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Created with Raphaël 2.2.022Sep211817161413111098765432131Aug3029282726252423222120191817161514131211643130Jul28272423222117167632130Jun2928272625242322Added a sum of memory and threadsAdded the -T argAdded executable to commandMerge remote-tracking branch 'origin/develop' into feature-pipeableUse piping after bwamemMade output of bwamem pipeableAdded samtools sortMade codeMemory readable from outsideAdded more to code styleStart on dev docsFix reference in varscanMerge branch 'feature-input_files_checking' into developMerge branch 'fix-remove_temp_files' into 'develop' Merge branch 'fix-sample_flag_summary_report' into 'develop' This will remove tempfiles on exitMerge branch 'feature-gatk_et_option' into 'develop' Still executes multisample jobs when all samples are given with --sample flagFix summary when --sample flag is used in multisample pipelinesMerge branch 'fix-report' into 'develop' Merge branch 'feature-external_examples' into 'develop' Fixed unit testsFastq sync is not intermediateFix protected packageAdd commentFixed case classChange nameAdd input files to pipelinesskip canRead when file does not existFastq sync is not intermediateDisable default toucanAdding input files to checkFix protected packageFix protected packageFix error cacheCode style fixFix importsSync with develop and fix build issuesFix importsMerge branch 'develop' into feature-cnvpipelineFix extensions