list-pipelinesLABSCO SUMMARY
The nf-core pipelines you cloned, made searchable where they sit.
It reads the repositories already in your workspace rather than fetching anything, so a question about how rnaseq configures a step is answered from the copy you will actually run. Adding a pipeline means cloning it into the directory — nothing else registers it.
What it is
A navigator for nf-core pipeline repositories on disk: it lists the pipelines in your workspace, searches their files, and reports the modules a pipeline is built from.
What you get
- Every nf-core pipeline in the workspace, with its configuration file status
- Module information for a named pipeline
- Search across pipeline files, optionally scoped to one pipeline
- Pipeline config and workflow available as resources, addressed as pipeline://{name}/config and pipeline://{name}/workflow
- New pipelines detected automatically once cloned into the workspace directory
Requirements
A workspace directory holding cloned nf-core repositories — rnaseq, sarek, modules and any others you use. Node with npm run build, or the Docker image with the workspace mounted at /app/workspace.
Setup effort
Run a container — build the image from the repository, then point your client at it
USE CASES
01
Seeing which pipelines you have locally
The listing includes whether each one's configuration file is in place, so a half-set-up clone is visible immediately.
02
Finding where a parameter is set
Search the pipeline's files by query rather than grepping across several repositories by hand.
03
Understanding what a pipeline is built from
Module information for the named pipeline, so the components are visible before you modify one.
04
Confirming a newly cloned pipeline was picked up
Re-list after cloning; a pipeline that does not appear is in the wrong directory.
05
Reading a pipeline's config without opening the repo
The config and workflow are exposed as resources, and search finds the section you need inside them.
3 tools
Listed in project docs. Your client may show a different list.
get-pipeline-modulessearch-pipelinesBEFORE YOU INSTALL
What to know first
Tools you get
3 tools named in the project's documentation.
Requires
git and docker on PATH
Where it runs
The documented client runs the server on your machine.
INSTALLATION
Connect your client
Build the image from the repository, then point your client at it.
Server setup
TERMINAL
git clone https://github.com/wjlim/nf-core_mcp.git
cd nf-core_mcp
docker build -t nf-core-mcp .MCP Clients
Cursor — Docker
CURSOR — DOCKER · JSON
{
"mcpServers": {
"nf-core": {
"command": "docker",
"args": [
"run",
"-i",
"--rm",
"-v",
"<YOUR_PATH_TO_WORKSPACE>:/app/workspace",
"nf-core-mcp"
]
}
}
}
