15 cicd tests (#24)

* Create main.yml

* files added

* singularity removed and args cleaned

* fix

.github/workflows/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,52 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+ - type: checkboxes
+ attributes:
+ label: Have you checked the docs?
+ description: I have checked the following places for my error
+ options:
+ - label: "[nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)"
+ required: true
+ - label: "[nf-core modules documentation](https://nf-co.re/docs/contributing/modules)"
+ required: true
+
+ - type: textarea
+ id: description
+ attributes:
+ label: Description of the bug
+ description: A clear and concise description of what the bug is.
+ validations:
+ required: true
+
+ - type: textarea
+ id: command_used
+ attributes:
+ label: Command used and terminal output
+ description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
+ render: console
+ placeholder: |
+ $ nextflow run ...
+
+ Some output where something broke
+
+ - type: textarea
+ id: files
+ attributes:
+ label: Relevant files
+ description: |
+ Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
+ Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
+
+ - type: textarea
+ id: system
+ attributes:
+ label: System information
+ description: |
+ * Nextflow version _(eg. 21.10.3)_
+ * Hardware _(eg. HPC, Desktop, Cloud)_
+ * Executor _(eg. slurm, local, awsbatch)_
+ * Container engine and version: _(e.g. Docker, Singularity)_
+ * OS and version: _(eg. CentOS Linux, macOS, Ubuntu 22.04)_
+ * Image tag: <!-- [e.g. biocontainers/platypus-variant:0.8.1.2] -->

.github/workflows/ISSUE_TEMPLATE/feature_reuest.yml

@@ -0,0 +1,32 @@
+name: Feature request
+description: Suggest an idea
+labels: feature
+title: "[FEATURE]"
+body:
+ - type: textarea
+ id: description
+ attributes:
+ label: Is your feature request related to a problem? Please describe
+ description: A clear and concise description of what the bug is.
+ placeholder: |
+ <!-- e.g. [I'm always frustrated when ...] -->
+ validations:
+ required: true
+
+ - type: textarea
+ id: solution
+ attributes:
+ label: Describe the solution you'd like
+ description: A clear and concise description of the solution you want to happen.
+
+ - type: textarea
+ id: alternatives
+ attributes:
+ label: Describe alternatives you've considered
+ description: A clear and concise description of any alternative solutions or features you've considered.
+
+ - type: textarea
+ id: additional_context
+ attributes:
+ label: Additional context
+ description: Add any other context about the feature request here.

.github/workflows/branch.yml

@@ -0,0 +1,44 @@
+name: branch protection
+# This workflow is triggered on PRs to master branch on the repository
+# It fails when someone tries to make a PR against the `master` branch instead of `dev`
+on:
+ pull_request_target:
+ branches: [master]
+
+jobs:
+ test:
+ runs-on: ubuntu-latest
+ steps:
+ # PRs to the master branch are only ok if coming from the repo `dev` or any `patch` branches
+ - name: Check PRs
+ if: github.repository == 'ghga-de/nf-aceseq'
+ run: |
+ { [[ ${{github.event.pull_request.head.repo.full_name }} == ghga-de/nf-aceseq ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+
+ # If the above check failed, post a comment on the PR explaining the failure
+ # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
+ - name: Post PR comment
+ if: failure()
+ uses: mshick/add-pr-comment@v1
+ with:
+ message: |
+ ## This PR is against the `master` branch :x:
+
+ * Do not close this PR
+ * Click _Edit_ and change the `base` to `dev`
+ * This CI test will remain failed until you push a new commit
+
+ ---
+
+ Hi @${{ github.event.pull_request.user.login }},
+
+ It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
+ The `master` branch on nf-core repositories should always contain code from the latest release.
+ Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+
+ You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
+ Note that even after this, the test will continue to show as failing until you push a new commit.
+
+ Thanks again for your contribution!
+ repo-token: ${{ secrets.GITHUB_TOKEN }}
+ allow-repeats: false

.github/workflows/code_linting.yml

@@ -0,0 +1,47 @@
+name: Code Linting
+on:
+ push:
+ branches:
+ - master
+ - dev
+ release:
+ types: [published]
+ pull_request:
+ branches: [master]
+ merge_group:
+ types: [checks_requested]
+ branches: [master]
+
+# Cancel if a newer run is started
+concurrency:
+ group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+ cancel-in-progress: true
+
+jobs:
+ Prettier:
+ runs-on: ubuntu-latest
+ steps:
+ - name: Check out repository
+ uses: actions/checkout@v3
+
+ - name: Install NodeJS
+ uses: actions/setup-node@v2
+
+ - name: Install Prettier
+ run: npm install -g prettier
+
+ - name: Run Prettier --check
+ run: prettier --check .
+
+ EditorConfig:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v3
+
+ - uses: actions/setup-node@v2
+
+ - name: Install editorconfig-checker
+ run: npm install -g editorconfig-checker
+
+ - name: Run ECLint check
+ run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)

.github/workflows/main.yml

@@ -0,0 +1,44 @@
+name: Main
+# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+on:
+ push:
+ branches:
+ - dev
+ - 15-cicd-tests
+ pull_request:
+ release:
+ types: [published]
+
+# Uncomment if we need an edge release of Nextflow again
+# env: NXF_EDGE: 1
+
+jobs:
+ test:
+ name: Run workflow tests
+ runs-on: ubuntu-latest
+ env:
+ NXF_VER: ${{ matrix.nxf_ver }}
+ NXF_ANSI_LOG: false
+ strategy:
+ matrix:
+ # Nextflow versions: check pipeline minimum and current latest
+ nxf_ver: ["22.10.6"]
+ steps:
+ - name: Check out pipeline code
+ uses: actions/checkout@v3
+
+ - name: Install Nextflow
+ env:
+ CAPSULE_LOG: none
+ run: |
+ wget -qO- get.nextflow.io | bash
+ sudo mv nextflow /usr/local/bin/
+ - name: HELPTEXT Run with the help flag
+ run: |
+ nextflow run ${GITHUB_WORKSPACE} --help
+ - name: DELAY to try address some odd behaviour with what appears to be a conflict between parallel htslib jobs leading to CI hangs
+ run: |
+ if [[ $NXF_VER = '' ]]; then sleep 1200; fi
+ - name: BASIC Run the basic pipeline only for ACE calling with docker
+ run: |
+ nextflow run ${GITHUB_WORKSPACE} -profile test,docker

conf/modules.config

@@ -51,7 +51,6 @@ process {
  ]
  }
  withName: 'ADD_HAPLOTYPES' {
- ext.args = ""
  publishDir = [
  path: {"${params.outdir}/${meta.id}/phasing"},
  pattern: "*{.tab.gz,.tab.gz.tbi}",
@@ -68,101 +67,140 @@ process {
  }
 
  withName: 'ADD_CREST|ADD_SVS' {
- ext.args = ""
  publishDir = [
  path: {"${params.outdir}/${meta.id}"},
  pattern: "*{.txt}",
  mode: params.publish_dir_mode
  ]
  }
  withName: GROUP_HAPLOTYPES {
- ext.args = ""
  publishDir = [
  path: {"${params.outdir}/${meta.id}/haploblocks"},
  pattern: "*{.tab}",
  mode: params.publish_dir_mode
  ]
  }
  withName: DEFINE_BREAKPOINTS {
- ext.args = ""
+ ext.args = '--libloc "" '
  publishDir = [
  path: {"${params.outdir}/${meta.id}"},
  pattern: "*{.txt.gz,.txt.gz.tbi,.pdf,.txt}",
  mode: params.publish_dir_mode
  ]
  }
  withName: CLUSTER_SEGMENTS {
- ext.args = ""
+ ext.args = '--out . --libloc "" --runInDebugMode false'
  publishDir = [
  path: {"${params.outdir}/${meta.id}"},
  pattern: "*{.txt.gz,.txt.gz.tbi,.txt,.pdf}",
  mode: params.publish_dir_mode
  ]
  }
  withName: "HOMOZYGOUS_DELETIONS|SEGMENTS_TO_DATA" {
- ext.args = ""
  publishDir = [
  path: {"${params.outdir}/${meta.id}"},
  pattern: "*{.txt.gz,.txt.gz.tbi}",
  mode: params.publish_dir_mode
  ]
  }
  withName: 'GC_BIAS|CONVERT_TO_JSON' {
- ext.args = ""
  publishDir = [
  path: {"${params.outdir}/${meta.id}/gc_bias"},
  pattern: "*{png,txt,tsv,json,tab.gz,txt.gz}",
  mode: params.publish_dir_mode
  ]
  }
  withName: 'CREATE_BAF_PLOTS' {
- ext.args = ""
+ ext.args = "--plot_Dir ."
  publishDir = [
  path: {"${params.outdir}/${meta.id}/baf_plots"},
  pattern: "*{png}",
  mode: params.publish_dir_mode
  ]
  }
  withName: GENERATE_PLOTS {
- ext.args = ""
+ ext.args = "--outDir ."
  publishDir = [
  path: {"${params.outdir}/${meta.id}/plots"},
- pattern: "*{.png}",
+ pattern: "*{png,txt}",
  mode: params.publish_dir_mode
  ]
  }
  withName: 'PURITY_PLOIDY' {
- ext.args = ""
+ ext.args = "--path ."
  publishDir = [
  path: {"${params.outdir}/${meta.id}"},
  pattern: "*{.json}",
  mode: params.publish_dir_mode
  ]
  }
- withName: GENERATE_PLOTS {
- ext.args = ""
+ withName: 'ESTIMATE_PEAKS' {
+ ext.args = "--out ."
+ publishDir = [
+ path: {"${params.outdir}/${meta.id}"},
+ pattern: "*{.txt}",
+ mode: params.publish_dir_mode
+ ]
+ }
+ withName: 'ESTIMATE_PURITY_PLOIDY' {
+ ext.args = "--out ."
+ publishDir = [
+ path: {"${params.outdir}/${meta.id}"},
+ pattern: "*{.txt}",
+ mode: params.publish_dir_mode
+ ]
+ }
+ withName: 'PSCBS_SEGMENTATION' {
+ ext.args = '--libloc "" '
+ publishDir = [
+ path: {"${params.outdir}/${meta.id}"},
+ pattern: "*{.txt}",
+ mode: params.publish_dir_mode
+ ]
+ }
+ withName: 'ESTIMATE_HDRSCORE' {
  publishDir = [
  path: {"${params.outdir}/${meta.id}"},
  pattern: "*{.txt}",
  mode: params.publish_dir_mode
  ]
  }
- withName: "ESTIMATE_PEAKS|ESTIMATE_PURITY_PLOIDY|PSCBS_SEGMENTATION|ESTIMATE_HDRSCORE|ESTIMATE_SEX" {
- ext.args = ""
+ withName: "ESTIMATE_SEX" {
  publishDir = [
  path: {"${params.outdir}/${meta.id}"},
  pattern: "*{.txt}",
  mode: params.publish_dir_mode
  ]
  }
- withName: 'MERGE_SNP|MERGE_CNV|GET_GENOTYPES' {
- ext.args = ""
+ withName: 'MERGE_CNV' {
+ ext.args = "--inputsuffix '.cnv.anno.tab.gz'"
+ publishDir = [
+ path: {"${params.outdir}/${meta.id}"},
+ pattern: "*{tab.gz,tab.gz.tbi}",
+ mode: params.publish_dir_mode
+ ]
+ }
+ withName: 'MERGE_SNP' {
+ publishDir = [
+ path: {"${params.outdir}/${meta.id}"},
+ pattern: "*{tab.gz,tab.gz.tbi}",
+ mode: params.publish_dir_mode
+ ]
+ }
+ withName: 'GET_GENOTYPES' {
  publishDir = [
  path: {"${params.outdir}/${meta.id}"},
  pattern: "*{tab.gz,tab.gz.tbi}",
  mode: params.publish_dir_mode
  ]
  }
+ withName: 'BEAGLE5_BEAGLE' {
+ publishDir = [
+ path: {"${params.outdir}/${meta.id}"},
+ pattern: "*{noting}",
+ mode: params.publish_dir_mode
+ ]
+ }
  withName: CUSTOM_DUMPSOFTWAREVERSIONS {
  publishDir = [
  path: { "${params.outdir}/pipeline_info" },
@@ -176,7 +214,7 @@ process {
 // Don't publish results for these processes
 //
 process { 
- withName: 'GREP_GENOTYPES|GETCHROMSIZES|EMBED_HAPLOTYPES|BEAGLE5_BEAGLE|CREATE_UNPHASED|FAKE_CONTROL|GET_GENOTYPES|MAKE_MOCK|WIN_GENERATOR|CREATE_FAKE_SAMPLES|PREPARE_BEAGLE_REF' {
+ withName: 'GETCHROMSIZES|EMBED_HAPLOTYPES|CREATE_UNPHASED|FAKE_CONTROL|MAKE_MOCK|WIN_GENERATOR|CREATE_FAKE_SAMPLES|PREPARE_BEAGLE_REF' {
  publishDir = [
  path: { "${params.outdir}/test" },
  enabled: false