Nf-core tools MCP (Unofficial)
About
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…
Details
- Author
- FloWuenne
- GitHub stars
- 1
- Downloads
- 122
- Categories
- Other
Jump to
- 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
Setting up with Highlight
This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:
- Download and install Highlight from highlightai.com/download
- Navigate to the plugins tab and select "Add Custom Plugin"
-
Configure the plugin with the settings below
Plugin Name
Nf-core tools MCP (Unofficial)Command (node, npx, python, etc.)Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
- Enable "Start Automatically" if you want the plugin to start when Highlight launches
From the repository
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.
Claude Desktop / Cursor
Paste into your MCP client config file to install this server.
{
"mcpServers": {
"nf-core tools mcp (unofficial)": {
"mcp-nf-core": {
"command": "uv",
"args": [
"venv"
]
}
}
}
}McpServers
{
"mcp-nf-core": {
"command": "uv",
"args": [
"venv"
]
}
}Nf-core tools MCP (Unofficial)
A repo to experiment with MCP capabilities for nf-core tools functions.Overview
This MCP provides a suite of tools for accessing nf-core tools for pipelines and modules:
- Create a pipeline using the nf-core template
- List nf-core modules
- Create a module using the nf-core modules template
- Install existing nf-core modules into your pipeline or modules repo
For testing purposes, tools were implemented from the command line (cli) and directly from the python package (python). Two different MCP server files exist for these two implementations:
1) nf-core.test-server.cli.py
2) nf-core.test-server.python.py
Installation
- Claude Desktop App
- Uv
- nf-core tools
Installing with FastMCP to use in Claude Desktop
1) Create a venv with uv:
uv venv
2) Activate the environment:
source .venv/bin/activate
3) Add required packages:
uv add "mcp[cli]" nf-core
4) Install the server
fastmcp install nf-core.test-server.cli.py ## CLI server
fastmcp install nf-core.test-server.python.py ## Python based server
Adding server to Cursor
{
"mcpServers": {
"mix_server": {
"command": "uv",
"args": [
"--directory",
"[Full path to the server directory (this repo folder)]]",
"run",
"server.py"
]
}
}
}
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