diff --git a/CHANGELOG.md b/CHANGELOG.md index 13573295bd794e798758dba326d8b8556b73f010..dec107859d6771adca59893efc99d29370d038da 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,53 +13,53 @@ version 2.1.0-dev --------------------------- + Updated parameter_meta sections for Minimap2 and TranscriptClean. + Updated cores variable for TALON. -+ Updated TALON to version 4.4 ++ Updated TALON to version 4.4. + Added parameter_meta sections to the following tools: + htseq + cutadapt + collect-columns + stringtie + fastqc -+ Updated star default image to 2.7.3a ++ Updated star default image to 2.7.3a. + Hisat2 now indexes the resulting BAM file. -+ Samtools index now also works without setting a path for the output -+ Bugfix: Biowdl-input-converter now makes sure the output directory exists ++ Samtools index now also works without setting a path for the output. ++ Bugfix: Biowdl-input-converter now makes sure the output directory exists. version 2.0.0 --------------------------- -+ TranscriptClean: Update TranscriptClean to version 2.0.2 ++ TranscriptClean: Update TranscriptClean to version 2.0.2. + Memory runtime attributes are now Strings indicating total memory, as opposed to Ints indicating memory per core. + Memory inputs for most tasks are now Strings, remaining Int memory inputs are renamed to "memoryGb". + Use the biowdl-input-converter container for JsonToYaml, to reduce the amount of containers needed. + Add biowdl-input-converter and remove SampleConfigToSampleReadgroupLists which it replaces. -+ GATK.GenotypeGVCFs: Increased memoryMultiplier from 2.0 to 3.0 -+ Minimap2: Add -k option to minimap2 mapping -+ Added bwakit task -+ Minimap2: Add the option for --MD tag -+ TALON: Update average memory needs for main TALON process ++ GATK.GenotypeGVCFs: Increased memoryMultiplier from 2.0 to 3.0 . ++ Minimap2: Add -k option to minimap2 mapping. ++ Added bwakit task. ++ Minimap2: Add the option for --MD tag. ++ TALON: Update average memory needs for main TALON process. version 1.0.0 --------------------------- -+ Common: Add "SampleConfigToSampleReadgroupLists" task -+ MultiQC: the "interactive" input is now set to true by default ++ Common: Add "SampleConfigToSampleReadgroupLists" task. ++ MultiQC: the "interactive" input is now set to true by default. + Removed deprecated tasks: + bioconda.installPrefix + mergecounts.MergeCounts -+ GATK.BaseRecalibrator: "knownIndelsSitesVCFs" and "knownIndelsSitesVCFIndexes" are no longer optional, but now have a default of "[]" -+ Removed BWA index task -+ Removed unused "picardJar" input from bwa.wdl -+ All inputs to bedtools Sort are now reflected in the generated command -+ TranscriptClean: Update TranscriptClean container to version 1.0.8 -+ Removed "pipefail" from command sections TALON and TranscriptClean -+ Add WDL task for Minimap2 -+ Add WDL task for TALON -+ Add WDL task for TranscriptClean -+ Fastqsplitter: fix mkdir command to work with biocontainer's busybox mkdir -+ Cutadapt: simplify interface -+ Bigger memory multiplier in mutect to take in account bigger vmem usage -+ Cutadapt: Remove default adapter ++ GATK.BaseRecalibrator: "knownIndelsSitesVCFs" and "knownIndelsSitesVCFIndexes" are no longer optional, but now have a default of "[]". ++ Removed BWA index task. ++ Removed unused "picardJar" input from bwa.wdl. ++ All inputs to bedtools Sort are now reflected in the generated command. ++ TranscriptClean: Update TranscriptClean container to version 1.0.8. ++ Removed "pipefail" from command sections TALON and TranscriptClean. ++ Add WDL task for Minimap2. ++ Add WDL task for TALON. ++ Add WDL task for TranscriptClean. ++ Fastqsplitter: fix mkdir command to work with biocontainer's busybox mkdir. ++ Cutadapt: simplify interface. ++ Bigger memory multiplier in mutect to take in account bigger vmem usage. ++ Cutadapt: Remove default adapter. + Fastqsplitter: use version 1.1. -+ Picard: Use version 2.20.5 of the biocontainer as this includes the R dependency ++ Picard: Use version 2.20.5 of the biocontainer as this includes the R dependency. + Common: Update dockerTag to dockerImage. + GATK: Add CombineVariants task that allows, e.g., to merge VCFs from different callers. + Mutect2: Add GATK tasks related to variant filtering (LearnReadOrientationModel, MergeStats, GetPileupSummaries, CalculateContamination and FilterMutectCalls).