I cloned the latest ncov of Nextstrain (3.0.3) from github (running the CLI environment in conda, Ubuntu) and when I run the snakefile for any example profile, I get to an 'augur filter' step that reports that the option '--output-strains' is invalid. When I check 'augur filter -h', sure enough, there is no '--output-strains' option listed.

Maybe I need to update the Nextstrain conda package? After much difficulty I got the latest version installed but it made no difference. Has this broken?