Addec config option to disable merging of countfiles



See merge request !392

Fix vcf filter test

Try to solve #333 with this

See merge request !386

Fix reporting of found Adapters with counts by Cutadapt in Json.

the adapters used by Cutadapt were not reported in the json. This fix will solve this.

fixes #319 
fixes #325 

See merge request !369

Fix gatk extension cleanup

Fixes #336 

See merge request !390

Toucan groups

Fixes #315 and adds some for #324 

See merge request !385

Added grep as extension



See merge request !388

Added exclusion for gatk tools

This is related to #332 

See merge request !382