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Created with Raphaël 2.2.020Jan1918171514121110865430Dec29282625242322211817161514131110764330Nov29272625242320191817161211109876543231Oct30292827262523222120191615141312Add pindel2vcf to pipelineMerge branch 'fix-260' into 'develop' Added cufflinksFixed typoAdded htseqCount jobAdded files to summaryFix bwa bug using freeVar=falseRevert "PindelVCF wrapper", does not belong to this branchPindelVCF wrapperPindelVCF wrapperAdded heatmap plotAdded general mergingMerge remote-tracking branch 'origin/feature-VarscanIntoShiva' into feature-VarscanIntoShivatypoMove script and init to main traitSet up more defaults.Merge branch 'fix-259' into 'develop' Style refactor of PindelCaller wrappersmallRNA pipelineIntegrating developRemove pindel from the list of default callersFixed unit testsAdded varscan_jar to test configRaise default memory for varscanAdded version to varscanAdded version to varscanFixed error message in bamutilsFixed styleMerge branch 'feature-update-cutadapt' into 'develop' add varscan test to shiva variantcalling testmove varscan wrapper to extensionsUpdate Cutadapt wrapper and style change (camelCaps instead of _)Update Cutadapt wrapperchanges to get rid of reference callsRefactor styledelete file name file on exit of pipelinechange sample name in varscan vcfremove function removeEmptyPile()Pindel outputpath fix.added fix mpileup.py scripts to scripts dir in shiva