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

Adding a timeout to testing

Fix biopet 546

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