diff --git a/CHANGELOG.md b/CHANGELOG.md index 9a546718279bc853ad32fff24257e442cda43271..4acadc5703053b97e13fa099779521768f7c742b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,23 @@ that users understand how the changes affect the new version. version 4.0.0-develop --------------------------- ++ Picard SortSam added as a task. ++ Md5 files are no longer created by default on Picard tasks that generate + BAM files. ++ Changed PicardMarkduplicates to use COMPRESSION_LEVEL=1 by default + speeding up execution by 2x at the cost of a 20% larger BAM file. ++ Added sambamba markdup and sambamba sort. NOTE: samtools sort is more + efficient and is recommended. ++ Correctly represent samtools inconsistent use of the threads flag. + Sometimes it means 'threads' sometimes it means 'additional threads'. + BioWDL tasks now use only threads. The `threads - 1` conversion is + applied where necessary for samtools tools that use additional threads. ++ Updated BWA MEM and BWA KIT tasks to use samtools sort version 1.10 for + sorting the BAM file. ++ Updated memory requirements on bcftools Stats, bwa mem, bwakit, GATK + ApplyBQSR, GATK BaseRecalibrator, GATK GatherBqsrReports, Gatk + HaplotypeCaller, Picard CollectMultipleMetrics, Picard GatherBamFiles, + samtools Flagstat, samtools sort and bcftools stats. + TALON: Update `FilterTalonTranscripts` to new version, which removes the pairingsFile and replaces this with datasetsFile. + TALON: Add `GetSpliceJunctions` & `LabelReads` tasks.