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)

lrp_4.0.19

Cleaned up short read workflows, minor feature additions (#461)

• Added docker image and WDL to backup workspaces.
• Added util-malaria-coi docker image.
• Fixed bug in SRFlowcell that preferentially pulled the existing aligned bam rather than the merged aligned bam.
• Cleaned up redundant / unnecessary inputs and outputs from SRWholeGenome.wdl
• Enabled SRWholeGenome.wdl and HaplotypeCaller.wdl to use an interval_list to call variants in subsets of the genome.
• Renamed ONTPfTypeDrugResistanceMarkers.wdl to PfalciparumTypeDrugResistanceMarkers.wdl.
• Renamed ONTPfHrp2Hrp3Status.wdl to PfalciparumHrp2Hrp3Status.wdl
• PfalciparumDrugResistanceSummary.wdl now produces individual drug resistances/sensitivites as additional outputs.
• PfalciparumDrugResistanceSummary.wdl is now deprecated.
• PfalciparumDrugResistanceMarkers.wdl now produces drug resistances/sensitivites as well as the summary file. This deprecates PfalciparumDrugResistanceSummary.wdl.
• Added PfalciparumPolygenomicityBarcodeEstimate.wdl to estimate CoI based on the 24 SNP molecular barcode.
• Cleaned up some outputs in SRJointCallGVCFsWithGenomicsDB.wdl.
• Added flag for dangling end recovery to HaplotypeCaller.wdl.
• Minor fixes for MiniWDL style suggestions (TrainCnnFilters.wdl, LRCNVs.wdl, AlignedMetrics.wdl, FastQC.wdl, SRUtils.wdl, Utils.wdl, VariantUtils.wdl, SRJointGenotyping.wdl, NanoPlot.wdl, Pf_Niare_HaplotypeCaller.wdl)