Nf test local subworkflows #937
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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] | |
| workflow_dispatch: | |
| env: | |
| NXF_ANSI_LOG: false | |
| NFT_MAX_SHARDS: 5 | |
| SOURCE_BRANCH: ${{ github.head_ref || github.ref_name }} | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test_all: | |
| name: Run ${{ matrix.filter }} tests | shard ${{ matrix.shard }} (${{ matrix.NXF_VER }}) | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-cmgg/germline') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "24.10.0" | |
| - "latest-everything" | |
| filter: | |
| - "process" | |
| - "workflow" | |
| - "pipeline" | |
| shard: [1, 2, 3, 4, 5] | |
| steps: | |
| - name: Free some space | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| with: | |
| fetch-depth: 0 | |
| - 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: Install nf-test | |
| run: | | |
| conda install -c bioconda nf-test | |
| - name: "Run ${{ matrix.filter }} tests | ${{ matrix.shard }}/${{ env.NFT_MAX_SHARDS }}" | |
| run: | | |
| if [ ${{ env.SOURCE_BRANCH }} == 'main' ]; then | |
| $CONDA/bin/nf-test test \ | |
| --ci \ | |
| --changed-since HEAD^ \ | |
| --shard ${{ matrix.shard }}/${{ env.NFT_MAX_SHARDS }} \ | |
| --filter ${{ matrix.filter }} \ | |
| --junitxml=default.xml | |
| else | |
| $CONDA/bin/nf-test test \ | |
| --ci \ | |
| --shard ${{ matrix.shard }}/${{ env.NFT_MAX_SHARDS }} \ | |
| --filter ${{ matrix.filter }} \ | |
| --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/ |