WIP Piper node mode

This doesn't handle sample-level job tracking yet w.r.t the database and also I need to add a Charon update into the sbatch file before checking the coverage to see if we can proceed with sample analysis, but the rest of it seems to work. I'm aware that parts of it are a little hacky (#fix later) but I'm open to suggestions for improvements as well.
I am seriously too tired now to follow this.... Monday we need to sit down go through the workflow (like sketch down a flowchart) so we know what is happening. In this way it will be easy to decide Charon fields