fix: correctly filter target regions

[FelixMoelder]

The filter group regions filters covered regions against a set of target regions if existing. If the target regions file exists filtering is done by bedtools intersect defined by {params.filter_targets}. In its current implementation the covered regions and target regions are being concatenated. This way we would end up with the whole set of target regions but also duplicate entries.

[dlaehnemann]

Looking through the commits that happened while I was away, I came across this one. I think we need to revisit this, as the rule's shell code now simply doesn't use {input.predefined}. So instead of using cat, we should probably be doing a proper bedtools intersect, here. I'll look into it when I'm officially back from vacation tomorrow.

[dlaehnemann]

Ah, never ming. @johanneskoester just explained it to me. The actual filtering happens via the get_filter_targets function result in params.filter_targets.