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: mcp-server-github
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
| Name | Required | Description | Default |
|---|---|---|---|
| pipeline | Yes |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Tool has no description.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Tool has no description.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Tool has no description.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Tool has no description.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
Tool has no description.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Tool has no description.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
| Name | Required | Description | Default |
|---|---|---|---|
No parameters | |||
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Tool has no description.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Tool has no description.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Tool has no description.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Tool has no description.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
Tool has no description.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Tool has no description.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
| Name | Required | Description | Default |
|---|---|---|---|
| pipeline | No | ||
| query | Yes |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Tool has no description.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Tool has no description.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Tool has no description.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Tool has no description.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
Tool has no description.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Tool has no description.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Recent tool additions, removals, and schema changes observed during successful MCP inspections.
v1.0.0get-pipeline-moduleslist-pipelinessearch-pipelinesScored across 3 tools
The three tools have clearly distinct purposes: get-pipeline-modules retrieves modules for a specific pipeline, list-pipelines enumerates available pipelines, and search-pipelines finds pipelines based on criteria. There is no overlap in functionality, making tool selection straightforward for an agent.
All tool names follow a consistent verb-noun pattern with hyphens (e.g., get-pipeline-modules, list-pipelines, search-pipelines). The naming is uniform and predictable, using clear action verbs paired with relevant nouns.
With only three tools, the server feels thin for a pipeline management domain, potentially lacking operations like create, update, or delete pipelines. However, the tools cover basic discovery and inspection, which might be sufficient for a limited scope.
The toolset is severely incomplete for pipeline management, missing essential CRUD operations such as creating, updating, or deleting pipelines. It only supports discovery and inspection, leaving significant gaps that could hinder agent workflows.
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