vjmarteau / bd_rhapsody_velocyto

Nextflow workflow to run velocyto.py on BD Rhapsody BAM files

Velocyto.py for BD Rhapsody

This is a minimal nextflow workflow to run velocyto.py on BAM files produces by the BD Rhapsody pipeline.

It consists of two steps:

• manipulating the BAM file to make it compatible with velocyto.
• running velocyto.py

Usage

nextflow run velocyto.nf -c nf_velocyto.config

The nf_velocyto.config defines all paths to input and reference files. Adjust it to your needs.