Nf-core tools MCP
by FloWuenne
This MCP provides a suite of tools for accessing nf-core tools for pipelines and modules. It allows users to create pipelines and modules, list nf-core modules, and install existing modules into their projects.
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What is Nf-core tools MCP?
This MCP (Meta-Compute Provider) is an experimental tool designed to integrate nf-core tools functionalities. It provides command-line and Python-based interfaces for managing nf-core pipelines and modules.
How to use Nf-core tools MCP?
To use this MCP, you need to install the required dependencies (Claude Desktop App, Uv, nf-core tools). Then, create a virtual environment using Uv, activate it, and add the necessary packages ('mcp[cli]' and nf-core). Finally, install the desired server (CLI or Python-based) using fastmcp install.
Key features of Nf-core tools MCP
Create nf-core pipelines from templates
List available nf-core modules
Create nf-core modules from templates
Install existing nf-core modules into pipelines or module repositories
Use cases of Nf-core tools MCP
Automating nf-core pipeline creation
Managing nf-core modules in a project
Integrating nf-core tools into a workflow
Experimenting with nf-core functionalities
FAQ from Nf-core tools MCP
What is nf-core?
What is nf-core?
nf-core is a community effort to collect a curated set of analysis pipelines built using Nextflow.
What is MCP?
What is MCP?
MCP stands for Meta-Compute Provider. In this context, it acts as a server to provide nf-core tools functionalities.
Which server should I use, CLI or Python?
Which server should I use, CLI or Python?
The choice depends on your preference. The CLI server uses command-line tools, while the Python server uses the Python package directly.
How do I add the server to Cursor?
How do I add the server to Cursor?
You can add the server to Cursor by configuring the mcpServers section in your Cursor settings, providing the command and arguments to run the server.
Where can I find more information about nf-core tools?
Where can I find more information about nf-core tools?
You can find more information on the official nf-core tools GitHub repository: https://github.com/nf-core/tools