Feature tarmac pipeline

Fixing config value

Recessive calls

parsing conf for the info which tumor samples match with which normal samples, for the case when this info is given with sample tags: samples -> <sampleName> -> tags -> type

Fixing broken link in carp

Fix biopet 685

Update mvn_scalafmt

Remove manual report call - maven plugin now does this

Fix file extension

Adding a tool to collect coverage from multiple bam files

Adding a tool to extract tags from a gtf file