Nextflow Developer Tools

Nextflow Developer Tools is an MCP server that integrates with a local clone of the Nextflow Git repository to facilitate internal Nextflow development and testing. Built with FastMCP, this server is designed specifically for developers contributing to the Nextflow engine and its core components, rather than for bioinformatics researchers authoring workflows. It connects AI assistants directly to the Nextflow codebase, enabling users to trigger builds from source, execute integration tests, run targeted test suites for plugins like nf-amazon, launch development versions of Nextflow, manage repository paths, and consult documentation. By exposing these build and test operations through standard Model Context Protocol tools, developers using clients such as Claude Desktop or Cursor can automate routine build tasks, evaluate code changes against regression suites, and troubleshoot engine modifications through conversational prompts without manually switching to a separate terminal session.

Category: Developer Tools & Code Intelligence

Tags: bioinformatics, git, nextflow, pipeline, workflow

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How to install and configure Nextflow Developer Tools

1. Ensure Python 3.8+, FastMCP, and a local clone of the Nextflow repository are installed. 2. Install the FastMCP CLI via pip: bash pip install fastmcp 3. Clone the server repository and navigate into it: bash git clone https://github.com/adamrtalbot/mcp-nextflow.git cd mcp-nextflow 4. For Claude Desktop, install the server directly using FastMCP, specifying your local Nextflow path: bash NEXTFLOW_DIR=/path/to/your/nextflow fastmcp install mcp-nextflow.py 5. For Cursor, add the server to your Cursor MCP configuration JSON: json { "mcpServers": { "nextflow-dev": { "command": "/path/to/your/.venv/bin/python", "args": ["/path/to/your/mcp-nextflow/mcp-nextflow.py"], "env": { "NEXTFLOW_DIR": "/path/to/your/nextflow" } } } }

What you can do with Nextflow Developer Tools

• Compiling Nextflow from local source code through AI chat commands to verify modifications before submitting pull requests. - Running specific plugin integration test suites, such as nf-amazon, to check compatibility during development. - Executing integration test commands and inspecting build failures directly within the Cursor agentic workspace. - Running the locally built development version of the Nextflow binary to test new workflow runtime features. - Managing local Nextflow directory paths and retrieving official development documentation while editing core engine files.

Key facts

• Open Source
• https://github.com/adamrtalbot/mcp-nextflow
• Developer Tools & Code Intelligence, DevOps, CI/CD & Version Control
• bioinformatics, git, nextflow, pipeline, workflow

Part of MCP Servers

What can Nextflow Developer Tools do?

Nextflow Developer Tools provides access to local Nextflow development operations. It allows AI clients to compile Nextflow from source, execute specific plugin and integration test suites, run development builds of Nextflow, manage local repository directories, and retrieve development documentation.

Can I use Nextflow Developer Tools to write Nextflow pipelines?

No. The server documentation explicitly notes that it is built for developing Nextflow itself, such as engine internals and plugins, rather than for writing, linting, or executing standard Nextflow analysis pipelines.

Which MCP clients work with Nextflow Developer Tools?

The server can be used with Claude Desktop and Cursor. Installation with Claude Desktop is handled via the FastMCP CLI, while Cursor integrates with the Python script using standard MCP server configuration files.

What are the prerequisites for running Nextflow Developer Tools?

You need Python 3.8 or higher with pip, the FastMCP package installed, a supported MCP client such as Claude Desktop or Cursor, and a locally cloned Git repository of Nextflow specified via the NEXTFLOW_DIR environment variable.

Is Nextflow Developer Tools open source?

Yes, Nextflow Developer Tools is open source. The codebase is publicly accessible on GitHub at https://github.com/adamrtalbot/mcp-nextflow for cloning, configuration, and inspection.