feat: update environments and tool usage #1
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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] | |
| env: | |
| CACHE_NUMBER: 0 # Increment this number to invalidate the cache | |
| 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/[email protected] | |
| with: | |
| extra_args: --all-files | |
| Testing: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - Pre-Commit | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| lfs: 'true' | |
| - name: Set up caches | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| .snakemake/conda | |
| ~/.cache/pre-commit/ | |
| key: snakemake-conda-${{ env.CACHE_NUMBER }} | |
| - name: Clean conda cache | |
| run: conda clean --all --yes | |
| - name: Test workflow - Preprocess | |
| uses: snakemake/[email protected] | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: > | |
| --use-conda | |
| --show-failed-logs | |
| --cores 3 | |
| --conda-cleanup-pkgs cache | |
| --latency-wait 5 | |
| preprocess__fastp | |
| preprocess__bowtie2 | |
| preprocess__kraken2 | |
| - name: Test workflow - Quantify | |
| uses: snakemake/[email protected] | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: > | |
| --use-conda | |
| --show-failed-logs | |
| --cores 3 | |
| --conda-cleanup-pkgs cache | |
| --latency-wait 5 | |
| quantify | |
| - name: Test workflow - Report | |
| uses: snakemake/[email protected] | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: > | |
| --use-conda | |
| --show-failed-logs | |
| --cores 3 | |
| --conda-cleanup-pkgs cache | |
| --latency-wait 5 | |
| report | |
| - uses: actions/upload-artifact@v4 | |
| if: failure() | |
| with: | |
| name: results | |
| path: | | |
| results/**/*.log | |
| # results/ | |
| # reports/ | |
| # !**/*.cram | |
| # !**/*.fq.gz | |
| # !**/*.bam | |
| # !**/*.bt2 |