.dockstore.yml

version: 1.2
workflows:

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# deprecated
- name: ONT10x
  subclass: wdl
  primaryDescriptorPath: /wdl/deprecated/ONT10x.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: PBCLRDemultiplexWholeGenome
  subclass: wdl
  primaryDescriptorPath: /wdl/deprecated/PBCLRDemultiplexWholeGenome.wdl
- name: PBCLRWholeGenome
  subclass: wdl
  primaryDescriptorPath: /wdl/deprecated/PBCLRWholeGenome.wdl
- name: DownloadFromHudsonAlpha
  subclass: wdl
  primaryDescriptorPath: /wdl/deprecated/DownloadFromHudsonAlpha.wdl

###################################################
# ONT
- name: ONTWholeGenome
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/ONT/VariantCalling/ONTWholeGenome.wdl
- name: ONTFlowcell
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/ONT/Preprocessing/ONTFlowcell.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: 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: ONTProcessBasecall
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/ONT/Preprocessing/ONTProcessBasecall.wdl
- name: ONTFlowcellFromMultipleBasecalls
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/ONT/Preprocessing/ONTFlowcellFromMultipleBasecalls.wdl

###################################################
# PacBio
- name: PBFlowcell
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/PacBio/Alignment/PBFlowcell.wdl
- name: PBCCSIsoSeq
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/PacBio/Utility/PBCCSIsoSeq.wdl
- name: PBCCSWholeGenome
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/PacBio/VariantCalling/PBCCSWholeGenome.wdl
- name: PBAssembleWithHifiasm
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/PacBio/Assembly/PBAssembleWithHifiasm.wdl
- name: PBMASIsoSeqQuantify
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/PacBio/Utility/PBMASIsoSeqQuantify.wdl
- name: PBMASIsoSeqDemultiplex
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/PacBio/Utility/PBMASIsoSeqDemultiplex.wdl

###################################################
# TechAgnostic - *mics data processing
- name: CallVariantsReadBased
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/VariantCalling/CallVariantsReadBased.wdl
- name: LRCNVs
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/VariantCalling/LRCNVs.wdl
- name: LRJointCallGVCFs
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/VariantCalling/LRJointCallGVCFs.wdl
- name: ConvertToHailMT
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/ConvertToHailMT.wdl
- name: LRConvertBCF
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/LRConvertBCF.wdl

###################################################
# TechAgnostic - *mics data QC & metrics
- name: ShardWholeGenome
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/ShardWholeGenome.wdl
- name: MergeSampleBamsAndCollectMetrics
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/MergeSampleBamsAndCollectMetrics.wdl
- name: AlignedBamQCandMetrics
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/AlignedBamQCandMetrics.wdl
- name: CollectBamFlagStats
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/CollectBamFlagStats.wdl
- name: CountTheBeans
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/CountTheBeans.wdl
- name: DystPeaker
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/DystPeaker.wdl
- name: FASTQstats
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/FASTQstats.wdl
- name: FilterBamByLength
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/FilterBamByLength.wdl
- name: LongReadsContaminationEstimation
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/LongReadsContaminationEstimation.wdl
- name: SexCheckNaive
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/SexCheckNaive.wdl
- name: VerifyFingerprint
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/VerifyFingerprint.wdl
- name: VerifyBamFingerprint
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/VerifyBamFingerprint.wdl

###################################################
# TechAgnostic - utility
- name: CleanupIntermediate
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/CleanupIntermediate.wdl
- name: DownloadFromSRA
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/DownloadFromSRA.wdl
- name: DownloadFromWeb
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/DownloadFromWeb.wdl
- name: SaveFilesToDestination
  subclass: wdl
  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/SaveFilesToDestination.wdl