Gomis had been forced to train away from the first team during the speculation but maintains that his departure will be amicable.
"I will stay until the end of the season," he told RMC.
"It was complicated but there is not problem. I have the confidence of managers and coaches. Everything that happened is ancient history. I will give everything for Lyon.
"You cannot erase everything that happened, but we have a common goal."
Gomiz scored as Lyon lost 2-1 to Monaco on Sunday.