Pipeline reference

This section is a deep reference for the MetaGEAR Nextflow pipeline — what each workflow does biologically, what it consumes, what it produces, and the parameters that change its behaviour.

Where this content lives

The pages under Workflows are mirrored at build time from the pipeline repository, schirmer-lab/metagear-pipeline-dev, under docs/workflows/. The pipeline repo is the source of truth; this site renders the same markdown with consistent navigation and search.

Editing

To change a workflow page, open a pull request against docs/workflows/ in the pipeline repo. Once merged, bump the ref in pipeline-docs.json on this site to publish the new content. The bump is a one-line PR.

Want to run the pipeline?

The pages here are reference — they describe what each workflow does in detail. If you’re trying to actually run the pipeline, start with Get started and the MetaGEAR Tools (CLI) page, which cover installation and end-to-end usage.