I am also encountering a similar. I can't figure out how to get transformation scripts to execute. I used the documentation here:
https://www.labkey.org/Documentation/wiki-page.view?name=programmaticQC&_docid=wiki%3A32d707ff-ed56-1034-b734-fe851e088836

which makes it look like you'll probably want $(runInfo) in the Program Command, at least if you want access to any of the run properties within the python script. I think Output File Name will be dependent on your use case - if you want the script to write any console output (like print statements or exceptions) to a file it will write the output to the file specified in Output File Name.

My confusion comes in being unable to tell whether the script is actually getting executed, and if not how to get it to execute. I have the engine set up with $(runInfo) in the Program Command, but when the module I've added my transform script to is used to upload data the script doesn't seem to do anything. I have it set to send an email to me and write a test file just to ensure it's working but neither action is happening.