Allows running the MCP server in a containerized environment with volume mounting to access workspace pipelines.
Enables cloning and managing nf-core pipeline repositories to make them available for the MCP server to interact with.
Provides tools for managing and navigating nf-core pipeline repositories, including listing pipelines, accessing configurations and workflows, searching through pipeline files, and exploring pipeline modules.
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
Docker Version
Adding nf-core Repositories
To add new nf-core pipeline repositories to the workspace:
- Clone the repositories:
- Directory Structure:
Your workspace should look like this:
- 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.
Available Tools
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
:
Using Docker
Add the following to your mcp.json
:
Example Usage
Using the MCP server in Cursor:
Running the Server
Using NPM
Using Docker
Development
License
MIT
local-only server
The server can only run on the client's local machine because it depends on local resources.
Enables users to manage and navigate nf-core bioinformatics pipeline repositories, allowing list, search, and explore operations on pipeline configurations, workflows, and modules.
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