Seemann, Torsten. “Ten recommendations for creating usable bioinformatics command line software.” GigaScience 2.1 (2013): 1-3. APA
This paper is written by someone with experience of CLI bioinformatics tools, covering 10 guidelines for greater CLI usability. Whilst I think I’m typically concerned with UIs, this may also be relevant.
They cover providing useful feedback a well a general programming-relevant guidelines like not hardcoding, managing dependencies, etc.
Overall these are reasonable and decent guidelines but probably not something I’ll refer to in the future.