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Created with Raphaël 2.2.029Sep282725242322211817161413111098765432131Aug3029282726252423222120191817161514131211643130Jul28272423222117167632130Jun2928272625Merge remote-tracking branch 'origin/feature-gears' into feature-gearsAdding KrakenToJSON tool, converting the kraken format to JSON.Added set limits to bash scriptFix for #210Merge remote-tracking branch 'origin/feature-gears' into feature-gearsoutput flag should be output-filenameChanged own vmemAdding summary statsFixed resourcesautogenerated stylesSet remote command for local executionAggregate threads and corememory for pipesCatch NullPointer from queue and convert is to null instead of an failureMoved codeHide null pointen from unit testsFixed single-end runsOverrider default shell from queueAdded depsFix fastqc dependencyFixed QcCommandadded scripts to copy sourcesMerge remote-tracking branch 'origin/feature-gears' into feature-gearsFix sambamba, all config must derive from 1 key only: "sambamba" (for all sub commands)replaced --output option definition + replaced with ,Added aggregate option for scoverageremoved qscript keyAdded gears as optional step into mappingRefactoring of gearsMerge remote-tracking branch 'origin/develop' into feature-scoverageRemove some test from shiva-gatksamples testingfix sample showfix importbedfix samplesImportmove old classes for later useAdded Aggregate moduleMove breaking classestiny fixdata sources testfix