Video demo, README header #107
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| name: Snakemake workflow | |
| on: [push] | |
| jobs: | |
| run_snakemake_workflow: | |
| name: Run snakemake workflow | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| environment-file: micromamba_env.yml | |
| cache-environment: true | |
| cache-environment-key: ${{ hashFiles('micromamba_env.yml') }} | |
| post-cleanup: 'none' | |
| - name: Install pip dependencies | |
| run: | | |
| micromamba run -n protein-runway pip install -r requirements.txt | |
| - name: Generate image artifacts | |
| run: | | |
| micromamba run -n protein-runway bash scripts/generate_snakemake_graphs.sh 5vde_example | |
| - name: Run snakemake | |
| run: | | |
| micromamba run -n protein-runway snakemake | |
| - name: Generate report | |
| run: | | |
| micromamba run -n protein-runway snakemake --report 04_extra/report.html | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: workflow-graphs | |
| path: | | |
| 04_extra/graphs/*.svg | |
| 04_extra/report.html |