Merge template 3.0.2 #1163
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 | |
| - master | |
| pull_request: | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| env: | |
| NXF_ANSI_LOG: false | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})" | |
| # Only run on push if this is the nf-core dev branch (merged PRs) | |
| if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mhcquant') }}" | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "24.04.2" | |
| - "latest-everything" | |
| profile: | |
| - "conda" | |
| - "docker" | |
| - "singularity" | |
| test_name: | |
| - "test" | |
| isMaster: | |
| - ${{ github.base_ref == 'master' }} | |
| # Exclude conda and singularity on dev | |
| exclude: | |
| - isMaster: false | |
| profile: "conda" | |
| - isMaster: false | |
| profile: "singularity" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
| - name: Set up Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: "${{ 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: Clean up Disk space | |
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
| - name: Run pipeline with test data | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results | |
| profile: | |
| name: Run profile tests | |
| if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mhcquant') }} | |
| runs-on: ubuntu-latest | |
| env: | |
| NXF_VER: ${{ matrix.nxf_ver }} | |
| NXF_ANSI_LOG: false | |
| strategy: | |
| matrix: | |
| include: | |
| # Test pipeline minimum Nextflow version | |
| - NXF_VER: "23.04.0" | |
| NXF_EDGE: "" | |
| # Test latest edge release of Nextflow | |
| - NXF_VER: "" | |
| NXF_EDGE: "1" | |
| tests: ["test_mokapot", "test_percolator", "test_ionannotator"] | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| env: | |
| NXF_VER: ${{ matrix.NXF_VER }} | |
| # Uncomment only if the edge release is more recent than the latest stable release | |
| # See https://github.com/nextflow-io/nextflow/issues/2467 | |
| # NXF_EDGE: ${{ matrix.NXF_EDGE }} | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline with profile ${{ matrix.tests }} | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker --spectrum_batch_size 5000 --outdir ./results | |
| # Define a second workflow only against main with additional tests: test_timstof and test_full | |
| profile_main: | |
| name: Run timsTOF profile tests | |
| if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' && github.repository == 'nf-core/mhcquant' }} | |
| runs-on: ubuntu-latest | |
| env: | |
| NXF_VER: ${{ matrix.nxf_ver }} | |
| NXF_ANSI_LOG: false | |
| strategy: | |
| matrix: | |
| include: | |
| # Test pipeline minimum Nextflow version | |
| - NXF_VER: "23.04.0" | |
| NXF_EDGE: "" | |
| # Test latest edge release of Nextflow | |
| - NXF_VER: "" | |
| NXF_EDGE: "1" | |
| tests: ["test_timstof"] | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v2 | |
| - name: Install Nextflow | |
| env: | |
| NXF_VER: ${{ matrix.NXF_VER }} | |
| # Uncomment only if the edge release is more recent than the latest stable release | |
| # See https://github.com/nextflow-io/nextflow/issues/2467 | |
| # NXF_EDGE: ${{ matrix.NXF_EDGE }} | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| - name: Run pipeline with profile ${{ matrix.tests }} | |
| run: | | |
| nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker --spectrum_batch_size 5000 --outdir ./results |