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GATK4 default jar conventions differ in M2 and CNV WDLs. #4072

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samuelklee opened this issue Jan 7, 2018 · 2 comments
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GATK4 default jar conventions differ in M2 and CNV WDLs. #4072

samuelklee opened this issue Jan 7, 2018 · 2 comments
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@davidbenjamin
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@samuelklee
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The default jar is taken to be the one bundled with the Docker in the CNV WDLs but is an exposed argument in the M2 WDLs.
@samuelklee samuelklee added the wdl label Jan 7, 2018
@LeeTL1220
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@samuelklee See upcoming WDL convention guide for GATK repo.

@LeeTL1220
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GATK CNV is correct.

@davidbenjamin davidbenjamin self-assigned this Jan 11, 2018
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@LeeTL1220 @davidbenjamin @samuelklee