How do I install the nf core mcp server?

Run it through your MCP client's configuration using `npx -y nf-core-mcp`. Add the server block to Claude Desktop's config file (or use `claude mcp add` for Claude Code), restart the client, and the tools appear automatically. Full snippets are on this page.

Does the nf core mcp server need an API key?

No API key is documented for this server, so it should start without additional credentials. Because it runs locally, it inherits whatever access your machine already has — worth keeping in mind when you decide what to point it at.

Nf Core MCP Server — Setup, Tools & Config

Name: Nf Core MCP Server
Author: wjlim

What is the Nf Core MCP MCP server?

Connect Nf Core MCP to Claude, Cursor or any other MCP client and it stops being a tab you switch to. MCP server for managing nf-core pipeline repositories. The nf core mcp mcp server is what makes that connection.

What the server does

List local nf-core repositories (rnaseq, sarek, modules, tools)
Access pipeline configurations and workflows
Search through pipeline files
Explore pipeline modules

Available tools

The toolset is worth reading before you wire it up, because it tells you what the integration is really for:

Parameters — - pipeline: Pipeline name (rnaseq, sarek, or modules)

Installation

Installation goes through your MCP client rather than a global install: point it at nf-core-mcp on npm and it is fetched when the client starts. The copy-paste blocks for Claude Desktop, Claude Code and Cursor are further down this page.

Where it fits

This sits in the developer tooling group, where several servers overlap in what they claim to do but differ sharply once you actually set them up. Nf Core MCP's toolset — Parameters — is a fair guide to whether it matches your workflow. It is maintained by wjlim; worth a glance at recent repository activity before you build anything load-bearing on it.

This entry was verified against Nf Core MCP's own documentation before publication; SyncDev keeps the directory reviewed rather than auto-generated.

Worth knowing first

It runs with your machine's permissions. That is convenient and also the reason to think about what you point it at before you approve a tool call.
Keep per-call confirmation enabled while you learn its behaviour; it is the cheapest safeguard you have.

Available tools

Tool	What it does
Parameters	- pipeline: Pipeline name (rnaseq, sarek, or modules)

How to install the Nf Core MCP MCP server

{
  "mcpServers": {
    "nf-core": {
      "command": "npx",
      "args": ["-y", "nf-core-mcp"]
    }
  }
}

Add to claude_desktop_config.json, then restart Claude Desktop.

Example prompts to try

“Use Nf Core MCP to Parameters.”

Frequently asked questions

It connects Nf Core MCP to MCP-compatible AI assistants such as Claude and Cursor, exposing 1 tool (Parameters) that the assistant can call on your behalf. Instead of copying data back and forth by hand, the assistant works with Nf Core MCP directly.

Nf Core MCP Server

What is the Nf Core MCP MCP server?

What the server does

Available tools

Installation

Where it fits

Worth knowing first

Available tools

How to install the Nf Core MCP MCP server

Example prompts to try

Frequently asked questions

Alternatives to the Nf Core MCP MCP server

Context7

Playwright

GitHub

Linear

Git

Time

Nf Core MCP Server

What is the Nf Core MCP MCP server?

What the server does

Available tools

Installation

Where it fits

Worth knowing first

Available tools

How to install the Nf Core MCP MCP server

Example prompts to try

Frequently asked questions

What does the nf core mcp server do?

How do I install the nf core mcp server?

Does the nf core mcp server need an API key?

Alternatives to the Nf Core MCP MCP server

Context7

Playwright

GitHub

Linear

Git

Time