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Release 3.0.0
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@DavyCats DavyCats released this 17 Mar 15:28
· 206 commits to develop since this release
v3.0.0
a644ca7

In version 3.0.0 the RNA-seq pipeline was brought up to date with the GATK best
practices pipeline. Several errors in the variant calling part of the pipeline
were fixed.

  • UMI deduplication stats collection is now optional.
  • Add scatterSize option to centrally control the scatter size
  • Multisample VCFs are no longer generated for RNA-seq by default as this is
    not GATK best practice. It can optionally be turned on again.
  • Add proper copyright headers to WDL files. So the free software license
    is clear to end users who wish to adapt and modify.
  • Added UMI based deduplication as an optional step.
  • Major fix: Joint genotyping is not performed on RNA-seq reads. Instead, each
    sample is genotyped seperately by the HaplotypeCaller.
  • Major fix: base recalibration is now applied after splitting the cigar reads.
    previously this was done in an erroneous manner.
  • Structs are removed from the input.
  • Fixed a typo in the inputs: detectNovelTranscipts -> detectNovelTranscripts.
  • Removed a number of unused inputs ("dbsnp", "targetIntervals",
    "ampliconIntervals" and "variantCalling") from the sample workflow.
  • Added input overview to docs.
  • Added WDL-AID to linting.
  • Update default htseq image version to 0.11.2
Assets 4