A container for holding items to be microbially deactivated in a reprocessor. The container is comprised of a generally cup shaped tray having a bottom wall and a continuous side wall extending to one side from the periphery of the bottom wall. The bottom wall and the side wall defining a cavity for receiving instruments and items to be microbially deactivated. A lid is attachable to the tray. The lid is dimensioned to cover the cavity. An inlet port is formed in the tray to communicate with the cavity. An outlet port is formed in the tray to communicate with the cavity. A barrier element is disposed within one of the ports. The barrier element controls flow through the one port. The barrier element is comprised of a material that is permeable to gas and water vapor but impermeable to liquid, bacteria and organisms. The barrier element is movable between a first position wherein fluid flow through the one port is restricted to flow through the barrier element a second position wherein fluid flow through the one port is unrestricted.