Bundled documentation

The keywords “MUST”, “MUST NOT”, “SHOULD”, etc. are to be interpreted as described in RFC 2119.

All documentation MUST be bundled with the pipeline code in the main repository, within a directory called docs.

Documentation MUST be hosted only on the nf-core website and GitHub. Hosting the documentation at a second location (such as custom readthedocs website, or GitHub pages) MUST NOT be permitted.

Rationale

This ensures that users of nf-core pipelines can always intuitively find the documentation for all nf-core pipelines in the same way, providing a consistent user experience.

Documentation MUST include at least the following files:

  • README.md
  • docs/usage.md
  • docs/output.md

Additional markdown pages (e.g., tutorials, FAQs) MAY be added under directories called docs/usage/ or docs/output/, and will be automatically rendered on the nf-core website pipeline page as sub-pages of the corresponding section. These will be only listed in the sidebar. Providing links to the sub-pages within the main usage.md or output.md is highly recommended. Markdown files elsewhere in docs/ are not rendered on the website: such a page displays correctly on GitHub but returns a 404 on nf-co.re.