Misc leftover changes discovered while updating protobuff version #3875

Job	Run time
Validate generated WDLs using womtools	13m 15s
build and push gatk docker to artifacts	21m 30s
Validate script WDLs using womtools	1m 40s
check if the environment has privileges	1s
WDL test RUN_CNV_GERMLINE_COHORT_WDL on cromwell	26m 42s
WDL test RUN_CNV_GERMLINE_CASE_WDL on cromwell	31m 4s
WDL test RUN_CNV_SOMATIC_WDL on cromwell	24m 34s
WDL test RUN_M2_WDL on cromwell	18m 53s
WDL test RUN_CNN_WDL on cromwell	16m 57s
WDL test RUN_VCF_SITE_LEVEL_FILTERING_WDL on cromwell	13m 6s
Java 17.0.6+10 build and test cloud	23m 50s
Java 17.0.6+10 build and test integration	31m 44s
Java 17.0.6+10 build and test unit	21m 9s
Java 17.0.6+10 test on docker integration	37m 11s
Java 17.0.6+10 test on docker unit	24m 55s
Java 17.0.6+10 test on docker variantcalling	31m 45s
Java 17.0.6+10 test on docker conda	33m 44s
	6h 12m 0s

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