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