If whole run is to be covered, I would go with green translucent. If part only, I would go with sheet metal. For skylight in coop, I would go with white, not clear. In that case, (skylight for coop) I would use a nail-down plastic bubble type, two surfaces to avoid it sweating. Use flashing all around and caulk into place using Sonneborne N P 1 sonolastic caulk. I would also make a place to put an interior panel to block most light in summer for keeping heat down.