Patch summary versions

Fix for Some(versions) in summary

See merge request !118

Patch seqstat

Fix for #121

See merge request !119

Conflicts:
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetrics.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetrics.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala

Feature scaladocs

Added scala docs to all extensions, utils and pipeline template.

See also #37

See merge request !116