there are a few ways to do this. the simplest is to follow the regular flow, being careful to select "SuperPixel" as the debayering method. other debayering methods will work, but they of course interpolate the data for the missing pixels in the bayer matrix. there are some debayering methods that look at, say, the G channel while processing the R channel, which would be a disaster here (no real signal in G which would then corrupt R). however i don't think PI implements any of those methods.
if you want to get fancy, you can try to split out the red channel early in the flow so you're not carrying around the G and B channels, unnecessarily costing disk space and processing time.
one method is to calibrate only, then use the BatchChannelExtraction script to pull out the red channel of each calibrated light.
a more advanced method is to use the SplitCFA process to extract the individual R, G, G, B images from all your input files (lights, flats, darks, bias) and then throw away the G,G,B images and proceed with calibration, registration and integration of the R images as though they came from a mono camera. however, this will require the use of ImageContainer which would allow SplitCFA to run as a batch process.
rob