Running nf-docs

Generate docs

nf-docs generate PIPELINE_PATH [OPTIONS]

# HTML — single shareable file
nf-docs generate . -f html -o site/

# Markdown — for static site generators
nf-docs generate . -f markdown -o docs/

# JSON — pipe to file or other tools
nf-docs generate . -f json > api.json

# Table — compact terraform-docs-style tables
nf-docs generate . -f table -o docs/

Other commands

# Print a summary without generating full docs
nf-docs inspect /path/to/pipeline

# Pre-download the Language Server JAR
nf-docs download-lsp

# Clear the extraction cache for a specific pipeline
nf-docs clear-cache /path/to/pipeline

# Clear the entire extraction cache
nf-docs clear-cache --all

Caching

nf-docs caches extraction results to avoid re-running the Language Server on every invocation. Cached data is stored in ~/.cache/nf-docs/ (respects $XDG_CACHE_HOME).

The cache is keyed by pipeline path, a SHA-256 hash of all pipeline source files, and the nf-docs version, so it is automatically invalidated whenever files change or nf-docs is upgraded.

Use --no-cache to skip the cache for a single run, or nf-docs clear-cache to remove entries manually.

Output formats

HTML

A single self-contained file with everything inlined:

• Three-column responsive layout with full-text search
• Deep linking to every section and item
• Source code links (GitHub, GitLab, Bitbucket)
• nf-core module documentation links
• Dark mode · mobile-friendly

Markdown

A directory of files, one per section:

docs/
├── index.md        # Pipeline overview
├── inputs.md       # Input parameters
├── config.md       # Config parameters
├── workflows.md    # Workflows
├── processes.md    # Processes
└── functions.md    # Functions

Table

A single README.md with compact Markdown tables — inspired by terraform-docs.

Supports marker-based injection into existing README files:

# My Pipeline

Some intro text.

<!-- BEGIN_NF_DOCS -->
<!-- END_NF_DOCS -->

Other content below.

Running nf-docs generate . -f table -o . will inject the generated tables between the markers, leaving the rest of the file untouched.

Selective sections with template tags

Control which sections appear by adding {{ section }} placeholders between the markers:

<!-- BEGIN_NF_DOCS -->

{{ inputs }}

{{ config }}

<!-- END_NF_DOCS -->

Available tags: {{ header }}, {{ inputs }}, {{ config }}, {{ workflows }}, {{ processes }}, {{ functions }}.

If no tags are present, all sections are rendered (the default).

JSON / YAML

Structured data for programmatic use, CI/CD pipelines, or custom tooling.

See the examples to get a feel for the structure.