Patch aln wrapper threads

@p.j.van_t_hof, @wyleung, and @a.h.b.bollen ~ for the threads behavior that we saw earlier today

See merge request !124

Feature test coverage

Removed aggregated scoverage module, now not breaking packaging anymore.

See merge request !117

Patch toucan

Fix output directory path in Toucan

See merge request !123

Conflicts:
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
	public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

Feature shiva

This will become a new version of the variantcalling pipeline.

See also issue #116 and #119

See merge request !110

Feature rcommandline

R commandline function cherry-picked

See merge request !121

Conflicts:
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala

Conflicts:
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/RscriptCommandLineFunction.scala

Patch mapping

Fix for #122

See merge request !120

Patch summary versions

Fix for Some(versions) in summary

See merge request !118