It is possible to use scripts to pre-process the new images automatically for example at the end of the nightly sequence.
You can now have your pre-processed files ready and immediately start the interesting part of the process. 😉
There is standard script you can use directly or if you have very specific needs you can modify them to make your own.
See here: https://www.ap-i.net/ccdciel/en/documentation/image_preprocessing