chore: update github CI #259
Workflow file for this run
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| name: Tests | |
| on: | |
| # always run tests when pushing to main | |
| push: | |
| branches: [ main ] | |
| # only run tests on pull requests which actually modify files that affect the tests | |
| pull_request: | |
| branches_ignore: [] | |
| # for now, the tests defined in this file are only run when any of the following paths are modified: | |
| paths: | |
| # workflow definitions | |
| - '.tests/**' | |
| # github workflow configurations | |
| - '.github/**' | |
| # 'base' files of snappy-pipeline | |
| - 'snappy_pipeline/*' | |
| - 'snappy_pipeline/workflows/abstract/**' | |
| # steps used in the test workflows | |
| - 'snappy_pipeline/workflows/ngs_mapping/**' | |
| - 'snappy_pipeline/workflows/somatic_variant_calling/**' | |
| - 'snappy_pipeline/workflows/somatic_variant_annotation/**' | |
| - 'snappy_pipeline/workflows/somatic_variant_filtration/**' | |
| # 'base' files of snappy_wrappers | |
| - 'snappy_wrappers/*' | |
| # wrappers used in the test workflows | |
| - 'snappy_wrappers/wrappers/alfred/**' | |
| - 'snappy_wrappers/wrappers/bcftools/**' | |
| - 'snappy_wrappers/wrappers/bwa/**' | |
| - 'snappy_wrappers/wrappers/link_in_bam/**' | |
| - 'snappy_wrappers/wrappers/mutect/**' | |
| - 'snappy_wrappers/wrappers/mutect_par/**' | |
| - 'snappy_wrappers/wrappers/mutect2/**' | |
| - 'snappy_wrappers/wrappers/mutect2_par/**' | |
| - 'snappy_wrappers/wrappers/ngs_chew/**' | |
| - 'snappy_wrappers/wrappers/somatic_variant_filtration/**' | |
| - 'snappy_wrappers/wrappers/vep/**' | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| jobs: | |
| Dryrun_Tests: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| lfs: 'true' | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: environment.yml | |
| channels: conda-forge,bioconda,nodefaults | |
| channel-priority: strict | |
| - name: Test workflow (local FASTQs) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .tests/test-workflow | |
| snakefile: .tests/test-workflow/workflow/Snakefile | |
| args: "--configfile .tests/test-workflow/config/config.yaml --use-conda --show-failed-logs -j 2 --conda-cleanup-pkgs cache --dryrun" | |
| show-disk-usage-on-error: true | |
| Tests: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: | |
| - "3.12" | |
| needs: | |
| - Dryrun_Tests | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| lfs: 'true' | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: environment.yml | |
| channels: conda-forge,bioconda,nodefaults | |
| channel-priority: strict | |
| activate-environment: test | |
| - name: Test workflow (local FASTQs) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .tests/test-workflow | |
| snakefile: .tests/test-workflow/workflow/Snakefile | |
| args: "--configfile .tests/test-workflow/config/config.yaml --use-conda --show-failed-logs -j 2 --conda-cleanup-pkgs cache" | |
| show-disk-usage-on-error: true | |