Only run C preprocessor in cmake?

I'm trying to use cmake to simplify distributing my OpenCL program. I have a kernel file which includes several headers and other source files, and I want to have a single self contained executable.

My plan is to have cmake run the C preprocessor on the kernel source, turning the cl file and its includes into a single unit which is easier to work with.

I can use add_custom_command to do it by calling gcc/clang with -E, but then I don't get the flags to include the right directories to find the various header files in the command, and I don't see an easy way to find all current include directories to use in the custom call to the compiler.

Is there a way to run only the C preprocessor on a file with the current cmake environment?