Is there a way to leave the phone plugged in, but schedule when to actually charge it? Under my normal daily use, my phone would have around 50~40% battery power left before I go to sleep.  I don't want to keep my phone plugged in to charge over night, but I do want it to be at 100% when I wake up.  Is there a way to disable charging while it is plugged in, and re-enable at a scheduled time?  i.e. one hour prior to I wake up.

Nexus 6 32GB rooted currently running CHROMA, using Motorola Turbo Charger.
Why don't you want to keep the phone plugged in overnight? Per Is it better to detach a charger when my Android device gets fully charged?, it sounds like sitting at 100% on the charger for ~6 hours is not considered harmful to the lithium-ion battery in your device.

That said, you can purchase a light timer for under $20, set it to only turn on for an hour or two in the morning, and plug your charger into it at night.

But actually, if your phone drains by over 50% during the day, this is probably not the ideal solution, because allowing the battery to drain further overnight until the timer kicks on means that it will discharge even more deeply than it currently does, which will wear down the battery's capacity far more quickly over time than being at 100% charge for 6 hours per day will.
So an optimum cycle might be to charge it to 100% in the afternoon, when it's only down to, say, 70% charge, instead of waiting for bedtime; and then put it on the timer as described above when you go to bed. Just be sure to give it a full discharge occasionally (once every 2-4 weeks sounds about right based on your usage).