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If rats can get in your coop, you might want to plug up the holes in both the coop and the run. Good idea to do that anyway, because if a rat can get in, so can a lot of other more lethal predators. If your coop is open and you free-range, I don't know what can be done.
I have the same issue for the past 2 weeks, I put a big rock in the hole, and fill it, he makes a new one. I added 10" of chicken screen down and over, it stoped him for a couple of days, now he found the edge and made a new tunnel. I put Cayenne pepper last night, I'll see how that works, I'll let you know.