Raw data processing pipeline for scTRIBE

This file contains a Nextflow pipeline for processing raw (sc) TRIBE data

General outline

Raw reads are processed closely following the GATK best-practices workflow for RNAseq short variant discovery. Raw reads go through the following steps:

1. Adapter and homopolymer sequence trimming
2. Depleting rRNA sequences
3. Aligning to the reference genome
4. Deduplication
5. Variant identification and filtering

See BioRXiv: doi: https://doi.org/10.1101/2021.06.21.449212 for context