Shopify is partnered with many payment gateways in Nigeria. @Zworthkey listed a few and you can see the full list of them from the help guide here.
It's definitley worth your while to research some of them and make sure you have the right fit for your business. Shopify wouldn't have any control or say about what these gateways allow as they are independent and third party.
How have you found Shopify so far? What are looking to sell? I'm here if you have any other questions!