Add bam input test #11
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| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - featurecount | |
| pull_request: | |
| branches_ignore: [] | |
| jobs: | |
| linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Linting | |
| uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/configs/star_config.yaml --lint" | |
| run-workflow: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - linting | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Test workflow (star) | |
| uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/configs/star_config.yaml --use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache" | |
| - name: Test workflow (bam) | |
| uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/configs/bam2bakR.yaml --use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache" |