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@DavyCats DavyCats released this 13 Mar 13:10
· 991 commits to develop since this release
v3.0.0
c651dcf
  • Update command section syntax Minimap2, Talon, TranscriptClean and Centrifuge.
  • Add CCS workflow WDL files (ccs.wdl, lima.wdl, isoseq3.wdl).
  • Update TALON version to 4.4.2.
  • The statsPrefix input for umitools dedup is now optional.
  • Allow setting the --emit-ref-confidence flag for HaplotypeCaller.
  • Add --output-mode flag to HaplotypeCaller.
  • Added rtg.Format and rtg.VcfEval tasks.
  • Added gatk.SelectVariants and gatk.VariantFiltration tasks.
  • Fixed a bug where the output directory was not created for bwa.Kit.
  • Add vt task for variants normalization and decomposition.
  • Update WDL task Picard (Add task RenameSample).
  • Update WDL task Samtools (Add task FilterShortReadsBam).
  • Add WDL task for BCFtools (bcf to vcf).
  • Add WDL task for SURVIVOR (merge).
  • Update WDL task Manta (Add germline SV calling).
  • Add WDL task for Delly.
  • Add WDL task for Clever (and Mate-Clever).
  • Add proper copyright headers to all WDL files. So the free software license
    is clear to end users who wish to adapt and modify.
  • Add pedigree input for HaplotypeCaller and GenotypeGVCFs.
  • Combined biopet.ScatterRegions and biopet.ReorderedGlobbedScatters into one.
    biopet.ScatterRegions now always returns correctly ordered scatters.
  • Add tasks for umi-tools dedup and extract.
  • Add GenomicsDBImport task for GATK.
  • Add annotationGroups input to GenotypeGVCFs to allow setting multiple
    annotation groups. The StandardAnnotation group is still used as default.
  • GenotypeGVCFs, only allow one input GVCF file, as the tool also only allows
    one input file.
  • Rename HaplotypeCallerGVCF to HaplotypeCaller. Add gvcf option to set
    whether output should be a GVCF.
  • Centrifuge: Add Krona task specific to Centrifuge.
  • Centrifuge: Fix Centrifuge tests, where sometimes the index files could still not be located.
  • Update parameter_meta for TALON, Centrifuge and Minimap2.
  • Centrifuge: Fix issue where Centrifuge Inspect did not get the correct index files location.
  • Add minimumContigLength input to PlotDenoisedCopyRatios and PlotModeledSegments.
  • Add commonVariantSitesIndex input to CollectAllelicCounts.
  • Centrifuge: Fix issue where Centrifuge could not locate index files.
  • Increase default memory of BWA mem to 32G (was 16G).
  • Add memory input to fastqc task.
  • Centrifuge: Fix issue where centrifuge would fail on incorrect paths.
  • Added GATK CNV calling tasks:
    • AnnotateIntervals
    • CallCopyRatioSegments
    • CollectAllelicCounts
    • CollectReadCounts
    • CreateReadCountPanelOfNormals
    • DenoiseReadCounts
    • ModelSegments
    • PlotDenoisedCopyRatios
    • PlotModeledSegments
    • PreprocessIntervals
  • Add common.TextToFile task.
  • Add bedtools.Intersect.
  • Add -o pipefail to bedtools.MergeBedFiles to prevent errors in BED files
    from going unnoticed.
  • Centrifuge: Fix -1/-U options for single end data.
  • 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.
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