filter germline consented samples in germline mode #870
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…y process germline samples in germline mode in a given list.
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Addressing #860
--germlinewill accept valuestrue,falseor a file.truewill perform analysis on all germline samples; a file will filter the germline channels to only include the samples in a valid file.The processes
GermlineDellyCall,GermlineRunManta,GermlineMergeDellyAndManta,GermlineRunHaplotypecaller,GermlineCombineHaplotypecallerVcf,GermlineRunStrelka2,GermlineCombineChannel,GermlineAnnotateMafare filtered butRunPolysolveris not.Behavior under the
watchmode is accounted for with the methodwatchGermline