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nf-core MCP Server

by wjlim

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

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

Install Server
A
security – no known vulnerabilities
F
license - not found
A
quality - confirmed to work

local-only server

The server can only run on the client's local machine because it depends on local resources.

사용자가 nf-core 생물정보학 파이프라인 저장소를 관리하고 탐색할 수 있도록 하여 파이프라인 구성, 워크플로 및 모듈에 대한 목록, 검색 및 탐색 작업을 수행할 수 있습니다.

  1. 특징
    1. 설치
      1. NPM 버전
      2. 도커 버전
    2. nf-core 저장소 추가
      1. 사용 가능한 도구
        1. 사용 가능한 리소스
          1. 커서 IDE와 함께 사용
            1. NPX 사용(권장)
            2. Docker 사용
          2. 사용 예
            1. 서버 실행
              1. NPM 사용하기
              2. Docker 사용
            2. 개발
              1. 특허

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