refactor: use snakehelpers #124
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| # Run tests over snakefile workflow | |
| --- | |
| name: Tests | |
| on: # yamllint disable-line rule:truthy | |
| push: | |
| branches: [main, devel] | |
| pull_request: | |
| branches: [main, devel] | |
| jobs: | |
| Pre-Commit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| lfs: 'true' | |
| - name: Run pre-commit on all files | |
| uses: pre-commit/action@v3.0.1 | |
| with: | |
| extra_args: --all-files | |
| Testing: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - Pre-Commit | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| lfs: 'true' | |
| - name: Cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: .snakemake/conda | |
| key: snakemake-conda | |
| - name: Download environments | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: > | |
| --use-conda | |
| --conda-create-envs-only | |
| --conda-frontend mamba | |
| --cores 1 | |
| - name: Test workflow | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: > | |
| --use-conda | |
| --show-failed-logs | |
| --cores 3 | |
| --conda-cleanup-pkgs cache | |
| --profile profile/default | |
| --all-temp | |
| - name: Cache - unlock permissions | |
| run: chmod -R 777 .snakemake/conda | |
| - name: Conda - make space | |
| run: mamba clean --all --yes |