Connects BaseRecalibrator, SortSam, ApplyBQSR
Connects BaseRecalibrator, SortSam, ApplyBQSR

Applies java and resource limits according to https://github.com/gatk-workflows/gatk4-data-processing/blob/8ffa26ff4580df4ac3a5aa9e272a4ff6bab44ba2/processing-for-variant-discovery-gatk4.hg38.wgs.inputs.json#L45-L66
Uses `default:` instead of `valueFrom:` to supply values, since the latter only supports strings or expressions.

Duke-GCB/bespin-cwl,Duke-GCB/bespin-cwl