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Darktable will process the cr2 files. You can invert the image using the contrast setting on the lowpass filter. You could also search youtube for developing negatives with darktable.
Better answer - Use the invert module in darktable. It's in the basic group, but you may have to add it from the more modules at the bottom
darktable does have a pretty steep learning curve. I've been using it for over a year and I'm still learning lots of things. If you brought a lot of images into darktable you could process one, copy the history stack from it, then paste the stack to the rest and they would be processed the same.