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@rhpvorderman rhpvorderman released this 28 Apr 13:12
· 25 commits to develop since this release
v5.1.0
c2b179a
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Learn about vigilant mode.
  • 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
    value.
  • 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
    (AnnotateSvTypes).
  • 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.
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