Instrument for processing cartridge for performing assays in a closed sample preparation and reaction system

An apparatus for processing and analyzing a sample comprising:

• a system that comprises a sample processing bay and an assay analysis module (AAM), the system including a processor coupled to a non-transitory computer readable medium, the non-transitory computer readable medium storing instructions directing the processor to:
• receive and read an Assay Definition File (ADF) from an external source comprising control parameters for processing a fluid sample, sensing parameters that are a function of a particular molecular detection taking place in the apparatus, and analysis parameters for analyzing the data, wherein the analysis parameters comprise the selection of one or more digital filters to be applied from a group of two or more digital filters to process the data;
• send control instructions based on the control parameters and the sensing parameters to the sample processing bay;
• send analysis instructions based on the analysis parameters to the AAM;
• receive the sample;
• utilize the ADF to process the sample;
• sense an analyte or molecule;
• and
• report results from sensing.