Use nf-schema for pipeline params #146
Workflow file for this run
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| name: build | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - develop | |
| pull_request: | |
| branches: | |
| - main | |
| - develop | |
| workflow_dispatch: | |
| env: | |
| NFT_DIFF: "pdiff" | |
| NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" | |
| NFT_VER: "0.9.1" | |
| NFT_WORKDIR: "~" | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| permissions: | |
| contents: read | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.11"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: "pip" | |
| - name: Install nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools | |
| pip install .[dev,test] | |
| - name: pytest | |
| if: always() | |
| run: | | |
| pytest tests | |
| - name: lint nxf | |
| if: always() | |
| run: | | |
| nf-core pipelines schema lint | |
| - name: Stub run | |
| if: always() | |
| continue-on-error: true # temporarily set this until we create containers for every process | |
| run: | | |
| mkdir tmp && cd tmp | |
| sinclair init | |
| sinclair run \ | |
| -stub \ | |
| -profile ci_stub,docker,test | |
| - name: "Upload Artifact" | |
| uses: actions/upload-artifact@v4 | |
| if: always() # run even if previous steps fail | |
| with: | |
| name: nextflow-log | |
| path: .nextflow.log | |
| nf-test-changes: | |
| name: Check for changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| nf_test_files: ${{ steps.list.outputs.components }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: List nf-test files | |
| id: list | |
| uses: adamrtalbot/[email protected] | |
| with: | |
| head: ${{ github.sha }} | |
| base: origin/${{ github.base_ref }} | |
| include: .github/include.yml | |
| - name: print list of nf-test files | |
| run: | | |
| echo ${{ steps.list.outputs.components }} | |
| test: | |
| name: "Run tests (${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }})" | |
| needs: [nf-test-changes] | |
| if: needs.nf-test-changes.outputs.nf_test_files != '[]' | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: | |
| - "24.04.2" | |
| - "latest-everything" | |
| nf_test_files: | |
| ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] | |
| profile: | |
| - "docker" | |
| isMaster: | |
| - ${{ github.base_ref == 'master' }} | |
| # Exclude conda and singularity on dev | |
| exclude: | |
| - isMaster: false | |
| profile: "singularity" | |
| - NXF_VER: "latest-everything" | |
| profile: "singularity" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Set up Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Set up Apptainer | |
| if: matrix.profile == 'singularity' | |
| uses: eWaterCycle/setup-apptainer@main | |
| - name: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| run: | | |
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
| - name: Install nf-test | |
| uses: nf-core/setup-nf-test@v1 | |
| with: | |
| version: ${{ env.NFT_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: Clean up Disk space | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Run nf-test | |
| run: | | |
| nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ 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 | |
| build-status: # https://github.com/orgs/community/discussions/4324#discussioncomment-3477871 | |
| runs-on: ubuntu-latest | |
| needs: [build, test] | |
| if: always() | |
| steps: | |
| - name: Successful build | |
| if: ${{ !(contains(needs.*.result, 'failure')) }} | |
| run: exit 0 | |
| - name: Failing build | |
| if: ${{ contains(needs.*.result, 'failure') }} | |
| run: exit 1 |