Remove required from config calls

...ala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala

...ala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

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

...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

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

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

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

...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala

...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala

...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala

...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala

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

...st/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala

...la/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala

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

...n/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala