GitHub Basics: GitHub Actions

The following describe the minimum GitHub actions that should be deployed with any production pipeline. The actions are automatically provided via the cookiecutter templates: NextFlow and Snakemake.

  1. Documentation (assumes mkdocs build; required for all repos)

    • These rules will automatically update any documentation built with mkdocs for all PR’s.
    • Rule Name(s): mkdocs_build –> pages-build-and-deployment

  2. Lintr (required for CCBR projects and new pipelines)

    • This rule will automatically perform a lintr with the data provided in the .test folder of the pipeline. Review the GitHub Best Practices - Test Data page for more information.

  3. Dry-run with test sample data for any PR to dev branch (required for CCBR projects and new pipelines)

    • This rule will automatically perform a dry-run with the data provided in the .test folder of the pipeline. Review the GitHub Best Practices - Test Data page for more information.

  4. Full-run with full sample data for any PR to main branch (required for CCBR projects and new pipelines)

    • This rule will automatically perform a full-run with the data provided in the .test folder of the pipeline. Review the GitHub Best Practices - Test Data page for more information.

  5. Auto pull/push from source (if applicable for CCBR projects and new pipelines)

    • If the pipeline is forked from another location and updating this forked pipeline is required, an action will automatically perform a pull from the source location at least once a week.

  6. Add assigned issues & PRs to user projects.

    When an issue or PR is assigned to a CCBR member, this action will automatically add it to their personal GitHub Project, if they have one. This file can be copy and pasted exactly as-is into any CCBR repo from here.