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pachterlab / kb_python

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
https://www.kallistobus.tools/
BSD 2-Clause "Simplified" License
141 stars 23 forks source link

kb ref can't handle blanks in path arguments #245

Closed NikTuzov closed 2 months ago

NikTuzov commented 2 months ago

Hello Delaney:

kb ref (and probably kb count also) cannot find the input files if the paths contain blanks. I have tried double and single quotes, to no avail. Is there a way around that, short of copying the input file(s)?

Regards, Nik Tuzov

Yenaled commented 2 months ago

Ooh, i haven’t looked into it but looks like that’s something that can only be addressed via an update, if true. I’ll make note of it. For now, you have to just create a symlink (ln -s) to the file.

NikTuzov commented 2 months ago

Thank you for a fast reply.