Conflicts:
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

Feature fix missing values

Fix for wrong messages when config value does not exist

Now also fix for #112

See merge request !89

Make a val for globalConfig, test should now be able to override it so unit test are not depending on a global var

Patch flexiprep fastqc

Found another bug because of incorrect type usage, which makes the pipeline output paths like `/my/path/Some(file.txt)` when it should be `/my/path/file.txt`. This pull request should fix it.

See merge request !91