How are CQL queries run?

You can use CQL with any data model. The examples in the Cooking with CQL, QDM, and FHIR® sessions are focused on using the Quality Data Model (QDM), which has a serialization as Quality Reporting Document Architecture (QRDA). QRDA is similar to the consolidated clinical document architecture (C-CDA) standard. QRDA and C-CDA are HL7 V3 standards.