Omprep produces the first intermediate image file, by converting the integer image in a raw image file into a real image and adding some keywords to the fits header. Omcosflag then adds a Quality image to this same file. Omflatfield then flatfields this image by dividing it by the master flatfield produced by omflatgen.
Please note that the latter image is only produced if there are 3 or 4 engineering-2 exposures.