nf-docs

Generate beautiful API documentation for Nextflow pipelines

Full documentation →

Choose from 4 different output formats:

HTML Single-file output Share anywhere, even offline Full-text search built in

Markdown Multiple files or tables by section Perfect for static site generators

JSON / YAML Machine-readable output Build custom integrations CI/CD friendly

What is nf-docs?

Important

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

Information is pulled from multiple sources to construct the docs (each only if available):

• README.md - Pipeline overview and description
• nextflow.config - Runtime configuration defaults
• nextflow_schema.json - Typed input parameters with descriptions and validation rules
• Language Server - Processes, workflows, functions with their Groovydoc comments
• meta.yml - nf-core module metadata (tools, keywords, authors)

The documentation for workflows, processes and functions is relatively unique. nf-docs extracts this from your Nextflow pipelines by querying the Nextflow Language Server. It produces structured API documentation similar to Sphinx for Python or Javadoc for Java.

Examples and docs

See https://ewels.github.io/nf-docs

Quick Start

With uv:

uvx nf-docs generate ./my_pipeline

With pip:

# Install
pip install nf-docs

# Generate HTML documentation
nf-docs generate ./my_pipeline

With Bioconda (requires channel setup):

pixi global install nf-docs
# or
conda install nf-docs

That's it! Open docs/index.html in your browser.

Document a single module

Pass a single .nf file to generate a focused, module-style README:

nf-docs generate modules/mytool/subtools/main.nf --format md

By default this writes README.md next to main.nf. Use --output to pick a different path, or --format json / --format yaml to print structured output to stdout instead.

Prek / pre-commit hook

nf-docs can generate pipeline documentation automatically before each commit using Prek or pre-commit:

repos:
  - repo: https://github.com/ewels/nf-docs
    rev: v0.3.0
    hooks:
      - id: nf-docs

Install the hook into your repo:

# With Prek (recommended)
prek install

# Or with pre-commit
pre-commit install

The hook defaults to nf-docs generate . --format html, which writes HTML output to docs/. Override args in your .pre-commit-config.yaml to use another format or output path:

repos:
  - repo: https://github.com/ewels/nf-docs
    rev: v0.3.0
    hooks:
      - id: nf-docs
        args: [., --format, markdown, --output, docs/api]

Development

See CONTRIBUTING.md for development setup, testing, and contribution guidelines.

License

Apache 2.0 - see LICENSE for details.