v1.0.0 #66

BarryDigby · 2022-12-13T10:39:03Z

DSL2 version of nf-core/circrna.

A few minor comments on the linting warnings:

I need some assistance configuring the full AWS test dataset. The data can be accessed via SRA, this should be straightforward using fetchngs.
Links to manuscripts / DOI links - I have a paper for the workflow currently under review, I'm hoping this will be accepted soon having addressed reviewer comments.

github-actions · 2023-02-01T10:53:05Z

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: 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 👍

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!

Thanks again for your contribution!

maxulysse · 2023-10-27T11:36:40Z

I feel like comments from #69 haven't been integrated in this PR yet.

github-actions · 2024-02-02T08:53:57Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 98923dd

+| ✅ 216 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-circrna_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-circrna_logo_light.png
files_exist - File found: docs/images/nf-core-circrna_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-circrna_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowCircrna.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: dev
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.tool= circexplorer2
nextflow_config - Config default value correct: params.bsj_reads= 0
nextflow_config - Config default value correct: params.tool_filter= 0
nextflow_config - Config default value correct: params.duplicates_fun= mean
nextflow_config - Config default value correct: params.save_intermediates= false
nextflow_config - Config default value correct: params.exon_boundary= 200
nextflow_config - Config default value correct: params.sjdboverhang= 100
nextflow_config - Config default value correct: params.chimJunctionOverhangMin= 10
nextflow_config - Config default value correct: params.alignSJDBoverhangMin= 10
nextflow_config - Config default value correct: params.limitSjdbInsertNsj= 1000000
nextflow_config - Config default value correct: params.chimSegmentMin= 10
nextflow_config - Config default value correct: params.seglen= 25
nextflow_config - Config default value correct: params.min_intron= 20
nextflow_config - Config default value correct: params.max_intron= 1000000
nextflow_config - Config default value correct: params.min_map_len= 40
nextflow_config - Config default value correct: params.min_fusion_distance= 200
nextflow_config - Config default value correct: params.bootstrap_samples= 30
nextflow_config - Config default value correct: params.save_unaligned= false
nextflow_config - Config default value correct: params.save_reference= true
nextflow_config - Config default value correct: params.hisat2_build_memory= 200.GB
nextflow_config - Config default value correct: params.skip_trimming= false
nextflow_config - Config default value correct: params.save_trimmed= false
nextflow_config - Config default value correct: params.skip_fastqc= false
nextflow_config - Config default value correct: params.min_trimmed_reads= 10000
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.max_cpus= 50
nextflow_config - Config default value correct: params.max_memory= 300.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-circrna_logo_light.png matches the template
files_unchanged - docs/images/nf-core-circrna_logo_light.png matches the template
files_unchanged - docs/images/nf-core-circrna_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (382 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
modules_config - CLEAN_FASTA found in conf/modules.config and Nextflow scripts.
modules_config - SEQKIT_SPLIT found in conf/modules.config and Nextflow scripts.
modules_config - BOWTIE_BUILD found in conf/modules.config and Nextflow scripts.
modules_config - BOWTIE2_BUILD found in conf/modules.config and Nextflow scripts.
modules_config - BWA_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - HISAT2_EXTRACTSPLICESITES found in conf/modules.config and Nextflow scripts.
modules_config - HISAT2_BUILD found in conf/modules.config and Nextflow scripts.
modules_config - STAR_GENOMEGENERATE found in conf/modules.config and Nextflow scripts.
modules_config - FILTER_BSJS found in conf/modules.config and Nextflow scripts.
modules_config - UPSET_SAMPLES found in conf/modules.config and Nextflow scripts.
modules_config - UPSET_ALL found in conf/modules.config and Nextflow scripts.
modules_config - ADD_BACKSPLICE found in conf/modules.config and Nextflow scripts.
modules_config - COMBINE_TRANSCRIPTOME_GTFS found in conf/modules.config and Nextflow scripts.
modules_config - EXCLUDE_OVERLONG_TRANSCRIPTS found in conf/modules.config and Nextflow scripts.
modules_config - MARK_CIRCULAR found in conf/modules.config and Nextflow scripts.
modules_config - TARGETSCAN_DATABASE found in conf/modules.config and Nextflow scripts.
modules_config - TARGETSCAN found in conf/modules.config and Nextflow scripts.
modules_config - MIRANDA found in conf/modules.config and Nextflow scripts.
modules_config - MIRNA_TARGETS found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-06-19 19:30:35

Segemehl update

Add support for ext.args in ciriquant

Update modules

Add support for setting strandedness in samplesheet

Co-authored-by: Nico Trummer <52698566+nictru@users.noreply.github.com>

Improve circRNA-miRNA interaction analysis

Add credits for mweyrich

Add output containing per-tool quantification

BarryDigby mentioned this pull request Dec 22, 2022

Important! Template update for nf-core/tools v2.7.2 #67

Closed

jfy133 assigned jfy133 and FriederikeHanssen Jan 19, 2023

jfy133 mentioned this pull request Jan 23, 2023

[Do not merge!] Pseudo PR for first release #69

Draft

nictru and others added 23 commits May 30, 2024 13:48

Update nf-core modules

43a1c4d

Update segemehl unify call

b81a30a

Merge pull request #123 from nf-core/segemehl-update

0e9cce3

Segemehl update

Add support for ext.args in ciriquant

0a98534

Merge pull request #124 from nf-core/ciriquant-args

d5967c5

Add support for ext.args in ciriquant

Add strandedness to samplesheet

0cc85b0

Add support for strandedness in ciriquant

30af702

Revise DCC parameters

9c58899

Implement ext.args interface for find_circ

f38c58c

Fix trimming indentation in modules.config

ca15b3a

Move segemehl index location in modules.config

2b54d43

Add strandedness to bowtie2 calls

022d66e

Add strandedness to find_circ

a41eab1

Add strandedness documentation

8957a7e

Add samplesheet validation for strandedness of runs of the same sample

c65e604

Update modules

0ea2e75

Merge pull request #132 from nf-core/module-updates_24-06

98c1070

Update modules

Merge pull request #131 from nf-core/strandedness

e17b3ac

Add support for setting strandedness in samplesheet

Add new STATISTICAL_TESTS subworkflow

8150c43

Implement CIRCTEST_PREPARE

7ef6b03

Implement circTest

5893d6d

Fix circtest problems

9c5906d

Re-enable circtest plots

21236c8

mweyrich28 and others added 30 commits August 7, 2024 22:09

Apply suggestions from code review

6479a53

Co-authored-by: Nico Trummer <52698566+nictru@users.noreply.github.com>

renaming mirna_vote to mirna_tool_filter

e52e401

applying prettier

e49b947

renaming mirna_tools in nextflow.config

edafce4

fixing indent

4d514b4

deleting redundant file

737da80

rewording usage

b112f0c

rewording usage

bd7cd36

reformatting compute correlations

7f165ba

reformatting normalization

5708f75

reformatting majority vote

3b7074d

reformatting majority vote py

6ac49fd

reformatting mirna filtering R

26e7599

reformatting mirna bindingsites

050bb4d

reformatting mirna prediction

1cd2841

fixing param mirna_tool_filter

80edcc5

checking if mirna_expression is null before passing it to file()

0106c3a

Apply suggestions from code review

2be53ee

Co-authored-by: Nico Trummer <52698566+nictru@users.noreply.github.com>

applying correct format to mirna_tools

e0afb0a

updating default format of mirna_tools

5082d4f

Merge pull request #166 from nf-core/sponging

b233bb8

Improve circRNA-miRNA interaction analysis

Add credits for mweyrich

6f69c93

Merge pull request #167 from nf-core/credits-mweyrich

3e1ce6f

Add credits for mweyrich

Implement count extraction

2977ef0

Implement per-tool count combination across samples

16695da

Restructure BSJ detection workflow

38c2e49

Update docs

a1acac7

Perform outer join on counts

d0f7cfe

Imporve BSJ_DETECTION order

7ac747e

Merge pull request #168 from nf-core/per-tool-quantification

c9a5eb7

Add output containing per-tool quantification

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

v1.0.0 #66

v1.0.0 #66

BarryDigby commented Dec 13, 2022

github-actions bot commented Feb 1, 2023

maxulysse commented Oct 27, 2023

github-actions bot commented Feb 2, 2024 •

edited

Loading

❗ Test warnings:

✅ Tests passed:

Run details

v1.0.0 #66

Are you sure you want to change the base?

v1.0.0 #66

Conversation

BarryDigby commented Dec 13, 2022

github-actions bot commented Feb 1, 2023

Python linting (black) is failing

maxulysse commented Oct 27, 2023

github-actions bot commented Feb 2, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

Python linting (`black`) is failing

github-actions bot commented Feb 2, 2024 •

edited

Loading

`nf-core lint` overall result: Passed ✅ ⚠️