This adds a small handful of bugfixes and improvements. Beginning with bugfixes:
Fixed usage of externally defined variables, they previously required an all or nothing approach to the definitions.
Fixed a copy-paste typo for constitutional GATK CNV which resulted in the tasks not rendering/running. #51
Regression bugfix from v1.2.0: v1.2.0 introduced a bug for the usage of scripts that exist within the pipeline/repo wherein the render would unintentionally update for certain tasks due to pathing changes for the pipeline's install location. Resulting in wasted compute. Fortunately these tasks are usually lightweight. This bugfix works best with Jetstream v1.7.4, but it's possible to use older Jetstream versions if some workarounds are in place.
Improvements:
Bumped deepvariant to v1.6.0 - this reportedly has improved performance for the NovaSeqX. Additionally this allows us to multithread the postprocess_variants task. The postprocess_variants task does require more memory in our testing.
Added filters to PASS for constitutional Manta, and we've added annotation via VEP. #52
This adds a small handful of bugfixes and improvements. Beginning with bugfixes:
Improvements: