I want to take a bunch or photos using RAW (without using indi / kstars, and then convert them to fits files that will be compatible with later lights, darks etc I take via kstars / indi. Then I can use them all in stacking software without confusion.

Can I convert RAW to FITS via command line or similar?

Why I want to do this:
I'm using a Canon EOS Ra and stellarmate
I have found that when running my camera through gphoto2, the camera quickly heats up when it is idle or taking short exposure photos (it cools down again when I start a sequence of longer exposures - 30 secs or more). This makes it really difficult to get a set of bias (in particular) frames at temperatures that match the lights / darks I take because it takes 2-3 secs per photo even when the exposure time is 1/1000 sec. The camera warms up by several degrees per minute while doing this, so I only get 1 or 2 frames at the temperature matching the lights, If I take a sequence of 24 bias frames, the sensor temperature will typically have risen by 10 - 12 C, and the readout noise is significantly worse.

If I take a burst sequence by hand of 24 frames, the temperature only changes by 1C at most. If I could then convert these to FITS that would match the other frames I take using ekos / indi it would make preparing Bias frames (and other short exposures frames like darkflats) much easier.

The heating up seems to be pretty much down to gphoto2, I have written a small test program that drives gphoto2 directly and as soon as I open the camera in gphoto2, the temperature starts climbing until I start taking longer exposure photos.

Siril can convert raw files to fits that are compatible with kstars/Ekos. Open Siril, click the Home button, select the folder with your raw files. Enter a name in the text box (eg. Bias) click the add button, select all your raw files. Click Convert and it'll be done in a few seconds - there'll be a Biasxxxx.fit file for each raw in the same folder.