Migrate to nf schema #747
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 | |
| jobs: | |
| test_all: | |
| name: Run nf-test with ${{ matrix.test }}-${{ matrix.NXF_VER }} | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-cmgg/germline') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.10.0" | |
| - "latest-everything" | |
| test: | |
| - "pipeline_default" | |
| - "pipeline_callers" | |
| - "pipeline_variations" | |
| - "pipeline_variations2" | |
| - "pipeline_gvcfs" | |
| - "cram_call_genotype_gatk4" | |
| - "cram_call_vardictjava" | |
| - "cram_prepare_samtools_bedtools" | |
| - "input_split_bedtools" | |
| - "vcf_annotation" | |
| - "vcf_extract_relate_somalier" | |
| - "vcf_ped_rtgtools" | |
| - "vcf_upd_updio" | |
| - "vcf_validate_small_variants" | |
| steps: | |
| - name: Free some space | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| - 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 }}" | |
| - name: Disk space cleanup | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Install nf-test | |
| run: | | |
| conda install -c bioconda nf-test | |
| - name: Run pipeline with test data | |
| run: | | |
| $CONDA/bin/nf-test test --tag ${{ matrix.test }} --junitxml=default.xml | |
| - name: Publish Test Report | |
| uses: mikepenz/action-junit-report@v3 | |
| if: always() # always run even if the previous step fails | |
| with: | |
| report_paths: "default.xml" | |
| - name: Upload log file artifact | |
| if: failure() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: nf-test-workdir | |
| path: .nf-test/ |