perf: update to dna-seq-varlociraptor 5.8.1 (#49) #191
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |