I use NINA to automate skyflats in the AM. I can send you a screenshot of my sequence in a few days.
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Basically after imaging my mount parks at HOME and waits for the sun angle to get to the desired elevation.?
Once the sun is at the desired elevation the Advanced sequencer commands a:
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Slew to Alt/AZ - 90/90 (this slews the mount to zenith)
Tracking Stopped
then it starts to take the sky flats.?
After sky flats are done it commands a slew back to HOME.?
Ryan Noonan