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filter germline consented samples in germline mode #870

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filter germline consented samples in germline mode #870

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Addressing #860

--germline will accept values true, false or a file. true will 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, GermlineAnnotateMaf are filtered but RunPolysolver is not.
Behavior under the watch mode is accounted for with the method watchGermline

@anoronh4
add support for file input in params.germline parameter to selectivel…
9dcb22c 
…y process germline samples in germline mode in a given list.
@anoronh4 anoronh4 changed the base branch from master to develop January 26, 2021 20:43
@anoronh4 anoronh4 requested a review from gongyixiao January 26, 2021 20:43
@anoronh4 anoronh4 marked this pull request as draft January 27, 2021 00:18
@gongyixiao gongyixiao linked an issue Jan 29, 2021 that may be closed by this pull request
enhance germline analysis to run subsets of samples #860
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@gongyixiao gongyixiao added the enhancement New feature or request label Jan 29, 2021
@anoronh4 anoronh4 marked this pull request as ready for review October 12, 2021 22:25
@anoronh4 anoronh4 marked this pull request as draft October 12, 2021 22:26
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@gongyixiao gongyixiao Awaiting requested review from gongyixiao

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enhance germline analysis to run subsets of samples
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