MCP Servers / development / nf-core MCP Server

nf-core MCP Server

JSON →
nonedevelopment

Manage and navigate local nf-core pipeline repositories.

github ↗
Install
How to run this server
[ { "cmd": "npx -y nf-core-mcp", "imports": [] } ]
server path: nf-core-mcp-server
Tools
What this server exposes
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 query), pipeline (optional, specific pipeline to search).
Configuration
Environment & auth
authnone
Resources
githubhttps://github.com/wjlim/nf-core_mcp ↗
nf-core MCP Server — MCP Server · libregistry