Merge branch 'develop' into feature-scoverage

.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

...cala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala

public/biopet-extensions/pom.xml

...umc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py

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

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

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

...ns/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Pbzip2.scala

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

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

...c/main/scala/nl/lumc/sasc/biopet/extensions/Sha1sum.scala