fix: ffpe event handling now correctly considers the provided purity #180
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| name: Tests | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| Formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Formatting | |
| uses: github/super-linter@v4 | |
| env: | |
| VALIDATE_ALL_CODEBASE: false | |
| DEFAULT_BRANCH: main | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
| Linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Lint workflow | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: "--lint" | |
| Testing: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - Linting | |
| - Formatting | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Test workflow (tumor/normal) | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-tumor_normal/config.yaml --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache" | |
| - name: Test report | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-tumor_normal/config.yaml --cores 1 --report report.zip" | |
| - name: Test workflow (tumor/normal, ffpe) | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-tumor_normal_ffpe/config.yaml --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp" | |
| stagein: | | |
| rm -rf .test/results | |
| - name: Test workflow (tumor only) | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-tumor_only/config.yaml --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp" | |
| stagein: | | |
| rm -rf .test/results | |
| - name: Test workflow (tumor only, ffpe) | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-tumor_only_ffpe/config.yaml --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp" | |
| stagein: | | |
| rm -rf .test/results |