Feature reorganize config

Step 1 for #89

First check this before i start writing unit tests

See merge request !57

Feature skip analyze covariates

Workaround for #17

See merge request !55

Feature multiple configs

see #88

See merge request !54

Feature runplot

for solving issue #17

See merge request !56

Feature fix disable mpileup

Small change in pipeline to skip raw caller

See merge request !53

Conflicts:
	biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
	biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

Feature no output test

For #58

See merge request !52

Feature basty generate fasta

for #31

See merge request !51