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.
not mega priority but I love when complex pipelines check the existence of this things at the very beginning. It is alway good to double check this also while running but it would be great have a small function testing that all needed variable are in place and make sense (e.g., check that the reference file exists)