This directory contains the official Nextflow documentation, built with Docusaurus 3.9.2 using the Seqera preset theme.

• Docusaurus 3.9.2: Modern static site generator
• MDX: Markdown with JSX/React component support
• Seqera Preset: Custom Docusaurus theme and configuration
• Node.js 20+: Required runtime environment
• Tailwind CSS: Utility-first CSS framework
• DaisyUI: Component library

cd .docusaurus_site
npm install
npm start

This starts a local development server at http://localhost:3000 with hot reload. Most changes are reflected live without restarting the server.

.docusaurus_site/            # Docusaurus project root
├── docs -> ../docs          # Symlink to the documentation content (at repo root)
├── src/                     # Custom React components and styling
│   └── custom.css           # Custom CSS styles
├── static/                  # Static assets served at root
├── build/                   # Generated static site (git-ignored)
├── docusaurus.config.js     # Main Docusaurus configuration
├── sidebars.js              # Sidebar navigation structure
└── package.json             # Node.js dependencies

docs/                        # Documentation content (.mdx files), at repo root
├── _static/                 # Static assets for documentation pages
├── developer/               # Developer/contributor documentation
├── guides/                  # How-to guides
├── migrations/              # Version migration guides
├── plugins/                 # Plugin documentation
├── reference/               # Language and runtime reference
├── snippets/                # Code snippet examples
└── tutorials/               # Step-by-step tutorials

netlify.toml                 # Netlify deployment configuration (at repo root)

• Use .mdx extension for all documentation files
• MDX supports standard Markdown plus JSX/React components
• Files are automatically processed and converted to HTML pages

• Add new pages to sidebars.js to appear in navigation
• Use relative paths for internal links: [link text](./other-page.mdx)
• Organize pages into categories using the sidebar structure

Docusaurus provides built-in admonitions for callouts:

:::note
This is a note
:::

:::tip
This is a helpful tip
:::

:::warning
This is a warning
:::

:::danger
This is a danger warning
:::

Use custom version tags for tracking feature changes:

<AddedInVersion version="25.10" />
<ChangedInVersion version="25.10" />
<DeprecatedInVersion version="25.04" />

Code blocks support syntax highlighting:

```groovy
workflow {
    println "Hello, Nextflow!"
}
```

Supported languages include: groovy, bash, python, javascript, java, yaml, json, and many more.

• Code snippets under docs/snippets/ are runnable and covered by the docs tests.

• Place images in docs/_static/ or static/
• Reference from docs using relative paths:
  • From docs/_static/: ![alt text](./_static/image.png)
  • From static/: ![alt text](/image.png) (served at root)

We welcome documentation contributions! Please:

1. Fork and create a branch for your changes
2. Test locally using npm run build
3. Follow existing patterns for consistency
4. Update sidebars.js if adding new pages
5. Check spelling and grammar
6. Submit a pull request with a clear description

See the main CONTRIBUTING.md for general contribution guidelines.

1. Clear the cache: npm run clear
2. Reinstall dependencies: rm -rf node_modules && npm install
3. Check for syntax errors in MDX files
4. Verify all internal links are correct

1. Restart the development server
2. Clear browser cache
3. Check for JavaScript errors in browser console

1. Ensure custom CSS imports in docusaurus.config.js
2. Check Tailwind configuration
3. Clear Docusaurus cache

Ensure you're using Node.js 20 or higher:

node --version

Nextflow documentation is distributed under the Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0) license.