viral-pipelines CI

add deduplication of sequences by ID in augur_from_assemblies #2678

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Run time

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Job	Run time
test_docs	1m 24s
test_docs	1m 24s
validate_wdl_miniwdl	1m 35s
validate_wdl_miniwdl	1m 35s
validate_wdl_womtool	2m 57s
validate_wdl_womtool	2m 57s
test_miniwdl	1m 7s
test_miniwdl	27m 19s
test_cromwell	3m 9s
test_cromwell	21m 6s
deploy_dnanexus	25m 56s
deploy_dnanexus	25m 56s
	1h 56m 25s