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Created with Raphaël 2.2.030Jun29262524232219181716151211109854228May20191815141311876130Apr282120151410987632131Mar3026252423201918161312119325Feb2420131211107654331Jan302928272423222120171615141310987617Dec12111096227Nov262519765131Oct3028159872127SepUse memory requirements based on WGSUse memory estimates from WGS sampleupdate sambamba memory requirements and parameter_metaFix bwakit commandSwitch sorting to samtools. Do not index as it is not required for marking duplicatesMerge pull request #225 from biowdl/pbmm2Remove additional thread nonsensecorrect additional threadsfix sambamba threadsuse validation stringency silent for sort samUpdate scriptsAdd bam index to outputproper threads for sambambasambamba creates index automaticalldo not require indexes on the markdup taskfix picard optional md5add outputsadd markdup taskIncrease time estimates for sort tasksAdd new tasks to talon.Do not create md5 file by default anymorePicard markduplicates has a default compression of 1update picardUpdate sortsam task with extra variablesActually sort the inputBam, not stdoutMerge branch 'BIOWDL-475' of https://github.com/biowdl/tasks into BIOWDL-475use correct memory for sambamacorrect memory calculationadd threads on index as wellFix sambamba index command in sortAdd sortSam taskupdate parameter_metaMake sure samtools uses memoryPut sorting back into bwakit taskRevert "Don't sort"use newer more experimental imageuse correct memory estimateremove other sorting bitsUpdate samtools sort to also indexDon't sort