Fitswork 4 works for me. It has a batch mode.
For debayering/converting to TIFF's.
Fitswork is not very straightforward but I figured it out.
Here's how to batch convert to TIFF (tiffs then can be converted to jpg elsewhere).

-- open Fitswork.
-- go to Settings | Save and make sure Scale TIFF Images is unchecked.
-- open one of your fits files in Fitswork.
-- go to Processing | Bayer Interpolation | Demosaic Camera Raw Image
-- select Linear Interpolation or Bayer Astro (didn't investigate the difference)
-- set your Bayer pattern (RGGB etc)
-- click on the Save button to save your Debayer settings to a *.fcm file. Then Cancel.
-- go to File | Batch Processing.
-- Start File - select the first file of your sequence. Fitswork will pick up the rest.
-- Destination File - anyname.tif - you need to specify the extension! *.tif will be saved as tif. *.jpg willl be saved as jpg.
-- All Files in Folder - unticked. Skip absent - ticked.
-- Click the arrow on the right (next step)
-- Choose Processing Function | Debayer Raw Images | Open the *.fcm file you saved before
-- START and you're done.

I just tried to convert to JPG and it didn't work (got white images) - maybe Fitswork settings can be adjusted to work with JPG.

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