nf-core Pipeline Manager

Example Use Cases

• 1

  List available nf-core pipelines in a local workspace and check configuration file status programmatically.

• 2

  Retrieve module metadata or inspect pipeline workflows and configuration files (pipeline://{name}/config and pipeline://{name}/workflow).

• 3

  Search across pipeline source files (globally or within a specific pipeline) to find references, tools, or steps like 'fastqc'.

Description

This MCP server exposes nf-core pipeline repositories (rnaseq, sarek, modules, tools, etc.) so agents and IDEs can list pipelines, read configurations and workflows, inspect modules, and search pipeline files. It can be run via npm or Docker and integrates with Cursor IDE through an mcp.json entry. The server is useful for local development workflows where quick navigation and programmatic access to pipeline contents are required.