refactor: use snakehelpers #128
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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@v1.25.1 | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: > | |
| --use-conda | |
| --conda-create-envs-only | |
| --cores 1 | |
| - name: Snakemake - Remove unused envs | |
| uses: snakemake/snakemake-github-action@v1.25.1 | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: > | |
| --use-conda | |
| --conda-cleanup-envs | |
| - name: Snakemake - Remove unused tarballs | |
| uses: snakemake/snakemake-github-action@v1.25.1 | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: > | |
| --use-conda | |
| --conda-cleanup-pkgs tarballs | |
| - name: Snakemake - Remove unused cache | |
| uses: snakemake/snakemake-github-action@v1.25.1 | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: > | |
| --use-conda | |
| --conda-cleanup-pkgs cache | |
| - name: Test workflow | |
| uses: snakemake/snakemake-github-action@v1.25.1 | |
| 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: sudo chmod -R 777 .snakemake/conda |