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nf-core MCP Server

nf-core MCP Server

Public
wjlim/nf-core_mcp

Manage and navigate nf-core pipeline repositories with an MCP server offering pipeline listing, configuration access, workflow exploration, module details, and powerful search capabilities.

typescript
0 tools
May 29, 2025
Updated Jun 4, 2025

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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:

  1. 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
  2. Directory Structure: Your workspace should look like this:

    workspace/
    ├── rnaseq/
    ├── sarek/
    ├── modules/
    └── your-new-pipeline/
    
  3. 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

  1. list-pipelines

    • Lists all nf-core pipelines in the workspace
    • Shows configuration file status
    • No parameters required
  2. get-pipeline-modules

    • Gets module information from a pipeline
    • Parameters:
      • pipeline: Pipeline name (rnaseq, sarek, or modules)
  3. search-pipelines

    • Searches through pipeline files
    • Parameters:
      • query: Search query
      • pipeline (optional): Specific pipeline to search

Available Resources

  1. pipeline-config

    • Gets pipeline configuration
    • URI format: pipeline://{name}/config
    • Parameters:
      • name: Pipeline name (rnaseq, sarek, or modules)
  2. 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

License

MIT

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