Nile cruises run between Luxor and Aswan in both directions — some itineraries sail from Luxor to Aswan, others the reverse — and the Nile cruise fleet operates specifically within that Upper Egypt stretch of river. The set of sites visited along the way is generally the same either way; it's the order that changes.
Why direction rarely matters much
In practice, direction rarely matters much to the traveler experience — the same temples, the same river scenery, the same onboard routine. What matters more is which city bookends the rest of your trip, since that shapes your flight connections; see How Do You Get From Cairo to Luxor? for the transport options at either end.
If you're combining the cruise with time in Cairo beforehand, starting in Luxor and ending in Aswan, or the reverse, is mostly a question of which flight or train connections work best for your overall itinerary rather than anything about the cruise itself.