I only Found a way to do that manually every time from the start.
I write code in angular2 with webstorm 11.
As Adrian said your transpiler needs to produce map info, which can also be generated into the js output file instead of a separate .map file.
One issue you may run into is that within lambda functions (aka arrow functions) you will not be able to see your variables, neither in chrome nor in WebStorm.
However, there is a setting in WebStorm that allows you to see your
this. variables properly within the WebStorm debugger:
Find Action, enter "registry".
In the registry check