Documentation update and added a full test #134
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 | |
| - documentation | |
| pull_request: | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| env: | |
| NXF_ANSI_LOG: false | |
| NFT_VER: "0.9.0" | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| # env var to force tests | |
| # TEST_SET: '["tests/workflows/mcmicro.nf.test", "subworkflows/local/utils_nfcore_mcmicro_pipeline/tests/initialisation.nf.test", "tests/main.nf.test"]' | |
| concurrency: | |
| group: "${{ 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 }} | |
| # nf_test_files: ${{ env.TEST_SET }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: List nf-test files | |
| id: list | |
| uses: adamrtalbot/detect-nf-test-changes@v0.0.4 | |
| with: | |
| head: ${{ github.sha }} | |
| # TODO: check that the following works on pull_request | |
| base: ${{ github.ref_name }} | |
| - 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] | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mcmicro')) && needs.nf-test-changes.outputs.nf_test_files != '[]' }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: | |
| - "24.04.2" | |
| - "latest-everything" | |
| nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] | |
| profile: | |
| # - "conda" | |
| - "docker" | |
| - "singularity" | |
| test_name: | |
| - "test" | |
| isMaster: | |
| - ${{ github.base_ref == 'master' }} | |
| # Exclude conda and singularity on dev | |
| exclude: | |
| - isMaster: false | |
| profile: "conda" | |
| - isMaster: false | |
| profile: "singularity" | |
| steps: | |
| - name: install curl | |
| run: sudo apt update && sudo apt install -y curl wget | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Set up Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ 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 }},ci" \ | |
| # --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) = ${{ toJSON(needs.*.result) }}" | |
| test_orig: | |
| name: Run pipeline with test data | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mcmicro') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-java@v4 | |
| with: | |
| distribution: "zulu" # See 'Supported distributions' for available options | |
| java-version: "21" | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - 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: Run pipeline with test data | |
| # TODO nf-core: You can customise CI pipeline run tests as required | |
| # For example: adding multiple test runs with different parameters | |
| # Remember that you can parallelise this by using strategy.matrix | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results |