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(Do not merge) Port of nvscorevariants into GATK, with a basic tool frontend #4677

(Do not merge) Port of nvscorevariants into GATK, with a basic tool frontend

(Do not merge) Port of nvscorevariants into GATK, with a basic tool frontend #4677

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1 error and 2 warnings

WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell

failed Sep 27, 2024 in 20m 18s