Not sure if my tagline catches my meaning, but I am struggling with an issue when I would like to take a working protocol, let’s say a basic normalisation protocol, as a basis for building a new protocol.
Just by changing the input file it seems that the protocol gets broken, I think there are some dependencies between files and functions (or something else) that stay in place in the background? Because if it was not so, then it should not make a difference for the functionality of the script which actual file it is that I call “file1”?