The public app on DNAnexus just runs the standard pipeline, equivalent to CNVkit's batch command. The app doesn't provide a way to run sub-commands like call.

However, the only step of the pipeline that is particularly resource-intensive is the coverage command, which is the first step in batch. Once you have the .cnn files from the cnvkit_batch app (and ideally .cnr and .cns, to save yourself some typing), you can easily run the rest on a laptop, even for WGS data. Try installing the cnvkit package with conda/Anaconda, or use the Docker image if you prefer. Either installation approach will give you access to the call command and the rest of CNVkit's functionality.