A vital reproducibility habit is to always write a master script. This script should run through all of your analyses in their proper order. It will
help readers know exactly how your steps are linked together;
reduce all labor required of readers to executing a single script; and
help you, the author, figure out if everything runs as you think, from top to bottom.
hover over a file;
click the dropdown menu that appears on it;
select 'Set as File to Run':
You'll then get a 'run' script, as shown above, that executes your main script. This file is a shell script and can be modified as you see fit to run your analyses -- and also to take care of system level commands (e.g. creating symbolic links).
What makes a good master script?
First, your run script should run headlessly, meaning that it does not require user input, nor expect a pop-up display, during runtime.
Second, you should presume that user will not be monitoring their runs continuously, Therefore, please:
have logical default parameters;
reproduce as many of your results as possible without users' needing to choose anything;
run continuously without pause or delay.