Clear output directory before resuming

[TCLamnidis]

With each successive reprocessing, more and more files get added to the output directory, but do not always overwrite the previous processing, since more sequencing data might have been added that trigger e.g. a libmerge bam to be created instead of a library bam.

This means end users need to be careful what data they use to ensure they are using the latest output.

TODO

Test if deleting the contents of the eager_output directory does not break resume, to only outputs from the same runs within the directories, instead of parts from different "versions" of the output all together.