Upgrade to scala 2.11

(cherry picked from commit b75b9047)

(cherry picked from commit e4baa723)

Fix biopet 607 2

Fixed BIOPET-584

Improved phrasing

Adding more output files to bamstats

compiling ssp-template files with scalate

no need to copy the template from classpath to a file, TemplateEngine is able to access the files also from there, and it's able also to find precompiled template classes when it's given the path to the ssp template

Test fail on format/git issues

# Conflicts:
#	Jenkinsfile

Changed VCFstats to check whether outputDir is a valid directory.