Enhancement/combine MergeBams and MarkDuplicates#875
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MergeBamsandMarkDuplicateswere combined into a single process namedMergeBamsAndMarkDuplicates. This is expected to reduce the size of the bam cache because the merged and unmarked bam is not written to permanent storage. The resource configuration files were adjusted by simply adopted the resources forMarkDuplicates. The container forMergeBamsbecame the container of the new process because it also contains gatk.i noticed that the original
resources_juno_genome.confighad 8 cpu* 1.GB forMergeBams, is there a reason it needs so many cpu for the combined process or will 2 cpu*5.GB cover it?