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wilkelab / cinful

A fully automated pipeline to identify microcins along with their associated immunity proteins and export machinery
GNU General Public License v3.0
6 stars 1 forks source link

input format and extention #25

Closed tijeco closed 2 years ago

tijeco commented 3 years ago

This really needs to be straightened out at some point. I don't know if it needs to be done through snakemake or the eventual python wrapper. Basically, input has to be provided. It will try to run anyway if it doesn't and give zero helpful error messages, when in reality the error message should simply be "NO files detected" or something like that. I kind of like requiring files to end in *fna but that has it's limits. I think configuration input files is the way to go. Users can either pass in a list of input files to what will eventually be --inputAssemblies, which will be placed into a configuration file, or they can simply provide their own configuration file! Either way, if no files are present, it really needs to not run, like at all

tijeco commented 2 years ago

I'm going to close this for now, the current setup is stable and works for the given format extension. This may be reopened for a future version update.