Merge remote-tracking branch 'remotes/origin/develop' into feature-qiime

biopet-aggregate/copy-src.sh

biopet-aggregate/pom.xml

biopet-aggregate/rm-src.sh

biopet-aggregate/src/.gitignore

...umc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala

...mc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala

...main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala

...nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp

...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

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

...e/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala

...ain/scala/nl/lumc/sasc/biopet/core/SampleLibraryTag.scala

...in/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala

...c/biopet/core/extensions/RscriptCommandLineFunction.scala

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

public/biopet-core/src/test/resources/fake_chrQ.dict

public/biopet-core/src/test/resources/fake_chrQ.fa

public/biopet-core/src/test/resources/fake_chrQ.fa.fai

public/biopet-core/src/test/resources/fake_chrQ_no_index.fa