I didn't see it explicitly stated, but hope (using GNU-make nomenclature) that outputs are targets and are checked in the same way and not remade if extant? This is handled using file timestamp in make, which is checked to specify whether to remake. Can you point to documentation on this if it exists for WDL?
Also is there forthcoming support for Docker (currently tagged as 'Broadies Only'). Would be great to get a Docker for 'standard' GATK processing direct from here.