Merge pull request #1274 from adamrtalbot/update_bam_markduplicates_p… #2481
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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) }}" |