Over on Michael Niehaus' Windows and Office deployment ramblings, Michael has documented how to deploy Nano Server by following four steps which I have listed below, but read his post to get the full details. Don't forget that Nano Server capabilities are included with Windows Server 2016 Standard and Datacenter, but it's important to note that you need Software Assurance if you are applying Nano Server in production.
Set up MDT with updated files to deploy a Nano Server OS.
Use the Nano Server Image Builder tool to create a Nano Server WIM that MDT can deploy.
Create the task sequence in MDT to deploy.
Deploy (using PXE, media, etc.).
He was even kind enough to make a video, and edit out the boring bits.