Build and Test

Replace GATK with FreeBayes for variant calling; upgrade Java tools to eliminate CVEs #243

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Run time

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Job	Run time
paths-filter	6s
get-version	6s
build-baseimage-amd64	18s
build-baseimage-arm64	25s
build-core-amd64	4m 8s
build-core-arm64	3m 31s
create-manifest-baseimage	20s
build-assemble-arm64	3m 26s
build-phylo-arm64	3m 7s
build-classify-arm64	2m 32s
build-mega-arm64	4m 14s
build-mega-amd64	4m 17s
create-manifest-core	20s
build-assemble-amd64	3m 4s
build-classify-amd64	3m 23s
build-phylo-amd64	2m 9s
test-core-arm64	2m 43s
test-core	3m 8s
create-manifest-phylo	17s
test-phylo-arm64	1m 53s
test-phylo	1m 37s
create-manifest-assemble	18s
create-manifest-classify	21s
test-assemble-arm64	2m 17s
test-assemble	2m 8s
test-classify	2m 8s
test-classify-arm64	2m 8s
create-manifest-mega	19s
scan-containers (mega)	2m 13s
scan-containers (assemble)	1m 47s
scan-containers (classify)	2m 7s
scan-containers (core)	2m 19s
scan-containers (baseimage)	39s
scan-containers (phylo)	1m 37s
all-tests-pass	3s
deploy-to-quay	0s
	1h 5m 28s