Merge with develop

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

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

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

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

.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala

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

...la/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala

...la/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala

...asc/biopet/extensions/breakdancer/BreakdancerCaller.scala

...c/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala

.../nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala

...cala/nl/lumc/sasc/biopet/extensions/conifer/Conifer.scala

...la/nl/lumc/sasc/biopet/extensions/delly/DellyCaller.scala

...main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala

...la/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala

.../nl/lumc/sasc/biopet/extensions/kraken/KrakenReport.scala

...in/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala

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

...la/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala

...in/scala/nl/lumc/sasc/biopet/extensions/seqtk/Seqtk.scala