We use a Ge-Si core-shell nanowire to realise a Josephson field-effect transistor with highly transparent contacts to superconducting leads. By changing the electric field we gain access to two distinct regimes not combined before in a single device: In the accumulation mode the device is highly transparent and the supercurrent is carried by multiple subbands, while near depletion supercurrent is carried by single-particle levels of a strongly coupled quantum dot operating in the few-hole regime. These results establish Ge-Si nanowires as an important platform for hybrid superconductor-semiconductor physics and Majorana fermions.