用于管理和导航 nf-core 管道存储库的 MCP 服务器。
列出本地 nf-core 存储库（rnaseq、sarek、模块、工具）
访问管道配置和工作流程
搜索管道文件
探索管道模块
Related MCP server: Bio-OS MCP Server
cd nf-core_mcp
npm install
# Build TypeScript
npm run build
# Start the server
npm start# 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要将新的 nf-core 管道存储库添加到工作区：
克隆存储库：
# 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目录结构：您的工作区应如下所示：
workspace/
├── rnaseq/
├── sarek/
├── modules/
└── your-new-pipeline/验证安装：启动 MCP 服务器后，使用list-pipelines命令验证是否检测到新管道：
list-pipelines注意：MCP 服务器将自动检测并管理工作区目录中的任何 nf-core 管道存储库。
list-pipelines
列出工作区中的所有 nf-core 管道
显示配置文件状态
无需参数
get-pipeline-modules
从管道获取模块信息
参数：
pipeline ：管道名称（rnaseq、sarek 或模块）
search-pipelines
搜索管道文件
参数：
query ：搜索查询
pipeline （可选）：要搜索的特定管道
pipeline-config
获取管道配置
URI 格式： pipeline://{name}/config
参数：
name ：管道名称（rnaseq、sarek 或模块）
pipeline-workflow
获取管道工作流程
URI 格式： pipeline://{name}/workflow
参数：
name ：管道名称（rnaseq、sarek 或模块）
将以下内容添加到您的mcp.json中：
{
"mcpServers": {
"nf-core": {
"command": "npx",
"args": ["-y", "nf-core-mcp"]
}
}
}将以下内容添加到您的mcp.json中：
{
"mcpServers": {
"nf-core": {
"command": "docker",
"args": [
"run",
"-i",
"--rm",
"-v",
"/path/to/your/workspace:/app/workspace",
"nf-core-mcp"
]
}
}
}在 Cursor 中使用 MCP 服务器：
# 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# If installed globally
nf-core-mcp
# If installed locally
npx nf-core-mcp
# Using npx without installation
npx -y nf-core-mcpdocker run -it --rm \
-v /path/to/your/workspace:/app/workspace \
nf-core-mcp# 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麻省理工学院
Unclaimed servers have limited discoverability.
If you are the server author, to access and configure the admin panel.
Create, browse, remix, collaborate on, and run durable AI workflow nodes from MCP hosts.
Connect AI assistants to GitHub - manage repos, issues, PRs, and workflows through natural language.
Generate SBOMs, scan vulnerabilities, and analyze dependencies from local projects or Git repos.
We provide all the information about MCP servers via our MCP API.
curl -X GET 'https://glama.ai/api/mcp/v1/servers/wjlim/nf-core_mcp'
If you have feedback or need assistance with the MCP directory API, please join our Discord server