Description

This repository holds various bioinformatic workflows. Each workflow is broken down as a main or sub workflow and has an associated .yaml file specifying inputs and are named to correspond with the workflow they are associated with. A list of each available workflow is provided below, for a more complete description of a specific workflow see the github wiki.

Main Worfklows

1. kallisto - Run kallisto from a bam file
2. hla_typing - Run optitype and xHLA from a bam file
3. hla_somatic_variants - Call somatic variants within the HLA region

Sub Workflows

1. bam2fastq - Convert a paired end bam file to fastq files.