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Nextflow Developer Tools MCP Server

Provides development tooling to build, test, and run Nextflow from source via an MCP interface.

Installation

Add the following to your MCP client configuration file.

Configuration

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

You can run Nextflow development and testing tasks through an MCP server built with FastMCP. This server helps you build Nextflow from source, run tests, and execute the development version of Nextflow from within Claude Desktop or Cursor, using a simple MCP client workflow.

How to use

You will interact with the MCP using an MCP client. Start by installing the MCP client and then connect to the Nextflow development MCP. In Claude Desktop, open the Tools menu and select Nextflow Developer Tools to access the server. In Cursor, ensure the MCP is installed, open your Nextflow project, and reference the MCP in a chat to run actions like building, testing, or running the development version of Nextflow.

How to install

Prerequisites include the Claude Desktop App, Python 3.8 or newer with pip, and a locally cloned Git repository for Nextflow development.

Install the FastMCP CLI tool and set up the MCP in Claude Desktop.

pip install fastmcp
```

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

```
fastmcp install mcp-nextflow.py

Additional configuration and usage notes

To run the MCP from Cursor, prepare a Python invocation that points to the MCP script and sets the development directory via NEXTFLOW_DIR. This enables Cursor to execute make test and other Nextflow development tasks through the MCP.

Environment variables used by the MCP example include NEXTFLOW_DIR, which should point to your Nextflow development directory.

Available tools

build Nextflow from source

Trigger the build process to compile Nextflow from its source code so you can run the development version locally.

run integration tests

Execute integration tests to verify that the development environment works as expected.

run specific tests

Run targeted tests, such as plugin tests, to validate individual components during development.

run development Nextflow

Launch the development version of Nextflow for experimentation and debugging.

manage development directory

Handle the Nextflow development directory, including updates and cleanup as you iterate on changes.

access Nextflow docs

Open or fetch Nextflow documentation relevant to the current development task.