Merge remote-tracking branch 'origin/develop' into feature-pipeable

Conflicts:
	public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
	public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala
	public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VepNormalizer.scala
	public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
	public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala