Nextflow Developer Tools

by adamrtalbot

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Streamlines Nextflow development by providing tools for building, testing, and executing pipelines directly from local repositories.

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Author: adamrtalbot
Repository: adamrtalbot/mcp-nextflow
Categories: Developer Tools, Infrastructure, Automation, Other, Productivity, Design, AI, Frontend
Tags: #integration

Setting up with Highlight

This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:

Download and install Highlight from highlightai.com/download
Navigate to the plugins tab and select "Add Custom Plugin"
Configure the plugin with the settings below
Plugin Name Nextflow Developer Tools

Command (node, npx, python, etc.) /path/to/your/.venv/bin/python
Arguments
- Argument 1 /path/to/your/mcp-nextflow/mcp-nextflow.py
Environment
- NEXTFLOW_DIR /path/to/your/nextflow
Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
Enable "Start Automatically" if you want the plugin to start when Highlight launches

Setting up with Cursor

Open Cursor's settings
Navigate to the MCP section
Click "Add new Global MCP server"
Copy and paste the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "nextflow developer tools": {
            "env": {
                "NEXTFLOW_DIR": "/path/to/your/nextflow"
            },
            "args": [
                "/path/to/your/mcp-nextflow/mcp-nextflow.py"
            ],
            "command": "/path/to/your/.venv/bin/python"
        }
    }
}

JSON

{
    "mcpServers": {
        "nextflow developer tools": {
            "env": {
                "NEXTFLOW_DIR": "/path/to/your/nextflow"
            },
            "args": [
                "/path/to/your/mcp-nextflow/mcp-nextflow.py"
            ],
            "command": "/path/to/your/.venv/bin/python"
        }
    }
}

JSON

{
    "mcpServers": {
        "nextflow developer tools": {
            "env": {
                "NEXTFLOW_DIR": "/path/to/your/nextflow"
            },
            "args": [
                "/path/to/your/mcp-nextflow/mcp-nextflow.py"
            ],
            "command": "/path/to/your/.venv/bin/python"
        }
    }
}

Setting up with Claude Desktop

Open Claude Desktop's settings
Go to the Integrations tab
Click "Add MCP Server"
Use the configuration below based on your operating system

Note: Make sure Claude Desktop is running before attempting to connect.

JSON

{
    "mcpServers": {
        "nextflow developer tools": {
            "env": {
                "NEXTFLOW_DIR": "/path/to/your/nextflow"
            },
            "args": [
                "/path/to/your/mcp-nextflow/mcp-nextflow.py"
            ],
            "command": "/path/to/your/.venv/bin/python"
        }
    }
}

JSON

{
    "mcpServers": {
        "nextflow developer tools": {
            "env": {
                "NEXTFLOW_DIR": "/path/to/your/nextflow"
            },
            "args": [
                "/path/to/your/mcp-nextflow/mcp-nextflow.py"
            ],
            "command": "/path/to/your/.venv/bin/python"
        }
    }
}

JSON

{
    "mcpServers": {
        "nextflow developer tools": {
            "env": {
                "NEXTFLOW_DIR": "/path/to/your/nextflow"
            },
            "args": [
                "/path/to/your/mcp-nextflow/mcp-nextflow.py"
            ],
            "command": "/path/to/your/.venv/bin/python"
        }
    }
}

Setting up with Windsurf

Open Windsurf's preferences
Go to the Integrations section
Click "Add MCP Integration"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "nextflow developer tools": {
            "env": {
                "NEXTFLOW_DIR": "/path/to/your/nextflow"
            },
            "args": [
                "/path/to/your/mcp-nextflow/mcp-nextflow.py"
            ],
            "command": "/path/to/your/.venv/bin/python"
        }
    }
}

JSON

{
    "mcpServers": {
        "nextflow developer tools": {
            "env": {
                "NEXTFLOW_DIR": "/path/to/your/nextflow"
            },
            "args": [
                "/path/to/your/mcp-nextflow/mcp-nextflow.py"
            ],
            "command": "/path/to/your/.venv/bin/python"
        }
    }
}

JSON

{
    "mcpServers": {
        "nextflow developer tools": {
            "env": {
                "NEXTFLOW_DIR": "/path/to/your/nextflow"
            },
            "args": [
                "/path/to/your/mcp-nextflow/mcp-nextflow.py"
            ],
            "command": "/path/to/your/.venv/bin/python"
        }
    }
}

Setting up with Cline

Open Cline's settings
Navigate to the Integrations section
Click "Add MCP Server"
Copy and paste the configuration below based on your operating system

Note: Make sure to restart Cline after adding the configuration.

JSON

{
    "mcpServers": {
        "nextflow developer tools": {
            "env": {
                "NEXTFLOW_DIR": "/path/to/your/nextflow"
            },
            "args": [
                "/path/to/your/mcp-nextflow/mcp-nextflow.py"
            ],
            "command": "/path/to/your/.venv/bin/python"
        }
    }
}

JSON

{
    "mcpServers": {
        "nextflow developer tools": {
            "env": {
                "NEXTFLOW_DIR": "/path/to/your/nextflow"
            },
            "args": [
                "/path/to/your/mcp-nextflow/mcp-nextflow.py"
            ],
            "command": "/path/to/your/.venv/bin/python"
        }
    }
}

JSON

{
    "mcpServers": {
        "nextflow developer tools": {
            "env": {
                "NEXTFLOW_DIR": "/path/to/your/nextflow"
            },
            "args": [
                "/path/to/your/mcp-nextflow/mcp-nextflow.py"
            ],
            "command": "/path/to/your/.venv/bin/python"
        }
    }
}

Setting up with Goose

Open Goose's preferences
Go to the Integrations tab
Select "MCP Servers"
Click "Add New Server"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "nextflow developer tools": {
            "env": {
                "NEXTFLOW_DIR": "/path/to/your/nextflow"
            },
            "args": [
                "/path/to/your/mcp-nextflow/mcp-nextflow.py"
            ],
            "command": "/path/to/your/.venv/bin/python"
        }
    }
}

JSON

{
    "mcpServers": {
        "nextflow developer tools": {
            "env": {
                "NEXTFLOW_DIR": "/path/to/your/nextflow"
            },
            "args": [
                "/path/to/your/mcp-nextflow/mcp-nextflow.py"
            ],
            "command": "/path/to/your/.venv/bin/python"
        }
    }
}

JSON

{
    "mcpServers": {
        "nextflow developer tools": {
            "env": {
                "NEXTFLOW_DIR": "/path/to/your/nextflow"
            },
            "args": [
                "/path/to/your/mcp-nextflow/mcp-nextflow.py"
            ],
            "command": "/path/to/your/.venv/bin/python"
        }
    }
}

From the repository

1. Install the FastMCP CLI tool:

pip install fastmcp

2. Clone this repository:

git clone https://github.com/yourusername/nextflow-dev-mcp.git
cd nextflow-dev-mcp

3. Install the MCP in Claude Desktop:

fastmcp install mcp-nextflow.py

This will make the MCP available in the Claude Desktop app.

1. Fetch the virtual environment path which includes the FastMCP CLI tool. If you are using uv this will be in the .venv directory.
1. Get the directory of your Nextflow cloned repository.
1. Add the following json to the cursor MCP servers:

{
    "mcpServers": {
        "server-name": {
            "command": "/path/to/your/.venv/bin/python",
            "args": [
                "/path/to/your/mcp-nextflow/mcp-nextflow.py"
            ],
            "env": {
                "NEXTFLOW_DIR": "/path/to/your/nextflow"
            }
        }
    }
}

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.

You can specify the Nextflow directory during installation:

NEXTFLOW_DIR=/path/to/your/nextflow fastmcp install mcp-nextflow.py

Claude Desktop / Cursor

Paste into your MCP client config file to install this server.

{
    "mcpServers": {
        "nextflow developer tools": {
            "env": {
                "NEXTFLOW_DIR": "/path/to/your/nextflow"
            },
            "args": [
                "/path/to/your/mcp-nextflow/mcp-nextflow.py"
            ],
            "command": "/path/to/your/.venv/bin/python"
        }
    }
}

Linux

{
    "env": {
        "NEXTFLOW_DIR": "/path/to/your/nextflow"
    },
    "args": [
        "/path/to/your/mcp-nextflow/mcp-nextflow.py"
    ],
    "command": "/path/to/your/.venv/bin/python"
}

Macos

{
    "env": {
        "NEXTFLOW_DIR": "/path/to/your/nextflow"
    },
    "args": [
        "/path/to/your/mcp-nextflow/mcp-nextflow.py"
    ],
    "command": "/path/to/your/.venv/bin/python"
}

Windows

{
    "env": {
        "NEXTFLOW_DIR": "/path/to/your/nextflow"
    },
    "args": [
        "/path/to/your/mcp-nextflow/mcp-nextflow.py"
    ],
    "command": "/path/to/your/.venv/bin/python"
}

An MCP server for Nextflow development and testing, which requires a local clone of the Nextflow Git repository.

A Model Context Protocol (MCP) server designed for Nextflow development and testing, built with FastMCP.

[!WARNING] This MCP is designed for developing Nextflow itself, not for writing Nextflow pipelines.

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

- Claude Desktop App
- Python 3.8+ with pip
- Git repository of Nextflow (cloned locally)

Installing with FastMCP to use in Claude Desktop

git clone https://github.com/yourusername/nextflow-dev-mcp.git cd nextflow-dev-mcp

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 usinguvthis will be in the.venvdirectory. - Get the directory of your Nextflow cloned repository. - Add the following json to the cursor MCP servers:

{ "mcpServers": { "server-name": { "command": "/path/to/your/.venv/bin/python", "args": [ "/path/to/your/mcp-nextflow/mcp-nextflow.py" ], "env": { "NEXTFLOW_DIR": "/path/to/your/nextflow" } } } }

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 runmake test module=plugins:nf-amazon.

You can specify the Nextflow directory during installation:

NEXTFLOW_DIR=/path/to/your/nextflow fastmcp install mcp-nextflow.py

Once installed, you can access the MCP in the Claude Desktop app:
- Open Claude Desktop
- Click on theToolsmenu button in the Claude interface
- SelectNextflow Developer Toolsfrom the list of installed MCPs

Cursoris 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 is a web browser that enables your coding agent, such as Claude Code, to visit websites on your behalf and assist you in identifying bugs or creating UI test cases.

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Agents make claims. Reelier writes receipts — record an agent's tool-call workflow once, replay it deterministically at 0 tokens, and diff runs to catch drift.

The Shipyard CLI provides an MCP server for agents to manage Shipyard environments directly: by pulling logs, comparing branches, running tests, and stopping/starting environments..

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Clean and audit messy MCP setups: stale servers, unused tools, context-heavy MCPs, outdated packages, and safe repair plans.

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Details

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Setting up with Highlight

From the repository

Claude Desktop / Cursor

Linux

Macos

Windows

Installing with FastMCP to use in Claude Desktop

Installing with FastMCP to use in Cursor

Install

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