+ 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.