nf-core/hisat2/build/tests/main.nf.test.snap +++ b/modules/nf-core/hisat2/build/tests/main.nf.test.snap @@ -1,64 +1,4 @@ { - "test - stub": { - "content": [ - { - "0": [ - - ], - "1": [ - - ], - "index": [ - - ], - "versions": [ - - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-20T17:29:31.567024" - }, - "Should run without failures - stub": { - "content": [ - { - "0": [ - [ - { - "id": "genome" - }, - [ - - ] - ] - ], - "1": [ - "versions.yml:md5,e36ef3cd73d19ccf2378c9358fe942c0" - ], - "index": [ - [ - { - "id": "genome" - }, - [ - - ] - ] - ], - "versions": [ - "versions.yml:md5,e36ef3cd73d19ccf2378c9358fe942c0" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-20T18:18:08.896422" - }, "Should run without failures": { "content": [ { @@ -104,10 +44,6 @@ ] } ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, "timestamp": "2023-10-16T14:42:22.381609786" } -} +} \ No newline at end of file diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf index 588a9947..b0c8513a 100644 --- a/modules/nf-core/hisat2/extractsplicesites/main.nf +++ b/modules/nf-core/hisat2/extractsplicesites/main.nf @@ -28,15 +28,4 @@ process HISAT2_EXTRACTSPLICESITES { hisat2: $VERSION END_VERSIONS """ - - stub: - def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - """ - touch ${gtf.baseName}.splice_sites.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - hisat2: $VERSION - END_VERSIONS - """ } diff --git a/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test b/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test index 14129cff..72eb6d53 100644 --- a/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test +++ b/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test @@ -32,30 +32,4 @@ nextflow_process { ) } } - - test("test - stub") { - - options "-stub" - - when { - params { - outdir = "$outputDir" - } - process { - """ - input[0] = Channel.of([ - [id:'genome'], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } } diff --git a/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test.snap b/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test.snap index 1dcd8af2..17f1c8eb 100644 --- a/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test.snap +++ b/modules/nf-core/hisat2/extractsplicesites/tests/main.nf.test.snap @@ -1,47 +1,10 @@ { - "test - stub": { - "content": [ - { - "0": [ - [ - { - "id": "genome" - }, - "genome.splice_sites.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - "versions.yml:md5,eeea7231fe197810659b8bad4133aff2" - ], - "txt": [ - [ - { - "id": "genome" - }, - "genome.splice_sites.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,eeea7231fe197810659b8bad4133aff2" - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-20T17:34:13.229903" - }, "Should run without failures": { "content": [ [ "versions.yml:md5,eeea7231fe197810659b8bad4133aff2" ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, "timestamp": "2024-01-18T20:56:30.71763" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 2121492d..ca39fb67 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.23 + - bioconda::multiqc=1.21 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 459dfea5..47ac352f 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,16 +3,14 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.23--pyhdfd78af_0' : - 'biocontainers/multiqc:1.23--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : + 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" path(multiqc_config) path(extra_multiqc_config) path(multiqc_logo) - path(replace_names) - path(sample_names) output: path "*multiqc_report.html", emit: report @@ -28,8 +26,6 @@ process MULTIQC { def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' - def replace = replace_names ? "--replace-names ${replace_names}" : '' - def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ @@ -37,8 +33,6 @@ process MULTIQC { $config \\ $extra_config \\ $logo \\ - $replace \\ - $samples \\ . cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 382c08cb..45a9bc35 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -29,19 +29,6 @@ input: type: file description: Optional logo file for MultiQC pattern: "*.{png}" - - replace_names: - type: file - description: | - Optional two-column sample renaming file. First column a set of - patterns, second column a set of corresponding replacements. Passed via - MultiQC's `--replace-names` option. - pattern: "*.{tsv}" - - sample_names: - type: file - description: | - Optional TSV file with headers, passed to the MultiQC --sample_names - argument. - pattern: "*.{tsv}" output: - report: type: file diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index 6aa27f4c..f1c4242e 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -17,8 +17,6 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] - input[4] = [] - input[5] = [] """ } } @@ -43,8 +41,6 @@ nextflow_process { input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] - input[4] = [] - input[5] = [] """ } } @@ -70,8 +66,6 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] - input[4] = [] - input[5] = [] """ } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 45e95e5d..bfebd802 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "23.10.1" }, - "timestamp": "2024-07-10T12:41:34.562023" + "timestamp": "2024-02-29T08:48:55.657331" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "23.10.1" }, - "timestamp": "2024-07-10T11:27:11.933869532" + "timestamp": "2024-02-29T08:49:49.071937" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "23.10.1" }, - "timestamp": "2024-07-10T11:26:56.709849369" + "timestamp": "2024-02-29T08:49:25.457567" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test b/modules/nf-core/samtools/flagstat/tests/main.nf.test index 3b648a37..24c3c04b 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test @@ -11,30 +11,9 @@ nextflow_process { test("BAM") { when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ]) - """ + params { + outdir = "$outputDir" } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("BAM - stub") { - - options "-stub" - - when { process { """ input[0] = Channel.of([ @@ -49,7 +28,8 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out.flagstat).match("flagstat") }, + { assert snapshot(process.out.versions).match("versions") } ) } } diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap index 23989c61..e9f85efa 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap @@ -1,72 +1,32 @@ { - "BAM - stub": { + "flagstat": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" - ], - "flagstat": [ - [ - { - "id": "test", - "single_end": false - }, - "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" ] - } + ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.04.3" }, - "timestamp": "2024-07-22T14:17:28.002887" + "timestamp": "2024-02-12T18:31:37.783927" }, - "BAM": { + "versions": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" - ] - ], - "1": [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" - ], - "flagstat": [ - [ - { - "id": "test", - "single_end": false - }, - "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" - ] - ], - "versions": [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" - ] - } + [ + "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T14:17:13.330971" + "timestamp": "2024-05-28T15:41:52.516253882" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test b/modules/nf-core/samtools/idxstats/tests/main.nf.test index 5fd1fc78..a2dcb27c 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test @@ -11,28 +11,9 @@ nextflow_process { test("bam") { when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ]) - """ + params { + outdir = "$outputDir" } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("bam - stub") { - options "-stub" - when { process { """ input[0] = Channel.of([ @@ -47,7 +28,9 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out.idxstats).match("idxstats") }, + { assert snapshot(process.out.versions).match("versions") } ) } - }} + } +} diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap index a5ac8104..4eacdb90 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap @@ -1,72 +1,32 @@ { - "bam - stub": { + "versions": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" - ], - "idxstats": [ - [ - { - "id": "test", - "single_end": false - }, - "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" - ] - } + [ + "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T14:17:56.180093" + "timestamp": "2024-05-28T15:46:46.617989517" }, - "bam": { + "idxstats": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" - ] - ], - "1": [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" - ], - "idxstats": [ - [ - { - "id": "test", - "single_end": false - }, - "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" - ] - ], - "versions": [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" ] - } + ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.04.3" }, - "timestamp": "2024-07-22T14:17:41.408704" + "timestamp": "2024-02-12T18:36:41.561026" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index e002585b..b523c21b 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -35,11 +35,10 @@ process SAMTOOLS_INDEX { """ stub: - def args = task.ext.args ?: '' - def extension = file(input).getExtension() == 'cram' ? - "crai" : args.contains("-c") ? "csi" : "bai" """ - touch ${input}.${extension} + touch ${input}.bai + touch ${input}.crai + touch ${input}.csi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test index ca34fb5c..bb7756d1 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -9,49 +9,11 @@ nextflow_process { tag "samtools/index" test("bai") { - when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - test("crai") { when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true) - ]) - """ + params { + outdir = "$outputDir" } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("csi") { - config "./csi.nextflow.config" - - when { process { """ input[0] = Channel.of([ @@ -65,38 +27,18 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot( - file(process.out.csi[0][1]).name, - process.out.versions - ).match() } + { assert snapshot(process.out.bai).match("bai") }, + { assert snapshot(process.out.versions).match("bai_versions") } ) } } - test("bai - stub") { - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } + test("crai") { - test("crai - stub") { - options "-stub" when { + params { + outdir = "$outputDir" + } process { """ input[0] = Channel.of([ @@ -110,16 +52,20 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out.crai).match("crai") }, + { assert snapshot(process.out.versions).match("crai_versions") } ) } } - test("csi - stub") { - options "-stub" + test("csi") { + config "./csi.nextflow.config" when { + params { + outdir = "$outputDir" + } process { """ input[0] = Channel.of([ @@ -133,7 +79,8 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert path(process.out.csi.get(0).get(1)).exists() }, + { assert snapshot(process.out.versions).match("csi_versions") } ) } } diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 799d199c..52756e85 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -1,250 +1,74 @@ { - "csi - stub": { + "crai_versions": { "content": [ - { - "0": [ - - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" - ], - "bai": [ - - ], - "crai": [ - - ], - "csi": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T16:51:53.9057" - }, - "crai - stub": { - "content": [ - { - "0": [ - - ], - "1": [ - - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" - ], - "bai": [ - - ], - "crai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "csi": [ - - ], - "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" - ] - } + [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T16:51:45.931558" + "timestamp": "2024-05-28T15:42:04.203740976" }, - "bai - stub": { + "csi_versions": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" - ], - "bai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "crai": [ - - ], - "csi": [ - - ], - "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" - ] - } + [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T16:51:34.807525" + "timestamp": "2024-05-28T15:42:09.57475878" }, - "csi": { + "crai": { "content": [ - "test.paired_end.sorted.bam.csi", [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.04.3" }, - "timestamp": "2024-07-22T16:52:55.688799" + "timestamp": "2024-02-12T18:41:38.446424" }, - "crai": { + "bai": { "content": [ - { - "0": [ - - ], - "1": [ - - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" - ] - ], - "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" - ], - "bai": [ - - ], - "crai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" - ] - ], - "csi": [ - - ], - "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" ] - } + ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.04.3" }, - "timestamp": "2024-07-22T16:51:17.609533" + "timestamp": "2024-02-12T18:40:46.579747" }, - "bai": { + "bai_versions": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" - ], - "bai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" - ] - ], - "crai": [ - - ], - "csi": [ - - ], - "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" - ] - } + [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T16:51:04.16585" + "timestamp": "2024-05-28T15:41:57.929287369" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 8e019099..596c6f7e 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -50,20 +50,10 @@ process SAMTOOLS_SORT { """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def extension = args.contains("--output-fmt sam") ? "sam" : - args.contains("--output-fmt cram") ? "cram" : - "bam" """ - touch ${prefix}.${extension} - if [ "${extension}" == "bam" ]; - then - touch ${prefix}.${extension}.csi - elif [ "${extension}" == "cram" ]; - then - touch ${prefix}.${extension}.crai - fi + touch ${prefix}.bam + touch ${prefix}.bam.csi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index c2ea9c72..fb38ed9b 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -32,16 +32,16 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.bam, - process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions - ).match()} + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } } + ).match("test_bam") + } ) } } test("cram") { - config "./nextflow_cram.config" + config "./nextflow.config" when { process { @@ -62,20 +62,23 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - process.out.cram.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.crai.collect { it.collect { it instanceof Map ? it : file(it).name } }, - process.out.versions - ).match()} + process.out.bam, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } } + ).match("test_cram") + } ) } } - test("bam - stub") { + test("bam_stub") { - options "-stub" config "./nextflow.config" + options "-stub" when { + params { + outdir = "$outputDir" + } process { """ input[0] = Channel.of([ @@ -93,35 +96,8 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("cram - stub") { - - options "-stub" - config "./nextflow_cram.config" - - when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) - ]) - input[1] = Channel.of([ - [ id:'fasta' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(file(process.out.bam[0][1]).name).match("bam_stub_bam") }, + { assert snapshot(process.out.versions).match("bam_stub_versions") } ) } } diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index da38d5d1..5a27de1d 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -7,159 +7,54 @@ "id": "test", "single_end": false }, - "test.sorted.cram" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.cram.crai" + "test.sorted.bam:md5,21c992d59615936b99f2ad008aa54400" ] - ], - [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "24.04.2" }, - "timestamp": "2024-07-22T17:19:37.196205" + "timestamp": "2024-05-31T08:13:54.512837189" }, - "bam - stub": { + "bam_stub_bam": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - - ], - "2": [ - - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" - ], - "bam": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "crai": [ - - ], - "cram": [ - - ], - "csi": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" - ] - } + "test.sorted.bam" ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "24.04.2" }, - "timestamp": "2024-07-22T15:54:46.580756" + "timestamp": "2024-05-31T07:29:00.761845507" }, - "cram - stub": { + "test_cram": { "content": [ - { - "0": [ - - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.cram:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - - ], - "4": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" - ], - "bam": [ - - ], - "crai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "cram": [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.cram:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "csi": [ - - ], - "versions": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,22b2093be34a7637f5fbc84272b89d06" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi" ] - } + ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "24.04.2" }, - "timestamp": "2024-07-22T15:57:30.505698" + "timestamp": "2024-05-31T09:16:51.924951855" }, - "bam": { + "test_bam": { "content": [ [ [ @@ -178,15 +73,42 @@ }, "test.sorted.bam.csi" ] - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-05-31T08:28:12.15952312" + }, + "bam_stub_versions": { + "content": [ [ "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-05-31T07:29:00.765038811" + }, + "bam": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,21c992d59615936b99f2ad008aa54400" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" }, - "timestamp": "2024-07-22T15:54:25.872954" + "timestamp": "2024-05-31T08:13:48.538030517" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/tests/nextflow_cram.config b/modules/nf-core/samtools/sort/tests/nextflow_cram.config deleted file mode 100644 index 3a8c0188..00000000 --- a/modules/nf-core/samtools/sort/tests/nextflow_cram.config +++ /dev/null @@ -1,8 +0,0 @@ -process { - - withName: SAMTOOLS_SORT { - ext.prefix = { "${meta.id}.sorted" } - ext.args = "--write-index --output-fmt cram" - } - -} diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test b/modules/nf-core/samtools/stats/tests/main.nf.test index 28a77db2..e3d5cb14 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test +++ b/modules/nf-core/samtools/stats/tests/main.nf.test @@ -11,6 +11,9 @@ nextflow_process { test("bam") { when { + params { + outdir = "$outputDir" + } process { """ input[0] = Channel.of([ @@ -34,59 +37,9 @@ nextflow_process { test("cram") { when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true) - ]) - input[1] = Channel.of([ - [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ]) - """ + params { + outdir = "$outputDir" } - } - - then { - assertAll( - {assert process.success}, - {assert snapshot(process.out).match()} - ) - } - } - - test("bam - stub") { - - options "-stub" - - when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ]) - input[1] = [[],[]] - """ - } - } - - then { - assertAll( - {assert process.success}, - {assert snapshot(process.out).match()} - ) - } - } - - test("cram - stub") { - - options "-stub" - - when { process { """ input[0] = Channel.of([ diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap index 3828f378..2747fd6c 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -29,80 +29,10 @@ } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T14:20:24.885816" - }, - "bam - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" - ], - "stats": [ - [ - { - "id": "test", - "single_end": false - }, - "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T14:20:39.310713" - }, - "cram - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" - ], - "stats": [ - [ - { - "id": "test", - "single_end": false - }, - "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T14:21:04.771199" + "timestamp": "2024-05-28T15:45:24.403941966" }, "bam": { "content": [ @@ -134,9 +64,9 @@ } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T14:19:06.645466" + "timestamp": "2024-05-28T15:45:06.711251947" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index dc611448..38df8576 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -13,15 +13,13 @@ process SAMTOOLS_VIEW { path qname output: - tuple val(meta), path("${prefix}.bam"), emit: bam, optional: true - tuple val(meta), path("${prefix}.cram"), emit: cram, optional: true - tuple val(meta), path("${prefix}.sam"), emit: sam, optional: true - tuple val(meta), path("${prefix}.${file_type}.bai"), emit: bai, optional: true - tuple val(meta), path("${prefix}.${file_type}.csi"), emit: csi, optional: true - tuple val(meta), path("${prefix}.${file_type}.crai"), emit: crai, optional: true - tuple val(meta), path("${prefix}.unselected.${file_type}"), emit: unselected, optional: true - tuple val(meta), path("${prefix}.unselected.${file_type}.{bai,csi,crsi}"), emit: unselected_index, optional: true - path "versions.yml", emit: versions + tuple val(meta), path("*.bam"), emit: bam, optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true + tuple val(meta), path("*.sam"), emit: sam, optional: true + tuple val(meta), path("*.bai"), emit: bai, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true + tuple val(meta), path("*.crai"), emit: crai, optional: true + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -29,13 +27,13 @@ process SAMTOOLS_VIEW { script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - prefix = task.ext.prefix ?: "${meta.id}" + def prefix = task.ext.prefix ?: "${meta.id}" def reference = fasta ? "--reference ${fasta}" : "" - file_type = args.contains("--output-fmt sam") ? "sam" : - args.contains("--output-fmt bam") ? "bam" : - args.contains("--output-fmt cram") ? "cram" : - input.getExtension() - readnames = qname ? "--qname-file ${qname} --output-unselected ${prefix}.unselected.${file_type}": "" + def readnames = qname ? "--qname-file ${qname}": "" + def file_type = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt bam") ? "bam" : + args.contains("--output-fmt cram") ? "cram" : + input.getExtension() if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ samtools \\ @@ -56,14 +54,14 @@ process SAMTOOLS_VIEW { stub: def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" - file_type = args.contains("--output-fmt sam") ? "sam" : - args.contains("--output-fmt bam") ? "bam" : - args.contains("--output-fmt cram") ? "cram" : - input.getExtension() + def prefix = task.ext.prefix ?: "${meta.id}" + def file_type = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt bam") ? "bam" : + args.contains("--output-fmt cram") ? "cram" : + input.getExtension() if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" - def index = args.contains("--write-index") ? "touch ${prefix}.${file_type}.csi" : "" + def index = args.contains("--write-index") ? "touch ${prefix}.csi" : "" """ touch ${prefix}.${file_type} diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml index 27be60d0..3dadafae 100644 --- a/modules/nf-core/samtools/view/meta.yml +++ b/modules/nf-core/samtools/view/meta.yml @@ -73,15 +73,6 @@ output: type: file description: optional CRAM file index pattern: "*.{crai}" - # unselected and unselected_index are created when passing a qname - - unselected: - type: file - description: optional file with unselected alignments - pattern: "*.unselected.{bam,cram,sam}" - - unselected_index: - type: file - description: index for the "unselected" file - pattern: "*.unselected.{bai,csi,crai}" - versions: type: file description: File containing software versions diff --git a/modules/nf-core/samtools/view/tests/main.nf.test b/modules/nf-core/samtools/view/tests/main.nf.test index 37b81a91..45a0defb 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test +++ b/modules/nf-core/samtools/view/tests/main.nf.test @@ -172,8 +172,6 @@ nextflow_process { { assert snapshot(process.out.crai).match("cram_to_bam_index_qname_crai") }, { assert snapshot(process.out.cram).match("cram_to_bam_index_qname_cram") }, { assert snapshot(process.out.sam).match("cram_to_bam_index_qname_sam") }, - { assert snapshot(file(process.out.unselected[0][1]).name).match("cram_to_bam_index_qname_unselected") }, - { assert snapshot(file(process.out.unselected_index[0][1]).name).match("cram_to_bam_index_qname_unselected_csi") }, { assert snapshot(process.out.versions).match("cram_to_bam_index_qname_versions") } ) } diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap index 6bcce9fe..eb0c577c 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap @@ -355,26 +355,6 @@ }, "timestamp": "2024-02-12T19:38:23.322874" }, - "cram_to_bam_index_qname_unselected": { - "content": [ - "test.unselected.bam" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:23.322874" - }, - "cram_to_bam_index_qname_unselected_csi": { - "content": [ - "test.unselected.bam.csi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:23.328458" - }, "bam_versions": { "content": [ [ @@ -497,7 +477,7 @@ }, "bam_stub_csi": { "content": [ - "test.bam.csi" + "test.csi" ], "meta": { "nf-test": "0.8.4", diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index ae67e004..8e9c48b1 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -81,8 +81,6 @@ process STAR_ALIGN { stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - echo "" | gzip > ${prefix}.unmapped_1.fastq.gz - echo "" | gzip > ${prefix}.unmapped_2.fastq.gz touch ${prefix}Xd.out.bam touch ${prefix}.Log.final.out touch ${prefix}.Log.out @@ -91,6 +89,8 @@ process STAR_ALIGN { touch ${prefix}.toTranscriptome.out.bam touch ${prefix}.Aligned.unsort.out.bam touch ${prefix}.Aligned.sortedByCoord.out.bam + touch ${prefix}.unmapped_1.fastq.gz + touch ${prefix}.unmapped_2.fastq.gz touch ${prefix}.tab touch ${prefix}.SJ.out.tab touch ${prefix}.ReadsPerGene.out.tab diff --git a/modules/nf-core/star/align/tests/main.nf.test b/modules/nf-core/star/align/tests/main.nf.test index 2d9f72dd..6ecd7786 100644 --- a/modules/nf-core/star/align/tests/main.nf.test +++ b/modules/nf-core/star/align/tests/main.nf.test @@ -9,367 +9,27 @@ nextflow_process { tag "star/align" tag "star/genomegenerate" - test("homo_sapiens - single_end") { - config "./nextflow.config" - - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test_fasta' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] - ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] - ]) - """ - } - } - } - - when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:true ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ] - ]) - input[1] = STAR_GENOMEGENERATE.out.index - input[2] = Channel.of([ - [ id:'test_gtf' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] - ]) - input[3] = false - input[4] = 'illumina' - input[5] = false - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - file(process.out.log_final[0][1]).name, - file(process.out.log_out[0][1]).name, - file(process.out.log_progress[0][1]).name, - process.out.bam, - process.out.bam_sorted, - process.out.bam_transcript, - process.out.bam_unsorted, - process.out.bedgraph, - process.out.fastq, - process.out.junction, - process.out.read_per_gene_tab, - process.out.sam, - process.out.spl_junc_tab, - process.out.tab, - process.out.wig, - process.out.versions - ).match() } - ) - } - } - - test("homo_sapiens - paired_end") { - config "./nextflow.config" - - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test_fasta' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] - ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] - ]) - """ - } - } - } - - when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) - ] - ]) - input[1] = STAR_GENOMEGENERATE.out.index - input[2] = Channel.of([ - [ id:'test_gtf' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] - ]) - input[3] = false - input[4] = 'illumina' - input[5] = false - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - file(process.out.log_final[0][1]).name, - file(process.out.log_out[0][1]).name, - file(process.out.log_progress[0][1]).name, - process.out.bam, - process.out.bam_sorted, - process.out.bam_transcript, - process.out.bam_unsorted, - process.out.bedgraph, - process.out.fastq, - process.out.junction, - process.out.read_per_gene_tab, - process.out.sam, - process.out.spl_junc_tab, - process.out.tab, - process.out.wig, - process.out.versions - ).match() } - ) - } - } - - test("homo_sapiens - paired_end - arriba") { - config "./nextflow.arriba.config" - - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test_fasta' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] - ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] - ]) - """ - } - } - } - - when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) - ] - ]) - input[1] = STAR_GENOMEGENERATE.out.index - input[2] = Channel.of([ - [ id:'test_gtf' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] - ]) - input[3] = false - input[4] = 'illumina' - input[5] = false - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - file(process.out.log_final[0][1]).name, - file(process.out.log_out[0][1]).name, - file(process.out.log_progress[0][1]).name, - process.out.bam, - process.out.bam_sorted, - process.out.bam_transcript, - process.out.bam_unsorted, - process.out.bedgraph, - process.out.fastq, - process.out.junction, - process.out.read_per_gene_tab, - process.out.sam, - process.out.spl_junc_tab, - process.out.tab, - process.out.wig, - process.out.versions - ).match() } - ) - } - } - - test("homo_sapiens - paired_end - starfusion") { - config "./nextflow.starfusion.config" - - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test_fasta' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] - ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] - ]) - """ - } - } - } - - when { + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" process { """ input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) - ] + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] ]) - input[1] = STAR_GENOMEGENERATE.out.index - input[2] = Channel.of([ + input[1] = Channel.of([ [ id:'test_gtf' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] ]) - input[3] = false - input[4] = 'illumina' - input[5] = false """ } } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - file(process.out.log_final[0][1]).name, - file(process.out.log_out[0][1]).name, - file(process.out.log_progress[0][1]).name, - process.out.bam, - process.out.bam_sorted, - process.out.bam_transcript, - process.out.bam_unsorted, - process.out.bedgraph, - process.out.fastq, - process.out.junction, - process.out.read_per_gene_tab, - process.out.sam, - process.out.spl_junc_tab, - process.out.tab, - process.out.wig, - process.out.versions - ).match() } - ) - } } - test("homo_sapiens - paired_end - multiple") { - config "./nextflow.config" - - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test_fasta' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] - ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] - ]) - """ - } - } - } - - when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) - ] - ]) - input[1] = STAR_GENOMEGENERATE.out.index - input[2] = Channel.of([ - [ id:'test_gtf' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] - ]) - input[3] = false - input[4] = 'illumina' - input[5] = false - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - file(process.out.log_final[0][1]).name, - file(process.out.log_out[0][1]).name, - file(process.out.log_progress[0][1]).name, - process.out.bam, - process.out.bam_sorted, - process.out.bam_transcript, - process.out.bam_unsorted, - process.out.bedgraph, - process.out.fastq, - process.out.junction, - process.out.read_per_gene_tab, - process.out.sam, - process.out.spl_junc_tab, - process.out.tab, - process.out.wig, - process.out.versions - ).match() } - ) - } - } - - test("homo_sapiens - single_end - stub") { - options "-stub" + test("homo_sapiens - single_end") { config "./nextflow.config" - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test_fasta' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] - ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] - ]) - """ - } - } - } - when { process { """ @@ -392,33 +52,29 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - single_end - log_final") }, + { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - single_end - log_out") }, + { assert snapshot(process.out.bam).match("homo_sapiens - single_end - bam") }, + { assert snapshot(process.out.bam_sorted).match("homo_sapiens - single_end - bam_sorted") }, + { assert snapshot(process.out.bam_transcript).match("homo_sapiens - single_end - bam_transcript") }, + { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - single_end - bam_unsorted") }, + { assert snapshot(process.out.bedgraph).match("homo_sapiens - single_end - bedgraph") }, + { assert snapshot(process.out.fastq).match("homo_sapiens - single_end - fastq") }, + { assert snapshot(process.out.junction).match("homo_sapiens - single_end - junction") }, + { assert snapshot(process.out.log_progress).match("homo_sapiens - single_end - log_progress") }, + { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - single_end - read_per_gene_tab") }, + { assert snapshot(process.out.sam).match("homo_sapiens - single_end - sam") }, + { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - single_end - spl_junc_tab") }, + { assert snapshot(process.out.tab).match("homo_sapiens - single_end - tab") }, + { assert snapshot(process.out.wig).match("homo_sapiens - single_end - wig") }, + { assert snapshot(process.out.versions).match("homo_sapiens - single_end - versions") } ) } } - test("homo_sapiens - paired_end - stub") { - options "-stub" + test("homo_sapiens - paired_end") { config "./nextflow.config" - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test_fasta' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] - ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] - ]) - """ - } - } - } - when { process { """ @@ -444,33 +100,29 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - log_final") }, + { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - log_out") }, + { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - bam") }, + { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - bam_sorted") }, + { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - bam_transcript") }, + { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - bam_unsorted") }, + { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - bedgraph") }, + { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - fastq") }, + { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - junction") }, + { assert snapshot(process.out.log_progress).match("homo_sapiens - paired_end - log_progress") }, + { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - read_per_gene_tab") }, + { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - sam") }, + { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - spl_junc_tab") }, + { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - tab") }, + { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - wig") }, + { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - versions") } ) } } - test("homo_sapiens - paired_end - arriba - stub") { - options "-stub" + test("homo_sapiens - paired_end - arriba") { config "./nextflow.arriba.config" - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test_fasta' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] - ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] - ]) - """ - } - } - } - when { process { """ @@ -496,33 +148,29 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - arriba - log_final") }, + { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - arriba - log_out") }, + { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - arriba - log_progress") }, + { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - arriba - bam") }, + { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - arriba - bam_sorted") }, + { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - arriba - bam_transcript") }, + { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - arriba - bam_unsorted") }, + { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - arriba - bedgraph") }, + { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - arriba - fastq") }, + { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - arriba - junction") }, + { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - arriba - read_per_gene_tab") }, + { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - arriba - sam") }, + { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - arriba - spl_junc_tab") }, + { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - arriba - tab") }, + { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - arriba - wig") }, + { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - arriba - versions") } ) } } - test("homo_sapiens - paired_end - starfusion - stub") { - options "-stub" + test("homo_sapiens - paired_end - starfusion") { config "./nextflow.starfusion.config" - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test_fasta' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] - ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] - ]) - """ - } - } - } - when { process { """ @@ -548,33 +196,29 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_final") }, + { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_out") }, + { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_progress") }, + { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - starfusion - bam") }, + { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - starfusion - bam_sorted") }, + { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - starfusion - bam_transcript") }, + { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - starfusion - bam_unsorted") }, + { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - starfusion - bedgraph") }, + { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - starfusion - fastq") }, + { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - starfusion - junction") }, + { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - starfusion - read_per_gene_tab") }, + { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - starfusion - sam") }, + { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - starfusion - spl_junc_tab") }, + { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - starfusion - tab") }, + { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - starfusion - wig") }, + { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - starfusion - versions") } ) } } - test("homo_sapiens - paired_end - multiple - stub") { - options "-stub" + test("homo_sapiens - paired_end - multiple") { config "./nextflow.config" - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test_fasta' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] - ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] - ]) - """ - } - } - } - when { process { """ @@ -602,7 +246,22 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - multiple - log_final") }, + { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - multiple - log_out") }, + { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - multiple - log_progress") }, + { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - multiple - bam") }, + { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - multiple - bam_sorted") }, + { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - multiple - bam_transcript") }, + { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - multiple - bam_unsorted") }, + { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - multiple - bedgraph") }, + { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - multiple - fastq") }, + { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - multiple - junction") }, + { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - multiple - read_per_gene_tab") }, + { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - multiple - sam") }, + { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - multiple - spl_junc_tab") }, + { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - multiple - tab") }, + { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - multiple - wig") }, + { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - multiple - versions") } ) } } diff --git a/modules/nf-core/star/align/tests/main.nf.test.snap b/modules/nf-core/star/align/tests/main.nf.test.snap index c814eb56..08edb914 100644 --- a/modules/nf-core/star/align/tests/main.nf.test.snap +++ b/modules/nf-core/star/align/tests/main.nf.test.snap @@ -1,1170 +1,382 @@ { - "homo_sapiens - single_end - stub": { + "homo_sapiens - paired_end - multiple - bam_sorted": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "10": [ - [ - { - "id": "test", - "single_end": true - }, - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "11": [ - [ - { - "id": "test", - "single_end": true - }, - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "12": [ - [ - { - "id": "test", - "single_end": true - }, - "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "13": [ - [ - { - "id": "test", - "single_end": true - }, - "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "14": [ - [ - { - "id": "test", - "single_end": true - }, - "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "15": [ - [ - { - "id": "test", - "single_end": true - }, - "test.Signal.UniqueMultiple.str1.out.bg:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": true - }, - "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" - ], - "4": [ - [ - { - "id": "test", - "single_end": true - }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "5": [ - [ - { - "id": "test", - "single_end": true - }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "6": [ - [ - { - "id": "test", - "single_end": true - }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "7": [ - [ - { - "id": "test", - "single_end": true - }, - "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "8": [ - [ - { - "id": "test", - "single_end": true - }, - [ - "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "9": [ - [ - { - "id": "test", - "single_end": true - }, - [ - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "bam": [ - [ - { - "id": "test", - "single_end": true - }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "bam_sorted": [ - [ - { - "id": "test", - "single_end": true - }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "bam_transcript": [ - [ - { - "id": "test", - "single_end": true - }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bam_unsorted": [ - [ - { - "id": "test", - "single_end": true - }, - "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bedgraph": [ - [ - { - "id": "test", - "single_end": true - }, - "test.Signal.UniqueMultiple.str1.out.bg:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "fastq": [ - [ - { - "id": "test", - "single_end": true - }, - [ - "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "junction": [ - [ - { - "id": "test", - "single_end": true - }, - "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "log_final": [ - [ - { - "id": "test", - "single_end": true - }, - "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "log_out": [ - [ - { - "id": "test", - "single_end": true - }, - "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "log_progress": [ - [ - { - "id": "test", - "single_end": true - }, - "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "read_per_gene_tab": [ - [ - { - "id": "test", - "single_end": true - }, - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "sam": [ - [ - { - "id": "test", - "single_end": true - }, - "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "spl_junc_tab": [ - [ - { - "id": "test", - "single_end": true - }, - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "tab": [ - [ - { - "id": "test", - "single_end": true - }, - [ - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "versions": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" - ], - "wig": [ - [ - { - "id": "test", - "single_end": true - }, - "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.sortedByCoord.out.bam:md5,ab07c21d63ab0a6c07d171d213c81d5a" ] - } + ] ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T15:16:04.712114" + "timestamp": "2023-12-04T18:01:19.968225733" }, - "homo_sapiens - paired_end - arriba - stub": { + "homo_sapiens - paired_end - multiple - wig": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "10": [ - [ - { - "id": "test", - "single_end": false - }, - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "11": [ - [ - { - "id": "test", - "single_end": false - }, - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "12": [ - [ - { - "id": "test", - "single_end": false - }, - "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "13": [ - [ - { - "id": "test", - "single_end": false - }, - "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "14": [ - [ - { - "id": "test", - "single_end": false - }, - "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "15": [ - [ - { - "id": "test", - "single_end": false - }, - "test.Signal.UniqueMultiple.str1.out.bg:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" - ], - "4": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "5": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "6": [ - [ - { - "id": "test", - "single_end": false - }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "7": [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "8": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "9": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "bam": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "bam_sorted": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "bam_transcript": [ - [ - { - "id": "test", - "single_end": false - }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bam_unsorted": [ - 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"test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "6": [ - [ - { - "id": "test", - "single_end": false - }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "7": [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "8": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "9": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "bam": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "bam_sorted": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "bam_transcript": [ - [ - { - "id": "test", - "single_end": false - }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bam_unsorted": [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "bedgraph": [ - [ - { - "id": "test", - "single_end": false - }, - "test.Signal.UniqueMultiple.str1.out.bg:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "fastq": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "junction": [ - [ - { - "id": "test", - "single_end": false - }, - "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "log_final": [ - [ - { - "id": "test", - "single_end": false - }, - "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "log_out": [ - [ - { - "id": "test", - "single_end": false - }, - "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "log_progress": [ - [ - { - "id": "test", - "single_end": false - }, - "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "read_per_gene_tab": [ - [ - { - "id": "test", - "single_end": false - }, - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "sam": [ - [ - { - "id": "test", - "single_end": false - }, - "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "spl_junc_tab": [ - [ - { - "id": "test", - "single_end": false - }, - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "tab": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "versions": [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" - ], - "wig": [ - [ - { - "id": "test", - "single_end": false - }, - "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } + "test.Log.out" ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T15:16:40.64399" + "timestamp": "2023-11-23T13:27:55.93945" } } \ No newline at end of file diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test b/modules/nf-core/star/genomegenerate/tests/main.nf.test index 4d619c47..c17c8ba4 100644 --- a/modules/nf-core/star/genomegenerate/tests/main.nf.test +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test @@ -28,15 +28,15 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString(), - process.out.versions) - .match() } + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_gtf_index") }, + { assert snapshot(process.out.versions).match("fasta_gtf_versions") } ) } } - test("fasta") { + test("fasta_gtf_stub") { + + options '-stub' when { process { @@ -45,7 +45,10 @@ nextflow_process { [ id:'test_fasta' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] ]) - input[1] = Channel.of([ [], [] ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) """ } } @@ -53,17 +56,13 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString(), - process.out.versions - ).match() } + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_gtf_stub_index") }, + { assert snapshot(process.out.versions).match("fasta_gtf_stub_versions") } ) } } - test("fasta_gtf_stub") { - - options '-stub' + test("fasta") { when { process { @@ -72,10 +71,7 @@ nextflow_process { [ id:'test_fasta' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] - ]) + input[1] = Channel.of([ [], [] ]) """ } } @@ -83,9 +79,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_index") }, + { assert snapshot(process.out.versions).match("fasta_versions") } ) } + } test("fasta_stub") { @@ -107,8 +105,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_stub_index") }, + { assert snapshot(process.out.versions).match("fasta_stub_versions") } ) } + } + } diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap index 207f4b4f..5653d6e6 100644 --- a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap @@ -1,148 +1,90 @@ { - "fasta_gtf": { + "fasta_gtf_versions": { "content": [ - "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]", [ "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.04.3" }, - "timestamp": "2024-07-22T14:55:35.478401" + "timestamp": "2024-02-01T15:54:31.798555" }, - "fasta_gtf_stub": { + "fasta_stub_versions": { "content": [ - { - "0": [ - [ - { - "id": "test_fasta" - }, - [ - "Genome:md5,d41d8cd98f00b204e9800998ecf8427e", - "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "SA:md5,d41d8cd98f00b204e9800998ecf8427e", - "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e", - "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "exonGeTrInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "exonInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "geneInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "sjdbInfo.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "sjdbList.fromGTF.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "sjdbList.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "transcriptInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "1": [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" - ], - "index": [ - [ - { - "id": "test_fasta" - }, - [ - "Genome:md5,d41d8cd98f00b204e9800998ecf8427e", - "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "SA:md5,d41d8cd98f00b204e9800998ecf8427e", - "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e", - "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "exonGeTrInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "exonInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "geneInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "sjdbInfo.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "sjdbList.fromGTF.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "sjdbList.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "transcriptInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "versions": [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" - ] - } + [ + "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-01T15:55:07.521209" + }, + "fasta_gtf_stub_index": { + "content": [ + "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-01T15:54:46.478098" + }, + "fasta_gtf_stub_versions": { + "content": [ + [ + "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.04.3" }, - "timestamp": "2024-07-22T14:55:57.247585" + "timestamp": "2024-02-01T15:54:46.491657" }, - "fasta_stub": { + "fasta_index": { "content": [ - { - "0": [ - [ - { - "id": "test_fasta" - }, - [ - "Genome:md5,d41d8cd98f00b204e9800998ecf8427e", - "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "SA:md5,d41d8cd98f00b204e9800998ecf8427e", - "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e", - "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "1": [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" - ], - "index": [ - [ - { - "id": "test_fasta" - }, - [ - "Genome:md5,d41d8cd98f00b204e9800998ecf8427e", - "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e", - "SA:md5,d41d8cd98f00b204e9800998ecf8427e", - "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e", - "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "versions": [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" - ] - } + "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]" ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.04.3" }, - "timestamp": "2024-07-22T14:56:07.01742" + "timestamp": "2024-02-01T15:54:57.552329" }, - "fasta": { + "fasta_versions": { "content": [ - "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]", [ "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-01T15:54:57.560541" + }, + "fasta_gtf_index": { + "content": [ + "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-01T15:54:31.786814" + }, + "fasta_stub_index": { + "content": [ + "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" }, - "timestamp": "2024-07-22T14:55:45.48784" + "timestamp": "2024-02-01T15:55:07.517472" } } \ No newline at end of file diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test b/modules/nf-core/stringtie/stringtie/tests/main.nf.test index 2204e849..00efe8f1 100644 --- a/modules/nf-core/stringtie/stringtie/tests/main.nf.test +++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test @@ -3,7 +3,6 @@ nextflow_process { name "Test Process STRINGTIE_STRINGTIE" script "../main.nf" process "STRINGTIE_STRINGTIE" - config "./nextflow.config" tag "modules" tag "modules_nfcore" tag "stringtie" @@ -11,6 +10,8 @@ nextflow_process { test("sarscov2 [bam] - forward strandedness") { + config "./nextflow.config" + when { process { """ @@ -26,17 +27,17 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.abundance, - process.out.transcript_gtf, - process.out.versions - ).match() } + { assert snapshot(process.out.transcript_gtf).match("fs_transcript_gtf") }, + { assert snapshot(process.out.abundance).match("fs_abundance") }, + { assert snapshot(process.out.versions).match("fs_versions") } ) } } test("sarscov2 [bam] - forward strandedness + reference annotation") { + config "./nextflow.config" + when { process { """ @@ -52,120 +53,17 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.abundance, - process.out.ballgown, - process.out.transcript_gtf, - process.out.versions - ).match() } + { assert snapshot(process.out.transcript_gtf).match("fs_gtf_transcript_gtf") }, + { assert snapshot(process.out.abundance).match("fs_gtf_abundance") }, + { assert snapshot(process.out.ballgown).match("fs_gtf_ballgown") }, + { assert snapshot(process.out.versions).match("fs_gtf_versions") } ) } } test("sarscov2 [bam] - reverse strandedness") { - when { - process { - """ - input[0] = [ - [ id:'test', strandedness:'reverse' ], // meta map - [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ] - ] - input[1] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.abundance, - process.out.transcript_gtf, - process.out.versions - ).match() } - ) - } - } - - test("sarscov2 [bam] - reverse strandedness + reference annotation") { - - when { - process { - """ - input[0] = [ - [ id:'test', strandedness:'reverse' ], // meta map - [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ] - ] - input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true) - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.abundance, - process.out.ballgown, - process.out.transcript_gtf, - process.out.versions - ).match() } - ) - } - } - - test("sarscov2 [bam] - forward strandedness - stub") { - - options "-stub" - - when { - process { - """ - input[0] = [ - [ id:'test', strandedness:'forward' ], // meta map - [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ] - ] - input[1] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("sarscov2 [bam] - forward strandedness + reference annotation - stub") { - - options "-stub" - - when { - process { - """ - input[0] = [ - [ id:'test', strandedness:'forward' ], // meta map - [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true) ] - ] - input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gtf", checkIfExists: true) - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("sarscov2 [bam] - reverse strandedness - stub") { - - options "-stub" + config "./nextflow.config" when { process { @@ -182,14 +80,16 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out.transcript_gtf).match("rs_transcript_gtf") }, + { assert snapshot(process.out.abundance).match("rs_abundance") }, + { assert snapshot(process.out.versions).match("rs_versions") } ) } } - test("sarscov2 [bam] - reverse strandedness + reference annotation - stub") { + test("sarscov2 [bam] - reverse strandedness + reference annotation") { - options "-stub" + config "./nextflow.config" when { process { @@ -206,7 +106,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out.transcript_gtf).match("rs_gtf_transcript_gtf") }, + { assert snapshot(process.out.abundance).match("rs_gtf_abundance") }, + { assert snapshot(process.out.ballgown).match("rs_gtf_ballgown") }, + { assert snapshot(process.out.versions).match("rs_gtf_versions") } ) } } diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap index 124dd4cb..bf751636 100644 --- a/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap +++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "sarscov2 [bam] - forward strandedness + reference annotation": { + "fs_abundance": { "content": [ [ [ @@ -7,44 +7,49 @@ "id": "test", "strandedness": "forward" }, - "test.gene.abundance.txt:md5,7d8bce7f2a922e367cedccae7267c22e" + "test.gene.abundance.txt:md5,d6f5c8cadb8458f1df0427cf790246e3" ] - ], + ] + ], + "timestamp": "2023-11-23T13:55:41.032044613" + }, + "fs_transcript_gtf": { + "content": [ [ [ { "id": "test", "strandedness": "forward" }, - [ - "e2t.ctab:md5,e981c0038295ae54b63cedb1083f1540", - "e_data.ctab:md5,6b4cf69bc03f3f69890f972a0e8b7471", - "i2t.ctab:md5,8a117c8aa4334b4c2d4711932b006fb4", - "i_data.ctab:md5,be3abe09740603213f83d50dcf81427f", - "t_data.ctab:md5,3b66c065da73ae0dd41cc332eff6a818" - ] + "test.transcripts.gtf:md5,569137af5be452413086b50653a97203" ] - ], + ] + ], + "timestamp": "2023-11-23T13:55:41.017978904" + }, + "rs_abundance": { + "content": [ [ [ { "id": "test", - "strandedness": "forward" + "strandedness": "reverse" }, - "test.transcripts.gtf:md5,f56cf8aba2c4a5673bc7963ba5f12d04" + "test.gene.abundance.txt:md5,d6f5c8cadb8458f1df0427cf790246e3" ] - ], + ] + ], + "timestamp": "2023-11-23T13:56:13.601112933" + }, + "fs_gtf_versions": { + "content": [ [ "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" ] ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T12:33:44.299962" + "timestamp": "2023-11-23T13:56:00.523797974" }, - "sarscov2 [bam] - forward strandedness": { + "fs_gtf_transcript_gtf": { "content": [ [ [ @@ -52,395 +57,50 @@ "id": "test", "strandedness": "forward" }, - "test.gene.abundance.txt:md5,d6f5c8cadb8458f1df0427cf790246e3" - ] - ], - [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.transcripts.gtf:md5,569137af5be452413086b50653a97203" + "test.transcripts.gtf:md5,f56cf8aba2c4a5673bc7963ba5f12d04" ] - ], - [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" ] ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T12:33:35.177738" - }, - "sarscov2 [bam] - forward strandedness - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" - ], - "abundance": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "ballgown": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "coverage_gtf": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "transcript_gtf": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T12:36:32.885078" + "timestamp": "2023-11-23T13:56:00.475164879" }, - "sarscov2 [bam] - forward strandedness + reference annotation - stub": { + "rs_versions": { "content": [ - { - "0": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" - ], - "abundance": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "ballgown": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "coverage_gtf": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "transcript_gtf": [ - [ - { - "id": "test", - "strandedness": "forward" - }, - "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T12:36:43.325777" - }, - "sarscov2 [bam] - reverse strandedness + reference annotation - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "strandedness": "reverse" - }, - "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "strandedness": "reverse" - }, - "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test", - "strandedness": "reverse" - }, - "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test", - "strandedness": "reverse" - }, - "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" - ], - "abundance": [ - [ - { - "id": "test", - "strandedness": "reverse" - }, - "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "ballgown": [ - [ - { - "id": "test", - "strandedness": "reverse" - }, - "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "coverage_gtf": [ - [ - { - "id": "test", - "strandedness": "reverse" - }, - "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "transcript_gtf": [ - [ - { - "id": "test", - "strandedness": "reverse" - }, - "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" - ] - } + [ + "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + ] ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T12:37:06.085936" + "timestamp": "2023-11-23T13:56:13.623892691" }, - "sarscov2 [bam] - reverse strandedness - stub": { + "rs_gtf_transcript_gtf": { "content": [ - { - "0": [ - [ - { - "id": "test", - "strandedness": "reverse" - }, - "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "strandedness": "reverse" - }, - "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test", - "strandedness": "reverse" - }, - "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test", - "strandedness": "reverse" - }, - "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" - ], - "abundance": [ - [ - { - "id": "test", - "strandedness": "reverse" - }, - "test.gene.abundance.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "ballgown": [ - [ - { - "id": "test", - "strandedness": "reverse" - }, - "test.ballgown:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "coverage_gtf": [ - [ - { - "id": "test", - "strandedness": "reverse" - }, - "test.coverage.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "transcript_gtf": [ - [ - { - "id": "test", - "strandedness": "reverse" - }, - "test.transcripts.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.transcripts.gtf:md5,bb346053a8c156b803b055133376c7fa" ] - } + ] ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T12:36:53.837578" + "timestamp": "2023-11-23T13:56:22.693599559" }, - "sarscov2 [bam] - reverse strandedness + reference annotation": { + "fs_gtf_abundance": { "content": [ [ [ { "id": "test", - "strandedness": "reverse" + "strandedness": "forward" }, - "test.gene.abundance.txt:md5,7385b870b955dae2c2ab78a70cf05cce" + "test.gene.abundance.txt:md5,7d8bce7f2a922e367cedccae7267c22e" ] - ], + ] + ], + "timestamp": "2023-11-23T13:56:00.482135418" + }, + "rs_gtf_ballgown": { + "content": [ [ [ { @@ -455,54 +115,72 @@ "t_data.ctab:md5,3b66c065da73ae0dd41cc332eff6a818" ] ] - ], + ] + ], + "timestamp": "2023-11-23T13:56:22.715698347" + }, + "rs_transcript_gtf": { + "content": [ [ [ { "id": "test", "strandedness": "reverse" }, - "test.transcripts.gtf:md5,bb346053a8c156b803b055133376c7fa" + "test.transcripts.gtf:md5,31c34aec2bf36bb0ea3c16c2afeeeb1f" ] - ], + ] + ], + "timestamp": "2023-11-23T13:56:13.590054035" + }, + "rs_gtf_versions": { + "content": [ [ "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" ] ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T12:34:03.114695" + "timestamp": "2023-11-23T13:56:22.725513476" }, - "sarscov2 [bam] - reverse strandedness": { + "fs_gtf_ballgown": { "content": [ [ [ { "id": "test", - "strandedness": "reverse" + "strandedness": "forward" }, - "test.gene.abundance.txt:md5,d6f5c8cadb8458f1df0427cf790246e3" + [ + "e2t.ctab:md5,e981c0038295ae54b63cedb1083f1540", + "e_data.ctab:md5,6b4cf69bc03f3f69890f972a0e8b7471", + "i2t.ctab:md5,8a117c8aa4334b4c2d4711932b006fb4", + "i_data.ctab:md5,be3abe09740603213f83d50dcf81427f", + "t_data.ctab:md5,3b66c065da73ae0dd41cc332eff6a818" + ] ] - ], + ] + ], + "timestamp": "2023-11-23T13:56:00.494299817" + }, + "fs_versions": { + "content": [ + [ + "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + ] + ], + "timestamp": "2023-11-23T13:55:41.049417582" + }, + "rs_gtf_abundance": { + "content": [ [ [ { "id": "test", "strandedness": "reverse" }, - "test.transcripts.gtf:md5,31c34aec2bf36bb0ea3c16c2afeeeb1f" + "test.gene.abundance.txt:md5,7385b870b955dae2c2ab78a70cf05cce" ] - ], - [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" ] ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T12:33:52.874479" + "timestamp": "2023-11-23T13:56:22.701059059" } -} \ No newline at end of file +} diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 0e2f3290..24ead871 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -72,25 +72,4 @@ process TRIMGALORE { END_VERSIONS """ } - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - if (meta.single_end) { - output_command = "echo '' | gzip > ${prefix}_trimmed.fq.gz ;" - output_command += "touch ${prefix}.fastq.gz_trimming_report.txt" - } else { - output_command = "echo '' | gzip > ${prefix}_1_trimmed.fq.gz ;" - output_command += "touch ${prefix}_1.fastq.gz_trimming_report.txt ;" - output_command += "echo '' | gzip > ${prefix}_2_trimmed.fq.gz ;" - output_command += "touch ${prefix}_2.fastq.gz_trimming_report.txt" - } - """ - ${output_command} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//') - cutadapt: \$(cutadapt --version) - END_VERSIONS - """ } diff --git a/modules/nf-core/trimgalore/tests/main.nf.test b/modules/nf-core/trimgalore/tests/main.nf.test index 2a3dbbb0..43904ac3 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test +++ b/modules/nf-core/trimgalore/tests/main.nf.test @@ -44,28 +44,6 @@ nextflow_process { } } - test("test_trimgalore_single_end - stub") { - - options "-stub" - - when { - process { - """ - input[0] = [ [ id:'test', single_end:true ], // meta map - [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - test("test_trimgalore_paired_end") { when { @@ -122,29 +100,4 @@ nextflow_process { ) } } - - test("test_trimgalore_paired_end - stub") { - - options "-stub" - - when { - process { - """ - input[0] = [ [ id:'test', single_end:false ], // meta map - [ - file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), - file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) - ] - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } } diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap index 6cb31c9f..082c5500 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test.snap +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -11,160 +11,6 @@ }, "timestamp": "2024-02-29T16:33:20.401347" }, - "test_trimgalore_single_end - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - - ], - "5": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" - ], - "html": [ - - ], - "log": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "reads": [ - [ - { - "id": "test", - "single_end": true - }, - "test_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "unpaired": [ - - ], - "versions": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" - ], - "zip": [ - - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T10:27:44.964166" - }, - "test_trimgalore_paired_end - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_1_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_2_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "test_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - - ], - "5": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" - ], - "html": [ - - ], - "log": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_1.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "test_2.fastq.gz_trimming_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "reads": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_1_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_2_trimmed.fq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "unpaired": [ - - ], - "versions": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" - ], - "zip": [ - - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-21T10:28:07.611496" - }, "test_trimgalore_paired_end": { "content": [ [ From b3c1ffd47d87a3d94fcd1bfac2b9d1aba187c7bc Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Tue, 6 Aug 2024 18:01:56 +0200 Subject: [PATCH 457/491] only updating necessary modules --- modules.json | 22 +- .../samtools/flagstat/tests/main.nf.test | 28 +- .../samtools/flagstat/tests/main.nf.test.snap | 78 ++++- .../samtools/idxstats/tests/main.nf.test | 29 +- .../samtools/idxstats/tests/main.nf.test.snap | 78 ++++- modules/nf-core/samtools/index/main.nf | 7 +- .../nf-core/samtools/index/tests/main.nf.test | 87 ++++- .../samtools/index/tests/main.nf.test.snap | 264 +++++++++++--- modules/nf-core/samtools/sort/main.nf | 14 +- .../nf-core/samtools/sort/tests/main.nf.test | 54 ++- .../samtools/sort/tests/main.nf.test.snap | 202 +++++++---- .../samtools/sort/tests/nextflow_cram.config | 8 + .../nf-core/samtools/stats/tests/main.nf.test | 57 ++- .../samtools/stats/tests/main.nf.test.snap | 82 ++++- modules/nf-core/samtools/view/main.nf | 40 ++- modules/nf-core/samtools/view/meta.yml | 9 + .../nf-core/samtools/view/tests/main.nf.test | 2 + .../samtools/view/tests/main.nf.test.snap | 22 +- .../tests/main.nf.test | 76 +++- .../tests/main.nf.test.snap | 326 +++++++++++++++--- 20 files changed, 1187 insertions(+), 298 deletions(-) create mode 100644 modules/nf-core/samtools/sort/tests/nextflow_cram.config diff --git a/modules.json b/modules.json index 35714771..abfb70e0 100644 --- a/modules.json +++ b/modules.json @@ -71,7 +71,7 @@ }, "bwa/index": { "branch": "master", - "git_sha": "086fa66260595e123b0ea47a6512539b72a9afa3", + "git_sha": "e0ff65e1fb313677de09f5f477ae3da30ce19b7b", "installed_by": [ "modules" ] @@ -155,7 +155,7 @@ }, "gnu/sort": { "branch": "master", - "git_sha": "ca199cfe5aa4f1ea3c41302158f0af2cfaa58957", + "git_sha": "a3cc42943548378b726610f45bb5a79ab3f0b633", "installed_by": [ "modules" ] @@ -197,28 +197,28 @@ }, "samtools/faidx": { "branch": "master", - "git_sha": "f153f1f10e1083c49935565844cccb7453021682", + "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", "installed_by": [ "modules" ] }, "samtools/flagstat": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "46eca555142d6e597729fcb682adcc791796f514", "installed_by": [ "bam_stats_samtools" ] }, "samtools/idxstats": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "46eca555142d6e597729fcb682adcc791796f514", "installed_by": [ "bam_stats_samtools" ] }, "samtools/index": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "46eca555142d6e597729fcb682adcc791796f514", "installed_by": [ "bam_sort_stats_samtools", "modules" @@ -226,7 +226,7 @@ }, "samtools/sort": { "branch": "master", - "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", + "git_sha": "46eca555142d6e597729fcb682adcc791796f514", "installed_by": [ "bam_sort_stats_samtools", "modules" @@ -234,14 +234,14 @@ }, "samtools/stats": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "46eca555142d6e597729fcb682adcc791796f514", "installed_by": [ "bam_stats_samtools" ] }, "samtools/view": { "branch": "master", - "git_sha": "0bd7d2333a88483aa0476acea172e9f5f6dd83bb", + "git_sha": "6c2309aaec566c0d44a6cf14d4b2d0c51afe2e91", "installed_by": [ "modules" ] @@ -301,14 +301,14 @@ "nf-core": { "bam_sort_stats_samtools": { "branch": "master", - "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", + "git_sha": "46eca555142d6e597729fcb682adcc791796f514", "installed_by": [ "subworkflows" ] }, "bam_stats_samtools": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab", "installed_by": [ "bam_sort_stats_samtools", "subworkflows" diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test b/modules/nf-core/samtools/flagstat/tests/main.nf.test index 24c3c04b..3b648a37 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test @@ -11,9 +11,30 @@ nextflow_process { test("BAM") { when { - params { - outdir = "$outputDir" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + """ } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("BAM - stub") { + + options "-stub" + + when { process { """ input[0] = Channel.of([ @@ -28,8 +49,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.flagstat).match("flagstat") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap index e9f85efa..23989c61 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap @@ -1,32 +1,72 @@ { - "flagstat": { + "BAM - stub": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + ], + "flagstat": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" ] - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-12T18:31:37.783927" + "timestamp": "2024-07-22T14:17:28.002887" }, - "versions": { + "BAM": { "content": [ - [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + ] + ], + "1": [ + "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + ], + "flagstat": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + ] + ], + "versions": [ + "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-28T15:41:52.516253882" + "timestamp": "2024-07-22T14:17:13.330971" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test b/modules/nf-core/samtools/idxstats/tests/main.nf.test index a2dcb27c..5fd1fc78 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test @@ -11,9 +11,6 @@ nextflow_process { test("bam") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -28,9 +25,29 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.idxstats).match("idxstats") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out).match() } ) } } -} + + test("bam - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + }} diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap index 4eacdb90..a5ac8104 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap @@ -1,32 +1,72 @@ { - "versions": { + "bam - stub": { "content": [ - [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + ], + "idxstats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-28T15:46:46.617989517" + "timestamp": "2024-07-22T14:17:56.180093" }, - "idxstats": { + "bam": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + ] + ], + "1": [ + "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + ], + "idxstats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + ] + ], + "versions": [ + "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" ] - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-12T18:36:41.561026" + "timestamp": "2024-07-22T14:17:41.408704" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index b523c21b..e002585b 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -35,10 +35,11 @@ process SAMTOOLS_INDEX { """ stub: + def args = task.ext.args ?: '' + def extension = file(input).getExtension() == 'cram' ? + "crai" : args.contains("-c") ? "csi" : "bai" """ - touch ${input}.bai - touch ${input}.crai - touch ${input}.csi + touch ${input}.${extension} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test index bb7756d1..ca34fb5c 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -9,11 +9,7 @@ nextflow_process { tag "samtools/index" test("bai") { - when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -27,18 +23,13 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.bai).match("bai") }, - { assert snapshot(process.out.versions).match("bai_versions") } + { assert snapshot(process.out).match() } ) } } test("crai") { - when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -52,20 +43,83 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.crai).match("crai") }, - { assert snapshot(process.out.versions).match("crai_versions") } + { assert snapshot(process.out).match() } ) } } test("csi") { - config "./csi.nextflow.config" when { - params { - outdir = "$outputDir" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.csi[0][1]).name, + process.out.versions + ).match() } + ) + } + } + + test("bai - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("crai - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true) + ]) + """ } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("csi - stub") { + options "-stub" + config "./csi.nextflow.config" + + when { process { """ input[0] = Channel.of([ @@ -79,8 +133,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert path(process.out.csi.get(0).get(1)).exists() }, - { assert snapshot(process.out.versions).match("csi_versions") } + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 52756e85..799d199c 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -1,74 +1,250 @@ { - "crai_versions": { + "csi - stub": { "content": [ - [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" - ] + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ], + "bai": [ + + ], + "crai": [ + + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-28T15:42:04.203740976" + "timestamp": "2024-07-22T16:51:53.9057" }, - "csi_versions": { + "crai - stub": { "content": [ - [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" - ] + { + "0": [ + + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ], + "bai": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-28T15:42:09.57475878" + "timestamp": "2024-07-22T16:51:45.931558" }, - "crai": { + "bai - stub": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ], + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "crai": [ + + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" ] - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-12T18:41:38.446424" + "timestamp": "2024-07-22T16:51:34.807525" }, - "bai": { + "csi": { "content": [ + "test.paired_end.sorted.bam.csi", [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" - ] + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-02-12T18:40:46.579747" + "timestamp": "2024-07-22T16:52:55.688799" }, - "bai_versions": { + "crai": { "content": [ - [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" - ] + { + "0": [ + + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ], + "3": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ], + "bai": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T16:51:17.609533" + }, + "bai": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ], + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ], + "crai": [ + + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-28T15:41:57.929287369" + "timestamp": "2024-07-22T16:51:04.16585" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 596c6f7e..8e019099 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -50,10 +50,20 @@ process SAMTOOLS_SORT { """ stub: + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + def extension = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt cram") ? "cram" : + "bam" """ - touch ${prefix}.bam - touch ${prefix}.bam.csi + touch ${prefix}.${extension} + if [ "${extension}" == "bam" ]; + then + touch ${prefix}.${extension}.csi + elif [ "${extension}" == "cram" ]; + then + touch ${prefix}.${extension}.crai + fi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index fb38ed9b..c2ea9c72 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -32,16 +32,16 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.bam, - process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } } - ).match("test_bam") - } + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match()} ) } } test("cram") { - config "./nextflow.config" + config "./nextflow_cram.config" when { process { @@ -62,23 +62,20 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot( - process.out.bam, - process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } } - ).match("test_cram") - } + process.out.cram.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.crai.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match()} ) } } - test("bam_stub") { + test("bam - stub") { - config "./nextflow.config" options "-stub" + config "./nextflow.config" when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -96,8 +93,35 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(file(process.out.bam[0][1]).name).match("bam_stub_bam") }, - { assert snapshot(process.out.versions).match("bam_stub_versions") } + { assert snapshot(process.out).match() } + ) + } + } + + test("cram - stub") { + + options "-stub" + config "./nextflow_cram.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index 5a27de1d..da38d5d1 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -7,54 +7,159 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,21c992d59615936b99f2ad008aa54400" + "test.sorted.cram" ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram.crai" + ] + ], + [ + "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-31T08:13:54.512837189" + "timestamp": "2024-07-22T17:19:37.196205" }, - "bam_stub_bam": { + "bam - stub": { "content": [ - "test.sorted.bam" + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-31T07:29:00.761845507" + "timestamp": "2024-07-22T15:54:46.580756" }, - "test_cram": { + "cram - stub": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,22b2093be34a7637f5fbc84272b89d06" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam.csi" + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + + ], + "4": [ + "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + ], + "bam": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cram": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" ] - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-31T09:16:51.924951855" + "timestamp": "2024-07-22T15:57:30.505698" }, - "test_bam": { + "bam": { "content": [ [ [ @@ -73,42 +178,15 @@ }, "test.sorted.bam.csi" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-05-31T08:28:12.15952312" - }, - "bam_stub_versions": { - "content": [ + ], [ "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-05-31T07:29:00.765038811" - }, - "bam": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.sorted.bam:md5,21c992d59615936b99f2ad008aa54400" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-31T08:13:48.538030517" + "timestamp": "2024-07-22T15:54:25.872954" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/tests/nextflow_cram.config b/modules/nf-core/samtools/sort/tests/nextflow_cram.config new file mode 100644 index 00000000..3a8c0188 --- /dev/null +++ b/modules/nf-core/samtools/sort/tests/nextflow_cram.config @@ -0,0 +1,8 @@ +process { + + withName: SAMTOOLS_SORT { + ext.prefix = { "${meta.id}.sorted" } + ext.args = "--write-index --output-fmt cram" + } + +} diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test b/modules/nf-core/samtools/stats/tests/main.nf.test index e3d5cb14..28a77db2 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test +++ b/modules/nf-core/samtools/stats/tests/main.nf.test @@ -11,9 +11,6 @@ nextflow_process { test("bam") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -37,9 +34,59 @@ nextflow_process { test("cram") { when { - params { - outdir = "$outputDir" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ } + } + + then { + assertAll( + {assert process.success}, + {assert snapshot(process.out).match()} + ) + } + } + + test("bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + {assert process.success}, + {assert snapshot(process.out).match()} + ) + } + } + + test("cram - stub") { + + options "-stub" + + when { process { """ input[0] = Channel.of([ diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap index 2747fd6c..3828f378 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -29,10 +29,80 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-28T15:45:24.403941966" + "timestamp": "2024-07-22T14:20:24.885816" + }, + "bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T14:20:39.310713" + }, + "cram - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T14:21:04.771199" }, "bam": { "content": [ @@ -64,9 +134,9 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-28T15:45:06.711251947" + "timestamp": "2024-07-22T14:19:06.645466" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index 38df8576..dc611448 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -13,13 +13,15 @@ process SAMTOOLS_VIEW { path qname output: - tuple val(meta), path("*.bam"), emit: bam, optional: true - tuple val(meta), path("*.cram"), emit: cram, optional: true - tuple val(meta), path("*.sam"), emit: sam, optional: true - tuple val(meta), path("*.bai"), emit: bai, optional: true - tuple val(meta), path("*.csi"), emit: csi, optional: true - tuple val(meta), path("*.crai"), emit: crai, optional: true - path "versions.yml", emit: versions + tuple val(meta), path("${prefix}.bam"), emit: bam, optional: true + tuple val(meta), path("${prefix}.cram"), emit: cram, optional: true + tuple val(meta), path("${prefix}.sam"), emit: sam, optional: true + tuple val(meta), path("${prefix}.${file_type}.bai"), emit: bai, optional: true + tuple val(meta), path("${prefix}.${file_type}.csi"), emit: csi, optional: true + tuple val(meta), path("${prefix}.${file_type}.crai"), emit: crai, optional: true + tuple val(meta), path("${prefix}.unselected.${file_type}"), emit: unselected, optional: true + tuple val(meta), path("${prefix}.unselected.${file_type}.{bai,csi,crsi}"), emit: unselected_index, optional: true + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -27,13 +29,13 @@ process SAMTOOLS_VIEW { script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" def reference = fasta ? "--reference ${fasta}" : "" - def readnames = qname ? "--qname-file ${qname}": "" - def file_type = args.contains("--output-fmt sam") ? "sam" : - args.contains("--output-fmt bam") ? "bam" : - args.contains("--output-fmt cram") ? "cram" : - input.getExtension() + file_type = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt bam") ? "bam" : + args.contains("--output-fmt cram") ? "cram" : + input.getExtension() + readnames = qname ? "--qname-file ${qname} --output-unselected ${prefix}.unselected.${file_type}": "" if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ samtools \\ @@ -54,14 +56,14 @@ process SAMTOOLS_VIEW { stub: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def file_type = args.contains("--output-fmt sam") ? "sam" : - args.contains("--output-fmt bam") ? "bam" : - args.contains("--output-fmt cram") ? "cram" : - input.getExtension() + prefix = task.ext.prefix ?: "${meta.id}" + file_type = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt bam") ? "bam" : + args.contains("--output-fmt cram") ? "cram" : + input.getExtension() if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" - def index = args.contains("--write-index") ? "touch ${prefix}.csi" : "" + def index = args.contains("--write-index") ? "touch ${prefix}.${file_type}.csi" : "" """ touch ${prefix}.${file_type} diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml index 3dadafae..27be60d0 100644 --- a/modules/nf-core/samtools/view/meta.yml +++ b/modules/nf-core/samtools/view/meta.yml @@ -73,6 +73,15 @@ output: type: file description: optional CRAM file index pattern: "*.{crai}" + # unselected and unselected_index are created when passing a qname + - unselected: + type: file + description: optional file with unselected alignments + pattern: "*.unselected.{bam,cram,sam}" + - unselected_index: + type: file + description: index for the "unselected" file + pattern: "*.unselected.{bai,csi,crai}" - versions: type: file description: File containing software versions diff --git a/modules/nf-core/samtools/view/tests/main.nf.test b/modules/nf-core/samtools/view/tests/main.nf.test index 45a0defb..37b81a91 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test +++ b/modules/nf-core/samtools/view/tests/main.nf.test @@ -172,6 +172,8 @@ nextflow_process { { assert snapshot(process.out.crai).match("cram_to_bam_index_qname_crai") }, { assert snapshot(process.out.cram).match("cram_to_bam_index_qname_cram") }, { assert snapshot(process.out.sam).match("cram_to_bam_index_qname_sam") }, + { assert snapshot(file(process.out.unselected[0][1]).name).match("cram_to_bam_index_qname_unselected") }, + { assert snapshot(file(process.out.unselected_index[0][1]).name).match("cram_to_bam_index_qname_unselected_csi") }, { assert snapshot(process.out.versions).match("cram_to_bam_index_qname_versions") } ) } diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap index eb0c577c..6bcce9fe 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap @@ -355,6 +355,26 @@ }, "timestamp": "2024-02-12T19:38:23.322874" }, + "cram_to_bam_index_qname_unselected": { + "content": [ + "test.unselected.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.322874" + }, + "cram_to_bam_index_qname_unselected_csi": { + "content": [ + "test.unselected.bam.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.328458" + }, "bam_versions": { "content": [ [ @@ -477,7 +497,7 @@ }, "bam_stub_csi": { "content": [ - "test.csi" + "test.bam.csi" ], "meta": { "nf-test": "0.8.4", diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test index 75b5b934..821a3cf5 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test @@ -19,9 +19,6 @@ nextflow_workflow { test("test_bam_sort_stats_samtools_single_end") { when { - params { - outdir = "$outputDir" - } workflow { """ input[0] = Channel.of([ @@ -41,9 +38,11 @@ nextflow_workflow { { assert workflow.success}, { assert workflow.out.bam.get(0).get(1) ==~ ".*.bam"}, { assert workflow.out.bai.get(0).get(1) ==~ ".*.bai"}, - { assert snapshot(workflow.out.stats).match("test_bam_sort_stats_samtools_single_end_stats") }, - { assert snapshot(workflow.out.flagstat).match("test_bam_sort_stats_samtools_single_end_flagstats") }, - { assert snapshot(workflow.out.idxstats).match("test_bam_sort_stats_samtools_single_end_idxstats") } + { assert snapshot( + workflow.out.flagstat, + workflow.out.idxstats, + workflow.out.stats, + workflow.out.versions).match() } ) } } @@ -51,9 +50,6 @@ nextflow_workflow { test("test_bam_sort_stats_samtools_paired_end") { when { - params { - outdir = "$outputDir" - } workflow { """ input[0] = Channel.of([ @@ -73,9 +69,65 @@ nextflow_workflow { { assert workflow.success}, { assert workflow.out.bam.get(0).get(1) ==~ ".*.bam"}, { assert workflow.out.bai.get(0).get(1) ==~ ".*.bai"}, - { assert snapshot(workflow.out.stats).match("test_bam_sort_stats_samtools_paired_end_stats") }, - { assert snapshot(workflow.out.flagstat).match("test_bam_sort_stats_samtools_paired_end_flagstats") }, - { assert snapshot(workflow.out.idxstats).match("test_bam_sort_stats_samtools_paired_end_idxstats") } + { assert snapshot( + workflow.out.flagstat, + workflow.out.idxstats, + workflow.out.stats, + workflow.out.versions).match() } + ) + } + } + + test("test_bam_sort_stats_samtools_single_end - stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out).match() } + ) + } + } + + test("test_bam_sort_stats_samtools_paired_end - stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out).match() } ) } } diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap index db063837..b7f4da17 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "test_bam_sort_stats_samtools_paired_end_flagstats": { + "test_bam_sort_stats_samtools_single_end": { "content": [ [ [ @@ -7,36 +7,18 @@ "id": "test", "single_end": false }, - "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" - }, - "timestamp": "2023-10-22T20:25:03.687121177" - }, - "test_bam_sort_stats_samtools_paired_end_idxstats": { - "content": [ + ], [ [ { "id": "test", "single_end": false }, - "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" - }, - "timestamp": "2023-10-22T20:25:03.709648916" - }, - "test_bam_sort_stats_samtools_single_end_stats": { - "content": [ + ], [ [ { @@ -45,15 +27,22 @@ }, "test.stats:md5,d32de3b3716a11039cef2367c3c1a56e" ] + ], + [ + "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1", + "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4", + "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1", + "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30", + "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-05-29T07:47:44.044172487" + "timestamp": "2024-07-22T17:02:44.34964" }, - "test_bam_sort_stats_samtools_paired_end_stats": { + "test_bam_sort_stats_samtools_paired_end": { "content": [ [ [ @@ -61,50 +50,281 @@ "id": "test", "single_end": false }, - "test.stats:md5,cca83e4fc9406fc3875b5e60055d6574" + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-05-29T07:47:51.426232891" - }, - "test_bam_sort_stats_samtools_single_end_idxstats": { - "content": [ + ], [ [ { "id": "test", "single_end": false }, - "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20" + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" - }, - "timestamp": "2024-01-18T17:10:02.84631" - }, - "test_bam_sort_stats_samtools_single_end_flagstats": { - "content": [ + ], [ [ { "id": "test", "single_end": false }, - "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53" + "test.stats:md5,cca83e4fc9406fc3875b5e60055d6574" ] + ], + [ + "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1", + "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4", + "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1", + "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30", + "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T17:03:02.583095" + }, + "test_bam_sort_stats_samtools_single_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1", + "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4", + "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1", + "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30", + "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5" + ], + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "csi": [ + + ], + "flagstat": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "idxstats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1", + "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4", + "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1", + "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30", + "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T17:03:22.328703" + }, + "test_bam_sort_stats_samtools_paired_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1", + "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4", + "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1", + "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30", + "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5" + ], + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "csi": [ + + ], + "flagstat": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "idxstats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1", + "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4", + "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1", + "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30", + "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-18T17:10:02.829756" + "timestamp": "2024-07-22T17:03:38.833662" } } \ No newline at end of file From 35ebe7575bab3920311bd518fa04a1acf8ad5bfb Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Tue, 6 Aug 2024 18:07:06 +0200 Subject: [PATCH 458/491] fixing pattern for input file of mirna_expression --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 21f3dfb1..ef992d4e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -66,7 +66,7 @@ "format": "file-path", "exists": true, "mimetype": "text/tsv", - "pattern": "^\\s+\\.tsv$", + "pattern": "^\\S+\\.tsv$", "description": "path to tab-separated file providing the expression counts of mirnas, which are created in pipeline 'smrnaseq'. \n\nmirna \t sample1 \t sample2 \t sample3 \t\nid1\t count_sample1 \t count_sample2 \t count_sample3 \t\nid2 \t ... \t ... \t ... \t \n", "fa_icon": "fas fa-file-tsv" }, From 399a16d3379c332b198142fc956af8fda591c991 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Wed, 7 Aug 2024 21:04:00 +0200 Subject: [PATCH 459/491] Adding missing html tag in output.md --- docs/output.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/output.md b/docs/output.md index 7c00df20..d706517c 100644 --- a/docs/output.md +++ b/docs/output.md @@ -369,6 +369,7 @@ The quantification is performed using psirc-quant, which is a wrapper around `ka - `*.marked.fasta`: Transcript sequences in FASTA format with the circRNA sequences marked with a `C` field in the header. - `*.tx2gene.tsv`: Transcript to gene mapping file. + ### Per sample
    From e550ec22544a86492b541ba004888069c207ba1b Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Wed, 7 Aug 2024 21:05:57 +0200 Subject: [PATCH 460/491] updating output.md in docs Updating the mirna_prediction section --- docs/output.md | 74 ++++++++++++++++++++++++++++++++++++++++++-------- 1 file changed, 63 insertions(+), 11 deletions(-) diff --git a/docs/output.md b/docs/output.md index d706517c..ea926cb2 100644 --- a/docs/output.md +++ b/docs/output.md @@ -24,9 +24,9 @@ The directories listed below will be created in the results directory after the - samples: Per sample quantification results - transcriptome: Combined linear and circular transcriptome, based on GTF file and detected BSJs - mirna_prediction - - miranda - - targetscan - - combined + - binding_sites + - correlation + - mirna_expression - statistical_tests - circtest - multiqc @@ -370,6 +370,7 @@ The quantification is performed using psirc-quant, which is a wrapper around `ka - `*.tx2gene.tsv`: Transcript to gene mapping file.
    + ### Per sample
    @@ -418,13 +419,22 @@ nf-core/circrna combines the sample-specific quantification results into proper ## miRNA Prediction -### miRanda +### Binding Sites + +#### Tools + +This section contains predicted binding sites for miRNA-target interactions generated by various computational tools. +Each tool utilizes unique algorithms and criteria to identify potential miRNA binding sites on target genomic sequences, providing complementary insights into miRNA regulatory networks. + +##### miRanda
    Output files -- `mirna_prediction/miranda/` - - `*.miRanda.txt`: Raw outputs from `miRanda`. +- `mirna_prediction/bindingsites/tools/miranda/output` + - `*.miranda.txt`: Raw predictions from `miRanda`. +- `mirna_prediction/bindingsites/tools/miranda/unified` + - `*.miranda.tsv`: Unified predictions from `miRanda`.
    @@ -433,24 +443,27 @@ nf-core/circrna combines the sample-specific quantification results into proper 1. First a dynamic programming local alignment is carried out between the query miRNA sequence and the reference sequence. This alignment procedure scores based on sequence complementarity and not on sequence identity. 2. Secondly, the algorithm takes high-scoring alignments detected from phase 1 and estimates the thermodynamic stability of RNA duplexes based on these alignments. This second phase of the method utilises folding routines from the `RNAlib` library, part of the [ViennaRNA](https://www.tbi.univie.ac.at/RNA/) package. -### TargetScan +##### TargetScan
    Output files -- `mirna_prediction/targetscan/` - - `*.targetscan.txt`: Raw outputs from `TargetScan`. +- `mirna_prediction/bindingsites/tools/targetscan/output` + - `*.targetscan.txt`: Raw predictions from `TargetScan`. +- `mirna_prediction/bindingsites/tools/targetscan/unified` + - `*.targetscan.tsv`: Unified predictions from `TargetScan`.
    [TargetScan](http://www.targetscan.org/vert_72/) predicts biological targets of miRNAs by searching for the presence of conserved 8mer, 7mer, and 6mer sites within the circRNA mature sequence that match the seed region of each miRNA. -### Combined + +#### Targets
    Output files -- `mirna_prediction/combined/` +- `mirna_prediction/binding_sites/targets` - `*_miRNA_targets.txt`: Filtered target miRNAs of circRNAs called by quantification tools. Columns are self explanatory: miRNA, Score, Energy_KcalMol, Start, End, Site_type.
    @@ -459,3 +472,42 @@ nf-core/circrna performs miRNA target filtering on `miRanda` and `TargetScan` pr 1. miRNA must be called by both `miRanda` and `TargetScan`. 2. If a site within the circRNA mature sequence shares duplicate miRNA ID's overlapping the same coordinates, the miRNA with the highest score is kept. + +#### Majority Vote + +
    +Output files + +- `mirna_prediction/binding_sites/majority_vote` + - `mirna.targets.tsv`: Stores miRNA-target mappings with all targets listed per miRNA, making it compact and suitable for bulk analyses. + - `mirna.majority.tsv`: Lists each miRNA-target interaction on a separate line, which is helpful for detailed analysis of each interaction independently. + +
    + +nf-core/circrna performs a majority vote on the predicted miRNA targets from [TargetScan](http://www.targetscan.org/vert_72/) and [miRanda](http://cbio.mskcc.org/miRNA2003/miranda.html) based on a +threshold specified by the user. + +### miRNA Expression + +
    +Output files + +- `mirna_prediction/mirna_expression/` + - `mirna.normalized_counts.tsv`: Contains normalized miRNA expression of all samples. + - `mirna.normalized_counts_filtered.tsv`: Contains miRNA expression after filtering. + +
    + +nf-core/circrna processes miRNA expression data by normalizing and filtering it for further analysis. + +### Correlation + +
    +Output files + +- `mirna_prediction/correlation` + - `*.tsv`: Files named after the specific miRNA containing correlation results for that miRNA with its target transcripts. + +
    + +nf-core/circrna computes correlations between miRNA and transcript expression levels and writes the results to individual tsv files for each miRNA-target interaction specified in the input binding sites file. From 8fef0f7cb7501a14b71af1c60da7181fd759994f Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Wed, 7 Aug 2024 21:17:44 +0200 Subject: [PATCH 461/491] capitalizing 'tsv' to TSV --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index ea926cb2..64599ac0 100644 --- a/docs/output.md +++ b/docs/output.md @@ -510,4 +510,4 @@ nf-core/circrna processes miRNA expression data by normalizing and filtering it
    -nf-core/circrna computes correlations between miRNA and transcript expression levels and writes the results to individual tsv files for each miRNA-target interaction specified in the input binding sites file. +nf-core/circrna computes correlations between miRNA and transcript expression levels and writes the results to individual TSV files for each miRNA-target interaction specified in the input binding sites file. From 740cc4372214078e59e159f927656ec018398add Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Wed, 7 Aug 2024 21:24:25 +0200 Subject: [PATCH 462/491] updating usage.md --- docs/usage.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 13a1b410..a8cbfcae 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -94,12 +94,15 @@ The output of the annotation step will be bundled with the outputs of the BSJ de ## miRNA prediction -This section allows looking for miRNA binding sites in the circRNAs. The following tools are currently supported: +This section allows looking for miRNA binding sites in the circRNAs. +The following tools are currently supported: - `miRanda` - `TargetScan` -This section will only be executed if the `mature` parameter is provided. The parameter should point to a FASTA file containing mature miRNA sequences. +This section will only be executed if the `mature` and `mirna_expression` parameters are provided. +The parameter `mature` should point to a FASTA file containing mature miRNA sequences. +The `mirna_expression` parameter should reference a TSV file containing the miRNA expression for each sample in your samplesheet. To view the outputs of the module, please see the output [documentation](https://nf-co.re/circrna/dev/output#mirna-prediction). From 5f9a7f98a425911fa31a16c87af2cb3a381a0dd2 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Wed, 7 Aug 2024 21:24:36 +0200 Subject: [PATCH 463/491] updating README.md --- README.md | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 6e8bb401..3f8b368f 100644 --- a/README.md +++ b/README.md @@ -54,9 +54,13 @@ If you want to contribute, feel free to create an issue or pull request on the [ - Merge circular transcriptome with linear transcriptome derived from provided GTF - Quantification of combined circular and linear transcriptome - [`psirc-quant`](https://github.com/Christina-hshi/psirc) -- miRNA binding affinity analysis (only if the `mature` parameter is provided) - - [`miRanda`](http://cbio.mskcc.org/miRNA2003/miranda.html) - - [`TargetScan`](http://www.targetscan.org/cgi-bin/targetscan/data_download.vert72.cgi) +- miRNA binding affinity analysis (only if the `mature` and `mirna_expression` parameter is provided) + - Normalizes miRNA expression + - Binding site prediction + - [`miRanda`](http://cbio.mskcc.org/miRNA2003/miranda.html) + - [`TargetScan`](http://www.targetscan.org/cgi-bin/targetscan/data_download.vert72.cgi) + - Perform majority vote on binding sites + - Compute correlations between miRNA and transcript expression levels - Statistical tests (only if the `phenotype` parameter is provided) - [`CircTest`](https://github.com/dieterich-lab/CircTest) - MultiQC report [`MultiQC`](http://multiqc.info/) From 596df450ca784369be156821bab66c5bdc0bf65b Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Wed, 7 Aug 2024 21:51:31 +0200 Subject: [PATCH 464/491] making mirna_expression parameter optional --- nextflow_schema.json | 1 - 1 file changed, 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index ef992d4e..bce90b44 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -59,7 +59,6 @@ "type": "object", "fa_icon": "fas fa-terminal", "description": "Define paths and threasholds for miRNA analysis.", - "required": ["mirna_expression"], "properties": { "mirna_expression": { "type": "string", From 6479a534f927fa92667aa7c598ae734918a89113 Mon Sep 17 00:00:00 2001 From: mweyrich28 <120316140+mweyrich28@users.noreply.github.com> Date: Wed, 7 Aug 2024 22:09:09 +0200 Subject: [PATCH 465/491] Apply suggestions from code review Co-authored-by: Nico Trummer <52698566+nictru@users.noreply.github.com> --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 3f8b368f..d856c31d 100644 --- a/README.md +++ b/README.md @@ -54,13 +54,13 @@ If you want to contribute, feel free to create an issue or pull request on the [ - Merge circular transcriptome with linear transcriptome derived from provided GTF - Quantification of combined circular and linear transcriptome - [`psirc-quant`](https://github.com/Christina-hshi/psirc) -- miRNA binding affinity analysis (only if the `mature` and `mirna_expression` parameter is provided) - - Normalizes miRNA expression +- miRNA binding affinity analysis (only if the `mature` parameter is provided) + - Normalizes miRNA expression (only if the `mirna_expression` parameter is provided) - Binding site prediction - [`miRanda`](http://cbio.mskcc.org/miRNA2003/miranda.html) - [`TargetScan`](http://www.targetscan.org/cgi-bin/targetscan/data_download.vert72.cgi) - Perform majority vote on binding sites - - Compute correlations between miRNA and transcript expression levels + - Compute correlations between miRNA and transcript expression levels (only if the `mirna_expression` parameter is provided) - Statistical tests (only if the `phenotype` parameter is provided) - [`CircTest`](https://github.com/dieterich-lab/CircTest) - MultiQC report [`MultiQC`](http://multiqc.info/) From e52e401b181b30c214cd65e6ee11902af5c43d6f Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Wed, 7 Aug 2024 22:25:04 +0200 Subject: [PATCH 466/491] renaming mirna_vote to mirna_tool_filter --- modules/local/majority_vote/templates/majority.py | 2 +- nextflow_schema.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/majority_vote/templates/majority.py b/modules/local/majority_vote/templates/majority.py index 2969ce54..b08d9c25 100644 --- a/modules/local/majority_vote/templates/majority.py +++ b/modules/local/majority_vote/templates/majority.py @@ -28,7 +28,7 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: df = df.groupby(['mirna', 'target'])['tool'].apply(set).reset_index() # performing majority vote keeping only mirna binding sites that meet the required number of votes -min_tools = int("${params.mirna_vote}") +min_tools = int("${params.mirna_tool_filter}") df = df[df['tool'].apply(len) >= min_tools].copy() df = df.drop('tool', axis=1) diff --git a/nextflow_schema.json b/nextflow_schema.json index bce90b44..8ab9ecdc 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -147,7 +147,7 @@ "default": "miranda, targetscan", "pattern": "^((miranda|targetscan|pita|tarpmir)?,?)*[^,]+$" }, - "mirna_vote": { + "mirna_tool_filter": { "type": "integer", "fa_icon": "fas fa-intersection", "description": "Specify the number of votes required for a miRNA to be further considered in downstream analysis.'", From e49b9477abf910aaddd2427784e9a186d436f8c6 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Thu, 8 Aug 2024 09:21:16 +0200 Subject: [PATCH 467/491] applying prettier --- README.md | 2 +- docs/output.md | 1 - modules.json | 189 +++++------------- modules/local/mirna_filtering/environment.yml | 2 +- 4 files changed, 49 insertions(+), 145 deletions(-) diff --git a/README.md b/README.md index d856c31d..5ea93d2c 100644 --- a/README.md +++ b/README.md @@ -59,7 +59,7 @@ If you want to contribute, feel free to create an issue or pull request on the [ - Binding site prediction - [`miRanda`](http://cbio.mskcc.org/miRNA2003/miranda.html) - [`TargetScan`](http://www.targetscan.org/cgi-bin/targetscan/data_download.vert72.cgi) - - Perform majority vote on binding sites + - Perform majority vote on binding sites - Compute correlations between miRNA and transcript expression levels (only if the `mirna_expression` parameter is provided) - Statistical tests (only if the `phenotype` parameter is provided) - [`CircTest`](https://github.com/dieterich-lab/CircTest) diff --git a/docs/output.md b/docs/output.md index 64599ac0..f7016c8b 100644 --- a/docs/output.md +++ b/docs/output.md @@ -457,7 +457,6 @@ Each tool utilizes unique algorithms and criteria to identify potential miRNA bi [TargetScan](http://www.targetscan.org/vert_72/) predicts biological targets of miRNAs by searching for the presence of conserved 8mer, 7mer, and 6mer sites within the circRNA mature sequence that match the seed region of each miRNA. - #### Targets
    diff --git a/modules.json b/modules.json index abfb70e0..c1bed414 100644 --- a/modules.json +++ b/modules.json @@ -8,292 +8,208 @@ "bedtools/getfasta": { "branch": "master", "git_sha": "cdcdd5e3d806f0ff3983c40c69e0b07bb44ec299", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/groupby": { "branch": "master", "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/intersect": { "branch": "master", "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/sort": { "branch": "master", "git_sha": "571a5feac4c9ce0a8df0bc15b94230e7f3e8db47", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bioawk": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/bioawk/bioawk.diff" }, "bowtie/align": { "branch": "master", "git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bowtie/build": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bowtie2/align": { "branch": "master", "git_sha": "e4bad511789f16d0df39ee306b2cd50418365048", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bowtie2/build": { "branch": "master", "git_sha": "1fea64f5132a813ec97c1c6d3a74e0aee7142b6d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bwa/index": { "branch": "master", "git_sha": "e0ff65e1fb313677de09f5f477ae3da30ce19b7b", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/cat": { "branch": "master", "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", "git_sha": "4fc983ad0b30e6e32696fa7d980c76c7bfe1c03e", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "circexplorer2/annotate": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "circexplorer2/parse": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "csvtk/join": { "branch": "master", "git_sha": "614abbf126f287a3068dc86997b2e1b6a93abe20", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "csvtk/split": { "branch": "master", "git_sha": "614abbf126f287a3068dc86997b2e1b6a93abe20", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "de45447d060b8c8b98575bc637a4a575fd0638e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/gtffilter": { "branch": "master", "git_sha": "a0aee18374b7f072aa0f89f4d66f5a3a9f8176d2", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/tx2gene": { "branch": "master", "git_sha": "ec155021a9104441bf6a9bae3b55d1b5b0bfdb3a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastqc": { "branch": "master", "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gawk": { "branch": "master", "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gnu/sort": { "branch": "master", "git_sha": "a3cc42943548378b726610f45bb5a79ab3f0b633", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "hisat2/align": { "branch": "master", "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "hisat2/build": { "branch": "master", "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "hisat2/extractsplicesites": { "branch": "master", "git_sha": "400037f54de4b0c42712ec5a499d9fd9e66250d1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "miranda": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/flagstat": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/idxstats": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": [ - "bam_sort_stats_samtools", - "modules" - ] + "installed_by": ["bam_sort_stats_samtools", "modules"] }, "samtools/sort": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": [ - "bam_sort_stats_samtools", - "modules" - ] + "installed_by": ["bam_sort_stats_samtools", "modules"] }, "samtools/stats": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/view": { "branch": "master", "git_sha": "6c2309aaec566c0d44a6cf14d4b2d0c51afe2e91", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "segemehl/align": { "branch": "master", "git_sha": "9a6b0745dbb5359286d36dee2183ffab240abba0", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "segemehl/index": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "star/align": { "branch": "master", "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "star/genomegenerate": { "branch": "master", "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "stringtie/stringtie": { "branch": "master", "git_sha": "b1b959609bda44341120aed1766329909f54b8d0", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "trimgalore": { "branch": "master", "git_sha": "a98418419ae6c9df3cf6cf108d1e1aba71037d5a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tximeta/tximport": { "branch": "master", "git_sha": "5d095e8413da1f4c72b7d07ce87f75c09482486f", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -302,41 +218,30 @@ "bam_sort_stats_samtools": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "bam_stats_samtools": { "branch": "master", "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab", - "installed_by": [ - "bam_sort_stats_samtools", - "subworkflows" - ] + "installed_by": ["bam_sort_stats_samtools", "subworkflows"] }, "utils_nextflow_pipeline": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} diff --git a/modules/local/mirna_filtering/environment.yml b/modules/local/mirna_filtering/environment.yml index 1aa60c3d..ddeffa11 100644 --- a/modules/local/mirna_filtering/environment.yml +++ b/modules/local/mirna_filtering/environment.yml @@ -1,4 +1,4 @@ -name: mirna_filtering +name: mirna_filtering channels: - conda-forge - defaults From edafce4825c5b541196d74ab4b86c063b4c7551f Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Thu, 8 Aug 2024 09:23:53 +0200 Subject: [PATCH 468/491] renaming mirna_tools in nextflow.config --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 21270121..f79cdd5b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -69,7 +69,7 @@ params { mirna_expression = null mirna_min_reads = 5 mirna_min_sample_percentage = 0.2 - mirna_tools = 'miranda, targetscan' + mirna_tool_filter = 'miranda, targetscan' mirna_vote = 1 mirna_correlation = 'pearson' From 4d514b405c8f758c9e395fe3347a091b4c6a7f53 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Thu, 8 Aug 2024 09:25:34 +0200 Subject: [PATCH 469/491] fixing indent --- modules/local/mirna_filtering/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/local/mirna_filtering/main.nf b/modules/local/mirna_filtering/main.nf index 035354d1..03efeea4 100644 --- a/modules/local/mirna_filtering/main.nf +++ b/modules/local/mirna_filtering/main.nf @@ -5,12 +5,12 @@ process MIRNA_FILTERING { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-base:4.2.1' : - 'biocontainers/r-base:4.2.1' }" + 'biocontainers/r-base:4.2.1' }" input: tuple val(meta), path(normalized_counts) - val(mirna_min_sample_percentage) - val(mirna_min_reads) + val(mirna_min_sample_percentage) + val(mirna_min_reads) output: tuple val(meta), path("${meta.id}.normalized_counts_filtered.tsv"), emit: filtered From 737da8027e5c14563cafd261a17a4454a1816dbb Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Thu, 8 Aug 2024 09:28:10 +0200 Subject: [PATCH 470/491] deleting redundant file --- modules/local/mirna_filtering/environment.yml | 4 ---- 1 file changed, 4 deletions(-) delete mode 100644 modules/local/mirna_filtering/environment.yml diff --git a/modules/local/mirna_filtering/environment.yml b/modules/local/mirna_filtering/environment.yml deleted file mode 100644 index ddeffa11..00000000 --- a/modules/local/mirna_filtering/environment.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: mirna_filtering -channels: - - conda-forge - - defaults From b112f0c9ec6314623123114096cfbbb1f3a6ee00 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Thu, 8 Aug 2024 09:35:36 +0200 Subject: [PATCH 471/491] rewording usage --- docs/usage.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index a8cbfcae..2dbeda74 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -100,9 +100,11 @@ The following tools are currently supported: - `miRanda` - `TargetScan` -This section will only be executed if the `mature` and `mirna_expression` parameters are provided. +This section will only be executed if the `mature` parameter is provided. The parameter `mature` should point to a FASTA file containing mature miRNA sequences. -The `mirna_expression` parameter should reference a TSV file containing the miRNA expression for each sample in your samplesheet. +By providing a TSV file containing the miRNA expression of all samples via `mirna_expression`, this +subworkflow will perform additional normalization and filtering of `mirna_expression` and `mature` before +executing the miRNA binding size prediction. To view the outputs of the module, please see the output [documentation](https://nf-co.re/circrna/dev/output#mirna-prediction). From bd7cd3690f64c588f1d2e101def8f100079a9397 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Thu, 8 Aug 2024 09:40:59 +0200 Subject: [PATCH 472/491] rewording usage --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index 2dbeda74..2f3b2166 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -103,7 +103,7 @@ The following tools are currently supported: This section will only be executed if the `mature` parameter is provided. The parameter `mature` should point to a FASTA file containing mature miRNA sequences. By providing a TSV file containing the miRNA expression of all samples via `mirna_expression`, this -subworkflow will perform additional normalization and filtering of `mirna_expression` and `mature` before +sub-workflow will perform additional normalization and filtering of `mirna_expression` and `mature` before executing the miRNA binding size prediction. To view the outputs of the module, please see the output [documentation](https://nf-co.re/circrna/dev/output#mirna-prediction). From 7f165bafe3166625887587170b62bd6fc7afba59 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Thu, 8 Aug 2024 09:52:29 +0200 Subject: [PATCH 473/491] reformatting compute correlations --- modules/local/compute_correlations/main.nf | 2 +- .../templates/compute_correlations.R | 51 ++++++++++--------- 2 files changed, 29 insertions(+), 24 deletions(-) diff --git a/modules/local/compute_correlations/main.nf b/modules/local/compute_correlations/main.nf index 773fddae..4a72b5eb 100644 --- a/modules/local/compute_correlations/main.nf +++ b/modules/local/compute_correlations/main.nf @@ -21,7 +21,7 @@ process COMPUTE_CORRELATIONS { script: template 'compute_correlations.R' - + stub: """ touch ${meta.id}.circrna_correlation.tsv diff --git a/modules/local/compute_correlations/templates/compute_correlations.R b/modules/local/compute_correlations/templates/compute_correlations.R index e60ccc73..d9976226 100644 --- a/modules/local/compute_correlations/templates/compute_correlations.R +++ b/modules/local/compute_correlations/templates/compute_correlations.R @@ -11,34 +11,34 @@ tx_expression <- scaleInfReps(tx_expression) tx_expression <- labelKeep(tx_expression) # Here one can perform custom filtering if (!any(mcols(tx_expression)\$keep)) { - stop('No transcripts left after filtering') + stop('No transcripts left after filtering') } result_cols <- c('stat', 'log2FC', 'pvalue', 'locfdr', 'qvalue') # Iterate rows of interactions for (i in 1:nrow(interactions)) { - # Get miRNA and target gene - miRNA <- interactions[i, 1] - targets <- unlist(strsplit(interactions[i, 2], ',')) - - mirna_expression <- mi_expression[miRNA,] - transcript_expression <- tx_expression[targets,] - - if (!any(mcols(transcript_expression)\$keep)) { - print(paste('No transcripts left after filtering for miRNA', miRNA)) - next - } - - # Add miRNA expression to colData so that it can be used for correlation - colData(transcript_expression) <- cbind( - colData(transcript_expression), - t(mirna_expression[, rownames(colData(transcript_expression))]) - ) - - result <- rowData(swish(transcript_expression, miRNA, cor = "${params.mirna_correlation}"))[, result_cols] - result <- result[complete.cases(result), ] - write.table(result, paste0(miRNA, '.tsv'), sep = '\\t') + # Get miRNA and target gene + miRNA <- interactions[i, 1] + targets <- unlist(strsplit(interactions[i, 2], ',')) + + mirna_expression <- mi_expression[miRNA,] + transcript_expression <- tx_expression[targets,] + + if (!any(mcols(transcript_expression)\$keep)) { + print(paste('No transcripts left after filtering for miRNA', miRNA)) + next + } + + # Add miRNA expression to colData so that it can be used for correlation + colData(transcript_expression) <- cbind( + colData(transcript_expression), + t(mirna_expression[, rownames(colData(transcript_expression))]) + ) + + result <- rowData(swish(transcript_expression, miRNA, cor = "${params.mirna_correlation}"))[, result_cols] + result <- result[complete.cases(result), ] + write.table(result, paste0(miRNA, '.tsv'), sep = '\\t') } ################################################ @@ -53,5 +53,10 @@ writeLines( c( '"${task.process}":', paste(' r-base:', r.version) - ), + ), 'versions.yml') + +################################################ +################################################ +################################################ +################################################ From 5708f75696627954ee666743521a1f2f2c0eed95 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Thu, 8 Aug 2024 09:52:48 +0200 Subject: [PATCH 474/491] reformatting normalization --- .../templates/deseq_normalization.R | 17 +++++------------ 1 file changed, 5 insertions(+), 12 deletions(-) diff --git a/modules/local/deseq2/normalization/templates/deseq_normalization.R b/modules/local/deseq2/normalization/templates/deseq_normalization.R index 131bfd54..91b366dc 100644 --- a/modules/local/deseq2/normalization/templates/deseq_normalization.R +++ b/modules/local/deseq2/normalization/templates/deseq_normalization.R @@ -2,16 +2,12 @@ library(DESeq2) -raw_counts <- read.table("$counts", sep = "\\t", - header = TRUE, - stringsAsFactors = FALSE, - check.names = FALSE) +raw_counts <- read.table("$counts", sep = "\\t", header = TRUE, stringsAsFactors = FALSE, check.names = FALSE) samples <- colnames(raw_counts)[-c(1)] row.names(raw_counts) <- raw_counts\$miRNA data <- raw_counts[, -1] -mirna_names <- data.frame(miRNA = raw_counts\$miRNA, - order = seq_len(nrow(raw_counts))) +mirna_names <- data.frame(miRNA = raw_counts\$miRNA, order = seq_len(nrow(raw_counts))) # normalize using DeSeq2, Library Size Estimation meta_data <- data.frame(samples) @@ -19,22 +15,19 @@ row.names(meta_data) <- meta_data\$samples all(colnames(data) %in% rownames(meta_data)) all(colnames(data) == rownames(meta_data)) -dds <- DESeqDataSetFromMatrix(countData = data, - colData = meta_data, - design = ~ 1) +dds <- DESeqDataSetFromMatrix(countData = data, colData = meta_data, design = ~ 1) dds <- estimateSizeFactors(dds) sizeFactors(dds) normalized_counts <- DESeq2::counts(dds, normalized = TRUE) # add miRNA IDs back to counts table merged_data <- merge(mirna_names, normalized_counts, - by.x = "miRNA", by.y = "row.names") + by.x = "miRNA", by.y = "row.names") merged_data <- merged_data[order(merged_data\$order), ] norm_data <- subset(merged_data, select = -c(order)) -write.table(norm_data, paste0("${meta.id}.normalized_counts.tsv"), - quote = FALSE, sep = "\\t", row.names = FALSE) +write.table(norm_data, paste0("${meta.id}.normalized_counts.tsv"), quote = FALSE, sep = "\\t", row.names = FALSE) # TODO: (Can be done later) Add support for Samplesheet so that we can eliminate batch effects From 3b7074d556dcd976e40aae62bf6a0e42f72a08b5 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Thu, 8 Aug 2024 09:54:11 +0200 Subject: [PATCH 475/491] reformatting majority vote --- modules/local/majority_vote/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/majority_vote/main.nf b/modules/local/majority_vote/main.nf index 7b58a67f..5161ca6d 100644 --- a/modules/local/majority_vote/main.nf +++ b/modules/local/majority_vote/main.nf @@ -4,12 +4,12 @@ process MAJORITY_VOTE { conda "bioconda::pandas=1.5.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : + 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : 'biocontainers/pandas:1.5.2' }" input: tuple val(meta), path(bindingsites) - + output: tuple val(meta), path("${meta.id}.majority.tsv"), emit: tsv From 6ac49fd1284f4202ef765b8d41de5ec8d35dfe0a Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Thu, 8 Aug 2024 09:54:58 +0200 Subject: [PATCH 476/491] reformatting majority vote py --- modules/local/majority_vote/templates/majority.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/majority_vote/templates/majority.py b/modules/local/majority_vote/templates/majority.py index b08d9c25..70c5dd91 100644 --- a/modules/local/majority_vote/templates/majority.py +++ b/modules/local/majority_vote/templates/majority.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python3 +#!/usr/bin/env python3 import pandas as pd import platform From 26e75994c2c73df08f529a181f3ffa651723d068 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Thu, 8 Aug 2024 09:56:00 +0200 Subject: [PATCH 477/491] reformatting mirna filtering R --- .../mirna_filtering/templates/mirna_filtering.R | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/modules/local/mirna_filtering/templates/mirna_filtering.R b/modules/local/mirna_filtering/templates/mirna_filtering.R index 32521c8e..588eb260 100644 --- a/modules/local/mirna_filtering/templates/mirna_filtering.R +++ b/modules/local/mirna_filtering/templates/mirna_filtering.R @@ -18,15 +18,15 @@ sample_nr_cutoff <- ceiling($mirna_min_sample_percentage * length(samples)) rows_to_keep <- c() for (i in seq_len(nrow(expression_norm))) { - mirna_per_sample <- 0 - for (j in 5:ncol(expression_norm)) { - if (expression_norm[i, j] >= $mirna_min_reads) { - mirna_per_sample <- mirna_per_sample + 1 + mirna_per_sample <- 0 + for (j in 5:ncol(expression_norm)) { + if (expression_norm[i, j] >= $mirna_min_reads) { + mirna_per_sample <- mirna_per_sample + 1 + } + } + if (mirna_per_sample >= sample_nr_cutoff) { + rows_to_keep <- append(rows_to_keep, i) } - } - if (mirna_per_sample >= sample_nr_cutoff) { - rows_to_keep <- append(rows_to_keep, i) - } } filtered_data <- expression_norm[rows_to_keep, ] From 050bb4d6db9ce0129695e2aea5a198dbf9e1e3af Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Thu, 8 Aug 2024 09:58:23 +0200 Subject: [PATCH 478/491] reformatting mirna bindingsites --- subworkflows/local/mirna/mirna_bindingsites.nf | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/mirna/mirna_bindingsites.nf b/subworkflows/local/mirna/mirna_bindingsites.nf index 7683524f..d81abae5 100644 --- a/subworkflows/local/mirna/mirna_bindingsites.nf +++ b/subworkflows/local/mirna/mirna_bindingsites.nf @@ -7,7 +7,7 @@ include { MIRNA_TARGETS } from '../../../modules/local/mirna_t include { CAT_CAT as COMBINE_BINDINGSITES } from '../../../modules/nf-core/cat/cat' include { MAJORITY_VOTE } from '../../../modules/local/majority_vote' -workflow MIRNA_BINDINGSITES { +workflow MIRNA_BINDINGSITES { take: transcriptome_fasta circrna_bed12 @@ -35,26 +35,26 @@ workflow MIRNA_BINDINGSITES { if (tools_selected.size() == 0) { error 'No tools selected for miRNA discovery.' } - + if (tools_selected.contains('targetscan')) { // // TARGETSCAN WORKFLOW: // TARGETSCAN( ch_transcriptome_batches, formatMiRNAForTargetScan( mirna_fasta ).collect() ) UNIFY_TARGETSCAN( TARGETSCAN.out.txt, [] ) - + ch_versions = ch_versions.mix(TARGETSCAN.out.versions) ch_versions = ch_versions.mix(UNIFY_TARGETSCAN.out.versions) ch_predictions = ch_predictions.mix(UNIFY_TARGETSCAN.out.output) } - + if (tools_selected.contains('miranda')) { // // MIRANDA WORKFLOW: // MIRANDA( ch_transcriptome_batches, mirna_fasta.map{meta, mature -> mature}.collect() ) UNIFY_MIRANDA( MIRANDA.out.txt, [] ) - + ch_versions = ch_versions.mix(MIRANDA.out.versions) ch_versions = ch_versions.mix(UNIFY_MIRANDA.out.versions) ch_predictions = ch_predictions.mix(UNIFY_MIRANDA.out.output) @@ -67,7 +67,7 @@ workflow MIRNA_BINDINGSITES { // consolidate_targets = TARGETSCAN.out.txt.join(MIRANDA.out.txt).join(circrna_bed12) consolidate_targets = TARGETSCAN.out.txt.join(MIRANDA.out.txt) - + MIRNA_TARGETS( consolidate_targets ) ch_versions = ch_versions.mix(MIRNA_TARGETS.out.versions) From 1cd2841e076db4e651340f9f2bcab74cab32cc26 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Thu, 8 Aug 2024 10:02:41 +0200 Subject: [PATCH 479/491] reformatting mirna prediction --- subworkflows/local/mirna_prediction.nf | 20 +++++++++----------- 1 file changed, 9 insertions(+), 11 deletions(-) diff --git a/subworkflows/local/mirna_prediction.nf b/subworkflows/local/mirna_prediction.nf index 48c64fbe..b3fc46cc 100644 --- a/subworkflows/local/mirna_prediction.nf +++ b/subworkflows/local/mirna_prediction.nf @@ -9,7 +9,7 @@ include { MIRNA_BINDINGSITES } from './mirna/mirna_bindingsites' workflow MIRNA_PREDICTION { - take: + take: transcriptome_fasta circrna_annotation ch_mature @@ -25,16 +25,16 @@ workflow MIRNA_PREDICTION { // if (params.mirna_expression) { - + ch_mirna_normalized = DESEQ2_NORMALIZATION( ch_mirna ).normalized ch_versions = ch_versions.mix(DESEQ2_NORMALIZATION.out.versions) - ch_mirna_filtered = MIRNA_FILTERING(ch_mirna_normalized, - params.mirna_min_sample_percentage, + ch_mirna_filtered = MIRNA_FILTERING(ch_mirna_normalized, + params.mirna_min_sample_percentage, params.mirna_min_reads ).filtered - + ch_versions = ch_versions.mix(MIRNA_FILTERING.out.versions) // @@ -52,8 +52,8 @@ workflow MIRNA_PREDICTION { .combine(ch_uniq_mirnas.map{ it -> [it]}) // Not sure why this mapping is necessary but I think it is .filter{ record, mirnas -> ch_uniq_mirnas.contains(record.id).value - }.map{ record, mirnas -> - ">${record.id}\n${record.seqString}" + }.map{ record, mirnas -> + ">${record.id}\n${record.seqString}" } .collectFile( name: 'mature_filtered.fa', newLine: true) .map{ it -> [[id: 'mature_filtered'], it]} @@ -70,10 +70,8 @@ workflow MIRNA_PREDICTION { .splitText(by: 100, file: true) .map{ meta, file -> [[id: "batch_" + file.baseName.split("\\.").last()], file]} - COMPUTE_CORRELATIONS( ch_binding_site_batches, - ch_mirna_filtered, - quantification_rds ) - + COMPUTE_CORRELATIONS(ch_binding_site_batches, ch_mirna_filtered, quantification_rds) + ch_correlation_results = COMPUTE_CORRELATIONS.out.correlations .map{meta, results -> results} .flatten().collect() From 80edcc51b2b8ad91a74857b325e7c1120f7f9be4 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Thu, 8 Aug 2024 10:06:44 +0200 Subject: [PATCH 480/491] fixing param mirna_tool_filter --- nextflow.config | 4 ++-- nextflow_schema.json | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/nextflow.config b/nextflow.config index f79cdd5b..3d2aa173 100644 --- a/nextflow.config +++ b/nextflow.config @@ -69,8 +69,8 @@ params { mirna_expression = null mirna_min_reads = 5 mirna_min_sample_percentage = 0.2 - mirna_tool_filter = 'miranda, targetscan' - mirna_vote = 1 + mirna_tools = 'miranda, targetscan' + mirna_tool_filter = 1 mirna_correlation = 'pearson' diff --git a/nextflow_schema.json b/nextflow_schema.json index 8ab9ecdc..d62d2493 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -151,7 +151,7 @@ "type": "integer", "fa_icon": "fas fa-intersection", "description": "Specify the number of votes required for a miRNA to be further considered in downstream analysis.'", - "help_text": "Controls the number of votes required for a binding site prediction to be considered valid. If a miRNA binding site was predicted by two different tools (e.g., miRanda and TargetScan), it receives two votes. By specifying additional tools for miRNA binding site prediction (using the 'mirna_tools' parameter), you can adjust the number of votes required for a binding site to be considered valid.", + "help_text": "Controls the number of votes required for a binding site prediction to be considered valid. If a miRNA binding site was predicted by two different tools (e.g., miRanda and TargetScan), it receives two votes. By specifying additional tools for miRNA binding site prediction (using the 'mirna_tool_filter' parameter), you can adjust the number of votes required for a binding site to be considered valid.", "default": 1, "minimum": 1, "maximum": 4 From 0106c3a59717200322518dffabf3664a8591aace Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Thu, 8 Aug 2024 10:16:15 +0200 Subject: [PATCH 481/491] checking if mirna_expression is null before passing it to file() --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index b5a47b01..9be3219c 100644 --- a/main.nf +++ b/main.nf @@ -60,7 +60,7 @@ workflow NFCORE_CIRCRNA { ch_mature = params.mature ? Channel.value([[id: "mature"], file(params.mature, checkIfExists:true)]) : Channel.empty() ch_phenotype = params.phenotype ? Channel.value([[id: "phenotype"], file(params.phenotype, checkIfExists:true)]) : Channel.empty() ch_annotation = params.annotation ? Channel.fromSamplesheet("annotation") : Channel.empty() - ch_mirna = params.mature ? Channel.value([[id: "mirna"], file(params.mirna_expression, checkIfExists:true)]) : Channel.empty() + ch_mirna = params.mature && params.mirna_expression ? Channel.value([[id: "mirna"], file(params.mirna_expression, checkIfExists:true)]) : Channel.empty() CIRCRNA ( ch_samplesheet, From 2be53ee11605ae70e54a1057aa938b4208cdfc0b Mon Sep 17 00:00:00 2001 From: mweyrich28 <120316140+mweyrich28@users.noreply.github.com> Date: Thu, 8 Aug 2024 10:25:57 +0200 Subject: [PATCH 482/491] Apply suggestions from code review Co-authored-by: Nico Trummer <52698566+nictru@users.noreply.github.com> --- nextflow_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index d62d2493..64c63c17 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -143,9 +143,9 @@ "type": "string", "fa_icon": "fas fa-wrench", "description": "Comma separated list of miRNA bindingsite prediction tools to use. Supported tools: miranda, targetscan.", - "help_text": "Select one or a combination of miRNA bindingsite prediction tools for the pipeline e.g:\n--tool 'miranda, targetscan'", + "help_text": "Select one or a combination of miRNA bindingsite prediction tools for the pipeline e.g:\n--mirna_tools 'miranda,targetscan'", "default": "miranda, targetscan", - "pattern": "^((miranda|targetscan|pita|tarpmir)?,?)*[^,]+$" + "pattern": "^((miranda|targetscan)?,?)*[^,]+$" }, "mirna_tool_filter": { "type": "integer", From e0afb0a42aaae49a7c85e9402dcea5e0df9478ba Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Thu, 8 Aug 2024 10:28:23 +0200 Subject: [PATCH 483/491] applying correct format to mirna_tools --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 3d2aa173..ff6b0bbc 100644 --- a/nextflow.config +++ b/nextflow.config @@ -69,7 +69,7 @@ params { mirna_expression = null mirna_min_reads = 5 mirna_min_sample_percentage = 0.2 - mirna_tools = 'miranda, targetscan' + mirna_tools = 'miranda,targetscan' mirna_tool_filter = 1 mirna_correlation = 'pearson' From 5082d4fad8e3d8b6bb51729c2f9c752b1df7b3f5 Mon Sep 17 00:00:00 2001 From: Malte Weyrich Date: Thu, 8 Aug 2024 10:37:20 +0200 Subject: [PATCH 484/491] updating default format of mirna_tools --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 64c63c17..ee8ea89c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -144,7 +144,7 @@ "fa_icon": "fas fa-wrench", "description": "Comma separated list of miRNA bindingsite prediction tools to use. Supported tools: miranda, targetscan.", "help_text": "Select one or a combination of miRNA bindingsite prediction tools for the pipeline e.g:\n--mirna_tools 'miranda,targetscan'", - "default": "miranda, targetscan", + "default": "miranda,targetscan", "pattern": "^((miranda|targetscan)?,?)*[^,]+$" }, "mirna_tool_filter": { From 6f69c930706939f7677eab9d21427244c416b453 Mon Sep 17 00:00:00 2001 From: Nico Trummer <52698566+nictru@users.noreply.github.com> Date: Thu, 8 Aug 2024 09:43:10 +0000 Subject: [PATCH 485/491] Add credits for mweyrich --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 5ea93d2c..a1e288e1 100644 --- a/README.md +++ b/README.md @@ -130,6 +130,7 @@ We thank the following people for their extensive assistance in the development - [Alexander Peltzer](https://github.com/apeltzer) - [Ben Whittle](https://github.com/bj-w) - [Kevin Menden](https://github.com/KevinMenden) +- [Malte Weyrich](https://github.com/mweyrich28) - [Marieke Vromman](https://github.com/MariekeVromman) - [Maxime Garcia](https://github.com/maxulysse) - [Phil Ewels](https://github.com/ewels) From 2977ef0b39aee0ee3cad6af18377c25c425ae162 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 8 Aug 2024 23:00:54 +0200 Subject: [PATCH 486/491] Implement count extraction --- conf/modules.config | 10 ++++++++++ subworkflows/local/bsj_detection.nf | 11 +++++++++++ 2 files changed, 21 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index 4f6fea71..68008694 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -652,6 +652,16 @@ process { ] } + withName: 'EXTRACT_COUNTS' { + // Add meta.id as header + // Keep columns 4,5 + ext.args = { "-v FS='\\t' -v OFS='\\t' 'BEGIN { print \"id\", \"${meta.id}\" } { print \$4, \$5 }'" } + ext.suffix = {"counts.tsv"} + publishDir = [ + enabled: false + ] + } + withName: UPSET_SAMPLES { ext.when = { params.tools.split(',').length > 1 } publishDir = [ diff --git a/subworkflows/local/bsj_detection.nf b/subworkflows/local/bsj_detection.nf index 5da9899f..f0e5187f 100644 --- a/subworkflows/local/bsj_detection.nf +++ b/subworkflows/local/bsj_detection.nf @@ -5,6 +5,7 @@ include { GNU_SORT as CONCAT_TOOLS_PER_SAMPLE } from '../../modules/nf-co include { BEDTOOLS_GROUPBY as COUNT_TOOLS } from '../../modules/nf-core/bedtools/groupby' include { GAWK as FILTER_MIN_TOOLS } from '../../modules/nf-core/gawk' include { GNU_SORT as CONCAT_SAMPLES } from '../../modules/nf-core/gnu/sort' +include { GAWK as EXTRACT_COUNTS } from '../../modules/nf-core/gawk' include { UPSET as UPSET_SAMPLES } from '../../modules/local/upset' include { UPSET as UPSET_ALL } from '../../modules/local/upset' include { BEDTOOLS_GETFASTA as FASTA_COMBINED } from '../../modules/nf-core/bedtools/getfasta' @@ -140,6 +141,16 @@ workflow BSJ_DETECTION { ch_versions = ch_versions.mix(CONCAT_SAMPLES.out.versions) ch_bsj_bed_combined = CONCAT_SAMPLES.out.sorted + // + // QUANTIFY BSJs PER TOOL + // + EXTRACT_COUNTS( ch_bsj_bed_per_sample_tool, [] ) + ch_versions = ch_versions.mix(EXTRACT_COUNTS.out.versions) + + EXTRACT_COUNTS.out.output.map{ meta, bed -> [[id: meta.tool], meta.id, bed]} + .groupTuple() + .view() + // // UPSET PLOTS // From 16695dae224ee87e7597883cee91dd69d11bfd38 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 8 Aug 2024 23:08:20 +0200 Subject: [PATCH 487/491] Implement per-tool count combination across samples --- conf/modules.config | 9 +++++++++ subworkflows/local/bsj_detection.nf | 8 +++++--- 2 files changed, 14 insertions(+), 3 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 68008694..1fc279cd 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -662,6 +662,15 @@ process { ] } + withName: 'COMBINE_COUNTS_PER_TOOL' { + ext.args = "-f 1 -t" + publishDir = [ + path: { "${params.outdir}/bsj_detection/tools/${meta.id}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + withName: UPSET_SAMPLES { ext.when = { params.tools.split(',').length > 1 } publishDir = [ diff --git a/subworkflows/local/bsj_detection.nf b/subworkflows/local/bsj_detection.nf index f0e5187f..4eac9741 100644 --- a/subworkflows/local/bsj_detection.nf +++ b/subworkflows/local/bsj_detection.nf @@ -6,6 +6,7 @@ include { BEDTOOLS_GROUPBY as COUNT_TOOLS } from '../../modules/nf-co include { GAWK as FILTER_MIN_TOOLS } from '../../modules/nf-core/gawk' include { GNU_SORT as CONCAT_SAMPLES } from '../../modules/nf-core/gnu/sort' include { GAWK as EXTRACT_COUNTS } from '../../modules/nf-core/gawk' +include { CSVTK_JOIN as COMBINE_COUNTS_PER_TOOL } from '../../modules/nf-core/csvtk/join' include { UPSET as UPSET_SAMPLES } from '../../modules/local/upset' include { UPSET as UPSET_ALL } from '../../modules/local/upset' include { BEDTOOLS_GETFASTA as FASTA_COMBINED } from '../../modules/nf-core/bedtools/getfasta' @@ -147,9 +148,10 @@ workflow BSJ_DETECTION { EXTRACT_COUNTS( ch_bsj_bed_per_sample_tool, [] ) ch_versions = ch_versions.mix(EXTRACT_COUNTS.out.versions) - EXTRACT_COUNTS.out.output.map{ meta, bed -> [[id: meta.tool], meta.id, bed]} - .groupTuple() - .view() + COMBINE_COUNTS_PER_TOOL( EXTRACT_COUNTS.out.output + .map{ meta, bed -> [[id: meta.tool], bed]} + .groupTuple() ) + ch_versions = ch_versions.mix(COMBINE_COUNTS_PER_TOOL.out.versions) // // UPSET PLOTS From 38c2e495ef752637f6b4a6cd42a4a09c7bfc667f Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 8 Aug 2024 23:19:28 +0200 Subject: [PATCH 488/491] Restructure BSJ detection workflow --- subworkflows/local/bsj_detection.nf | 69 +++++++++++++++-------------- 1 file changed, 35 insertions(+), 34 deletions(-) diff --git a/subworkflows/local/bsj_detection.nf b/subworkflows/local/bsj_detection.nf index 4eac9741..fdcb8027 100644 --- a/subworkflows/local/bsj_detection.nf +++ b/subworkflows/local/bsj_detection.nf @@ -45,7 +45,7 @@ workflow BSJ_DETECTION { main: ch_versions = Channel.empty() - ch_bed = Channel.empty() + ch_bsj_bed_per_sample_tool = Channel.empty() ch_multiqc_files = Channel.empty() fasta = ch_fasta.map{meta, fasta -> fasta} gtf = ch_gtf.map{meta, gtf -> gtf} @@ -68,59 +68,71 @@ workflow BSJ_DETECTION { if (tools_selected.contains('segemehl')) { SEGEMEHL( reads, fasta, params.segemehl ) - ch_versions = ch_versions.mix(SEGEMEHL.out.versions) - ch_bed = ch_bed .mix(SEGEMEHL.out.bed) + ch_versions = ch_versions.mix(SEGEMEHL.out.versions) + ch_bsj_bed_per_sample_tool = ch_bsj_bed_per_sample_tool.mix(SEGEMEHL.out.bed) } if (tools_selected.contains('circexplorer2')) { CIRCEXPLORER2( gtf, fasta, STAR2PASS.out.junction ) - ch_versions = ch_versions.mix(CIRCEXPLORER2.out.versions) - ch_bed = ch_bed .mix(CIRCEXPLORER2.out.bed) + ch_versions = ch_versions.mix(CIRCEXPLORER2.out.versions) + ch_bsj_bed_per_sample_tool = ch_bsj_bed_per_sample_tool.mix(CIRCEXPLORER2.out.bed) } if (tools_selected.contains('circrna_finder')) { CIRCRNA_FINDER( fasta, STAR2PASS.out.sam, STAR2PASS.out.junction, STAR2PASS.out.tab ) - ch_versions = ch_versions.mix(CIRCRNA_FINDER.out.versions) - ch_bed = ch_bed .mix(CIRCRNA_FINDER.out.bed) + ch_versions = ch_versions.mix(CIRCRNA_FINDER.out.versions) + ch_bsj_bed_per_sample_tool = ch_bsj_bed_per_sample_tool.mix(CIRCRNA_FINDER.out.bed) } if (tools_selected.contains('find_circ')) { FIND_CIRC( reads, bowtie2_index, ch_fasta ) - ch_versions = ch_versions.mix(FIND_CIRC.out.versions) - ch_bed = ch_bed .mix(FIND_CIRC.out.bed) + ch_versions = ch_versions.mix(FIND_CIRC.out.versions) + ch_bsj_bed_per_sample_tool = ch_bsj_bed_per_sample_tool.mix(FIND_CIRC.out.bed) } if (tools_selected.contains('ciriquant')) { CIRIQUANT( reads, ch_gtf, ch_fasta, bwa_index, hisat2_index ) - ch_versions = ch_versions.mix(CIRIQUANT.out.versions) - ch_bed = ch_bed .mix(CIRIQUANT.out.bed) + ch_versions = ch_versions.mix(CIRIQUANT.out.versions) + ch_bsj_bed_per_sample_tool = ch_bsj_bed_per_sample_tool.mix(CIRIQUANT.out.bed) } if (tools_selected.contains('dcc')) { DCC( reads, ch_fasta, ch_gtf, star_index, STAR2PASS.out.junction, star_ignore_sjdbgtf, seq_platform, seq_center, bsj_reads ) - ch_versions = ch_versions.mix(DCC.out.versions) - ch_bed = ch_bed .mix(DCC.out.bed) + ch_versions = ch_versions.mix(DCC.out.versions) + ch_bsj_bed_per_sample_tool = ch_bsj_bed_per_sample_tool.mix(DCC.out.bed) } if (tools_selected.contains('mapsplice')) { MAPSPLICE( reads, gtf, fasta, bowtie_index, chromosomes, STAR2PASS.out.junction ) - ch_versions = ch_versions.mix(MAPSPLICE.out.versions) - ch_bed = ch_bed .mix(MAPSPLICE.out.bed) + ch_versions = ch_versions.mix(MAPSPLICE.out.versions) + ch_bsj_bed_per_sample_tool = ch_bsj_bed_per_sample_tool.mix(MAPSPLICE.out.bed) } - ch_bed = FILTER_BSJS( ch_bed, [] ).output - ch_versions = ch_versions.mix(FILTER_BSJS.out.versions) + ch_bsj_bed_per_sample_tool = FILTER_BSJS( ch_bsj_bed_per_sample_tool, [] ).output + ch_versions = ch_versions.mix(FILTER_BSJS.out.versions) + + // + // QUANTIFY BSJs PER TOOL + // + + EXTRACT_COUNTS( ch_bsj_bed_per_sample_tool, [] ) + ch_versions = ch_versions.mix(EXTRACT_COUNTS.out.versions) + + COMBINE_COUNTS_PER_TOOL( EXTRACT_COUNTS.out.output + .map{ meta, bed -> [[id: meta.tool], bed]} + .groupTuple() ) + ch_versions = ch_versions.mix(COMBINE_COUNTS_PER_TOOL.out.versions) // // MERGE BED FILES // - MASK_SCORES( ch_bed, [] ) + MASK_SCORES( ch_bsj_bed_per_sample_tool, [] ) ch_versions = ch_versions.mix(MASK_SCORES.out.versions) - ch_bsj_bed_per_sample_tool = MASK_SCORES.out.output + ch_bsj_bed_per_sample_tool_masked = MASK_SCORES.out.output .filter{ meta, bed -> !bed.empty } CONCAT_TOOLS_PER_SAMPLE( @@ -142,29 +154,18 @@ workflow BSJ_DETECTION { ch_versions = ch_versions.mix(CONCAT_SAMPLES.out.versions) ch_bsj_bed_combined = CONCAT_SAMPLES.out.sorted - // - // QUANTIFY BSJs PER TOOL - // - EXTRACT_COUNTS( ch_bsj_bed_per_sample_tool, [] ) - ch_versions = ch_versions.mix(EXTRACT_COUNTS.out.versions) - - COMBINE_COUNTS_PER_TOOL( EXTRACT_COUNTS.out.output - .map{ meta, bed -> [[id: meta.tool], bed]} - .groupTuple() ) - ch_versions = ch_versions.mix(COMBINE_COUNTS_PER_TOOL.out.versions) - // // UPSET PLOTS // - UPSET_SAMPLES( ch_bsj_bed_per_sample_tool + UPSET_SAMPLES( ch_bsj_bed_per_sample_tool_masked .map{ meta, bed -> [meta.id, meta.tool, bed]} .groupTuple() .map{ sample, tools, beds -> [[id: sample], tools, beds]} ) ch_multiqc_files = ch_multiqc_files.mix(UPSET_SAMPLES.out.multiqc) ch_versions = ch_versions.mix(UPSET_SAMPLES.out.versions) - UPSET_ALL( ch_bsj_bed_per_sample_tool + UPSET_ALL( ch_bsj_bed_per_sample_tool_masked .map{ meta, bed -> ["all", meta.tool, bed] } .groupTuple() .map{ sample, tools, beds -> [[id: sample], tools, beds]} ) @@ -185,7 +186,7 @@ workflow BSJ_DETECTION { ch_bsj_bed12_per_sample = ANNOTATE_PER_SAMPLE.out.bed ch_bsj_gtf_per_sample = ANNOTATE_PER_SAMPLE.out.gtf - ANNOTATE_PER_SAMPLE_TOOL( ch_bsj_bed_per_sample_tool, ch_gtf, exon_boundary, ch_annotation ) + ANNOTATE_PER_SAMPLE_TOOL( ch_bsj_bed_per_sample_tool_masked, ch_gtf, exon_boundary, ch_annotation ) ch_versions = ch_versions.mix(ANNOTATE_PER_SAMPLE_TOOL.out.versions) ch_bsj_bed12_per_sample_tool = ANNOTATE_PER_SAMPLE_TOOL.out.bed ch_bsj_gtf_per_sample_tool = ANNOTATE_PER_SAMPLE_TOOL.out.gtf @@ -202,7 +203,7 @@ workflow BSJ_DETECTION { ch_versions = ch_versions.mix(FASTA_PER_SAMPLE.out.versions) ch_bsj_fasta_per_sample = FASTA_PER_SAMPLE.out.fasta - FASTA_PER_SAMPLE_TOOL( ch_bsj_bed_per_sample_tool, fasta ) + FASTA_PER_SAMPLE_TOOL( ch_bsj_bed_per_sample_tool_masked, fasta ) ch_versions = ch_versions.mix(FASTA_PER_SAMPLE_TOOL.out.versions) ch_bsj_fasta_per_sample_tool = FASTA_PER_SAMPLE_TOOL.out.fasta From a1acac7b2557ed9514f589fdd32743d61f2696b3 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 8 Aug 2024 23:44:03 +0200 Subject: [PATCH 489/491] Update docs --- docs/output.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/output.md b/docs/output.md index f7016c8b..f60c28a0 100644 --- a/docs/output.md +++ b/docs/output.md @@ -154,6 +154,7 @@ The rough workflow for the BSJ detection looks like this: - `annotated`: Based on `masked`, but with additional columns for the circRNA type, the host gene(s), host transcript(s) and potential database hits. Contains a BED and a GTF file for each sample. - `fasta`: Extracted sequences of the circRNAs in FASTA format. Based on `masked`. - `intermediates`: Contains intermediate files generated by the BSJ detection tools, as explained below. +- `${tool}.csv`: Number of reads that the tool found supporting the BSJ.
    From d0f7cfeed6e86c3f6a76cc5e53b46605c8777cb5 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 8 Aug 2024 23:56:24 +0200 Subject: [PATCH 490/491] Perform outer join on counts --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 1fc279cd..b23ea157 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -663,7 +663,7 @@ process { } withName: 'COMBINE_COUNTS_PER_TOOL' { - ext.args = "-f 1 -t" + ext.args = "-f 1 -t -O" publishDir = [ path: { "${params.outdir}/bsj_detection/tools/${meta.id}" }, mode: params.publish_dir_mode, From 7ac747efcd42c0c0e9df9c53b0d975e78aa4e2f1 Mon Sep 17 00:00:00 2001 From: Nico Trummer Date: Thu, 8 Aug 2024 23:56:45 +0200 Subject: [PATCH 491/491] Imporve BSJ_DETECTION order --- subworkflows/local/bsj_detection.nf | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/bsj_detection.nf b/subworkflows/local/bsj_detection.nf index fdcb8027..89ddec4e 100644 --- a/subworkflows/local/bsj_detection.nf +++ b/subworkflows/local/bsj_detection.nf @@ -111,9 +111,6 @@ workflow BSJ_DETECTION { ch_bsj_bed_per_sample_tool = ch_bsj_bed_per_sample_tool.mix(MAPSPLICE.out.bed) } - ch_bsj_bed_per_sample_tool = FILTER_BSJS( ch_bsj_bed_per_sample_tool, [] ).output - ch_versions = ch_versions.mix(FILTER_BSJS.out.versions) - // // QUANTIFY BSJs PER TOOL // @@ -126,11 +123,19 @@ workflow BSJ_DETECTION { .groupTuple() ) ch_versions = ch_versions.mix(COMBINE_COUNTS_PER_TOOL.out.versions) + // + // APPLY bsj_reads FILTER + // + + ch_bsj_bed_per_sample_tool_filtered = FILTER_BSJS( ch_bsj_bed_per_sample_tool, [] ).output + ch_versions = ch_versions.mix(FILTER_BSJS.out.versions) + + // // MERGE BED FILES // - MASK_SCORES( ch_bsj_bed_per_sample_tool, [] ) + MASK_SCORES( ch_bsj_bed_per_sample_tool_filtered, [] ) ch_versions = ch_versions.mix(MASK_SCORES.out.versions) ch_bsj_bed_per_sample_tool_masked = MASK_SCORES.out.output .filter{ meta, bed -> !bed.empty }
    Process Name \\", + " \\ Software Version
    CUSTOM_DUMPSOFTWAREVERSIONSpython3.11.7
    yaml5.4.1
    TOOL1tool10.11.9
    TOOL2tool21.9
    WorkflowNextflow
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