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nf-docs

Generate beautiful API documentation for Nextflow pipelines.

nf-docs demo

nf-docs extracts structured API documentation from Nextflow pipelines via the Nextflow Language Server — similar to Sphinx for Python or Javadoc for Java.

Info

This is not an official Nextflow project. It's a fun side-project by Phil Ewels. Please use at your own risk :)

Output formats

  • HTML

    Single self-contained file with full-text search, deep linking, dark mode, source links, and mobile-friendly layout.

  • Markdown

    One file per section — integrates with static site generators like Astro, MkDocs, Zensical and Docusaurus.

  • Table

    Compact terraform-docs-style Markdown tables with marker injection and selective section rendering.

  • JSON & YAML

    Machine-readable structured data for CI/CD pipelines and custom integrations.