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Created with Raphaël 2.2.025Sep242322211817161413111098765432131Aug3029282726252423222120191817161514131211643130Jul28272423222117167632130Jun2928272625Fix 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 testfixadd cmd function to nicely format cmdLine in human readable formatFix importreformat some sentencesadded some extra information. Changed some typosadd root value to all children of ManweAdded FilePipesChanged menuannotate-bed and annotate-vcfManwe Datasources extensionsmove output argument to main Manwe class.manwe samplesAdding getting startedFix dirfix camelcaseChanged repo link of Gatkmanwe stubAdded support to have a pipe as input fileMerge branch 'fix-varscan' into 'develop'