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  • v5.2.0
    + Update cutadapt version to 4.4
    + Update FastQC version to 0.12.1
  • v5.1.0
    version 5.1.0
    + Add the `highlyDiploidPercentage` and `somaticMinPuritySpread` inputs to the
      hmtools PURPLE task.
    + Add a task for fastp.
    + Add a task for picard CollectInsertSizeMetrics.
    + Increased the timeMinutes runtime attribute for manta (somatic and germline) to `2880`.
    + Add a task for GRIDSS somatic filtering.
    + Add a task to generate a panel of normals BED and BEDPE file for GRIDSS.
    + Add a task to filter a GRIDSS PON.
    + Add a task for delly somatic filtering.
    + Delly CallSV's `bamFile` and `bamIndex` inputs are not arrays of files, allowing
      for multiple samples to be included.
    + Add `samples` input to bcftools view to select samples included in the output vcf.
    + Add a separatorChar input to the tagUmi task.
    + Bug fix: Add space between flag and the value provided for macs2
    + Add optional inputs to macs2, aiming to allow adhering to Encode ATACs-seq. Inputs added:
      + nomodel
      + gensz
      + extsize
      + shiftsize
      + pval_thres
      + bdg
      + keepdup
      + callsummits
    + Update samtools image to version 1.16.
    + Add targetsFile input for samtools View.
    + Mateclever's runtime attribute defaults were changed to:
      + memory: `"250GiB"`
      + timeMinutes: `2880`
    + Clever's Prediction task's runtime attribute defaults were changed to:
      + memory: `"80GiB"`
      + timeMinutes: `2200`
    + The GRIDSS AnnotateSvTypes task now also removes the second breakend of
      the breakpoints and single breakends. This will prepare the output better
      to be passed into survivor.
    + Updated SURVIVOR version to 1.0.7
    + Add a combined samtools dict and samtools faidx task.
    + Add a BWA index task.
    + Move all memory notation to `KiB`, `MiB` and `GiB` from `K`, `M` and `G`
      previously. The WDL spec clearly distuingishes between SI and binary
      notations. Since Java always takes `K`, `M` and `G` to mean `KiB`, `MiB` and
      `GiB` this means java tasks such as GATK, FastQC and Picard will always
      receive enough memory now.
    + Purple's `somaticRainfallPlot` output is now optional and included in
      the `plots` output as well.
    + Bedtools coverage's timeMinutes now defaults to `320`.
    + Gridss' runtime attribute defaults were changed to:
      + jvmHeapSizeGb: `64`
      + nonJvmMemoryGb: `10`
      + threads: `12`
    + Virusbreakend's runtime attribute defaults were changed to:
      + threads: `12`
      + timeMinutes: `320`
    + Cobalt's timeMinutes now defaults to `480`.
    + Orange's timeMinutes now defaults to 10.
    + Sage's runtime attributes were changed to:
      + threads: `32`
      + javaXmx: `"16G"`
      + memory: `"20G"`
      + timeMinutes: `720`
    + Sambamba's runtimeMinutes nor defaults to `320`.
    + Added a task for CupGenerateReport.
    + Updated Cuppa to version 1.6.
    + Added a task for Gripss.
    + Fixed the HealthChecker task's determination of the `succeeded` output
    + Updated Linx to version 1.18.
    + Added a task for LinxVisualization.
    + Added a task for HMFtools Orange.
    + Added a task for HMFtools Pave.
    + Updated Purple to version 3.2.
    + Added plot and table outputs of Sage to task outputs.
    + Updated virus-interpreter to version 1.2.
    + Updated Peach to version 1.5.
    + Added a task to add SVTYPE annotations to GRIDSS results
    + The GRIDSS task will now run tabix separately if GRIDSS doesn't
      produce a vcf index.
    + Add a script to subtract UMI's from the read name and add them as
      a BAM tag for each BAM record. The script is in umi.BamReadNameToUmiTag.
    + Add fgbio.AnnotateBamWithUmis.
    + Add picard.UmiAwareMarkDuplicatesWithMateCigar.
    + Added a task for SnpEff.
    + Adjusted runtime settings for sambamba Markdup.
    + Added a task for sambamba Flagstat.
    + Added a task for Picard CollectWgsMetrics.
    + Added a task for Peach.
    + Added tasks for HMFtools:
      + Amber
      + Cobalt
      + Cuppa
      + CuppaChart
      + GripssApplicationKt
      + GripssHardFilterApplicationKt
      + HealthChecker
      + Linx
      + Protect
      + Purple
      + Sage
      + VirusInterpreter
    + Added a task for VirusBreakend.
    + Added a task for GridssAnnotateVcfRepeatmasker.
    + Bumped GRIDSS version to 2.12.2.
    + Adjusted GRIDSS runtime settings.
    + Added optional inputs to GRIDSS:
      + blacklistBed
      + gridssProperties
    + Added a task for GRIDSS AnnotateInsertedSequence.
    + Added a task for ExtractSigPredictHRD.
    + Added a task for DeconstructSigs.
    + Added option useSoftclippingForSupplementary (default false) to
      BWA mem.
    + Adjusted BWA mem runtime settings.
    + Added a task for bedtools coverage.
    + Added a task for bcftools filter.
    + Adjusted runtime settings for bcftools annotate.
    + Added optional inputs to bcftools annotate:
      + inputFileIndex
      + annsFileIndex
    + Update parameter_meta for macs2
    + Add sample position in array task.
  • v5.0.1
    Release 5.0.1
  • v5.0.0
    Release v5.0.0
  • v4.0.0
    version 4.0.0
    + Picard MergeVcf now uses compression level 1 by default.
    + bwa mem, bwa mem+kit and hisat2 have their samtools sort threads tweaked. The
      number of threads is now related to the number of threads on the aligner.
      Using more threads reduces the chance of the samtools sort pipe getting
      blocked if it's full.
    + Renamed a few inputs in centrifuge.wdl, isoseq3.wdl, talon.wdl,
      transcriptclean.wdl to be more descriptive.
    + Renamed outputs of tasks used in the TALON-WDL, PacBio-subreads-processing &
      sequence-classification pipelines.
    + Reworked bcf2vcf task into bcftools view task.
    + Removed the redundant format flag from the htseq interface. This is
      autodetected in newer versions of htseq.
    + Update docker images for samtools, bcftools, picard, GATK, cutadapt, htseq
      and chunked-scatter.
    + Default docker images for bwa, bwakit and hisat2 updated to include samtools
    + Alignment tasks (STAR, Hisat2, BWA) now produce BAM files at level 1
    + Hisat2 task has added controls for samtools.
    + Alignment tasks no longer produce BAM indexes as these are not needed
      by the markduplicates step.
    + Picard Markduplicates now uses 7G of RAM just like in GATK's best practice
      example pipeline.
    + Picard SortSam added as a task.
    + Md5 files are no longer created by default on Picard tasks that generate
      BAM files.
    + Changed PicardMarkduplicates to use COMPRESSION_LEVEL=1 by default with
      the htsjdk deflater.
      This makes the task finish in 32% less time at the cost of a 8% larger BAM
    + Added sambamba markdup and sambamba sort. NOTE: samtools sort is more
      efficient and is recommended.
    + Correctly represent samtools inconsistent use of the threads flag.
      Sometimes it means 'threads' sometimes it means 'additional threads'.
      BioWDL tasks now use only threads. The `threads - 1` conversion is
      applied where necessary for samtools tools that use additional threads.
    + Updated BWA MEM  and BWA KIT tasks to use samtools sort version 1.10 for
      sorting the BAM file.
    + Updated memory requirements on bcftools Stats, bwa mem, bwakit, GATK
      ApplyBQSR, GATK BaseRecalibrator, GATK GatherBqsrReports, Gatk
      HaplotypeCaller, Picard CollectMultipleMetrics, Picard GatherBamFiles,
      samtools Flagstat, samtools sort and bcftools stats.
    + TALON: Update `FilterTalonTranscripts` to new version, which removes the
      pairingsFile and replaces this with datasetsFile.
    + TALON: Add `GetSpliceJunctions` & `LabelReads` tasks.
    + TALON: Update to version 5.0.
    + Add tasks for pbmm2, the PacBio wrapper for minimap2.
    + Update the image for chunked-scatter and make use of new features from 0.2.0.
    + Tuned resource requirements for GATK VariantEval, MultiQC, Picard metrics and
    + Added a new task for [scatter-regions](
      that replaces biopet-scatterregions.
    + The FastQC task now talks to the Java directly instead of using the included
      Perl wrapper for FastQC. This has the advantage that memory and threads can
      be set independently. A rather high maximum heap size of 1750MB (Xmx1750M)
      was set, as OOM errors occurred frequently on some fastqs.
    + STAR: Add options regarding alignment score (regarding read length as well)
      for tweaking when processing rRNA depleted samples.
    + TALON: Update `minimumIdentity` to correct type (float, was integer)
      & set new default according to developers (0.8, was 0).
    + Added GATK VariantEval task.
    + Added a log output for STAR.
    + Added report output to Hisat2.
    + Added output with all reports to gffcompare.
    + Change MultiQC inputs. It now accepts an array of reports files. It does not
      need access to a folder with the reports anymore. MultiQC can now be used
      as a normal WDL task without hacks.
    + Picard: Make all outputs in `CollectMultipleMetrics` optional. This will make sure the
      task will not fail if one of the metrics is set to false.
    + The struct `BowtieIndex` was removed, as it has become obsolete.
    + The task `ReorderGlobbedScatters` was removed, as it has become obsolete.
    + Adjusted the memory settings of many tools, especially java tools.
      They should now more accurately represent actual memory usage (as
      opposed to virtual memory).
    + Added `-XX:ParallelGCThreads=1` to the java options of java tasks.
    + Added `timeMinutes` input to many tasks, this indicates a maximum
      number of minutes that the job will run. The associated runtime
      attribute is `time_minutes` which can be used to inform
      a scheduler (eg. slurm) of the run time of the job.
    + Added STAR GenomeGenerate task.
    + GATK.HaplotypeCaller: Add `--dont-use-soft-clipped-bases` and
      `--standard-min-confidence-threshold-for-calling` options. These are
      required for RNA seq variant calling according to GATK best practices.
    + Samtools: Fix quotations in sort command.
    + Samtools SortByName is now called Sort.
    + Generalize sort task to now also sort by position, instead of just read name.
    + Add CreateSequenceDictionary task to picard.
    + Add faidx task to samtools.
    + Isoseq3: Remove dirname command from output folder creation step.
    + Isoseq3: Requires more memory by default, is now 2G.
    + Isoseq3: Remove cp commands and other bash magic, file naming is now solved by pipeline.
    + Lima: Replace mv command with cp.
    + Add WDL task for smoove (lumpy) sv-caller.
  • v3.1.0
    a28a3634 · stable changelog ·
    version 3.1.0
    + Default threads for BWA in bwa.Kit task: 4. Samtools sort in the
      same task: 1. Output BAM compression level to 1.
    + Lima: Add missing output to parameter_meta.
    + Lima: Remove outputPrefix variable from output section.
    + Isoseq3: Make sure stderr log file from Refine is unique and not overwritten.
    + Isoseq3: Add workaround in Refine for glob command not locating files in output directory.
    + Isoseq3: Fix --min-polya-length argument syntax.
    + Lima: Add workaround for glob command not locating files in output directory.
    + CCS: Add missing backslash.
    + Cutadapt now explicitly calls the `--compression-level` flag with compression
      level 1 to prevent cutadapt from using very high gzip compression level 6
      that uses 400% more cpu time.
    + Update default docker image for cutadapt and fastqc.
    + Default number of cores for cutadapt and bwamem to 4 cores.
  • v3.0.0
    + 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.
  • v2.1.0
    + 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.
  • v2.0.0
    e2559dbc · update changelog version ·
    version 2.0.0
    + 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
  • v1.0.0
    3fc501f2 · fixed version ·
    Release 1.0.0
  • v1.0
    3fc501f2 · fixed version ·
    BIOWDL tasks version 1
  • v0.3
    53dbf148 · add scripts submodule ·
    Most tasks now work with containers.
  • v0.1.1
    639024ae · fix issues with stringtie ·
  • v0.2
    221aab4c · Setting version to 0.2 ·
    Releasing 0.2
  • v0.1
    5a4ddaa9 · Setting version to 0.1 ·
    Releasing 0.1
  • phhv1reassembly
    8ffea620 · tweak spades memory ·
    Tasks used for the reassembly of phhv1
  • phhv1assembly
    Tasks used or the phhv1assembly