Run errthing like it's a sample

So this basically just runs variant calling always all the time. Things I still need to add include:
 - If we get new data and sample analysis is already running, I need to notify somebody to decide what to do manually (probably by setting a flag in Charon)
 - This doesn't yet actually parse and of the alignment results or populate Charon with the coverage information (do we need to do this?)

There's probably some other stuff I'm forgetting but it's ready to test.
No in this case it's in a for loop so it is indented properly