Restructure as Python package with Docker/CI support #5
Workflow file for this run
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| name: Snakemake Validation | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| validate: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| environment-file: environment.yml | |
| cache-environment: true | |
| - name: Install package | |
| run: pip install -e . | |
| shell: micromamba-shell {0} | |
| - name: Validate Snakefile syntax | |
| run: | | |
| cd workflows | |
| # Use Python syntax check since --lint returns non-zero for style warnings | |
| python -m py_compile Snakefile.example || exit 1 | |
| # Run lint but don't fail on warnings (informational only) | |
| snakemake -s Snakefile.example --lint || true | |
| shell: micromamba-shell {0} |