PCAWG uniform alignment workflow uses the popular short read aligner tool BWA MEM (https://github.com/lh3/bwa)
with BioBAMBAM (https://github.com/gt1/biobambam) for BAM sorting, merging and marking duplicate.
The alignment workflow has been dockerized and packaged using CWL workflow language, the source code
is available on GitHub at: https://github.com/ICGC-TCGA-PanCancer/Seqware-BWA-Workflow.

Run the workflow with your own data

Prepare compute environment and install software packages

This is a companion discussion topic for the original entry at quay.io/pancancer/pcawg-bwa-mem-workflow