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.

lrp_4.0.53

Fixes to runtime attributes for workflows for new GCP Batch engine (#501)

• Fixed all bootDiskSizeGb entries to be ints.

lrp_4.0.52

Set Conda py version for miniwdl (#502)

• set to use latest miniwdl version

• set python version to 3.12 in CI/CD

• set python version to 3.13 in CI/CD, set conda environment to 3.12

• Added composite action.yml

• added checkout before setup env action

• new line in setup env yml

• setting lfs set to true

• setting lfs set to true to cd and ci_nightly

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Co-authored-by: bshifaw [email protected]

lrp_4.0.51

Added base_bucket parameter to reports to fix issue. (#499)

lrp_4.0.50

Create stand-alone workflow for short read malaria QC (#498)

• Added QCAssessment workflow to run stand-alone QC on ILMN samples. (Primarily for malaria work)
• Added QC WDL to dockstore.