chore: use composite snakemake action [test] #1984
Workflow file for this run
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| name: Tests | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches-ignore: [] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| 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@v5 | |
| 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 | |
| with: | |
| fetch-depth: 0 | |
| - name: Lint workflow | |
| uses: snakemake/snakemake-github-action@use-conda-instead-of-docker | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: "--lint" | |
| Testing: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - Linting | |
| - Formatting | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| case: | |
| - name: local input (dryrun) | |
| args: > | |
| --configfile .test/config-simple/config.yaml --use-conda | |
| --show-failed-logs -j 10 --conda-cleanup-pkgs cache --dryrun | |
| report: false | |
| cleanup: false | |
| - name: local input | |
| args: > | |
| --configfile .test/config-simple/config.yaml --use-conda | |
| --show-failed-logs -j 10 --conda-cleanup-pkgs cache | |
| report: true | |
| cleanup: false | |
| - name: testcase generation | |
| args: > | |
| results/testcases/one/freebayes/IX:314200 --configfile .test/config-simple/config.yaml | |
| report: false | |
| cleanup: false | |
| - name: target regions | |
| args: > | |
| --configfile .test/config-target-regions/config.yaml | |
| report: true | |
| cleanup: false | |
| - name: target regions, multiple BEDs | |
| args: > | |
| --configfile .test/config-target-regions/config_multiple_beds.yaml | |
| report: true | |
| cleanup: false | |
| - name: no candidate filtering | |
| args: > | |
| --configfile .test/config-no-candidate-filtering/config.yaml | |
| report: true | |
| cleanup: false | |
| - name: primers | |
| args: > | |
| --configfile .test/config_primers/config.yaml | |
| report: true | |
| cleanup: false | |
| - name: sra download | |
| args: > | |
| --configfile .test/config-sra/config.yaml | |
| report: true | |
| cleanup: false | |
| name: test ${{ matrix.case.name }} | |
| steps: | |
| - name: update apt | |
| run: sudo apt-get update | |
| - name: Free Disk Space (Ubuntu) | |
| if: ${{ matrix.case.cleanup }} | |
| uses: jlumbroso/free-disk-space@v1.3.0 | |
| 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: false | |
| swap-storage: true | |
| - uses: actions/checkout@v2 | |
| - name: run workflow | |
| uses: snakemake/snakemake-github-action@use-conda-instead-of-docker | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: > | |
| ${{ matrix.case.args }} --sdm conda --cores 10 | |
| --conda-cleanup-pkgs cache | |
| show-disk-usage-on-error: true | |
| - name: generate report | |
| if: ${{ matrix.case.report }} | |
| uses: snakemake/snakemake-github-action@use-conda-instead-of-docker | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: > | |
| ${{ matrix.case.args }} --sdm conda --report report.zip | |
| show-disk-usage-on-error: true |