Merge remote-tracking branch 'origin/develop' into fix-BIOPET-593

.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

.../test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala

...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Awk.scala

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

...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala

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

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

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

...c/main/scala/nl/lumc/sasc/biopet/extensions/GffRead.scala

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

.../scala/nl/lumc/sasc/biopet/extensions/GtfToGenePred.scala

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

...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Sed.scala

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

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

...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala

.../lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala

...mc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala

...l/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala

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