nf-core Claude Code Plugin

A Claude Code plugin for nf-core Nextflow pipeline development. Skills mirror the nf-core CLI structure for intuitive use. Agents handle autonomous tasks like lint fixing, module creation, and code review.

Features

Skills (4)

Skill	Description	Maps to CLI
`pipelines`	Create, lint, schema, sync, and release pipelines	`nf-core pipelines <action>`
`modules`	Create, install, update, patch, and lint modules/subworkflows	`nf-core modules/subworkflows <action>`
`nf-test`	Run and manage nf-test tests	`nf-test`
`best-practices`	Quick reference for nf-core conventions	—

Agents (6)

Agent	Description
`pipeline-explorer`	Explore and analyze pipeline structure (read-only)
`pipeline-architect`	Plan pipeline migrations and refactoring
`lint-fixer`	Autonomously fix lint errors
`nf-core-reviewer`	Review code for nf-core compliance
`test-writer`	Create nf-test tests
`module-creator`	Create new modules from scratch

Hooks

PostToolUse: Validates Nextflow syntax after editing .nf and .config files
PreToolUse: Checks nf-core conventions before writing files

Installation

Option 1: Clone and use directly

git clone https://github.com/jonasscheid/claude-nfcore-plugin.git
claude --plugin-dir ./claude-nfcore-plugin

Option 2: Add to Claude Code settings

Add to your ~/.claude/settings.json:

{
  "enabledPlugins": {
    "/absolute/path/to/claude-nfcore-plugin": true
  }
}

Usage

Once installed, use skills with the /nf-core: prefix:

/nf-core:pipelines lint          # Lint your pipeline
/nf-core:pipelines create        # Create a new pipeline
/nf-core:modules install fastqc  # Install a module
/nf-core:modules create bwa/mem  # Create a new module
/nf-core:nf-test                 # Run tests
/nf-core:best-practices          # View conventions reference

Requirements

Claude Code CLI
Python environment with nf-core tools, nf-test, and Nextflow

Installation Options

Conda/Mamba (Recommended)

mamba create -n nf-core nf-core nf-test nextflow -c conda-forge -c bioconda

pip

pip install nf-core
# nf-test and Nextflow must be installed separately:
# nf-test: curl -fsSL https://get.nf-test.com | bash
# Nextflow: curl -s https://get.nextflow.io | bash

uv pip install nf-core
# nf-test and Nextflow must be installed separately

First-Use Setup

On first skill invocation, you'll be asked which package manager you use. Your preference is stored in nf-core.local.md within the plugin directory and used for all subsequent commands.

nf-core Conventions Enforced

Nextflow Strict Syntax (Q2 2026 Deadline)

Automatic validation of .nf and .config files via hooks
Error detection for removed syntax (for/while loops, switch, imports, etc.)
Warning detection for deprecated patterns (Channel., implicit closures, shell:)

nf-core Best Practices

Lowercase channel. instead of Channel.
Parameter names in snake_case
Boolean parameters with negative naming (skip_X not run_X)
Prefix-based output patterns (path("${prefix}.ext") not path("*.ext"))
PRs target dev branch for nf-core repos

Directory Structure

.
├── .claude-plugin/
│   └── plugin.json       # Plugin manifest
├── agents/               # 6 autonomous agents
├── hooks/
│   └── hooks.json        # Validation hooks
├── scripts/              # Hook scripts
├── shared/               # Reference docs read by skills and agents
│   ├── conventions.md    # nf-core conventions, strict syntax, naming
│   ├── module-template.md # Module structure and templates
│   └── test-patterns.md  # nf-test patterns and assertions
└── skills/               # 4 user-invocable skills
    ├── best-practices/
    ├── modules/
    ├── nf-test/
    └── pipelines/

License

MIT

Name	module-create
Description	Create a new nf-core module from scratch. Use when creating custom modules, wrapping new bioinformatics tools, or contributing modules to nf-core/modules repository.

module-create

SKILL.md