General refactor Biopet

...sc/biopet/core/extensions/PythonCommandLineFunction.scala

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

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

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

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

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

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

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

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

.../scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala

...scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie2.scala

...asc/biopet/extensions/breakdancer/BreakdancerConfig.scala

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

.../lumc/sasc/biopet/extensions/conifer/ConiferAnalyze.scala

...ain/scala/nl/lumc/sasc/biopet/extensions/gmap/Gsnap.scala

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

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

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

.../nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala

...nl/lumc/sasc/biopet/extensions/qiime/AssignTaxonomy.scala