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

More unit tests



See merge request !403

Init bed check

fixes #298 

See merge request !401

Changes arg parser with getOrElse(throw new IllegalArgumentException)

Fixes #342 

See merge request !402

Fixed fifo job names

Fixes #334 

See merge request !399