github.com/MilanParikh/infercnv_workflow

Automatic Tools and Workflows
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infercnv_workflow

Terra workflow for inferCNV with cell caching

Automation Script Jupyter Notebook

This notebook/script helps you set up the input files and bash scripts to run the R version of inferCNV on Terra from a Python (ScanPy) environment

Instructions contained within the comments show where to configure paths, Google buckets, Terra information, your email, etc.

There are two options:

  1. Per Sample (Recommended) - This will split up each of your samples into it’s own parallel T
This is a companion discussion topic for the original entry at github.com/MilanParikh/infercnv_workflow