MCP Nf Core

🚀 Nf-core Tool MCP (Unofficial)

A MCP repository for experimenting with the features of the nf-core tool.

🚀 Quick Start

✨ Features

This MCP provides a set of tools to access nf-core tools for pipelines and modules:

• Create pipelines using the nf-core template.
• List nf-core modules.
• Create modules using the nf-core module template.
• Install existing nf-core modules into your pipeline or module repository.

For testing purposes, these tools are implemented both from the command line (CLI) and directly from the Python package. There are two different MCP server files for these two implementations:

1. nf-core.test-server.cli.py
2. nf-core.test-server.python.py

📦 Installation

• Claude Desktop App
• Uv
• nf-core tools

Install in Claude Desktop using FastMCP

1. Create a virtual environment with uv:

uv venv

2. Activate the environment:

source .venv/bin/activate

3. Add the required packages:

uv add "mcp[cli]" nf-core

4. Install the servers:

fastmcp install nf-core.test-server.cli.py ## CLI-based server
fastmcp install nf-core.test-server.python.py ## Python-based server

Add the server to Cursor

{
  "mcpServers": {
    "mix_server": {
      "command": "uv",
      "args": [
        "--directory",
        "[Full path to the server directory (this repository folder)]",
        "run",
        "server.py"
      ]
    }
  }
}