Remove the need of merging the defaults anymore

.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

...cala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala

.../scala/nl/lumc/sasc/biopet/core/config/Configurable.scala

...c/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala

.../main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

...scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

.../main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala

...asc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala

...n/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala