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Created with Raphaël 2.2.023Sep22211817161413111098765432131Aug3029282726252423222120191817161514131211643130Jul28272423222117167632130Jun29282726252423Adding getting startedFix dirfix camelcaseChanged repo link of Gatkmanwe stubAdded support to have a pipe as input fileMerge branch 'fix-varscan' into 'develop' Remove count testsRefactor flexiprep, more pipes are used nowAdding a QC commandRemove intermediateFixed output pipelineReference is not used in hereBetter memory handling for pipesRemove old codeAdding classpath and memory to beforeGraphConvert mapping to sortsam for pipesConvert pipe to SortSam againChange temp filesFix compile errorsMoved sam filestyle changeAdded 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 pipelines