On a rooted nexus device with Lollipop (Android 5.0) the common OTA-updates fails. The reason is: there are some additional security checks while the OTA-update, which fails on rooted devices.
But if you know how to handle the adb-tools, it’s easy to make a manually update. Just download the matching factory image for your android device and extract the following files: boot.img, recovery.img and system.img.
adb reboot bootloader fastboot flash system system.img fastboot flash boot boot.img fastboot flash recovery recovery.img fastboot format cache fastboot reboot
That’s it! All your private files won’t be deleted.
I’ve tested it with my nexus 10 and I couldn’t guarantee that this is true for other devices.