nf-core MCP Server

nf-core MCP Server is an MCP server that enables AI assistants to inspect, manage, and navigate local nf-core pipeline repositories. Designed for bioinformaticians, computational biologists, and workflow developers, it bridges local Nextflow pipelines with Model Context Protocol clients. The server connects directly to the directory trees, workflow scripts, configuration files, and module structures of installed nf-core pipelines. By exposing these assets through standardized tool calls and resources, it allows developers to quickly look up parameter definitions, process declarations, subworkflows, and documentation without manually parsing deep directory hierarchies. Teams working with genomics workflows can use it to maintain standard practices across pipelines, review pipeline configurations, and write code compatible with nf-core guidelines. It streamlines the day-to-day maintenance of complex Nextflow setups by providing intelligent context to LLM-powered developer environments.

Category: Data & Analytics

Tags: bioinformatics, genomics, nextflow, pipelines, workflow

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How to install and configure nf-core MCP Server

1. Review the official documentation on the server registry page at https://mcpservers.org/servers/wjlim/nf-core_mcp to check for specific runtime dependencies such as Node.js or Python. 2. Clone or download the nf-core MCP server code to your local machine. 3. Open your MCP client configuration file, such as the Claude Desktop configuration (claude_desktop_config.json) or your Cursor workspace settings. 4. Add the server definition under the mcpServers section, specifying the command and script path to run the server alongside your local repository paths. 5. Save the configuration and restart your client to connect to the server.

What you can do with nf-core MCP Server

• Inspect local nf-core pipeline structures, processes, and subworkflows directly from your AI coding assistant during bioinformatics project development. * Review Nextflow configuration files and parameter profiles across multiple pipeline instances to verify execution settings and pipeline integrity. * Locate specific bioinformatics modules within local nf-core repositories to speed up updates and ensure adherence to community guidelines. * Query pipeline documentation, input samplesheet requirements, and output schemas to automate workflow validation before launching genomic analyses on compute clusters.

Key facts

• Open Source
• Data & Analytics, Developer Tools & Code Intelligence
• bioinformatics, genomics, nextflow, pipelines, workflow

Part of MCP Servers

What can nf-core MCP Server do?

The nf-core MCP Server allows supported AI clients to explore and manage local nf-core pipeline repositories. It exposes tools to traverse directory structures, inspect Nextflow scripts, review module configurations, and check pipeline documentation, helping bioinformaticians develop and troubleshoot genomic workflows.

Which MCP clients work with nf-core MCP Server?

Any client that complies with the Model Context Protocol can connect to the nf-core MCP Server. Commonly used clients include Claude Desktop, Cursor, and other custom developer environments configured to run local MCP stdio or SSE server instances.

Is nf-core MCP Server open source?

Yes, nf-core MCP Server is open source software. Users can inspect the implementation, contribute improvements, and configure the server locally to match their specific Nextflow development workflows.

How do I install nf-core MCP Server?

Installation details depend on the project implementation. Refer to the server registry page at https://mcpservers.org/servers/wjlim/nf-core_mcp for required installation commands and configuration parameters, then register the execution path within your client configuration file.