Clean up some old code #287

Job	Run time
quick-tests (sanity)	4m 20s
quick-tests (dry-run)	3m 59s
quick-tests (utilities)	4m 7s
quick-tests (report)	4m 5s
quick-tests (scripts)	4m 13s
functional-tests (qc-seq)	12m 0s
functional-tests (snv-indels)	20m 57s
functional-tests (itd)	11m 17s
functional-tests (fusion)	11m 42s
functional-tests (test-hamlet-targetted-RNA)	39m 13s
functional-tests (test-hamlet-chrM)	49m 18s
	2h 45m 11s

Provide feedback