Scanning a spring boot or shaded jar should be relatively simple.
> dependency-check.sh --project boot -l run.log -s /path/to/boot.jar -o .
If an error occurs, the contents of the run.log file will be helpful in figuring out what the problem is.
Note, dependency-check only supports Shaded Jars - other tools like onejar, uberjar, etc. do not appear to include enough information to identify the combined dependencies.