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artic-network / fieldbioinformatics

The ARTIC field bioinformatics pipeline
MIT License
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Not seeing default argument values in pipeline.py #27

Closed jbeaulaurier closed 4 years ago

jbeaulaurier commented 4 years ago

Hello,

I see that there is some code in place using ArgumentParserWithDefaults to include the specified argument defaults in the help string, but it's not picking them up for me. As a result, all the default values are hidden when you use artic <subcommand> -h. This tripped me up because I thought that simply removing --normalise <N> from artic minion would drop the normalisation step (instead it defaulted to --normalise 100). Not sure where the argparser it's going wrong, but it'd be great if someone with a sharper eye than me could take a look.

Thanks, John

nickloman commented 4 years ago

There is a default value set of 100 in there. I think if you set normalise to 0 it will do what you want!