Hello, I got across https://www.protocols.io/ and kind of liked what I saw. In my understanding it is a semi-formal way to mix scripts with verbal descriptions to reach for scientific goals. You could also say that these are columns in our excel sheet, except that these do not need a software package on their own, it is just a representation of the methods section of a paper.
We have enough to do for our packaging already. Still, you may find this useful to prioritize your packaging work. Or just to learn how some packages that you are already familiar with are used. Best, Steffen