A system for performing a nucleic acid amplification assay that includes a receptacle holder formed from a thermally conductive material and having a receptacle well for receiving a lower portion of a vial; a thermal element for cycling the temperature of the receptacle holder; a signal detection module in optical communication with the receptacle well; and a robotic pipettor. The receptacle holder supports a capped vial having a plastic, opaque cap in a snap-fit with a single plastic vial containing a nucleic acid amplification reagent. An upper portion of the cap includes a probe recess that is configured to be removably engaged by an end of a probe of the robotic pipettor. A lower portion of the vial is contained within the receptacle well, and the cap is situated above a top surface of the receptacle holder.