CLAM-NF pipeline

A pipeline for generating pathology slide embeddings using CLAM.

Requirements

• Unix-like operating system
• Java 11

Quickstart

1. Install docker

2. Install nextflow:

   curl -s https://get.nextflow.io | bash
   

3. Launch the pipeline execution using docker

   ./nextflow run msk-mind/clam-nf -profile standard,docker --samples_csv samples.csv
   

   samples.csv is a csv file where the first column is the slide ID and the second is the path to the slide.

4. When the execution completes, results will be in the results directory