Introducing nf-core docs version 2
Good documentation is the quiet backbone of any thriving open-source community. It’s what helps a newcomer run their first pipeline, guides a developer through a tricky edge case, and gives a contributor the confidence to open their first pull request.
Documentation has been a pain point for the nf-core community. At the Barcelona Summit 2025, we announced an initiative to rebuild the nf-core documentation from the ground up, rather than incrementally reorganise things while the wheels were still turning.
Thank you to everyone who flagged issues with the old documentation and contributed to this effort, especially those who joined the documentation team during the March 2026 hackathon: Meng Yuan, Fadinda Shafira, Jen Reeve, Manasvi Ghonge, Mrunali Thokadiwala, Kurayi Chawatama, Jess Kan, Peter Smith, Matthias Hörtenhuber, Priyal Tripathi, Saurabh, Iris, Beumjin, @ihlee-1014, and nf-core-bot.
We are excited to share that the initial migration of the docs is complete, and we have shipped the new and improved version.
What’s changed?
The most visible changes are refreshed landing pages and a clearer structure, which organises content into seven focused sections:
- Getting Started: Learn the basics and run your first pipeline
- Running: Run and configure nf-core pipelines
- Developing: Create and maintain pipelines using the nf-core template, components, and configs
- Contributing: Contribute to the nf-core community
- Specifications: Technical specifications for nf-core pipelines, components, and test data
- Community: Community resources and guidelines
- nf-core/tools: Command line tools and API for working with nf-core
Beyond structure, the content itself has been refreshed, with our brand-new style guide front of mind. Pages are more targeted and less verbose. We’ve tried to give each piece of content a clear purpose, whether that’s a how-to guide, a conceptual explanation, or a reference. While some content is new, other pieces have been rewritten to better fit their intended format.
A note on broken links
Rebuilding from scratch inevitably means that URLs have changed. We’ve put significant effort into adding redirects to carry over as many existing links as possible, but given the scale and complexity of the restructure, we expect this will cover ~95% of old pages. However, some links, particularly those shared in older issues, forum posts, or external resources, may no longer work as expected.
If you land on a 404, we’re sorry for the inconvenience.
The best course of action is to use the new navigation or search to find what you’re looking for, and if something important seems to be missing entirely, drop us a message in the #documentation channel or create a GitHub issue so we can investigate.
If you are looking for older documentation, you can access it on our archival site.
We’re not done yet
We want to be upfront: there are still gaps. Rebuilding documentation from scratch is a significant task, and we made a conscious decision to ship something solid and lay the foundation rather than wait for perfection. We know there are areas that need more depth, pages that still need to be written, and corners of the ecosystem that aren’t yet well represented.
Our plan is to continue identifying these gaps, prioritise them with input from you, the community, and work through them steadily. This is an ongoing project, not a one-time release.
Documentation is a team sport. If you spot something that’s unclear, outdated, or just plain missing, please let us know. Open an issue, suggest an edit, or contribute a page. Whether you’re a long-time pipeline developer, an occasional contributor, or someone who just ran their first nf-core pipeline, your perspective is valuable and helps us improve the docs.
We’re also always open to broader feedback. If something about the structure or content doesn’t work for the way you use nf-core, let us know on the #documentation channel.
We are always looking for more team members to help maintain and improve the nf-core documentation!
If you’re interested in joining the documentation team, reach out on the #documentation Slack channel or slide into our DMs.
