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phac-nml / staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Apache License 2.0
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PlasmidFinder database enterobacteriaceae no longer an option #169

Closed eam12 closed 1 year ago

eam12 commented 1 year ago

For the --plasmidfinder-database-type flag, it appears that enterobacteriaceae is no longer an option in PlasmidFinder 2.1. When you try to specify enterobacteriaceae you get the following message:

2023-03-09 15:35:58 INFO: PlasmidFinder database type [enterobacteriaceae] is out of date, switching to [enterobacteriales]

I think the --help message just needs to be updated to remove enterobacteriaceae as an option.

apetkau commented 1 year ago

Thanks for pointing this out. Yes, looks like we may have to update the help message here.