I have found Google provides some guidelines on how to run Nodejs on a custom runtime environment. Everything seems fine and I am managing to start my Nodejs app on local machin
As far as I can see, you need to provide the parameter --debug-brk= to node upon startup - this will enable debugging. After that, access the specified port on your docker container. You probably have to expose it or tunnel (using ssh).
After that, point the Webstorm remote debugger at the specified port, and you should be set.