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Created with Raphaël 2.2.04Dec330Nov29272625242320191817161211109876543231Oct30292827262523222120191615141312987652130Sep2928272524232221181716141311109876Create sub script for krakenfixed typoFixed version commandAdding multisample level gearsRename old Gears to GearsSingleUpgrade queue to 3.5Added plotFixed report with regionsFixed wrong tagStyle fixesMerge remote-tracking branch 'remotes/origin/develop' into shiva-refactorFixed vcf index filesAdded bam index file as output fileFix graph issuesAdded index to vt jobsRemove old codeStyle fixFixed haplotypecaller index filesFixed md5sumsFix dict generateCheck for bowtie2-Index files in bowtie2Check for bowtie2-Index files in bowtie2Fix bcftools executeablesFix vcf statsFix bowtie2 readgroupMerge branch 'fix-samplestsvtojson' into 'develop' changes in tool, since the checking for samples starting with a number went wrong.Fix default values and conditionals instead of optionalsFix typoStyle fixesMove mini pipeline dellyMerge branch 'feature-delly-merge' into shiva-refactorAdded CatVariantsStyle reformat after compilingSet defaults for Boolean values (missed the ignore_quals)Set defaults for Boolean valuesAdd bowtie2 to Mapping (and add wrapper for bowtie2)Remove whitespaceFixed outputDirsConvert breakdancer to sub pipeline of shiva