New RFC: `AGENTS.md` and AI steering document

Have you read the RFC docs?

• Yes, I have read and understood the RFC docs

Summary

AI agents are an increasingly used tool in software development, and Nextflow pipelines are no exception. As it stands, nf-core has some guidance on AI use, but no specific steering files for AI agents. This RFC proposes introducing a minimal AGENTS.md file to the template, as well as a larger remote steering file, to ensure agents have a basic understanding of nf-core best practices when working in template-based repositories.

Champion

@itrujnara

Background & Motivation

AI agents are systems that combine a Large Language Model with multiple deterministic tools to partially or fully automate software development. Apart from the user's prompts, they rely on several types of fixed input (steering files), including project instructions and skills. While there are differences in how agents from different vendors discover these files, AGENTS.md (https://agents.md/) has become a de facto standard. All popular agents are now set up to read this file before working in a directory.
nf-core currently has no specific AGENTS.md or other agent steering files. This requires extra work from developers to ensure that the agent output complies with nf-core standards, and creates room for divergence in practices. To promote uniformity and reduce the issue of non-compliant AI contributions, it would be prudent to introduce some basic guidance into the template, so that it affects every project automatically after the next update.
Concerns have been rightly raised about keeping the main steering file up to date, given the limited template release schedule and the dynamic nature of the AI sector. To address that, we propose to introduce a minimal AGENTS.md, consisting mostly of references to other, more updateable files.
Some community members have argued that CONTRIBUTING.md is a sufficient file to guide agents as well as human programmers. While this file is valuable, it is not automatically introduced into agent context, and thus should be explicitly included by reference. Furthermore, it is optimized for humans, so agent guidance should extend beyond this file.
There was previously an RFC on this topic, but it has gone stale months ago.

Goals

• Add a minimal AGENTS.md to the template, with references to CONTRIBUTING.md and other steering files
• Add a general AGENTS_nfcore.md to a public repository (website or otherwise), referenced by AGENTS.md
• Add a pipeline-specific AGENTS_[pipeline].md to the template, initially near-empty, intended for pipeline-specific coding standards and referenced by the main AGENTS.md

Non-Goals

• Overload the template with extensive agent steering (e.g. skills); this should be handled with an extension
• Create lag and/or undue maintenance burden; all steering files should be updateable with a simple PR

References

• Previous RFC: https://github.com/nf-core/proposals/issues/61
• Slack discussion 1 (#rfc-suggestions): https://nfcore.slack.com/archives/C08TXM0GGMT/p1779271876671859
• Slack discussion 2 (#team-maintainers): https://nfcore.slack.com/archives/C043UU89KKQ/p1779271926707799
• General information on AGENTS.md: https://agents.md/
• Module developer Claude extension: https://github.com/vagkaratzas/nf-core-module-dev

Start by reviewing the proposed AGENTS.md, CONTRIBUTING.md, AGENTS_nfcore.md, and AGENTS_[pipeline].md files, along with the previous RFC and linked discussions. Clarify the file locations, references, maintenance approach, and template integration. Done means the community has agreed on a concrete, maintainable proposal.