REFACTOR: change `args` for specific arguments

[atteggiani]

Overview

Many of the functions in this repo's scripts accept the entire parsed arguments args.
This is often not necessary and it might be preferable to only pass the specific arguments that each function requires.

Solution

Change instances of args in functions with the specific arguments needed.
Something like:

- def myfunc(args, arg2, arg3):
+ def myfunc(args.specific_arg1, args.specific_arg2, arg2, arg3):
    ...

- myfunc(args, arg2, arg3):
+ myfunc(args.specific_arg1, args.specific_arg2, arg2, arg3):
    ...