update CHANGELOG #3125
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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/detect-nf-test-changes@v0.0.2 | ||
| 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) }}" | ||
