There are no new features nor behavior changes in CWL v1.2.1 as compared to CWL v1.2.0. v1.2.1 fixes only typos, adds clarifications, and adds additional conformance tests. Some changes to the schema defining CWL have been made to aid the auto-generation of libraries for the reading and writing of CWL documents.
Documents should continue to specify cwlVersion: v1.2. However, when reporting results from running the CWL conformance tests, please do report all three components; for example "99% of CWL v1.2.0 required tests" or "100% of CWL v1.2.1 required tests".
For full details, see the CWL v1.2.1 changelogs for the Workflow and CommandLineTool standards.