NGI_pipeline first working version

This is a real working version of the NGI pipeline to run piper.
  - need to find consensus on folder name convention, right now it is overcomplecated
  - rerun --> sthm2UUSNP fails if re-run: NGIpipeline must handle this case
  - what happens when multiple samples are present.... we will see monday
Create a new directory as sthlm2UUSNP doesn't choke on the non-standard filenames