Fix for trim_primers_3end parameter and primer sequences containing ambiguous nucleotides
#219
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| name: Lint Code Base | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| workflow_dispatch: | |
| jobs: | |
| formatting: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: read | |
| statuses: write | |
| steps: | |
| - name: Checkout Code | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Lint | |
| uses: github/super-linter@v5 | |
| env: | |
| VALIDATE_ALL_CODEBASE: true | |
| DEFAULT_BRANCH: master | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
| VALIDATE_PYTHON_FLAKE8: true | |
| VALIDATE_R: true | |
| linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Linting | |
| uses: snakemake/snakemake-github-action@v1.23.0 | |
| with: | |
| directory: '.tests' | |
| snakefile: workflow/Snakefile | |
| args: "--lint" |