Update bam_markduplicates_picard subworkflow #2469
Workflow file for this run
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| name: nf-core CI | |
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| release: | |
| types: [published] | |
| env: | |
| NXF_ANSI_LOG: false | |
| NFT_VER: "0.8.4" | |
| NFT_WORKDIR: "~" | |
| NFT_DIFF: "pdiff" | |
| NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| star_salmon: | |
| name: Test STAR Salmon with workflow parameters | |
| if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| parameters: | |
| - "--skip_qc" | |
| - "--skip_trimming" | |
| - "--min_mapped_reads 90" | |
| - "--with_umi" | |
| - "--with_umi --skip_trimming" | |
| - "--remove_ribo_rna --skip_qualimap" | |
| - "--bam_csi_index" | |
| - "--save_align_intermeds --save_reference" | |
| - "--featurecounts_group_type false" | |
| - "--trimmer fastp" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v4 | |
| - name: Setup Nextflow | |
| uses: nf-core/[email protected] | |
| - name: Run pipeline with STAR and various parameters | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results | |
| star_rsem: | |
| name: Test STAR RSEM with workflow parameters | |
| if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| parameters: | |
| - "--skip_qc" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v4 | |
| - name: Setup Nextflow | |
| uses: nf-core/[email protected] | |
| - name: Run pipeline with RSEM STAR and various parameters | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results | |
| hisat2: | |
| name: Test HISAT2 with workflow parameters | |
| if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| parameters: | |
| - "--skip_qc" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v4 | |
| - name: Setup Nextflow | |
| uses: nf-core/[email protected] | |
| - name: Run pipeline with HISAT2 and various parameters | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results | |
| pseudo: | |
| name: Test Pseudoaligners with workflow parameters | |
| if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| parameters: | |
| - "--pseudo_aligner salmon --skip_qc" | |
| - "--pseudo_aligner salmon --skip_alignment --skip_pseudo_alignment" | |
| - "--pseudo_aligner kallisto --skip_qc" | |
| - "--pseudo_aligner kallisto --skip_alignment --skip_pseudo_alignment" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v4 | |
| - name: Setup Nextflow | |
| uses: nf-core/[email protected] | |
| - name: Run pipeline with Salmon or Kallisto and various parameters | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }} --outdir ./results | |
| nf-test-changes: | |
| name: Check for changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| changes: ${{ steps.changed_files.outputs.any_modified }} | |
| tags: ${{ steps.list.outputs.tags }} | |
| steps: | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| architecture: "x64" | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: tj-actions/changed-files@v42 | |
| id: changed_files | |
| with: | |
| dir_names: "true" | |
| output_renamed_files_as_deleted_and_added: "true" | |
| # Define list of additional rules for testing paths | |
| # Mostly, we define additional 'pipeline' or 'all' tests here | |
| files_yaml: | | |
| ".": | |
| - .github/workflows/** | |
| - nf-test.config | |
| - nextflow.config | |
| tests: | |
| - assets/* | |
| - bin/* | |
| - conf/* | |
| - main.nf | |
| - nextflow_schema.json | |
| files_ignore: | | |
| .git* | |
| .gitpod.yml | |
| .prettierignore | |
| .prettierrc.yml | |
| **.md | |
| **.png | |
| modules.json | |
| pyproject.toml | |
| tower.yml | |
| - name: print-changed-dirs | |
| run: | | |
| echo ${{ steps.changed_files.outputs.any_modified }} | |
| echo ${{ steps.changed_files.outputs.all_changed_files }} | |
| echo ${{ steps.changed_files.outputs.changed_keys }} | |
| - name: nf-test list tags | |
| id: list | |
| if: ${{ steps.changed_files.outputs.any_modified }} | |
| run: | | |
| echo tags=$(python \ | |
| .github/python/find_changed_files.py \ | |
| -t pipeline workflow process \ | |
| -p ${{ steps.changed_files.outputs.all_changed_files }} ${{ steps.changed_files.outputs.changed_keys }} \ | |
| ) >> $GITHUB_OUTPUT | |
| - name: print-test-tags | |
| run: | | |
| echo ${{ steps.list.outputs.tags }} | |
| test: | |
| name: ${{ matrix.tags }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }} | |
| needs: [nf-test-changes] | |
| if: needs.nf-test-changes.outputs.tags != '[]' | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: | |
| # - "latest-everything" | |
| - "23.04.0" | |
| tags: ["${{ fromJson(needs.nf-test-changes.outputs.tags) }}"] | |
| profile: | |
| - "docker" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v4 | |
| - name: Setup Nextflow | |
| uses: nf-core/[email protected] | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.11" | |
| architecture: "x64" | |
| - name: Install pdiff to see diff between nf-test snapshots | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pdiff | |
| - name: Cache nf-test installation | |
| id: cache-software | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| /usr/local/bin/nf-test | |
| /home/runner/.nf-test/nf-test.jar | |
| key: ${{ runner.os }}-${{ env.NFT_VER }}-nftest | |
| - name: Install nf-test | |
| if: steps.cache-software.outputs.cache-hit != 'true' | |
| run: | | |
| wget -qO- https://code.askimed.com/install/nf-test | bash | |
| sudo mv nf-test /usr/local/bin/ | |
| - name: Run nf-test | |
| run: | | |
| nf-test test --verbose --tag ${{ matrix.tags }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap | |
| - uses: pcolby/tap-summary@v1 | |
| with: | |
| path: >- | |
| test.tap | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| sudo apt install bat > /dev/null | |
| batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log | |
| - name: Publish Test Report | |
| uses: mikepenz/action-junit-report@v3 | |
| if: always() # always run even if the previous step fails | |
| with: | |
| report_paths: test.xml | |
| confirm-pass: | |
| runs-on: ubuntu-latest | |
| needs: [test, star_salmon, star_rsem, hisat2, pseudo] | |
| if: always() | |
| steps: | |
| - name: All tests ok | |
| if: ${{ !contains(needs.*.result, 'failure') }} | |
| run: exit 0 | |
| - name: One or more tests failed | |
| if: ${{ contains(needs.*.result, 'failure') }} | |
| run: exit 1 | |
| - name: debug-print | |
| if: always() | |
| run: | | |
| echo ${{ needs.nf-test-changes.outputs.changes }} | |
| echo "toJSON(needs) = ${{ toJSON(needs) }}" | |
| echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |