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broadinstitute / viral-ngs

Viral genomics analysis pipelines
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More robust determination of GATK version #1004

Open notestaff opened 4 years ago

notestaff commented 4 years ago

When determining GATK version (e.g. for choosing version-specific switches), base it on the actual GATK jar, rather than on tools.gatk.TOOL_VERSION_TUPLE . Fix how GATK jar is extracted in refine_2x_and_plot task.

This PR includes the GATK URL updates from #1003 to make testing work.