I use the following in my yml file. It concats the lcovs from karma and mocha, then sends them along.
after_script:
- ./node_modules/karma/bin/karma start
- istanbul cover ./node_modules/mocha/bin/_mocha server/api/**/*.spec.js
- cat ./coverage/lcov.info ./coverage/karma/**/*.info > lcov.info
- node node_modules/lcov-filter/index.js lcov.info config | ./node_modules/coveralls/bin/coveralls.js && rm -rf ./coverage