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Changing output names of drug resistances in Pf drug resistance WDLs. #463

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Aug 7, 2024
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Changing output names of drug resistances in Pf drug resistance WDLs. #463

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12 changes: 6 additions & 6 deletions wdl/pipelines/TechAgnostic/TertiaryAnalysis/PfalciparumDrugResistanceSummary.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
}
}

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12 changes: 6 additions & 6 deletions wdl/pipelines/TechAgnostic/TertiaryAnalysis/PfalciparumTypeDrugResistanceMarkers.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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