Updates to make the malaria comparison pipelines run to completion on the new test sets#510
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jonn-smith merged 16 commits intomainfrom Dec 10, 2025
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…_2_JointVariantCalling
- Added bcftools plugins directory from the build stage to the final image stage. This enables bcftools plugins, such as `+split`.
- Added `SplitMultiSampleVCF.wdl` which contains a single task to split a multi-sample VCF into individual sample VCFs. Uses bcftools `+split`. - Added `SplitMultiSampleVCF` to dockstore.
- Updated internal name of SRJointCallGVCFsWithGenomicsDB_Pf_Niare_VETS.wdl to reflect the actual workflow name. - Modified GenotypeGVCFs runtime attributes for BroadOnPremMalariaPipeline_2_JointVariantCalling.wdl
- Utils::SplitContigToIntervals was returning interval lists with numerical positions in their names. These lists were then being sorted by name, which was causing problems with coordinate sorting (lexicographic sorts put `10` ahead of `8`). The outputs of this task now use 0-padded positions to fix this.
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