fix: Fixing workflow for single-end sequencing (#70) #94
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| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches_ignore: [] | |
| jobs: | |
| formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout with submodules | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| fetch-depth: 0 | |
| - name: Formatting | |
| uses: github/super-linter@v5 | |
| env: | |
| VALIDATE_ALL_CODEBASE: false | |
| DEFAULT_BRANCH: master | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
| linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Linting | |
| uses: snakemake/[email protected] | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config_complex/config.yaml --lint" | |
| run-workflow: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - linting | |
| - formatting | |
| steps: | |
| - name: Checkout repository with submodules | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| - name: Test workflow (basic model, no batch_effects) | |
| uses: snakemake/[email protected] | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config_basic/config.yaml --use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache" | |
| - name: Test report (basic model, no batch_effects) | |
| uses: snakemake/[email protected] | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config_basic/config.yaml --report report.zip" | |
| - name: Test workflow (multiple variables_of_interest, include batch_effects) | |
| uses: snakemake/[email protected] | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config_complex/config.yaml --use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache" | |
| - name: Test report (multiple variables_of_interest, include batch_effects) | |
| uses: snakemake/[email protected] | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config_complex/config.yaml --report report.zip" |