Abstract: Described embodiments relate to a chemical processing instrument configured to receive one or more sample cartridges, to process one or more corresponding fluid samples. The chemical processing instrument comprises: a reagent dispenser configured to dispense one or more fluid reagents into a reagent vessel via an open top of the reagent vessel; and a pneumatic module configured to connect to a primary pneumatic port of a primary reaction vessel and selectively adjust a pressure within the primary reaction vessel when the lid is closed to draw fluid from the reagent vessel through a primary reagent channel into the primary reaction vessel.