What would you need to do exactly?
Do you need to Delete Some file at End of Day Script Processing?
Do you need to Remove Some Data files from End of Day Script?
Generally, Across all AS/400 Systems, There will End of Day(or Week) Processing. Which will update the Database Files(Based on Application) and will be Purging data(Which has been stored from long time and no longer required).
I think you should be Purging the old data not to delete Data files.
There might be possiblity that, your application might be having some temporary files that needs be deleted daily.
List the little more details of your requirement and brief description of your current script.