feat(experiment): 🚀 FWD/REV(/UMI) reads can be splitted into n files before merging #641
Workflow file for this run
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| --- | |
| 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/[email protected] | |
| # 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/[email protected] | |
| # with: | |
| # directory: .test | |
| # snakefile: workflow/Snakefile | |
| # args: "--configfile config/example_config.yaml --report report.zip" |