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Created with Raphaël 2.2.013Jul97632130Jun29262524232219181716151211109854228May20191815141311876130Apr282120151410987632131Mar3026252423201918161312119325Feb2420131211107654331Jan302928272423222120171615141310987617Dec12111096227Nov262519765131Oct3028Request less memory for htseq-countSASC-1333SASC-1333add function to get the list of chromosomesadd vep taskUse more sort threads for alignment if more alignment threads are usedupdate changelogMerge pull request #228 from biowdl/usepicardUpdate changelogusepicardusepicardUse htsjdk inflaters and deflaters for markduplicatesupdate changeloguse samtools 1.10 and hisat 2.2.0Add outputBAMcompression to STARAdd samtools controls to hisat2Merge pull request #227 from biowdl/BIOWDL-475add parameter_metaadd forgotten Mupdate changelogMerge remote-tracking branch 'origin' into BIOWDL-4752GB per thread is sufficientuse 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/pbmm2