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3.2.2 (Caribou)

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@RoanKanninga RoanKanninga released this 03 May 12:55
· 1546 commits to master since this release
  • Changed CoveragePerBase protocol into CoverageCalculations
  • Added Coverage calculations for subset bed files (LEVER, NEURO, SSID and GEO)
  • Changed output for coverage per target and coverage per base
  • CoveragePerBase added missing make genesOnly file + VariantCalling bug (double brackets)
  • increased memory for MarkDuplicates
  • improved the copy prmtotmp data (when prm is not available on zinc-finger it will download it from calculon)
  • bugfix in CheckIlluminaEncoding (where '++' is not used anymore, it is now '+1')
  • added automating:
    • start of pipeline
    • copying to prm
    • copying to zinc-finger
  • fixed the duplication rate in the QC report
  • Made new QCReport (in html)
  • fix issue with samples on multiple lanes and counting number of samples in

Release notes of older updates are below (track changes are lost in moving to own repo, older versions can be downloaded from


Major changes:

  • Replaced Picard tools SortBam, MergeBam and MarkDuplicates for Sambamba tools
  • renamed CheckSex protocol to GenderCheck
  • Splitted the metrics calculations
  • added CramConversion (turned off in workflow)
  • added CoveragePerTarget
  • updated to new compute version v15.12.4
  • upgraded to Java 8

Minor changes + bugfixes

  • fixed GenderCheck for a WGS sample
  • extended walltime for Delly and added more memory
  • changed PERCENTAGE_DUPLICATES to PERCENT_DUPLICATION in dedup metrics (QC report)
  • added new batch options (per chr or 1 batch)
  • added #string project to every protocol
  • fixed VariantCalling bug (sex is Unknown bug)


  • UPDATED the old version numbers, newest NGS_DNA version is now in the directory NGS_DNA
  • added DellyAnnotator
  • fixed >200-samples issue
  • added pipeline version to QCReport
  • bugfixes
  • removed IndelRealigment step
  • splitted collect metrics step into 4 steps