Add flag to select tool used for marking/removing duplicates

[JulianMohr]

I would suggest to add a new flag, with which you can select the tool used for marking or removing duplicate reads. The choices would be then

1. picard (in particular MarkDuplicates) or
2. sambamba (in particular markdup).

With this feature, the pipeline remains backwards compatible to users who want to run Picard's MarkDuplicates for any reason, but who similarily want new updates or features introduced in later versions than v1.9.1.