RFC stage 3: AGENTS.md and agent steering#143
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ewels
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ewels
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Nice! Made a few minor suggested changes but all small potatoes.
I wonder if a simpler repo name would be nf-core/agents, but maybe it's just because I'm allergic to hyphens in repository names 🤧 😆
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| The pipeline-specific section contains any standards and practices specific to a given pipeline. Developing it and keeping it up to date is the resposibility of the maintainers of the pipeline. This section should not recapitulate any general nf-core standards. | ||
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| `nf-core/modules` may utilize this section to explain the specifics of the repository. |
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I think this confuses things a bit, as nf-core/modules doesn't use the pipeline template.
Instead, better to have a separate section of the RFC specifically for non-pipeline nf-core repositories. Modules is one of them, see also website, tools, even proposals 😅 All could / perhap should have a comparable AGENTS.md but it'll have to be created one by one.
| - commit and PR discipline (scopes, message format), | ||
| - pre-commit routine (linting, tests, prek), | ||
| - self-disclosure rules for fully autonomous agents, | ||
| - references to nf-core documentation as required. |
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It might be nice for the file to be fairly minimal and have separate skill files for all of these things, revealed with progressive disclosure. Some may be better as dedicated skills.
Not sure that the RFC really has to go into this detail, but thought I'd mention it here whilst thinking about it.
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Skills are deliberately out of scope for this RFC, but I expect them to be considered in some fashion soon
| - a description of nf-core tools, list of commands, and examples for the most common operations in pipeline development, | ||
| - a description of nf-test and basic testing concepts, | ||
| - commit and PR discipline (scopes, message format), | ||
| - pre-commit routine (linting, tests, prek), |
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both nf-core and nextflow strict sntax lints
Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
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I have addressed the first batch of comments. I like the ring of |
JoseEspinosa
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JoseEspinosa
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Very nice! I just made a few minor suggestions but really anything important.
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| 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. | ||
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| There was previously an RFC on this topic, but it has gone stale months ago. |
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Might be nice to reference it
| There was previously an RFC on this topic, but it has gone stale months ago. | |
| There was previously an [RFC](https://github.com/nf-core/proposals/issues/61) on this topic, but it has gone stale months ago and thus "closed as not planned". |
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I saw now that is referenced at the end, but maybe still we can keep it the link here
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| This RFC does not specify a rigid structure or contents, but the following elements will tentatively be included (in some order): | ||
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| - a treemap of the template with explanations of directories and files, |
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I have a couple of suggestions here, but not sure whether they are already superficially covered by this point for the two first items (treemap):
- How the different configs relate to each other.
- How nf-core uses workflows, subworkflows and modules.
- Common Nextflow pitfalls to avoid (this actually could be a different file linked to it).
- Meta map convention (as it is very nf-core specific.
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Summary
This is the stage 3 PR for the
AGENTS.mdand steering RFC (approved on 2026-05-28 at #141).This RFC adds a minimal
AGENTS.mdto the pipeline template and a comprehensive remoteAGENTS.mdhosted in a new repository.Companion implementation PRs
None yet, will be added in due course
This RFC should only be merged after the implementation plan is completed and all companion PRs are closed.
Review plan
The content of the files will be discussed in the companion PRs.