Merge branch 'main' into rlim/add-output-csv-short-read #1588

Job	Run time
linters	1m 13s
list-workflow-dirs	10s
cancel-previous	3s
wdl-ci (amr)	3m 20s
wdl-ci (benchmark)	3m 3s
wdl-ci (consensus-genome)	3m 26s
wdl-ci (host-genome-generation)	2m 9s
wdl-ci (legacy-host-filter)	3m 21s
wdl-ci (long-read-mngs)	3m 20s
wdl-ci (phylotree-ng)	3m 18s
wdl-ci (short-read-mngs)	3m 23s
	26m 46s

Provide feedback