feat: update envs and wrappers #1450
Workflow file for this run
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
| name: Tests | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches_ignore: [] | |
| jobs: | |
| Formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| # Full git history is needed to get a proper | |
| # list of changed files within `super-linter` | |
| fetch-depth: 0 | |
| - name: Formatting | |
| uses: github/super-linter@v4 | |
| env: | |
| VALIDATE_ALL_CODEBASE: false | |
| DEFAULT_BRANCH: master | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
| Linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Lint workflow | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| stagein: "mamba install -y -n snakemake --channel conda-forge pyarrow=6.0" | |
| args: "--lint" | |
| Testing: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - Linting | |
| - Formatting | |
| steps: | |
| - name: Free Disk Space (Ubuntu) | |
| uses: jlumbroso/[email protected] | |
| with: | |
| # this might remove tools that are actually needed, | |
| # if set to "true" but frees about 6 GB | |
| tool-cache: false | |
| # all of these default to true, but feel free to set to | |
| # "false" if necessary for your workflow | |
| android: true | |
| dotnet: true | |
| haskell: true | |
| large-packages: true | |
| docker-images: true | |
| swap-storage: true | |
| - uses: actions/checkout@v2 | |
| - name: Test workflow (local FASTQs) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-simple/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache" | |
| show-disk-usage-on-error: true | |
| - name: Test testcase generation | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "results/testcases/a/freebayes/IX:314200 --configfile .test/config-simple/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache" | |
| show-disk-usage-on-error: true | |
| - name: Test report | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-simple/config.yaml --report report.zip" | |
| show-disk-usage-on-error: true | |
| - name: Test workflow (local FASTQs, target regions) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-target-regions/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache" | |
| stagein: | | |
| rm -rf .test/results | |
| show-disk-usage-on-error: true | |
| - name: Test workflow (local FASTQs, multiple target regions BED files) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-target-regions/config_multiple_beds.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache" | |
| stagein: | | |
| rm -rf .test/results | |
| show-disk-usage-on-error: true | |
| - name: Test workflow (local FASTQs, no candidate filtering) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-no-candidate-filtering/config.yaml --dryrun --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache" | |
| stagein: | | |
| rm -rf .test/results | |
| show-disk-usage-on-error: true | |
| - name: Test workflow (local FASTQs primer) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config_primers/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache" | |
| stagein: | | |
| rm -rf .test/results | |
| show-disk-usage-on-error: true | |
| - name: Test workflow (SRA FASTQs) | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--configfile .test/config-sra/config.yaml --show-failed-logs --use-conda -n -j 10 --conda-cleanup-pkgs cache" | |
| stagein: | | |
| rm -rf .test/results | |
| show-disk-usage-on-error: true |