fix: mm10 gmap chr10 inversion; correct eagle gmap template; CI badge #3
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: [main, dev, "feat/**"] | |
| pull_request: | |
| concurrency: | |
| group: ci-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| dryrun: | |
| name: pytest + snakemake dry-run (py${{ matrix.python-version }}) | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.11", "3.13"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install snakemake + DAG-parse deps | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install "snakemake>=9" snakemake-storage-plugin-http snakemake-storage-plugin-fs \ | |
| pandas numpy pyyaml pulp pytest | |
| - name: pytest (DAG dry-run, all modes x JSON/TSV) | |
| run: pytest tests/ | |
| - name: snakemake dry-run on a real sample sheet (HCC1395, chr16) | |
| run: | | |
| set -euo pipefail | |
| # Stub only the references not bundled in resources/data/; a dry-run just | |
| # builds the DAG, so empty files are enough. | |
| R=.test-run/HCC1395/reference | |
| mkdir -p "$R/target_positions" "$R/phasing_panel" | |
| : > "$R/hg38.fa" | |
| : > "$R/gencode.hg38.gtf.gz" | |
| : > "$R/genetic_map_hg38_withX.txt.gz" | |
| : > "$R/target_positions/target.chr16.pos.gz" | |
| : > "$R/target_positions/target.chr16.pos.gz.tbi" | |
| : > "$R/phasing_panel/chr16.genotypes.bcf" | |
| : > "$R/phasing_panel/chr16.genotypes.bcf.csi" | |
| snakemake -n -c1 -s workflow/Snakefile --configfile tests/data/HCC1395/config.yaml |