Enables testing of the nf-amazon plugin for Nextflow, providing integration capabilities with Amazon Web Services for Nextflow workflows.
Supports interaction with Git repositories for Nextflow development, including cloning and managing the local Nextflow repository.
Provides a comprehensive suite of development tools for Nextflow, including building from source, running tests (integration and plugin tests), executing development versions, managing development directories, and accessing documentation.
Nextflow Developer Tools MCP
A Model Context Protocol (MCP) server designed for Nextflow development and testing, built with FastMCP.
This MCP is designed for developing Nextflow itself, not for writing Nextflow pipelines.
Overview
This MCP provides a suite of tools for Nextflow development, including:
Building Nextflow from source
Running tests (integration tests, specific tests, plugin tests)
Running the development version of Nextflow
Managing the Nextflow development directory
Accessing Nextflow documentation
Installation
Prerequisites
Python 3.8+ with pip
Git repository of Nextflow (cloned locally)
Installing with FastMCP to use in Claude Desktop
Install the FastMCP CLI tool:
Clone this repository:
Install the MCP in Claude Desktop:
This will make the MCP available in the Claude Desktop app.
Installing with FastMCP to use in Cursor
Fetch the virtual environment path which includes the FastMCP CLI tool. If you are using
uv
this will be in the.venv
directory.Get the directory of your Nextflow cloned repository.
Add the following json to the cursor MCP servers:
Then, you should be able to use the MCP in Cursor. In Agentic mode, ask the agent to "test the nf-amazon plugin" and it should run make test module=plugins:nf-amazon
.
Setting Environment Variables
You can specify the Nextflow directory during installation:
Using with Claude
Once installed, you can access the MCP in the Claude Desktop app:
Open Claude Desktop
Click on the Tools menu button in the Claude interface
Select Nextflow Developer Tools from the list of installed MCPs
Using with Cursor
Cursor is an AI-powered code editor that works with Claude. To use the MCP with Cursor:
Make sure you've installed the MCP as described above
Open your Nextflow project in Cursor
In a chat with Claude in Cursor, you can reference the MCP:
Using the Nextflow Developer Tools, run the integration tests for the nf-amazon plugin
This server cannot be installed
local-only server
The server can only run on the client's local machine because it depends on local resources.
A Model Context Protocol server designed to facilitate Nextflow development and testing, providing tools for building from source, running tests, and managing the Nextflow development environment.
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