update CHANGELOG #3125
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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: | ||
| pull_request: | ||
| release: | ||
| types: [published] | ||
| workflow_dispatch: | ||
| env: | ||
| NFT_DIFF: "pdiff" | ||
| NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" | ||
| NFT_VER: "0.9.0" | ||
| 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 | ||
| jobs: | ||
| 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.yaml | ||
| - 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: nf-test-changes.outputs.nf_test_files != '[]' | ||
|
Check failure on line 47 in .github/workflows/ci.yml
|
||
| 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: | ||
| - "conda" | ||
| - "docker" | ||
| - "singularity" | ||
| isMaster: | ||
| - ${{ github.base_ref == 'master' }} | ||
| # Exclude conda and singularity on dev | ||
| exclude: | ||
| - isMaster: false | ||
| profile: "conda" | ||
| - isMaster: false | ||
| profile: "singularity" | ||
| - profile: "conda" | ||
| nf_test_files: "tests/default.nf.test" | ||
| - profile: "conda" | ||
| nf_test_files: "tests/featurecounts_group_type.nf.test" | ||
| - profile: "conda" | ||
| nf_test_files: "tests/hisat2.nf.test" | ||
| - profile: "conda" | ||
| nf_test_files: "tests/kallisto.nf.test" | ||
| - profile: "conda" | ||
| nf_test_files: "tests/min_mapped_reads.nf.test" | ||
| - profile: "conda" | ||
| nf_test_files: "tests/remove_ribo_rna.nf.test" | ||
| - profile: "conda" | ||
| nf_test_files: "tests/salmon.nf.test" | ||
| - profile: "conda" | ||
| nf_test_files: "tests/skip_qc.nf.test" | ||
| - profile: "conda" | ||
| nf_test_files: "tests/skip_trimming.nf.test" | ||
| - profile: "conda" | ||
| nf_test_files: "tests/star_rsem.nf.test" | ||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | ||
| - name: Set up Nextflow | ||
| uses: nf-core/setup-nextflow@v2 | ||
| with: | ||
| version: "${{ 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: Set up Miniconda | ||
| if: matrix.profile == 'conda' | ||
| uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 | ||
| with: | ||
| miniconda-version: "latest" | ||
| auto-update-conda: true | ||
| conda-solver: libmamba | ||
| channels: conda-forge,bioconda | ||
| - name: Set up Conda | ||
| if: matrix.profile == 'conda' | ||
| run: | | ||
| echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | ||
| echo $(realpath python) >> $GITHUB_PATH | ||
| - 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 | ||
| confirm-pass: | ||
| runs-on: ubuntu-latest | ||
| needs: [test] | ||
| if: always() | ||
| steps: | ||
| - name: All tests ok | ||
| if: ${{ !contains(needs.*.result, 'failure') }} | ||
| run: exit 0 | ||
| - name: One or more tests failed | ||
| if: ${{ contains(needs.*.result, 'failure') }} | ||
| run: exit 1 | ||
| - name: debug-print | ||
| if: always() | ||
| run: | | ||
| echo "toJSON(needs) = ${{ toJSON(needs) }}" | ||
| echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" | ||
