Merge remote-tracking branch 'remotes/origin/develop' into fix-coverage_piping

.../lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala

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

.../main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala

...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala

...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala

...n/scala/nl/lumc/sasc/biopet/core/ToolCommandFuntion.scala

...ore/src/main/scala/nl/lumc/sasc/biopet/core/Version.scala

...in/scala/nl/lumc/sasc/biopet/core/extensions/Md5sum.scala

...scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala

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

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

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

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

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

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

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