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