Added more filter options

fixes #316 

See merge request !410

remove gatk-specific parts from license

Fixes #343 

@h.mei @p.j.van_t_hof Could you check this? Thanks :-). 

See merge request !406

Fix mapping plot in report

Fixes #349 

See merge request !411

Somehow the rootpath was broken

fixes #347 

See merge request !408

Fix vcf files from SV calling output to contain samplename

The SV callers in our pipeline name the samples 'default', ideally all of these 'default' should be named to the sample called accordingly. Otherwise we have issues later on in the SV merging.

fixes #321 

See merge request !365

Added check on unused config values

Fixes #327 

See merge request !400

Added singletons to summary



See merge request !404

Reference index generation



See merge request !396