How do I install the mcp nextflow mcp server?

Use a recorded configuration for your client, replace example credential values and paths, and verify the documented runtime. Restart or reconnect the client, then inspect the available tools.

What credentials does it need?

It reads `NEXTFLOW_DIR` from the environment. Store these in your client's env block or a secrets manager — never commit them to a repository — and grant the narrowest scope that still covers your use case.

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MCP Nextflow MCP Server

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

Local serverstdioPython

What is the MCP Nextflow MCP Server?

MCP Nextflow lets Claude, Cursor and other MCP clients work with MCP Nextflow directly. A Model Context Protocol (MCP) server designed for Nextflow development and testing, built with FastMCP.

What MCP Nextflow does

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

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

Requirements

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

Practical notes

Maintained by adamrtalbot, written in Python.

More MCP options

Compare MCP servers by category, or browse hosted MCP servers if you prefer an endpoint over a local process.

Maintainer setup documentation.

How to install the MCP Nextflow MCP Server

{
  "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"
      }
    }
  }
}

From the project documentation. Replace placeholders and example paths before connecting.

Configuration

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

Variable	Description	Required
NEXTFLOW_DIR	Declared in the maintainer’s client configuration.	Check documentation

Example prompts to try

“Use MCP Nextflow to Prerequisites.”

Frequently asked questions

A Model Context Protocol (MCP) server designed for Nextflow development and testing, built with FastMCP. Confirm the tools offered by your installed version in the connected client. Tool availability and permissions depend on the server and account configuration.