Nf-test #770
Workflow file for this run
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| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | ||
| name: nf-core CI | ||
| on: | ||
| pull_request: | ||
| release: | ||
| types: [published] | ||
| merge_group: | ||
| types: | ||
| - checks_requested | ||
| branches: | ||
| - master | ||
| - dev | ||
| env: | ||
| NXF_ANSI_LOG: false | ||
| NFTEST_VER: "0.8.1" | ||
| concurrency: | ||
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | ||
| cancel-in-progress: true | ||
| jobs: | ||
| test: | ||
| name: ${{ matrix.profile }} NF ${{ matrix.NXF_VER }} | ||
| needs: [changes, define_nxf_versions] | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| NXF_VER: | ||
| - "23.04.0" | ||
| - "latest-everything" | ||
| profile: | ||
| [ | ||
| "tests/main_pipeline_alevin.test", | ||
| "tests/main_pipeline_cellranger.test", | ||
| "tests/main_pipeline_kallisto.test", | ||
| "tests/main_pipeline_star.test", | ||
| ] | ||
| steps: | ||
| - name: Free some space | ||
| run: | | ||
| sudo rm -rf /usr/share/dotnet | ||
| sudo rm -rf /opt/ghc | ||
| sudo rm -rf "/usr/local/share/boost" | ||
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v4 | ||
| - name: Install Nextflow | ||
| uses: nf-core/setup-nextflow@v1 | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
| - 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.NFTEST_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 "${{ matrix.profile }}" --junitxml=test.xml | ||
| - 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 | ||
