feat: Assignment long read support with pbmm2 #625
Workflow file for this run
This file contains hidden or 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: # yamllint disable-line rule:truthy | |
| push: | |
| branches: [master, development] | |
| pull_request: | |
| branches: [master, development] | |
| jobs: | |
| docs: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v6 | |
| - name: install micromamba | |
| uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| environment-file: docs/environment.yml | |
| environment-name: sphinx | |
| - name: Run sphinx | |
| shell: bash -l {0} | |
| run: | | |
| cd docs && make SPHINXOPTS="-W" html | |
| Formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v6 | |
| with: | |
| fetch-depth: 0 | |
| - name: Formatting | |
| uses: super-linter/super-linter@v8 | |
| env: | |
| LINTER_RULES_PATH: . | |
| 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 | |
| SNAKEMAKE_SNAKEFMT_CONFIG_FILE: pyproject.toml | |
| VALIDATE_R: true | |
| SAVE_SUPER_LINTER_SUMMARY: true | |
| Linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v6 | |
| - name: Lint workflow | |
| uses: snakemake/snakemake-github-action@v2 | |
| with: | |
| directory: . | |
| snakefile: workflow/Snakefile | |
| args: "--lint --configfile config/example_config.yaml --config skip_version_check=True" | |
| # 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" |