Change to option types

...ain/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala

...l/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala

...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

...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala

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

.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala

...src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala

...ain/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala

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

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

.../nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala

...l/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala

...nl/lumc/sasc/biopet/extensions/picard/MergeSamFiles.scala

.../scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala

...la/nl/lumc/sasc/biopet/extensions/picard/SamToFastq.scala

...umc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala

...scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala

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