Can a prenuptial agreement control child custody upon divorce?

My husband and I drafted a prenuptial agreement before we married that stated if we divorced, I would retain full custody of any children we have together. We did this because my husband has previously had mental health issues and we both agreed any children would be better in my care if we were no longer living together. We are now in the process of divorce and have two young children. He is saying he wants equal time with them and will not honor our agreement. How will a judge look at our prenuptial agreement in the divorce process? Can the judge still enforce it even if he no longer agrees? I want to be able to make the court aware of my husband’s past issues and the concern about the safety of our children if my husband challenges the agreement. Do I need to include anything about the prenuptial in my divorce filing?