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Created with Raphaël 2.2.06Jul32130Jun29262524232219181716151211109854228May20191815141311876130Apr282120151410987632131Mar3026252423201918161312119325Feb2420131211107654331Jan302928272423222120171615141310987617Dec12111096227Nov262519765131Oct302815987use less memory on bcftools stats.Comment on real life use for sambamba markdupOnly little memory is needed for gatherbqsrreportsReduce flagstat memoryupdate haplotypecaller memoryMerge pull request #226 from biowdl/BIOWDL-426Address last comment.Address comments.Update threads and memories.BIOWDL-426BIOWDL-426Merge branch 'develop' into BIOWDL-426Update tasks.make md5 file optionalBIOWDL-475BIOWDL-475make compression level optional for gather bam filesincrease time for gatherbamfix samtools mergeAdd threads to samtoolsUse 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 variables