M

MCP Nf Core

An experimental nf-core tools MCP project that provides functions such as pipeline creation and module management
2 points
39

What is the Nf-core Tools MCP Server?

This is an experimental server based on the Model Context Protocol (MCP) that specifically provides interface services for nf-core tools. It allows users to access the functions of nf-core through a standardized protocol, including creating analysis workflows and managing modules.

How to use the Nf-core Tools MCP Server?

You can connect to this MCP server through the Claude desktop application or the Cursor editor. After installation and configuration, you can call various functions of the nf-core tools through the standard interface.

Use cases

Suitable for bioinformatics researchers and data analysts, especially those who use the nf-core framework to build standardized analysis workflows.

Main features

Create an analysis workflowCreate a new bioinformatics analysis workflow using the nf-core template
List modulesView all available nf-core modules
Create a moduleCreate a new analysis module using the nf-core module template
Install a moduleInstall an existing nf-core module into your workflow or module repository

Advantages and limitations

Advantages
Provide a standardized interface to access the functions of nf-core tools
Support two implementation methods (CLI and Python package)
Easy to integrate into existing workflows
Simplify the usage process of nf-core tools
Limitations
Currently an experimental implementation, and the functions may be unstable
Require pre - installation of nf-core tools and related dependencies
May have a learning curve for non - technical users

How to use

Create a virtual environment
Create a Python virtual environment using the uv tool
Activate the environment
Activate the newly created virtual environment
Install dependencies
Install the required Python packages
Install the server
Select and install the server implementation that suits your needs

Usage examples

Create a new analysis workflowUse the MCP server to create a new bioinformatics analysis workflow through the nf-core template
Install an existing moduleInstall an existing nf-core module into your project

Frequently Asked Questions

What is the difference between the CLI and Python implementation methods?
What software do I need to install in advance?
What nf-core functions does this MCP server support?

Related resources

Claude desktop application
The client application required to connect to the MCP server
uv package manager
A fast Python package management tool
nf-core tools
The official nf-core tool library
Installation
Copy the following command to your Client for configuration
Note: Your key is sensitive information, do not share it with anyone.
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