Run the KCCG GATK4 Mutect2 somatic variant calling pipeline using the Cromwell workflow engine.
For running the pipeline on the local cluster or the Google Cloud Platform, a Cromwell server must be first set up on the local cluster. Cromwell handles orchestrating the pipeline and submitting each task to either the cluster or GCP.
Cromwell is not required for running the pipeline on DNAnexus. For instructions for that platform, see below.
This is a companion discussion topic for the original entry at github.com/mgeaghan-garvan/cromwell-kccg-mutect2-chip/cromwell-kccg-mutect2-annotate-annovar-batch