What is the Nextflow Developer Tools MCP?

The Nextflow Developer Tools MCP (Model Context Protocol) server is designed to streamline Nextflow development and testing. It provides tools for building Nextflow from source, running tests, managing development versions, and accessing documentation.

Who is this MCP intended for?

This MCP is specifically designed for developers working on the Nextflow project itself, rather than for writing Nextflow pipelines.

What are the prerequisites for installing this MCP?

• Claude Desktop App or Cursor
• Python 3.8+ with pip
• Git repository of Nextflow (cloned locally)

How do I install the MCP for use with Claude Desktop?

1. Install the FastMCP CLI tool using pip install fastmcp.
2. Clone the MCP repository.
3. Run fastmcp install mcp-nextflow.py in the cloned repository.

How do I install the MCP for use with Cursor?

1. Locate the virtual environment path containing the FastMCP CLI.
2. Get the directory of your Nextflow cloned repository.
3. Add the provided JSON configuration to Cursor’s MCP servers settings, adjusting the paths to match your environment.

What environment variables do I need to set?

The most important environment variable is NEXTFLOW_DIR, which should point to the directory where you have cloned the Nextflow repository. You can set this during installation or in your shell environment.

How do I use the MCP with Claude?

Once installed, you can access the MCP from the Tools menu in the Claude Desktop app. Select ‘Nextflow Developer Tools’ to access the available functionalities.

How do I use the MCP with Cursor?

Open your Nextflow project in Cursor and interact with Claude in a chat. You can reference the MCP in your prompts, for example: “Using the Nextflow Developer Tools, run the integration tests for the nf-amazon plugin.”

What can I do with this MCP?

You can use it to build Nextflow from source, run various tests (integration, specific, plugin), manage development versions, and access documentation. It aims to simplify and accelerate the Nextflow development process.

Can I use this MCP to develop Nextflow pipelines?

No, this MCP is designed for developing Nextflow itself, not for writing Nextflow pipelines. It provides tools for those contributing to the Nextflow project.