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Created with Raphaël 2.2.04Dec330Nov29272625242320191817161211109876543231Oct30292827262523222120191615141312987652130Sep292827252423222118171614131110987Convert gears to subscriptsCreate sub script for extract unmappen readsCreate 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 whitespace