# Conflicts:
#	Jenkinsfile

Changed VCFstats to check whether outputDir is a valid directory.

Remove hard-coded settings in XhmmMatrix.

Improvement biopet 561

Fix biopet 585

Fixed that the timeout in on node time instead of including queue time

added some if-s so that sv calling wouldn't fail when there's only one sample or when only one tool is being used for the analysis

Adding a timeout to testing

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.