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.

lrp_4.0.49

Added stand-alone workflow for barcode/fingerprint extraction (#497)

• Added workflow to extract SNP barcodes / fingerprints from a VCF (ExtractSnpBarcodeFromVcfFile)
• Added ExtractSnpBarcodeFromVcfFile to dockstore.

lrp_4.0.48

Changed docker image for mosdepth to use gcr instead of quay (#496)

lrp_4.0.47

Improvement: Add updated bubble plots to summary reports (#495)

• fix reading drug resistance text file and change page title

• fix another spot parsing the DR text file

• add new bubble plot with support for hom/het/missing variants

• update docker image tag to latest

• change source of drug resistances to workspace table, not text file

lrp_4.0.46

Fixed drug resistance calculations for missing data; added marker output to data table (#494)

• Fixed bug where functionally annotated output VCF would only be set if the gcs_output dir was specified.

• Removed all finalization steps from PfalciparumTypeDrugResistanceMarkers.

• Fixed drug res analysis to handle missing vs hom_ref

• Updated CreateDrugResistanceSummary to use missing and hom_ref

• Added individual marker outputs.