A roof cap assembly for a fuel cell system includes a housing, and a cover assembly disposed on the housing and configured to move between a first position and a second position. The cover assembly includes a cover comprising a first opening and a second opening, and a door connected to the cover and configured to selectively open and close the second opening. When the cover assembly is in the first position, the door closes the second opening, such that the reaction exhaust and the cabinet exhaust are directed through the first opening. When the cover assembly is in the second position, the door opens the second opening, such that the cabinet exhaust is directed through first opening and the reaction exhaust is directed through the second opening.