chore: change logs location #27
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| name: Tests | ||
| on: | ||
| push: | ||
| branches: [ main ] | ||
| pull_request: | ||
| branches: [ main ] | ||
| jobs: | ||
| Formatting: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: Formatting | ||
| uses: github/super-linter@v4 | ||
| env: | ||
| VALIDATE_ALL_CODEBASE: false | ||
| DEFAULT_BRANCH: main | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| VALIDATE_SNAKEMAKE_SNAKEFMT: true | ||
| Linting-assembly: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: Lint workflow | ||
| uses: snakemake/[email protected] | ||
| with: | ||
| directory: . | ||
| snakefile: workflow/Snakefile-assembly | ||
| args: "--lint" | ||
| Linting-cluster: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: Lint workflow | ||
| uses: snakemake/[email protected] | ||
| with: | ||
| directory: . | ||
| snakefile: workflow/Snakefile-cluster | ||
| args: "--lint" | ||
| Linting-consensus: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: Lint workflow | ||
| uses: snakemake/[email protected] | ||
| with: | ||
| directory: . | ||
| snakefile: workflow/Snakefile-consensus | ||
| args: "--lint" | ||
| Testing: | ||
| runs-on: ubuntu-latest | ||
| needs: | ||
| - Linting | ||
| - Formatting | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: Test workflow | ||
| uses: snakemake/[email protected] | ||
| with: | ||
| directory: .test | ||
| snakefile: workflow/Snakefile | ||
| args: "--use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp" | ||
| - name: Test report | ||
| uses: snakemake/[email protected] | ||
| with: | ||
| directory: .test | ||
| snakefile: workflow/Snakefile | ||
| args: "--report report.zip" | ||
