MCP Nextflow

🚀 Next-Generation Process Development Tool - MCP

A Model Context Protocol (MCP) server designed for Nextflow development and testing, built with FastMCP.

⚠️ Important Note

This MCP is specifically designed for Nextflow's own development and is not intended for writing Nextflow pipelines.

🚀 Quick Start

Overview

This MCP provides a set of tools for Nextflow development, including:

• Building Nextflow from source code.
• Running tests (integration tests, specific tests, plugin tests).
• Running the development version of Nextflow.
• Managing the Nextflow development directory.
• Accessing Nextflow documentation.

📦 Installation

Prerequisites

• Claude Desktop Application
• Python 3.8+ with pip
• A locally cloned Nextflow code repository

Installing in Claude Desktop using FastMCP

1. Install the FastMCP CLI tool:

pip install fastmcp

2. Clone this repository:

git clone https://github.com/yourusername/nextflow-dev-mcp.git
cd nextflow-dev-mcp

3. Install the MCP in Claude Desktop:

fastmcp install mcp-nextflow.py

This will make the MCP available in the Claude desktop application.

Installing in Cursor using FastMCP

1. Obtain the path to the virtual environment containing the FastMCP CLI tool. If using uv, it is located in the .venv directory.
2. Get the directory where your cloned Nextflow code repository is located.
3. Add the following JSON to Cursor's MCP server configuration:

{
    "mcpServers": {
        "server-name": {
            "command": "/path/to/your/.venv/bin/python",
            "args": [
                "/path/to/your/mcp-nextflow/mcp-nextflow.py"
            ],
            "env": {
                "NEXTFLOW_DIR": "/path/to/your/nextflow"
            }
        }
    }
}

Then, you should be able to use the MCP in Cursor. In Agentic mode, tell the agent to run make test module=plugins:nf-amazon to test the nf-amazon plugin.

Setting Environment Variables

You can specify the Nextflow directory during installation:

NEXTFLOW_DIR=/path/to/your/nextflow fastmcp install mcp-nextflow.py

💻 Usage Examples

Using in Claude

Once installed, you can access the MCP in the Claude desktop application:

1. Open Claude Desktop.
2. Click the Tools menu button in the Claude interface.
3. Select Nextflow Developer Tools from the list of installed MCPs.

Using in Cursor

Cursor is an AI-enhanced code editor that works with Claude. To use the MCP in Cursor:

1. Ensure you have installed the MCP following the steps above.
2. Open your Nextflow project in Cursor.
3. In the chat with Claude, you can reference the MCP:

Use the Nextflow development tools to run integration tests for the nf-amazon plugin.