I wrote a post some time ago back in October 2015 on how to run a Minecraft server on Debian 8. You may find this useful? It is rather old now so I'm not completely sure how relevant it still is.

• Installing Minecraft Server on Debian 8

You're looking for something like screen to keep the SSH session persistent. Context on these two commands below is given in the above link.

sudo apt-get install screen 

screen ./run-minecraft-server.sh

There are other choices outside of screen but this should suffice.