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The bam-to-gvcf and jointgenotyping subworkflows were combined in a single
gatk-variantcalling pipeline. This allowed for eliminating some
inefficiencies that were caused by communication between these pipelines.
Simplify the pipelines so they use less subworkflows. This reduces
the complexity for cromwell and reduces inefficiencies that are caused
by waiting for the subworkflows to finish.
It also makes configuring memory or cpu requirements for tasks in the
workflow a lot easier, as these are not as deeply nested anymore.
separated somatic and germline variant calling into their own workflows