EASTER IS COMING: Was Jesus really nailed to the cross? (Meredith J. Warren, The Conversation). The Gospel of John (20:25) is the earliest source to assert this explicitly, although (not noted in the article) Luke 24:39-40 (40 may be secondary) imply there was something notable about the resurrected Jesus' hands and feet, presumably nail scars. But these sources were written long after the event and we don't know what actually happened.
Some past posts dealing with the macabre structural mechanics of crucifixion by nailing are here, here, here, here, here, and here.