GitLab

Fix biopet 582

Fix adapters fetch from fastqc

when no variants have been found then CatVariants now outputs a file that does have VCF-file header lines

gatk.tools.CatVariants outputs an empty file when input files don't contain anything, added a script that writes 2 VCF-file header lines to that empty output file

when Delly doesn't find variants from data then it doesn't generate an output file either, in Biopet it's needed that there would be at least an empty VCF-file after running the tool, so added script that does that, generates an empty VCF file when Delly hasn't found anything

Adding possibility to change metrics on preprocess bam

Centrifuge documentation changes.

Fixing dependency issue

Disable merging for specific variantcallers

Fixing GATK 3.7 compatible extensions