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.
Here I also need to change this so it wil copy in any pre-existing alignment data before the sample processing can begin. I'm gonna think a little about when this should happen but again I'm open to suggestions.