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176 lines (176 loc) · 7.24 KB
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version: 1.2
workflows:
- name: ONT10x
subclass: wdl
primaryDescriptorPath: /wdl/deprecated/ONT10x.wdl
- name: ONTWholeGenome
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/ONT/VariantCalling/ONTWholeGenome.wdl
- name: ONTFlowcell
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/ONT/Preprocessing/ONTFlowcell.wdl
- name: PBFlowcell
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/PacBio/Alignment/PBFlowcell.wdl
- name: PBCCS
subclass: wdl
primaryDescriptorPath: /wdl/deprecated/PBCCS.wdl
- name: PBCCS10x
subclass: wdl
primaryDescriptorPath: /wdl/deprecated/PBCCS10x.wdl
- name: PBCCSDemultiplex
subclass: wdl
primaryDescriptorPath: /wdl/deprecated/PBCCSDemultiplex.wdl
- name: PBCCSDemultiplexWholeGenome
subclass: wdl
primaryDescriptorPath: /wdl/deprecated/PBCCSDemultiplexWholeGenome.wdl
- name: PBCCSIsoSeq
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/PacBio/Utility/PBCCSIsoSeq.wdl
- name: PBCCSWholeGenome
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/PacBio/VariantCalling/PBCCSWholeGenome.wdl
- name: PBCLRDemultiplexWholeGenome
subclass: wdl
primaryDescriptorPath: /wdl/deprecated/PBCLRDemultiplexWholeGenome.wdl
- name: PBCLRWholeGenome
subclass: wdl
primaryDescriptorPath: /wdl/deprecated/PBCLRWholeGenome.wdl
- name: LRCNVs
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/VariantCalling/LRCNVs.wdl
- name: ONTBasecall
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/ONT/Preprocessing/ONTBasecall.wdl
- name: ONTAssembleWithCanu
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/ONT/Assembly/ONTAssembleWithCanu.wdl
- name: ONTAssembleWithFlye
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/ONT/Assembly/ONTAssembleWithFlye.wdl
- name: VerifyFingerprint
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/VerifyFingerprint.wdl
- name: DownloadFromHudsonAlpha
subclass: wdl
primaryDescriptorPath: /wdl/deprecated/DownloadFromHudsonAlpha.wdl
- name: PBAssembleWithHifiasm
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/PacBio/Assembly/PBAssembleWithHifiasm.wdl
- name: ONTMethylation
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/ONT/Epigenomics/ONTMethylation.wdl
- name: ONTPfHrp2Hrp3Status
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/ONT/MultiAnalysis/ONTPfHrp2Hrp3Status.wdl
- name: ONTPfTypeDrugResistanceMarkers
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/ONT/MultiAnalysis/ONTPfTypeDrugResistanceMarkers.wdl
- name: PBMASIsoSeqQuantify
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/PacBio/Utility/PBMASIsoSeqQuantify.wdl
- name: PBMASIsoSeqDemultiplex
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/PacBio/Utility/PBMASIsoSeqDemultiplex.wdl
- name: SRBamToFq
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/SRBamToFq.wdl
- name: SRIndexBam
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/SRIndexBam.wdl
- name: SRWholeGenome
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/ILMN/VariantCalling/SRWholeGenome.wdl
- name: SRFlowcell
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/ILMN/Alignment/SRFlowcell.wdl
- name: SRJointCallGVCFsWithGenomicsDB
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/VariantCalling/SRJointCallGVCFsWithGenomicsDB.wdl
- name: LRJointCallGVCFs
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/VariantCalling/LRJointCallGVCFs.wdl
- name: ConvertToHailMT
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/ConvertToHailMT.wdl
- name: ConvertToZarrStore
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/ConvertToZarrStore.wdl
- name: LRConvertBCF
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/LRConvertBCF.wdl
- name: DownloadFromSRA
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/DownloadFromSRA.wdl
- name: DownloadFromWeb
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/DownloadFromWeb.wdl
- name: ONTProcessBasecall
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/ONT/Preprocessing/ONTProcessBasecall.wdl
- name: ONTFlowcellFromMultipleBasecalls
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/ONT/Preprocessing/ONTFlowcellFromMultipleBasecalls.wdl
- name: CleanupIntermediate
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/CleanupIntermediate.wdl
- name: BenchmarkVCFs
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/BenchmarkVCFs.wdl
- name: CompareVcfBenchmarks
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/CompareVcfBenchmarks.wdl
- name: PanelProcessMalariaBarcodesForRh
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/TertiaryAnalysis/PanelProcessMalariaBarcodesForRh.wdl
- name: ProcessMalariaBarcodesDemo
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/TertiaryAnalysis/ProcessMalariaBarcodesDemo.wdl
- name: ExtractRegionsFromBam
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/ExtractRegionsFromBam.wdl
- name: PfalciparumDrugResistanceSummary
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/TertiaryAnalysis/PfalciparumDrugResistanceSummary.wdl
- name: SRWholeGenome_Pf_Niare_VQSR
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/Z_One_Off_Analyses/SRWholeGenome_Pf_Niare_VQSR.wdl
- name: SRWholeGenome_Pf_Niare_VETS
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/Z_One_Off_Analyses/SRWholeGenome_Pf_Niare_VETS.wdl
- name: SRJointCallGVCFsWithGenomicsDB_Pf_Niare_VQSR
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/Z_One_Off_Analyses/SRJointCallGVCFsWithGenomicsDB_Pf_Niare_VQSR.wdl
- name: SRJointCallGVCFsWithGenomicsDB_Pf_Niare_VETS
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/Z_One_Off_Analyses/SRJointCallGVCFsWithGenomicsDB_Pf_Niare_VETS.wdl
- name: ExpandedDrugResistanceMarkerExtraction
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/TertiaryAnalysis/ExpandedDrugResistanceMarkerExtraction.wdl
- name: ExpandedDrugResistanceMarkerAggregation
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/TertiaryAnalysis/ExpandedDrugResistanceMarkerAggregation.wdl
- name: SRDownsampleBam
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/SRDownsampleBam.wdl
- name: SRFlowcellDecontaminate
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/ILMN/Alignment/SRFlowcellDecontaminate.wdl
- name: SvQCPlots
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Visualization/SvQCPlots.wdl
- name: SRWholeGenomeBootstrap
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/ILMN/VariantCalling/SRWholeGenomeBootstrap.wdl
- name: SRJointCallGVCFsWithGenomicsDBBootstrap
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/VariantCalling/SRJointCallGVCFsWithGenomicsDBBootstrap.wdl
- name: SRReblockGVCFs
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/ILMN/VariantCalling/SRReblockGVCFs.wdl
- name: ExtractCoverageStats
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/ExtractCoverageStats.wdl
- name: DownloadFromFTP
subclass: wdl
primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/DownloadFromFTP.wdl