Tools like tar accept a path to a compression tool by using --use-compress-program
It would be good if FLASH could support something like this as I'd be able to use pigz to make use of some of the 64 cores I have available! I'm not sure how tools like tar handle command line arguments that should be passed to the compression tools. e.g. number of threads etc.
I implemented this for FLASH-1.2.4. The option is --compress-prog (and also --compress-prog-args and --output-suffix). Test it out and let me know if there are any problems!