FloWuenne/mcp-nf-core
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A repo to experiment with MCP capabilities for nf-core tools functions.
The Nf-core tools MCP (Unofficial) provides a suite of tools for accessing nf-core tools for pipelines and modules. It allows users to create pipelines using the nf-core template, list nf-core modules, create modules using the nf-core modules template, and install existing nf-core modules into their pipeline or modules repository. The tools are implemented for testing purposes from the command line (CLI) and directly from the Python package. Two different MCP server files exist for these implementations: nf-core.test-server.cli.py for CLI and nf-core.test-server.python.py for Python.
Features
- Create a pipeline using the nf-core template
- List nf-core modules
- Create a module using the nf-core modules template
- Install existing nf-core modules into your pipeline or modules repo
Usages
fastmcp with Claude Desktop
uv venv source .venv/bin/activate uv add "mcp[cli]" nf-core fastmcp install nf-core.test-server.cli.py ## CLI server fastmcp install nf-core.test-server.python.py ## Python based server
cursor integration
{
"mcpServers": {
"mix_server": {
"command": "uv",
"args": [
"--directory",
"[Full path to the server directory (this repo folder)]]",
"run",
"server.py"
]
}
}
}
