VS-1490 - Refactor python code from extract dir into a scripts directory. #4801

Job	Run time
build and push gatk docker to artifacts	42m 41s
Validate script WDLs using womtools	3m 58s
check if the environment has privileges	1s
Validate generated WDLs using womtools	13m 44s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	55m 14s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	52m 40s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	48m 27s
WDL test RUN_M2_WDL on cromwell	56m 52s
WDL test RUN_CNN_WDL on cromwell	41m 53s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	44m 2s
Java 17.0.6+10 build and test cloud	17m 8s
Java 17.0.6+10 build and test integration	34m 37s
Java 17.0.6+10 build and test unit	20m 38s
Java 17.0.6+10 test on docker integration	37m 30s
Java 17.0.6+10 test on docker unit	24m 10s
Java 17.0.6+10 test on docker variantcalling	32m 57s
Java 17.0.6+10 test on docker conda	29m 43s
	9h 16m 15s

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