Merging development branch from Malaria project - decontamination, pipelines for organisms with no variant truth set, etc.#451

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brosula wants to merge 84 commits intomainfrom

rrb_malaria_from_main

Commits on Jan 30, 2024

Commits on Apr 16, 2024

Reintroduced `ReblockGVCF` step.
jonn-smith
committed

Commits on Apr 17, 2024

Commits on Apr 18, 2024

Disabled QC when running on a singe bam file input.
jonn-smith
committed

Commits on Apr 19, 2024

Commits on Apr 22, 2024

Updating tasks to use `SSD` rather than `LOCAL` disk.
jonn-smith
committed
Merge remote-tracking branch 'origin/jts_updates_to_malaria_for_joint_calling' into rrb_malaria_from_main
brosula
committed
Merge _Bootstrap wdls into rrb_malaria_from_main branch, add standalone SRReblockGVCFs wdl
brosula
committed

Commits on Apr 26, 2024

Update HaplotypeCallerBootstrap.wdl to GATK v4.5.0
brosula
authored

Commits on May 2, 2024

Commits on May 6, 2024

Add contaminated bam/metrics to SRFlowcell output
brosula
committed

Commits on May 18, 2024

Commits on May 25, 2024

Change handling of optional decontamination/contamination outputs
brosula
committed

Commits on May 28, 2024

Specify intervals for manual sharding in SRJointCallGVCFsWithGenomicsDB
brosula
committed

Commits on May 29, 2024

Commits on May 31, 2024

Commits on Jun 26, 2024

Update SRWholeGenomeBootstrap.wdl to default to False for pileup detection
brosula
authored

Commits on Oct 16, 2024

Commits on Mar 20, 2025

Update SRFlowcellDecontaminate.wdl
brosula
authored

Commits on Jun 27, 2025

Update GetCurrentTimeStampString
brosula
authored