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Split CIs for dev and master PRs #203
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,130 @@ | ||
| name: nf-core CI master | ||
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors upon master PR | ||
| on: | ||
| pull_request: | ||
| branches: | ||
| - master | ||
| release: | ||
| types: [published] | ||
| workflow_dispatch: | ||
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|
||
| 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 }} | ${{ matrix.profile }})" | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| NXF_VER: | ||
| - "24.10.4" | ||
| - "latest-everything" | ||
| profile: | ||
| - "docker" | ||
| - "singularity" | ||
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|
||
| - "conda" | ||
| test_name: | ||
| - "test" | ||
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|
||
| - "test_conda" | ||
| - "test_pdb" | ||
| - "test_nosheet" | ||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | ||
|
|
||
| - name: Set up Nextflow | ||
| uses: nf-core/setup-nextflow@v2 | ||
| with: | ||
| version: "${{ 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 | ||
| echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | ||
| echo $(realpath python) >> $GITHUB_PATH | ||
|
|
||
| - 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 | ||
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|
||
|
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||
| - name: Clean up Disk space | ||
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | ||
|
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||
| - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" | ||
| if: "${{ (matrix.test_name != 'test' && matrix.profile == 'conda') || (matrix.test_name != 'test_conda' && matrix.profile != 'conda') }}" | ||
| run: | | ||
| nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results | ||
|
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||
| parameters_stub: | ||
| name: Stub run | ||
|
|
||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| NXF_VER: | ||
| - "24.10.4" | ||
| - "latest-everything" | ||
| profile: | ||
| - "docker" | ||
| - "singularity" | ||
| params: | ||
| - "--skip_stats" | ||
| - "--skip_eval" | ||
| - "--skip_visualisation" | ||
| - "--skip_validation" | ||
| - "--skip_preprocessing" | ||
| - "--skip_compression" | ||
| - "--skip_shiny" | ||
| test_name: | ||
| - "test" | ||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 | ||
| with: | ||
| fetch-depth: 0 | ||
|
|
||
| - 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: Clean up Disk space | ||
| uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | ||
|
|
||
| - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" | ||
| run: | | ||
| nextflow run ${GITHUB_WORKSPACE} -profile test,${{ matrix.profile }} ${{ matrix.params }} --outdir ./results | ||
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