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Nf-core tools MCP (Unofficial)

@FloWuenne

Repository

Basic information

Category

Other

Transports

stdio

Author

FloWuenne

About Nf-core tools MCP

Unofficial MCP server for nf-core tools.

Nf-core tools MCP config

Add this server to your MCP-compatible client using the configuration below.

{
  "mcpServers": {
    "mcp-nf-core": {
      "command": "uv",
      "args": [
        "venv"
      ]
    }
  }
}

Nf-core tools MCP tools

Tool list not available yet

This listing does not currently have a tool list to display. This does not mean the server has no tools; check its documentation for supported capabilities.

We auto-extract tools from the README. The maintainer can list them under a ## Tools heading to populate this section.

Overview

What is Nf-core tools MCP (Unofficial)?

This is an experimental MCP (Model Context Protocol) server that provides programmatic access to key nf-core tools functions. It allows users to create pipelines, list and create modules, and install existing modules—all through MCP-compatible clients like Claude Desktop or Cursor. It is designed for nf-core developers and bioinformaticians who want to integrate nf-core workflows into AI-assisted environments.

How to use Nf-core tools MCP (Unofficial)?

Installation requires Claude Desktop or Cursor, Uv, and nf-core tools. Create a virtual environment with uv venv, activate it, then add packages with uv add "mcp[cli]" nf-core. Finally, install one of the two server files using fastmcp install nf-core.test-server.cli.py (CLI-based) or fastmcp install nf-core.test-server.python.py (Python-based). To add the server to Cursor, configure a JSON entry pointing to the repo directory with uv run server.py.

Key features of Nf-core tools MCP (Unofficial)

  • Create a pipeline using the nf-core template
  • List available nf-core modules
  • Create a module using the nf-core modules template
  • Install existing nf-core modules into a pipeline or modules repo
  • Two implementations: CLI-based and Python-based
  • Integrates with Claude Desktop and Cursor via MCP

Use cases of Nf-core tools MCP (Unofficial)

  • Bootstrapping a new nf-core pipeline without leaving an MCP client
  • Browsing the nf-core modules registry and installing modules into an existing pipeline
  • Automating module creation during pipeline development workflows
  • Experimenting with MCP capabilities for nf-core tooling in AI-assisted environments

Frequently asked questions

1

What does Nf-core tools MCP (Unofficial) do?

It provides MCP-compatible tools that wrap nf-core command-line functions, enabling users to create pipelines, list and create modules, and install modules directly from MCP clients.

2

What are the prerequisites for using this server?

You need Claude Desktop or Cursor, [Uv](https://pypi.org/project/uv/), and [nf-core tools](https://github.com/nf-core/tools) installed on your system.

3

How do I install the server?

Create a virtual environment with `uv venv`, activate it, add the required packages (`uv add "mcp[cli]" nf-core`), then run `fastmcp install` with either the CLI or Python server file.

4

What are the two server implementations?

The CLI-based server (`nf-core.test-server.cli.py`) calls nf-core commands via subprocess, while the Python-based server (`nf-core.test-server.python.py`) uses the nf-core Python package directly. Both provide identical tools.

5

Is this an official nf-core project?

No, this is an unofficial experiment by the repository author to explore MCP capabilities for nf-core tools functions.

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