CHANGELOG.md

Changelog

version 2.2.0-dev

• Add -o pipefail to bedtools.MergeBedFiles to prevent errors in BED files from going unnoticed.
• Add bedtools.Complement, bedtools.Merge, and add a task to combine multiple bed files called bedtools.MergeBedFiles. This task combines bedtools merge and sort.
• Change g parameter on bedtools.Sort to genome.
• Add ploidity and excludeIntervalList to gatk.HaplotypeCallerGvcf.
• Update centrifuge tasks.
• Removed unused "cores" inputs from transcriptclean tasks.
• Removed unused "cores" inputs from talon tasks.
• Removed unused "threads" input from ModifyStrelka.
• Removed the "installDir" inputs from the somaticseq tasks.
• Removed the "installDir" input from CombineVariants.
• Removed the "extraArgs" input from FilterMutectCalls.
• Removed unused "verbose" and "quiet" inputs from multiqc.
• Added parameter_meta sections to a variety of tasks.
• Picard's BedToIntervalList outputPath input is now optional (with a default of "regions.interval_list")
• TALON: Fix SQLite error concerning database/disk space being full.
• Update htseq to default image version 0.11.2
• Update biowdl-input-converter in common.wdl to version 0.2.1.
• Update TALON section to now include the new annotation file output, and add config file creation to the TALON task.
• Removed unused inputs (trimPrimer and format) for cutadapt.
• Various minor command tweaks to increase stability.
• Fixed unused inputs in bedtools sort (inputs are now used).
• Added miniwdl check to linting.
• Update TALON default image to version 4.4.1.

version 2.1.0

• Make intervals optional for GATK CombineGVCFs.
• Updated biowdl-input-converter version.
• GATK CombineGVCFs memory was tripled to prevent it from using a lot of CPU in Garbage Collection mode.
• Updated parameter_meta sections for Minimap2 and TranscriptClean to wdl-aid format.
• Updated cores variable for TALON, the default is now 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.
• 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.

version 2.0.0

• 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.

version 1.0.0

• 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.
• Fastqsplitter: use version 1.1.
• 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).
• Mutect2: Add "--germline-resource" and "--f1r2-tar-gz" inputs, requiring an update to GATK 4.1.2.0.
• Mutect2: Add necessary missing index attribute for panel of normals.
• MultiQC: Add memory variable to multiqc task.
• GATK: SplitNCigarReads, BaseRecalibration and ApplyBQSR do no longer need regions files as required inputs.
• VarDict: Add user definable flags (-M, -A, -Q, -d, -v, -f) to the paired VCF filtering script.
• Cutadapt: If the output is a gzipped file, compress with level 1 (instead of default 6).
• Cutadapt: Fix issues with read2output when using single-end reads.
• Add feature type, idattr and additional attributes to htseq-count.
• Added allow-contain option to bowtie.
• Added a changelog to keep track of changes.
• Added sortByName task in samtools to support more memory efficient execution of HTSeqCount.
• Removed the bam index from HTSeqCount's inputs.