Add master script to run end-2-end example

To be able to create a Nextflow pipeline, I will need to have a master script file 
https://github.com/raphael-group/hotnet2/blob/master/paper/paper_commands.sh

UPDATE:
@wanpinglee Can you assign this to you? 
I am checking the Genome in a Bottle bams now and I will subsample one to be able to progress with this this week.