Medaka output for consensus chromosomes is split into 2 subdirectories

[georgiesamaha]

Flye and Trycycler output different files as they employ different methods. Trycycler consensus assemblies are output in a confusing way at the cluster level, rather than the barcode level. Can these be combined or output to the same directory? It is not readily clear to the end user what clusters are and why they are to be kept separate.