nf-core MCP Server

An MCP server for managing and navigating nf-core pipeline repositories.

Features

List local nf-core repositories (rnaseq, sarek, modules, tools)
Access pipeline configurations and workflows
Search through pipeline files
Explore pipeline modules

Installation

NPM Version

cd nf-core_mcp npm install # Build TypeScript npm run build # Start the server npm start

Docker Version

# Build the Docker image cd nf-core_mcp docker build -t nf-core-mcp . # Run the container docker run -i --rm \ -v "/path/to/your/workspace:/app/workspace" \ nf-core-mcp

Adding nf-core Repositories

To add new nf-core pipeline repositories to the workspace:

Clone the repositories:
# Navigate to your workspace directory (example for Windows) cd /path/to/your/workspace # Clone desired nf-core repositories git clone https://github.com/nf-core/rnaseq.git git clone https://github.com/nf-core/sarek.git git clone https://github.com/nf-core/modules.git # Add any other nf-core pipeline you want to manage
Directory Structure: Your workspace should look like this:
workspace/ ├── rnaseq/ ├── sarek/ ├── modules/ └── your-new-pipeline/
Verify Installation: After starting the MCP server, use the list-pipelines command to verify that your new pipelines are detected:
list-pipelines

Note: The MCP server will automatically detect and manage any nf-core pipeline repositories in your workspace directory.

Available Tools

list-pipelines
- Lists all nf-core pipelines in the workspace
- Shows configuration file status
- No parameters required
get-pipeline-modules
- Gets module information from a pipeline
- Parameters:
  - pipeline: Pipeline name (rnaseq, sarek, or modules)
search-pipelines
- Searches through pipeline files
- Parameters:
  - query: Search query
  - pipeline (optional): Specific pipeline to search

Available Resources

pipeline-config
- Gets pipeline configuration
- URI format: pipeline://{name}/config
- Parameters:
  - name: Pipeline name (rnaseq, sarek, or modules)
pipeline-workflow
- Gets pipeline workflow
- URI format: pipeline://{name}/workflow
- Parameters:
  - name: Pipeline name (rnaseq, sarek, or modules)

Usage with Cursor IDE

Using NPX (Recommended)

Add the following to your mcp.json:

{ "mcpServers": { "nf-core": { "command": "npx", "args": ["-y", "nf-core-mcp"] } } }

Using Docker

Add the following to your mcp.json:

{ "mcpServers": { "nf-core": { "command": "docker", "args": [ "run", "-i", "--rm", "-v", "/path/to/your/workspace:/app/workspace", "nf-core-mcp" ] } } }

Example Usage

Using the MCP server in Cursor:

# List available pipelines list-pipelines # Get modules from rnaseq pipeline get-pipeline-modules pipeline=rnaseq # Search in all pipelines search-pipelines query="fastqc" # Search in specific pipeline search-pipelines query="fastqc" pipeline=rnaseq # Access pipeline configuration pipeline://rnaseq/config # Access workflow pipeline://rnaseq/workflow

Running the Server

Using NPM

# If installed globally nf-core-mcp # If installed locally npx nf-core-mcp # Using npx without installation npx -y nf-core-mcp

Using Docker

docker run -it --rm \ -v /path/to/your/workspace:/app/workspace \ nf-core-mcp

Development

# Install dependencies npm install # Build TypeScript npm run build # Run in development mode npm run dev # Run tests npm test # Run linter npm run lint