[1.12.2] only run matter fabricator with scrap

There is not a setting for it, but you could detect the amount of scrap in a buffer with a comparator and apply a redstone signal to the massfab ifthe amount of scrap in the buffer is too low.

Since you're using 1.12, sort of. Right now the Mass Fabricator will only work when given scrap, but it will take 1M EU to produce UU (ie the scrap has no bonus multiplier) and produces solid UU. It also has no recipe, nor does the UU Assembly Bench which is designed to turn the solid UU into useful things. So if you wanted you could add your own recipe for it, a recipe to convert solid UU into liquid and then just drop the energy requirement in the config for UU down to 1/6. The Matter Fabricator doesn't have any option for scrap only operation.

If this is more of an in world only run it whilst it has it question rather than a balance one, the Matter Fabricator will output a comparator signal whilst it has scrap. So you could connect one of those, invert it (using a simple redstone torch NOT gate) then loop it back. You'll most likely need a redstone repeater as the signal will be weak if there's not much scrap left (although you might want this), but it will stop when given a redstone signal.

Ah, sniped by Aroma

I think you could only use the MASS fabricator by cheating / debugging.

HOWEVER, if you are willing to have 64 scrap unused, you could have an external storage with Redstone output, such as the hopper. The MATTER fabricator would always have 64 scrap, but once the hopper ran out, it (or a comparator) would stop sending a signal. You could use that signal to stop the matter fabricator.

I have not done this, so please use my wordsonly as an idea on what to actually design