nf-core

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: Load persistently via shell alias

To avoid passing --plugin-dir every time:

alias claude='claude --plugin-dir /absolute/path/to/claude-nfcore-plugin'

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

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

Links

• nf-core
• nf-core/tools
• Claude Code Documentation
• Claude Code GitHub