Substrate processing apparatus having a transport chamber, a linear array of substrate holding modules alongside the transport chamber, and a substrate transport located in the chamber. The chamber can hold an isolated atmosphere, and defines more than one substantially linear transport paths extending longitudinally along the transport chamber. The transport in the chamber is capable of transporting the substrate along the linear transport paths. The transport has a transporter capable of holding and moving the substrate. The transporter interfaces a wall of the transport chamber for moving along at least one of linear paths. The transport chamber has interfaces for mating with other substrate holding modules at opposite ends of the transport chamber. Each interface has an opening through which at least one of the more than one linear transport paths extends, and the transport chamber has a selectably variable longitudinal length between the interfaces.