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

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

...umc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

...ain/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala

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

...scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

...rc/main/resources/nl/lumc/sasc/biopet/extensions/cnmops.R

...ain/resources/nl/lumc/sasc/biopet/extensions/cnmops_wes.R

...rces/nl/lumc/sasc/biopet/extensions/freec/freec_BAFPlot.R

...rces/nl/lumc/sasc/biopet/extensions/freec/freec_CNVPlot.R

.../sasc/biopet/extensions/freec/freec_assess_significance.R

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

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

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

...in/scala/nl/lumc/sasc/biopet/extensions/freec/FreeC.scala

...biopet/extensions/freec/FreeCAssessSignificancePlot.scala

...a/nl/lumc/sasc/biopet/extensions/freec/FreeCBAFPlot.scala

...a/nl/lumc/sasc/biopet/extensions/freec/FreeCCNVPlot.scala

...ala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala

...umc/sasc/biopet/extensions/sambamba/SambambaMpileup.scala

...main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala