Merge branch 'develop' into feature-FilterOnMappingQualityCarp

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

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

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala

.../sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala

...asc/biopet/extensions/picard/CollectMultipleMetrics.scala

...test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala

.../main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala

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

...a/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala

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

...cala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala

...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

.../lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.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