Update CHANGELOG.md.

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).