Release 3.0.0
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