Pass input profiles in text file to inStrain compare

[jdwinkler-lanzatech]

Hi,

I might be processing a fairly large number of samples via inStrain compare soon, and I suspect I'll hit the limit on the length of the CLI argument used if I go through bash or something similar. Is it possible to add a CLI option containing a list of input folders (one folder per line) to avoid that issue? Thanks for the help again!

[MrOlm]

Yeah this is a great feature request- I'll try and add it in the next inStrain update. I'll note that after ~100 profiles or so things can get really slow because profiles are compared in a pair-wise manner. I'm working on a greedy clustering algorithm to get around this, but it won't be ready any time soon.

Best,
Matt

[jdwinkler-lanzatech]

Yeah, that'll probably put a damper on my analysis then. Thanks for the head's up!