diff --git a/wdl/pipelines/TechAgnostic/TertiaryAnalysis/PfalciparumDrugResistanceSummary.wdl b/wdl/pipelines/TechAgnostic/TertiaryAnalysis/PfalciparumDrugResistanceSummary.wdl index d112f78a5..6c1eb51c5 100644 --- a/wdl/pipelines/TechAgnostic/TertiaryAnalysis/PfalciparumDrugResistanceSummary.wdl +++ b/wdl/pipelines/TechAgnostic/TertiaryAnalysis/PfalciparumDrugResistanceSummary.wdl @@ -36,12 +36,12 @@ workflow PfalciparumDrugResistanceSummary { output { File drug_resistance_summary = select_first([FinalizeDrugResistanceSummary.gcs_path, CreateDrugResistanceSummary.resistance_summary]) - String chloroquine_status = CreateDrugResistanceSummary.chloroquine_status - String pyrimethamine_status = CreateDrugResistanceSummary.pyrimethamine_status - String sulfadoxine_status = CreateDrugResistanceSummary.sulfadoxine_status - String mefloquine_status = CreateDrugResistanceSummary.mefloquine_status - String artemisinin_status = CreateDrugResistanceSummary.artemisinin_status - String piperaquine_status = CreateDrugResistanceSummary.piperaquine_status + String drug_status_chloroquine = CreateDrugResistanceSummary.chloroquine_status + String drug_status_pyrimethamine = CreateDrugResistanceSummary.pyrimethamine_status + String drug_status_sulfadoxine = CreateDrugResistanceSummary.sulfadoxine_status + String drug_status_mefloquine = CreateDrugResistanceSummary.mefloquine_status + String drug_status_artemisinin = CreateDrugResistanceSummary.artemisinin_status + String drug_status_piperaquine = CreateDrugResistanceSummary.piperaquine_status } } diff --git a/wdl/pipelines/TechAgnostic/TertiaryAnalysis/PfalciparumTypeDrugResistanceMarkers.wdl b/wdl/pipelines/TechAgnostic/TertiaryAnalysis/PfalciparumTypeDrugResistanceMarkers.wdl index 0b96c9f25..5ab70f91f 100644 --- a/wdl/pipelines/TechAgnostic/TertiaryAnalysis/PfalciparumTypeDrugResistanceMarkers.wdl +++ b/wdl/pipelines/TechAgnostic/TertiaryAnalysis/PfalciparumTypeDrugResistanceMarkers.wdl @@ -75,12 +75,12 @@ workflow PfalciparumTypeDrugResistanceMarkers { File drug_resistance_summary = select_first([FinalizeDRSummary.gcs_path, CreateDrugResistanceSummary.resistance_summary]) File raw_drug_res_report = select_first([FinalizeDRReport.gcs_path, CallDrugResistanceMutations.report]) - String chloroquine_status = CreateDrugResistanceSummary.chloroquine_status - String pyrimethamine_status = CreateDrugResistanceSummary.pyrimethamine_status - String sulfadoxine_status = CreateDrugResistanceSummary.sulfadoxine_status - String mefloquine_status = CreateDrugResistanceSummary.mefloquine_status - String artemisinin_status = CreateDrugResistanceSummary.artemisinin_status - String piperaquine_status = CreateDrugResistanceSummary.piperaquine_status + String drug_status_chloroquine = CreateDrugResistanceSummary.chloroquine_status + String drug_status_pyrimethamine = CreateDrugResistanceSummary.pyrimethamine_status + String drug_status_sulfadoxine = CreateDrugResistanceSummary.sulfadoxine_status + String drug_status_mefloquine = CreateDrugResistanceSummary.mefloquine_status + String drug_status_artemisinin = CreateDrugResistanceSummary.artemisinin_status + String drug_status_piperaquine = CreateDrugResistanceSummary.piperaquine_status File? annotated_vcf = final_annotated_vcf File? annotated_vcf_index = final_annotated_vcf_index