Closed FelixMoelder closed 1 year ago
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.
Ah, never ming. @johanneskoester just explained it to me. The actual filtering happens via the get_filter_targets
function result in params.filter_targets
.
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.