Patch release 0.3.2 #1065
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 | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| permissions: | |
| checks: write | |
| jobs: | |
| test: | |
| name: Run pipeline with test data | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'genomic-medicine-sweden/nallo') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| parameters: | |
| - "" | |
| - "--preset ONT_R10 --input https://github.com/genomic-medicine-sweden/test-datasets/raw/e2266a34c14d1e0a9ef798de3cd81a76c9216fc1/testdata/samplesheet_multisample_bam_ont.csv --parallel_alignments 2 --parallel_snv 1" | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Run pipeline with test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }} | |
| nftest: | |
| name: ${{ matrix.tags }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: | |
| - "latest-everything" | |
| - "23.04.0" | |
| tags: | |
| - "SHORT_VARIANT_CALLING" | |
| - "SNV_ANNOTATION" | |
| - "samplesheet" | |
| - "samplesheet_multisample_bam" | |
| profile: | |
| - "docker" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - uses: nf-core/setup-nf-test@v1 | |
| - 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: 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 |