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
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.