When running without a --loc and without supplying a value to --config, CATS will look for config.yml in the current directory. As this is a generic file name, there's a chance that this could clash with a config file used for an unrelated purpose. Perhaps the default file name could be something like cats-config.yml?

I'd also recommend checking for the .yaml file extension, as in testing I'd accidentally named mine config.yaml and it took me a while to figure out why it wasn't working.

(this isn't part of my JOSS review, I just think CATS is pretty neat and wanted to help out!)