.github

This is the special .github repository for the Waldron Lab GitHub organization. It contains two types of shared resources:

Organization Profile

profile/README.md is displayed on the Waldron Lab's public GitHub organization page. It introduces the lab, its research focus (cancer genomics, microbiome profiling, and biostatistics), and community resources such as BugSigDB and the Microbiome Virtual International Forum.

Reusable Workflows

Reusable GitHub Actions workflows live in .github/workflows/ and can be called from any repository in the organization.

bioc-pr-cmdcheck-pkgdown.yml

A reusable workflow for Bioconductor R packages that performs the following steps on both pull requests and branch pushes:

1. R CMD check — runs rcmdcheck against the package.
2. BiocCheck — runs BiocCheck to enforce Bioconductor-specific guidelines.
3. Test coverage — collects coverage with covr on devel branch pushes and uploads results to Codecov (optional, requires CODECOV_TOKEN secret).
4. pkgdown site — builds and deploys a pkgdown site to GitHub Pages when pushing to a RELEASE_* branch (optional, enabled by default).
5. Docker image — builds and pushes a Docker image to Docker Hub when a Dockerfile is present and pushing to the devel branch (optional, requires DOCKERHUB_USERNAME and DOCKERHUB_TOKEN secrets).

Usage

Call this workflow from a repository in the organization with:

jobs:
  bioc-check:
    uses: waldronlab/.github/.github/workflows/bioc-pr-cmdcheck-pkgdown.yml@devel
    secrets:
      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
      DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
      DOCKERHUB_TOKEN: ${{ secrets.DOCKERHUB_TOKEN }}

Inputs

Input	Type	Default	Description
cran	string	https://p3m.dev/cran/__linux__/noble/latest	CRAN-like repository URL
enable_pkgdown	boolean	true	Build and deploy pkgdown site on RELEASE_* branch pushes
enable_docker	boolean	true	Build and push Docker image on devel branch pushes
dockerfile_path	string	inst/docker/pkg/Dockerfile	Path to the Dockerfile to build