feat: add prokka and bakta for annotation #18
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| name: CI | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| Formatting: | |
| runs-on: ubuntu-latest | |
| if: ${{ github.actor != 'github-actions[bot]' }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Test formatting | |
| uses: super-linter/super-linter@v7 | |
| env: | |
| VALIDATE_ALL_CODEBASE: false | |
| DEFAULT_BRANCH: main | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
| VALIDATE_YAML_PRETTIER: true | |
| Linting: | |
| runs-on: ubuntu-latest | |
| if: ${{ github.actor != 'github-actions[bot]' }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Test linting workflow | |
| uses: snakemake/snakemake-github-action@v2.0.0 | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: "--lint" | |
| Testing: | |
| runs-on: ubuntu-latest | |
| if: ${{ github.actor != 'github-actions[bot]' }} | |
| needs: | |
| - Formatting | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Test run workflow | |
| uses: snakemake/snakemake-github-action@v2.0.0 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--sdm conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache" | |
| - name: Test report | |
| uses: snakemake/snakemake-github-action@v2.0.0 | |
| with: | |
| directory: .test | |
| snakefile: workflow/Snakefile | |
| args: "--cores 1 --report report.zip -n" |