feat: add CI for a scaled down version of a cancer WES pipeline #11
Workflow file for this run
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| name: Tests | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches_ignore: [] | |
| jobs: | |
| Dryrun_Tests: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| lfs: 'true' | |
| - 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 | |
| needs: | |
| - Dryrun_Tests | |
| steps: | |
| - name: update apt | |
| run: sudo apt-get update | |
| - uses: actions/checkout@v4 | |
| with: | |
| lfs: 'true' | |
| - 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 | |