refactor!: No min max length for bbmap. default mapq is 30. (#131) #331
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, development] | |
| pull_request: | |
| branches: [master, development] | |
| jobs: | |
| docs: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: install micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: docs/environment.yml | |
| environment-name: sphinx | |
| - name: Run sphinx | |
| shell: bash -l {0} | |
| run: | | |
| cd docs && make html | |
| Formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Formatting | |
| uses: super-linter/super-linter@v6 | |
| env: | |
| VALIDATE_ALL_CODEBASE: false | |
| DEFAULT_BRANCH: master | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| VALIDATE_PYTHON_FLAKE8: true | |
| PYTHON_FLAKE8_CONFIG_FILE: .flake8 | |
| VALIDATE_JSON: true | |
| VALIDATE_YAML: true | |
| YAML_CONFIG_FILE: .yamllint.yml | |
| VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
| VALIDATE_R: true | |
| Linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Lint workflow | |
| uses: snakemake/snakemake-github-action@v1 | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: "--lint --configfile config/example_config.yaml" | |
| # Testing: | |
| # runs-on: ubuntu-latest | |
| # needs: | |
| # - Linting | |
| # - Formatting | |
| # steps: | |
| # - uses: actions/checkout@v2 | |
| # - name: Test workflow | |
| # uses: snakemake/snakemake-github-action@v1.24.0 | |
| # with: | |
| # directory: .test | |
| # snakefile: workflow/Snakefile | |
| # args: "--configfile config/example_config.yaml --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache" | |
| # - name: Test report | |
| # uses: snakemake/snakemake-github-action@v1.24.0 | |
| # with: | |
| # directory: .test | |
| # snakefile: workflow/Snakefile | |
| # args: "--configfile config/example_config.yaml --report report.zip" |