ci: update config files and create new marvin profiles #7
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| name: Snakemake dry run | |
| on: | |
| push: | |
| branches: | |
| - develop | |
| - main | |
| pull_request: | |
| branches: | |
| - develop | |
| - main | |
| workflow_dispatch: | |
| jobs: | |
| snakemake-dry-run: | |
| name: Run snakemake dry run for cpu mode | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: 3.9 | |
| - name: Install requirements.txt | |
| run: | | |
| pip install -r requirements.txt | |
| - name: Install requirements.test.txt | |
| run: | | |
| pip install -r requirements.test.txt | |
| - name: snakemake dry run cpu mode | |
| working-directory: .tests/integration | |
| run: | | |
| snakemake -n -s ../../workflow/Snakefile --configfile config/config.yaml --config aligner=bwa_cpu --config snp_caller=deepvariant_cpu |