I am working on a project which requires many raspberry pi's to be set up pretty much the same way. In order to set up the pi's we put NOOBS on the micro SD card and then install raspbian onto the pi. We then go through a series of steps where we make a specific directory, clone a git repo, make a startup script, and set the pi to not sleep. I have managed to write a script that does all of this when run. I was wondering if it is possible to include this file somewhere in the NOOBS files so that when Raspbian is fully installed and launched, this script is just sitting on the home screen waiting to be clicked. We do not want to just copy the sd cards of the pi's because not all of them should be the same, also we did a time trial and it took longer to make a copy than to set it up manually. So is there a way to include this file like I specified above?
I'm puzzled about your time trial. I don't see how you can
put NOOBS on the micro SD card
My advice would be to get a Pi built with the exact config you want (including your script on the desktop), make an image on a fast Linux (or Mac) computer with a fast card reader, burn that image onto the target cards using DD, boot up on the target Pis and edit the config as required.
Hint: If you're using a Mac, use
rdisk in the output file path to speed things up a bit.