nf-core

nf-core-skills

Agent Skills for nf-core — Nextflow pipelines, modules, subworkflows, and the nf-core toolchain.

These skills follow the Agent Skills specification so they can be used by any skills-compatible agent, including Claude Code, Codex CLI, OpenCode, and Cursor.

Will eventually live at nf-core/skills.

Installation

Claude Code

/plugin marketplace add nf-core/skills
/plugin install nf-core@nf-core-skills

Codex CLI

Copy the skills/ directory into your Codex skills path (typically ~/.codex/skills).

OpenCode

Clone the repository into the OpenCode skills directory:

git clone https://github.com/nf-core/skills.git ~/.opencode/skills/nf-core-skills

OpenCode auto-discovers SKILL.md files under ~/.opencode/skills/.

Cursor

Place the repository contents under .cursor/skills/ in your project (or globally where Cursor reads skills from).

Manual

Drop the skills/ directory contents into any agent harness that follows the Agent Skills specification.

Skills

Skill	Description
nf-core-pipeline	Create and modify nf-core pipelines following community standards
nf-core-lint	Run and interpret nf-core pipelines lint to validate pipeline compliance

Development

This repo uses prek to validate skills before commit. Install hooks once:

prek install

Run one hook:

prek run <hook-id> --all-files

Run all hooks:

prek run --all-files

Shared cross-agent hook IDs:

• guard-nfcore-modules
• lint-schema
• check-param-drift
• lint-local-module
• check-nftest-exists
• check-changelog

See prek.toml for the configured checks, AGENTS.md for the agent-facing map, and docs/ARCHITECTURE.md for the layout.

The design follows OpenAI's harness engineering principles: a small AGENTS.md table of contents, mechanical enforcement of repo structure, and progressive disclosure of detail.

License

MIT — see LICENSE.