Merge pull request #127 from hydra-genetics/apptainer_install #464
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| name: Snakemake dry run | |
| on: | |
| push: | |
| branches: | |
| - develop | |
| - master | |
| pull_request: | |
| branches: | |
| - develop | |
| - master | |
| workflow_dispatch: | |
| jobs: | |
| snakemake-dry-run: | |
| name: Run snakemake dry run | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: 3.8 | |
| - 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, merge | |
| working-directory: .tests/integration | |
| run: | | |
| snakemake --cores 2 -n -s ../../workflow/Snakefile --configfile config.yaml | |
| - name: snakemake dry run, fastp + merge | |
| working-directory: .tests/integration | |
| run: | | |
| snakemake --cores 2 -n -s ../../workflow/Snakefile --configfile config.yaml configs/fastp_merge_config.yaml | |
| - name: snakemake dry run pbmarkdup | |
| working-directory: .tests/integration | |
| run: | | |
| snakemake -n -s ../../workflow/Snakefile --configfile config_pacbio.yaml |