lrp_4.0.29

Increased minimum boot disk size to 25Gb for all tasks. (#476)

Fixed critical issue with boot disk size in Terra. Google likely changed their image and the boot disk is no longer big enough. Updated boot disk sizes to be 25 gb (or larger) by default.

lrp_4.0.28

Added more QC metrics and a pass / fail assessment to SRFlowcell (#475)

• Changed read quality stratification numbers to better suit ILMN data in SRFlowcell.
• Added QC pass / fail assessment to SRFlowcell. Defaults are set up for P. falciparum short read data, but can be adapted to other use cases.

lrp_4.0.27

Added support for giving background samples to joint calling workflow. (#474)

This adds in the ability to specify an Array[Array[File]] containing GVCFs to include as background samples in a joint call in SRJointCallGVCFsWithGenomicsDB. This input is optional.

lrp_4.0.26

Updates for Malaria pipelines: human read decontamination and WDLs for on-prem Malaria pipelines (#473)

• Added WDLS for Broad on-prem Malaria Pipelines
• Updated dockstore with Broad on prem malaria pipelines
• Finished implementing bowtie2 based read decontamination
• Enabled read decontamination in SRFlowcell
• Updated Utils.SortSam to use samtools

lrp_4.0.25

Updated interval extraction for short read joint calling for sharding. (#471)

lrp_4.0.24

Fixed JVM memory spec for VariantUtils::AnnotateVcfWithBedRegions (#469)

lrp_4.0.23

Updated drug resistance marker code to account for het genotypes. (#467)

• Updated drug resistance marker code.

• Now PfalciparumTypeDrugResistanceMarkers::CallDrugResistanceMutations pulls info directly from
  the VCF file using pysam, rather than a series of shell commands.
• Now PfalciparumTypeDrugResistanceMarkers::CallDrugResistanceMutations preserves het/hom
  genotype information in the raw output file.
• PfalciparumDrugResistanceSummary.wdl now calls into
  PfalciparumTypeDrugResistanceMarkers for
  CreateDrugResistanceSummary.
• Minor refactoring of names.

• Added VCF Index as input to PfalciparumTypeDrugResistanceMarkers.wdl
• Fixed output names in PfalciparumDrugResistanceSummary.wdl.

lrp_4.0.22

Updates to ONT workflows to bring them closer to current conventions (#466)

• Documentation updates for SRWholeGenome.wdl and ONTWholeGenome.wdl
• VariantUtils::MergeAndSortVCFs now has a fall-back to bcftools concat with normal compression if --naive fails.
• Fixed VariantUtils::MergeAndSortVCFs to use lr-basic:0.1.2
• CallVariantsONT.wdl now takes a ref_map instead of reference fasta/fai/dict.
• CallVariantsONT.wdl now filters out the mt_chr_name if call_small_vars_on_mitochondria is set to false.

lrp_4.0.21

Hotfix for BackupWorkspace.wdl and minor change to the hrp2/hrp3 detection wdl. (#464)

• Added volatile: true to `BackupWorkspace.wdl task.

• Increased disk space for PfalciparumHrp2Hrp3Status.wdl

• Fixed disk size to depend on all inputs for PfalciparumHrp2Hrp3Status.wdl

lrp_4.0.20

Changed output names of drug resistances in Pf drug resistance WDLs. (#463)

• Names of drug resistance outputs in PfalciparumTypeDrugResistanceMarkers.wdl have been changed to the form: drug_status_DRUGNAME (e.g. drug_status_chloroquine)