The hardest part of genomics for me has honestly been figuring out which open source poorly maintained tool I should use for a particular problem. and which options should be run and how the data need to be preprocessed before hand. I mean has anyone ever actually read the documentation of the GATK? It is famously dreadful. And that's professionally maintained. Honestly a nice addition here would be a "so you want to…
have you ever looked at the test suites for Picard? All regression tests and the library is OO hell lols I was taught a decade ago that rolling your own in genomics isn't as bad of a decision as it seems.
This is sadly very true, especially if you have any real software training.