lrp_4.0.63

Removed default runtime attr overrides for gnarly genotyper. (#512)

• Pulled out default runtime attrs from call to GnarlyGenotyper to expose them in the Terra UI. This enabled a large joint call with ~30000 Plasmodium falciparum samples from The Gambia and elsewhere.

lrp_4.0.62

Updated short read whole genome pipelines for scalability and speed, bugfixes (#511)

• Added simplified processing WDLs for SRFlowcell, SRWholeGenome, and SRJointCallGVCFsWithGenomicsDB.

• Added new wdls to dockstore.

• Fixed issue in FASTQ output (fastq2 not properly set).

----- Details below -----

• Added SRFlowcell_Simplified.wdl which removes two localization steps
  by combining sorting directly into main operations.

• Added SRWholeGenome_Simplified.wdl which uses a simplified version
  of the HaplotypeCaller workflow to run faster. This was accomplished
  by removing the scatter by interval. This workflow will not scatter
  by interval when performing variant calling. This is OK for small
  genomes / organisms.

• Added HaplotypeCaller_Simplified.wdl which performs germline variant
  calling on an input bam file without any scattering.

• Added SRJointCallGVCFsWithGenomicsDB_simplified.wdl

lrp_4.0.61

Minor bug fixes and updates to make the malaria comparison pipelines run to completion on the new test sets (#510)

• Updated ReblockGVCFs docker image to broadinstitute/gatk-nightly:2025-08-29-4.6.2.0-17-g2a1f41bf3-NIGHTLY-SNAPSHOT to fix exception with certain spanning deletions.
• Updates to malaria workflows for comparisons (BroadOnPremMalariaPipeline_2_JointVariantCalling.wdl, SRJointCallGVCFsWithGenomicsDB_Pf_Niare_VETS.wdl, SRJointCallGVCFsWithGenomicsDB_Pf_Niare_VQSR.wdl, BroadOnPremMalariaPipelineTasks.wdl)
• Fixed bug in SplitContigToIntervals that caused resulting bed files to sort out of order.
• Added SplitMultiSampleVCF.wdl which splits a multi-sample VCF into an array of single-sample VCFs using bcftools +split
• Added SplitMultiSampleVCF.wdl to dockstore.
• Added bcftools plugins to lr-basic docker image.
• Updated lr-basic to v0.1.3

lrp_4.0.60

Various bug fixes for the WDLization of old on-prem malaria variant calling pipelines (#509)

• Fixed read decontamination in BroadOnPremMalariaPipeline_1
• Added ChangeReadGroup task to Utils.wdl
• Fixed small bug in bwa-mem2 read group parsing.
• Fixing gvcf extension in on-prem wdl.
• Added program group hack / fix for on-prem pipeline.

lrp_4.0.59

Added RemoveSingleOrganismContamination to dockstore. (#500)

• Added RemoveSingleOrganismContamination to .dockstore.yml.
• moved RemoveSingleOrganismContamination.wdl to pipelines folder.

lrp_4.0.58

Various updates to long read processing to make ONT Malaria data processing easier (#508)

• Added ability to include background gvcf files when joint calling with GLNexus to enable population-level comparisons.

• Added optional flags to GLNexus joint calling to use DP field instead of DP_MIN. This was to allow for short-read / GATK-derived variants to be used in GLNexus along with long-read derived variants.

• Added a config file override for GLNexus.

• Various fixes to zones to comply with new Batch processing on GCP (As of May 19, 2025, all requested zones must be in the same GCP region. This fix addresses may zone requests that were mixed between regions (resulting in errors before the fix).

• Added task: CopyDP_MINToDP

lrp_4.0.57

New release of lr-basic (0.1.2) (#507)

• Several updates to lr-basic docker image.
  • Updated base docker image to ubuntu:22.04.
  • Updated samtools to 1.22.1
  • Updated bcftools to 1.22
  • Incremented lr-basic docker image version to 0.1.2

lrp_4.0.56

Updated to GATK 4.6.1.0 and added new parameter for extra memory for joint calling (#505)

• Updated to GATK 4.6.1.0 for joint genotyping.

• Updated the following tasks to use GATK 4.6.1.0:
  • GnarlyGenotypeGVCFs
  • GenotypeGVCFs
  • ImportGVCFs

• Added parameter for extra memory to ImportGVCFs

lrp_4.0.55

Added workaround for batch python issue. (#504)

lrp_4.0.54

Fix to HRP2/3 deletion detection for GCP batch backend. (#503)

• Updated HRP2/3 workflow to fix Batch backend issues.

• Now uses File for the bam file input.