`miga get` conflict between `--file` and `--db`

bio-miga / miga

MiGA: Microbial Genomes Atlas

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`miga get` conflict between `--file` and `--db` #154

Closed lmrodriguezr closed 6 months ago

lmrodriguezr commented 1 year ago

When passing a --file, the default database (nuccore) is kept regardless of the --db value. A workaround is to include a db column in the file, but this should be resolved.

lmrodriguezr commented 6 months ago

In fact, all parameters are currently being ignored if --file is passed, it's not specific to --db. This is unexpected behaviour and should be corrected.