Move wdl files to central directory called wdl (#393)

* moved wdls to wdl folder, updated testing location for wdl validation * updated wdl paths in dockstore.yml * renamed 'deprecated_wdl' to 'deprecated', updated docstore.yml accordingly --------- Co-authored-by: bshifaw <bshifaw@broadinstitute.com>
broadinstitute · Apr 11, 2023 · 475331a · 475331a
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Showing 114 changed files with 31 additions and 31 deletions.
diff --git a/.dockstore.yml b/.dockstore.yml
@@ -2,88 +2,88 @@ version: 1.2
 workflows:
 - name: ONT10x
   subclass: wdl
-  primaryDescriptorPath: /deprecated_wdl/ONT10x.wdl
+  primaryDescriptorPath: /wdl/deprecated/ONT10x.wdl
 - name: ONTWholeGenome
   subclass: wdl
-  primaryDescriptorPath: /pipelines/ONT/VariantCalling/ONTWholeGenome.wdl
+  primaryDescriptorPath: /wdl/pipelines/ONT/VariantCalling/ONTWholeGenome.wdl
 - name: ONTFlowcell
   subclass: wdl
-  primaryDescriptorPath: /pipelines/ONT/Preprocessing/ONTFlowcell.wdl
+  primaryDescriptorPath: /wdl/pipelines/ONT/Preprocessing/ONTFlowcell.wdl
 - name: PBFlowcell
   subclass: wdl
-  primaryDescriptorPath: /pipelines/PacBio/Alignment/PBFlowcell.wdl
+  primaryDescriptorPath: /wdl/pipelines/PacBio/Alignment/PBFlowcell.wdl
 - name: PBCCS
   subclass: wdl
-  primaryDescriptorPath: /deprecated_wdl/PBCCS.wdl
+  primaryDescriptorPath: /wdl/deprecated/PBCCS.wdl
 - name: PBCCS10x
   subclass: wdl
-  primaryDescriptorPath: /deprecated_wdl/PBCCS10x.wdl
+  primaryDescriptorPath: /wdl/deprecated/PBCCS10x.wdl
 - name: PBCCSDemultiplex
   subclass: wdl
-  primaryDescriptorPath: /deprecated_wdl/PBCCSDemultiplex.wdl
+  primaryDescriptorPath: /wdl/deprecated/PBCCSDemultiplex.wdl
 - name: PBCCSDemultiplexWholeGenome
   subclass: wdl
-  primaryDescriptorPath: /deprecated_wdl/PBCCSDemultiplexWholeGenome.wdl
+  primaryDescriptorPath: /wdl/deprecated/PBCCSDemultiplexWholeGenome.wdl
 - name: PBCCSIsoSeq
   subclass: wdl
-  primaryDescriptorPath: /pipelines/PacBio/Utility/PBCCSIsoSeq.wdl
+  primaryDescriptorPath: /wdl/pipelines/PacBio/Utility/PBCCSIsoSeq.wdl
 - name: PBCCSWholeGenome
   subclass: wdl
-  primaryDescriptorPath: /pipelines/PacBio/VariantCalling/PBCCSWholeGenome.wdl
+  primaryDescriptorPath: /wdl/pipelines/PacBio/VariantCalling/PBCCSWholeGenome.wdl
 - name: PBCLRDemultiplexWholeGenome
   subclass: wdl
-  primaryDescriptorPath: /deprecated_wdl/PBCLRDemultiplexWholeGenome.wdl
+  primaryDescriptorPath: /wdl/deprecated/PBCLRDemultiplexWholeGenome.wdl
 - name: PBCLRWholeGenome
   subclass: wdl
-  primaryDescriptorPath: /pipelines/PacBio/VariantCalling/PBCLRWholeGenome.wdl
+  primaryDescriptorPath: /wdl/pipelines/PacBio/VariantCalling/PBCLRWholeGenome.wdl
 - name: LRCNVs
   subclass: wdl
-  primaryDescriptorPath: /pipelines/TechAgnostic/VariantCalling/LRCNVs.wdl
+  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/VariantCalling/LRCNVs.wdl
 - name: ONTBasecall
   subclass: wdl
-  primaryDescriptorPath: /pipelines/ONT/Preprocessing/ONTBasecall.wdl
+  primaryDescriptorPath: /wdl/pipelines/ONT/Preprocessing/ONTBasecall.wdl
 - name: ONTAssembleWithCanu
   subclass: wdl
-  primaryDescriptorPath: /pipelines/ONT/Assembly/ONTAssembleWithCanu.wdl
+  primaryDescriptorPath: /wdl/pipelines/ONT/Assembly/ONTAssembleWithCanu.wdl
 - name: ONTAssembleWithFlye
   subclass: wdl
-  primaryDescriptorPath: /pipelines/ONT/Assembly/ONTAssembleWithFlye.wdl
+  primaryDescriptorPath: /wdl/pipelines/ONT/Assembly/ONTAssembleWithFlye.wdl
 - name: VerifyFingerprint
   subclass: wdl
-  primaryDescriptorPath: /pipelines/TechAgnostic/Utility/VerifyFingerprint.wdl
+  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/VerifyFingerprint.wdl
 - name: DownloadFromHudsonAlpha
   subclass: wdl
-  primaryDescriptorPath: /deprecated_wdl/DownloadFromHudsonAlpha.wdl
+  primaryDescriptorPath: /wdl/deprecated/DownloadFromHudsonAlpha.wdl
 - name: PBAssembleWithHifiasm
   subclass: wdl
-  primaryDescriptorPath: /pipelines/PacBio/Assembly/PBAssembleWithHifiasm.wdl
+  primaryDescriptorPath: /wdl/pipelines/PacBio/Assembly/PBAssembleWithHifiasm.wdl
 - name: ONTMethylation
   subclass: wdl
-  primaryDescriptorPath: /pipelines/ONT/Epigenomics/ONTMethylation.wdl
+  primaryDescriptorPath: /wdl/pipelines/ONT/Epigenomics/ONTMethylation.wdl
 - name: ONTPfHrp2Hrp3Status
   subclass: wdl
-  primaryDescriptorPath: /pipelines/ONT/MultiAnalysis/ONTPfHrp2Hrp3Status.wdl
+  primaryDescriptorPath: /wdl/pipelines/ONT/MultiAnalysis/ONTPfHrp2Hrp3Status.wdl
 - name: ONTPfTypeDrugResistanceMarkers
   subclass: wdl
-  primaryDescriptorPath: /pipelines/ONT/MultiAnalysis/ONTPfTypeDrugResistanceMarkers.wdl
+  primaryDescriptorPath: /wdl/pipelines/ONT/MultiAnalysis/ONTPfTypeDrugResistanceMarkers.wdl
 - name: PBMASIsoSeqQuantify
   subclass: wdl
-  primaryDescriptorPath: /pipelines/PacBio/Utility/PBMASIsoSeqQuantify.wdl
+  primaryDescriptorPath: /wdl/pipelines/PacBio/Utility/PBMASIsoSeqQuantify.wdl
 - name: PBMASIsoSeqDemultiplex
   subclass: wdl
-  primaryDescriptorPath: /pipelines/PacBio/Utility/PBMASIsoSeqDemultiplex.wdl
+  primaryDescriptorPath: /wdl/pipelines/PacBio/Utility/PBMASIsoSeqDemultiplex.wdl
 - name: LRJointCallGVCFs
   subclass: wdl
-  primaryDescriptorPath: /pipelines/TechAgnostic/VariantCalling/LRJointCallGVCFs.wdl
+  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/VariantCalling/LRJointCallGVCFs.wdl
 - name: ConvertToHailMT
   subclass: wdl
-  primaryDescriptorPath: /pipelines/TechAgnostic/Utility/ConvertToHailMT.wdl
+  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/ConvertToHailMT.wdl
 - name: LRConvertBCF
   subclass: wdl
-  primaryDescriptorPath: /pipelines/TechAgnostic/Utility/LRConvertBCF.wdl
+  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/LRConvertBCF.wdl
 - name: DownloadFromSRA
   subclass: wdl
-  primaryDescriptorPath: /pipelines/TechAgnostic/Utility/DownloadFromSRA.wdl
+  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/DownloadFromSRA.wdl
 - name: DownloadFromWeb
   subclass: wdl
-  primaryDescriptorPath: /pipelines/TechAgnostic/Utility/DownloadFromWeb.wdl
+  primaryDescriptorPath: /wdl/pipelines/TechAgnostic/Utility/DownloadFromWeb.wdl
diff --git a/test/test_scripts/test_wdl_validity.py b/test/test_scripts/test_wdl_validity.py
@@ -9,8 +9,8 @@
 @pytest.mark.parametrize(
     "tool, subcommand, dir_names",
     (
-        ["womtool", "validate", ["pipelines", "tasks", "deprecated_wdl"]],
-        ["miniwdl",  "check", ["pipelines", "tasks"]],  # miniwdl validation is stricter and takes more time than womtool, so we only run it on 'pipelines' and 'tasks' since 'deprecated_wdl' will eventually be deleted.
+        ["womtool", "validate", ["wdl"]],
+        ["miniwdl",  "check", ["wdl/pipelines", "wdl/tasks"]],  # miniwdl validation is stricter and takes more time than womtool, so we only run it on 'pipelines' and 'tasks' since 'deprecated' will eventually be deleted.
     )
 )
 def test_wdl_validity(script_runner, tool: str, subcommand: str, dir_names: list):

diff --git a/deprecated_wdl/.gitignore → wdl/deprecated/.gitignore b/deprecated_wdl/.gitignore → wdl/deprecated/.gitignore
diff --git a/deprecated_wdl/DownloadFromHudsonAlpha.wdl → wdl/deprecated/DownloadFromHudsonAlpha.wdl b/deprecated_wdl/DownloadFromHudsonAlpha.wdl → wdl/deprecated/DownloadFromHudsonAlpha.wdl
diff --git a/deprecated_wdl/ONT10x.wdl → wdl/deprecated/ONT10x.wdl b/deprecated_wdl/ONT10x.wdl → wdl/deprecated/ONT10x.wdl
diff --git a/deprecated_wdl/PBCCS.wdl → wdl/deprecated/PBCCS.wdl b/deprecated_wdl/PBCCS.wdl → wdl/deprecated/PBCCS.wdl
diff --git a/deprecated_wdl/PBCCS10x.wdl → wdl/deprecated/PBCCS10x.wdl b/deprecated_wdl/PBCCS10x.wdl → wdl/deprecated/PBCCS10x.wdl
diff --git a/deprecated_wdl/PBCCSDemultiplex.wdl → wdl/deprecated/PBCCSDemultiplex.wdl b/deprecated_wdl/PBCCSDemultiplex.wdl → wdl/deprecated/PBCCSDemultiplex.wdl
diff --git a/...cated_wdl/PBCCSDemultiplexWholeGenome.wdl → ...eprecated/PBCCSDemultiplexWholeGenome.wdl b/...cated_wdl/PBCCSDemultiplexWholeGenome.wdl → ...eprecated/PBCCSDemultiplexWholeGenome.wdl
diff --git a/...cated_wdl/PBCLRDemultiplexWholeGenome.wdl → ...eprecated/PBCLRDemultiplexWholeGenome.wdl b/...cated_wdl/PBCLRDemultiplexWholeGenome.wdl → ...eprecated/PBCLRDemultiplexWholeGenome.wdl
diff --git a/...PostprocessCCSedDemultiplexedSMRTCell.wdl → ...PostprocessCCSedDemultiplexedSMRTCell.wdl b/...PostprocessCCSedDemultiplexedSMRTCell.wdl → ...PostprocessCCSedDemultiplexedSMRTCell.wdl
diff --git a/...d_wdl/PreprocessBarcodedCCSedSMRTCell.wdl → ...cated/PreprocessBarcodedCCSedSMRTCell.wdl b/...d_wdl/PreprocessBarcodedCCSedSMRTCell.wdl → ...cated/PreprocessBarcodedCCSedSMRTCell.wdl
diff --git a/deprecated_wdl/README.md → wdl/deprecated/README.md b/deprecated_wdl/README.md → wdl/deprecated/README.md
diff --git a/deprecated_wdl/TestCromwell.wdl → wdl/deprecated/TestCromwell.wdl b/deprecated_wdl/TestCromwell.wdl → wdl/deprecated/TestCromwell.wdl
diff --git a/deprecated_wdl/tasks/AnnotateAdapters.wdl → wdl/deprecated/tasks/AnnotateAdapters.wdl b/deprecated_wdl/tasks/AnnotateAdapters.wdl → wdl/deprecated/tasks/AnnotateAdapters.wdl
diff --git a/deprecated_wdl/tasks/Busco.wdl → wdl/deprecated/tasks/Busco.wdl b/deprecated_wdl/tasks/Busco.wdl → wdl/deprecated/tasks/Busco.wdl
diff --git a/deprecated_wdl/tasks/C3POa.wdl → wdl/deprecated/tasks/C3POa.wdl b/deprecated_wdl/tasks/C3POa.wdl → wdl/deprecated/tasks/C3POa.wdl
diff --git a/deprecated_wdl/tasks/CCSLima.wdl → wdl/deprecated/tasks/CCSLima.wdl b/deprecated_wdl/tasks/CCSLima.wdl → wdl/deprecated/tasks/CCSLima.wdl
diff --git a/deprecated_wdl/tasks/CuteSV.wdl → wdl/deprecated/tasks/CuteSV.wdl b/deprecated_wdl/tasks/CuteSV.wdl → wdl/deprecated/tasks/CuteSV.wdl
diff --git a/deprecated_wdl/tasks/GATKBestPractice.wdl → wdl/deprecated/tasks/GATKBestPractice.wdl b/deprecated_wdl/tasks/GATKBestPractice.wdl → wdl/deprecated/tasks/GATKBestPractice.wdl
diff --git a/deprecated_wdl/tasks/Longshot.wdl → wdl/deprecated/tasks/Longshot.wdl b/deprecated_wdl/tasks/Longshot.wdl → wdl/deprecated/tasks/Longshot.wdl
diff --git a/deprecated_wdl/tasks/Methylation.wdl → wdl/deprecated/tasks/Methylation.wdl b/deprecated_wdl/tasks/Methylation.wdl → wdl/deprecated/tasks/Methylation.wdl
diff --git a/deprecated_wdl/tasks/Nanopolish.wdl → wdl/deprecated/tasks/Nanopolish.wdl b/deprecated_wdl/tasks/Nanopolish.wdl → wdl/deprecated/tasks/Nanopolish.wdl
diff --git a/deprecated_wdl/tasks/Pacasus.wdl → wdl/deprecated/tasks/Pacasus.wdl b/deprecated_wdl/tasks/Pacasus.wdl → wdl/deprecated/tasks/Pacasus.wdl
diff --git a/deprecated_wdl/tasks/Peregrine.wdl → wdl/deprecated/tasks/Peregrine.wdl b/deprecated_wdl/tasks/Peregrine.wdl → wdl/deprecated/tasks/Peregrine.wdl
diff --git a/deprecated_wdl/tasks/PhaseReads.wdl → wdl/deprecated/tasks/PhaseReads.wdl b/deprecated_wdl/tasks/PhaseReads.wdl → wdl/deprecated/tasks/PhaseReads.wdl
diff --git a/deprecated_wdl/tasks/SMRTtools.wdl → wdl/deprecated/tasks/SMRTtools.wdl b/deprecated_wdl/tasks/SMRTtools.wdl → wdl/deprecated/tasks/SMRTtools.wdl
diff --git a/deprecated_wdl/tasks/SVIM.wdl → wdl/deprecated/tasks/SVIM.wdl b/deprecated_wdl/tasks/SVIM.wdl → wdl/deprecated/tasks/SVIM.wdl
diff --git a/deprecated_wdl/tasks/Tama.wdl → wdl/deprecated/tasks/Tama.wdl b/deprecated_wdl/tasks/Tama.wdl → wdl/deprecated/tasks/Tama.wdl
diff --git a/deprecated_wdl/tasks/Ten_X_Tool.wdl → wdl/deprecated/tasks/Ten_X_Tool.wdl b/deprecated_wdl/tasks/Ten_X_Tool.wdl → wdl/deprecated/tasks/Ten_X_Tool.wdl
diff --git a/deprecated_wdl/tasks/UnalignedMetrics.wdl → wdl/deprecated/tasks/UnalignedMetrics.wdl b/deprecated_wdl/tasks/UnalignedMetrics.wdl → wdl/deprecated/tasks/UnalignedMetrics.wdl
diff --git a/...ks/dsde_pipelines_tasks/BamProcessing.wdl → ...ks/dsde_pipelines_tasks/BamProcessing.wdl b/...ks/dsde_pipelines_tasks/BamProcessing.wdl → ...ks/dsde_pipelines_tasks/BamProcessing.wdl
diff --git a/...elines_tasks/GermlineVariantDiscovery.wdl → ...elines_tasks/GermlineVariantDiscovery.wdl b/...elines_tasks/GermlineVariantDiscovery.wdl → ...elines_tasks/GermlineVariantDiscovery.wdl
diff --git a/...ted_wdl/tasks/dsde_pipelines_tasks/Qc.wdl → ...recated/tasks/dsde_pipelines_tasks/Qc.wdl b/...ted_wdl/tasks/dsde_pipelines_tasks/Qc.wdl → ...recated/tasks/dsde_pipelines_tasks/Qc.wdl
diff --git a/...wdl/tasks/dsde_pipelines_tasks/Readme.txt → ...ted/tasks/dsde_pipelines_tasks/Readme.txt b/...wdl/tasks/dsde_pipelines_tasks/Readme.txt → ...ted/tasks/dsde_pipelines_tasks/Readme.txt
diff --git a/.../tasks/dsde_pipelines_tasks/Utilities.wdl → .../tasks/dsde_pipelines_tasks/Utilities.wdl b/.../tasks/dsde_pipelines_tasks/Utilities.wdl → .../tasks/dsde_pipelines_tasks/Utilities.wdl
diff --git a/...dsde_pipelines_tasks/cnv_common_tasks.wdl → ...dsde_pipelines_tasks/cnv_common_tasks.wdl b/...dsde_pipelines_tasks/cnv_common_tasks.wdl → ...dsde_pipelines_tasks/cnv_common_tasks.wdl
diff --git a/...s/dsde_pipelines_tasks/variantcalling.wdl → ...s/dsde_pipelines_tasks/variantcalling.wdl b/...s/dsde_pipelines_tasks/variantcalling.wdl → ...s/dsde_pipelines_tasks/variantcalling.wdl
diff --git a/pipelines/.gitignore → wdl/pipelines/.gitignore b/pipelines/.gitignore → wdl/pipelines/.gitignore
diff --git a/...ines/ONT/Assembly/ONTAssembleWithCanu.wdl → ...ines/ONT/Assembly/ONTAssembleWithCanu.wdl b/...ines/ONT/Assembly/ONTAssembleWithCanu.wdl → ...ines/ONT/Assembly/ONTAssembleWithCanu.wdl
diff --git a/...ines/ONT/Assembly/ONTAssembleWithFlye.wdl → ...ines/ONT/Assembly/ONTAssembleWithFlye.wdl b/...ines/ONT/Assembly/ONTAssembleWithFlye.wdl → ...ines/ONT/Assembly/ONTAssembleWithFlye.wdl
diff --git a/pipelines/ONT/Epigenomics/ONTMethylation.wdl → ...elines/ONT/Epigenomics/ONTMethylation.wdl b/pipelines/ONT/Epigenomics/ONTMethylation.wdl → ...elines/ONT/Epigenomics/ONTMethylation.wdl
diff --git a/...ONT/MultiAnalysis/ONTPfHrp2Hrp3Status.wdl → ...ONT/MultiAnalysis/ONTPfHrp2Hrp3Status.wdl b/...ONT/MultiAnalysis/ONTPfHrp2Hrp3Status.wdl → ...ONT/MultiAnalysis/ONTPfHrp2Hrp3Status.wdl
diff --git a/...alysis/ONTPfTypeDrugResistanceMarkers.wdl → ...alysis/ONTPfTypeDrugResistanceMarkers.wdl b/...alysis/ONTPfTypeDrugResistanceMarkers.wdl → ...alysis/ONTPfTypeDrugResistanceMarkers.wdl
diff --git a/pipelines/ONT/Preprocessing/ONTBasecall.wdl → ...pelines/ONT/Preprocessing/ONTBasecall.wdl b/pipelines/ONT/Preprocessing/ONTBasecall.wdl → ...pelines/ONT/Preprocessing/ONTBasecall.wdl
diff --git a/pipelines/ONT/Preprocessing/ONTFlowcell.wdl → ...pelines/ONT/Preprocessing/ONTFlowcell.wdl b/pipelines/ONT/Preprocessing/ONTFlowcell.wdl → ...pelines/ONT/Preprocessing/ONTFlowcell.wdl
diff --git a/...nes/ONT/VariantCalling/ONTWholeGenome.wdl → ...nes/ONT/VariantCalling/ONTWholeGenome.wdl b/...nes/ONT/VariantCalling/ONTWholeGenome.wdl → ...nes/ONT/VariantCalling/ONTWholeGenome.wdl
diff --git a/pipelines/PacBio/Alignment/PBFlowcell.wdl → ...pipelines/PacBio/Alignment/PBFlowcell.wdl b/pipelines/PacBio/Alignment/PBFlowcell.wdl → ...pipelines/PacBio/Alignment/PBFlowcell.wdl
diff --git a/...PacBio/Assembly/PBAssembleWithHifiasm.wdl → ...PacBio/Assembly/PBAssembleWithHifiasm.wdl b/...PacBio/Assembly/PBAssembleWithHifiasm.wdl → ...PacBio/Assembly/PBAssembleWithHifiasm.wdl
diff --git a/pipelines/PacBio/Utility/PBCCSIsoSeq.wdl → wdl/pipelines/PacBio/Utility/PBCCSIsoSeq.wdl b/pipelines/PacBio/Utility/PBCCSIsoSeq.wdl → wdl/pipelines/PacBio/Utility/PBCCSIsoSeq.wdl
diff --git a/...PacBio/Utility/PBMASIsoSeqDemultiplex.wdl → ...PacBio/Utility/PBMASIsoSeqDemultiplex.wdl b/...PacBio/Utility/PBMASIsoSeqDemultiplex.wdl → ...PacBio/Utility/PBMASIsoSeqDemultiplex.wdl
diff --git a/...es/PacBio/Utility/PBMASIsoSeqQuantify.wdl → ...es/PacBio/Utility/PBMASIsoSeqQuantify.wdl b/...es/PacBio/Utility/PBMASIsoSeqQuantify.wdl → ...es/PacBio/Utility/PBMASIsoSeqQuantify.wdl
diff --git a/.../PacBio/Utility/TrioBinChildLongReads.wdl → .../PacBio/Utility/TrioBinChildLongReads.wdl b/.../PacBio/Utility/TrioBinChildLongReads.wdl → .../PacBio/Utility/TrioBinChildLongReads.wdl
diff --git a/...acBio/VariantCalling/PBCCSWholeGenome.wdl → ...acBio/VariantCalling/PBCCSWholeGenome.wdl b/...acBio/VariantCalling/PBCCSWholeGenome.wdl → ...acBio/VariantCalling/PBCCSWholeGenome.wdl
diff --git a/...acBio/VariantCalling/PBCLRWholeGenome.wdl → ...acBio/VariantCalling/PBCLRWholeGenome.wdl b/...acBio/VariantCalling/PBCLRWholeGenome.wdl → ...acBio/VariantCalling/PBCLRWholeGenome.wdl
diff --git a/...tation/AnnotateTranscriptomeWithGuide.wdl → ...tation/AnnotateTranscriptomeWithGuide.wdl b/...tation/AnnotateTranscriptomeWithGuide.wdl → ...tation/AnnotateTranscriptomeWithGuide.wdl
diff --git a/...hAgnostic/Utility/CleanupIntermediate.wdl → ...hAgnostic/Utility/CleanupIntermediate.wdl b/...hAgnostic/Utility/CleanupIntermediate.wdl → ...hAgnostic/Utility/CleanupIntermediate.wdl
diff --git a/.../TechAgnostic/Utility/ConvertToHailMT.wdl → .../TechAgnostic/Utility/ConvertToHailMT.wdl b/.../TechAgnostic/Utility/ConvertToHailMT.wdl → .../TechAgnostic/Utility/ConvertToHailMT.wdl
diff --git a/.../TechAgnostic/Utility/DownloadFromFTP.wdl → .../TechAgnostic/Utility/DownloadFromFTP.wdl b/.../TechAgnostic/Utility/DownloadFromFTP.wdl → .../TechAgnostic/Utility/DownloadFromFTP.wdl
diff --git a/.../TechAgnostic/Utility/DownloadFromSRA.wdl → .../TechAgnostic/Utility/DownloadFromSRA.wdl b/.../TechAgnostic/Utility/DownloadFromSRA.wdl → .../TechAgnostic/Utility/DownloadFromSRA.wdl
diff --git a/.../TechAgnostic/Utility/DownloadFromWeb.wdl → .../TechAgnostic/Utility/DownloadFromWeb.wdl b/.../TechAgnostic/Utility/DownloadFromWeb.wdl → .../TechAgnostic/Utility/DownloadFromWeb.wdl
diff --git a/.../TechAgnostic/Utility/FindBamIdentity.wdl → .../TechAgnostic/Utility/FindBamIdentity.wdl b/.../TechAgnostic/Utility/FindBamIdentity.wdl → .../TechAgnostic/Utility/FindBamIdentity.wdl
diff --git a/...nes/TechAgnostic/Utility/LRConvertBCF.wdl → ...nes/TechAgnostic/Utility/LRConvertBCF.wdl b/...nes/TechAgnostic/Utility/LRConvertBCF.wdl → ...nes/TechAgnostic/Utility/LRConvertBCF.wdl
diff --git a/...echAgnostic/Utility/VerifyFingerprint.wdl → ...echAgnostic/Utility/VerifyFingerprint.wdl b/...echAgnostic/Utility/VerifyFingerprint.wdl → ...echAgnostic/Utility/VerifyFingerprint.wdl
diff --git a/...es/TechAgnostic/VariantCalling/LRCNVs.wdl → ...es/TechAgnostic/VariantCalling/LRCNVs.wdl b/...es/TechAgnostic/VariantCalling/LRCNVs.wdl → ...es/TechAgnostic/VariantCalling/LRCNVs.wdl
diff --git a/...ostic/VariantCalling/LRJointCallGVCFs.wdl → ...ostic/VariantCalling/LRJointCallGVCFs.wdl b/...ostic/VariantCalling/LRJointCallGVCFs.wdl → ...ostic/VariantCalling/LRJointCallGVCFs.wdl
diff --git a/structs/Structs.wdl → wdl/structs/Structs.wdl b/structs/Structs.wdl → wdl/structs/Structs.wdl
diff --git a/tasks/.gitignore → wdl/tasks/.gitignore b/tasks/.gitignore → wdl/tasks/.gitignore
diff --git a/...Alignment/AlignAndCheckFingerprintCCS.wdl → ...Alignment/AlignAndCheckFingerprintCCS.wdl b/...Alignment/AlignAndCheckFingerprintCCS.wdl → ...Alignment/AlignAndCheckFingerprintCCS.wdl
diff --git a/tasks/Alignment/AlignReads.wdl → wdl/tasks/Alignment/AlignReads.wdl b/tasks/Alignment/AlignReads.wdl → wdl/tasks/Alignment/AlignReads.wdl
diff --git a/tasks/Assembly/Canu.wdl → wdl/tasks/Assembly/Canu.wdl b/tasks/Assembly/Canu.wdl → wdl/tasks/Assembly/Canu.wdl
diff --git a/tasks/Assembly/Flye.wdl → wdl/tasks/Assembly/Flye.wdl b/tasks/Assembly/Flye.wdl → wdl/tasks/Assembly/Flye.wdl
diff --git a/tasks/Assembly/Hifiasm.wdl → wdl/tasks/Assembly/Hifiasm.wdl b/tasks/Assembly/Hifiasm.wdl → wdl/tasks/Assembly/Hifiasm.wdl
diff --git a/tasks/Assembly/Racon.wdl → wdl/tasks/Assembly/Racon.wdl b/tasks/Assembly/Racon.wdl → wdl/tasks/Assembly/Racon.wdl
diff --git a/...Preprocessing/CollectParentsKmerStats.wdl → ...Preprocessing/CollectParentsKmerStats.wdl b/...Preprocessing/CollectParentsKmerStats.wdl → ...Preprocessing/CollectParentsKmerStats.wdl
diff --git a/tasks/Preprocessing/Guppy.wdl → wdl/tasks/Preprocessing/Guppy.wdl b/tasks/Preprocessing/Guppy.wdl → wdl/tasks/Preprocessing/Guppy.wdl
diff --git a/tasks/Preprocessing/Longbow.wdl → wdl/tasks/Preprocessing/Longbow.wdl b/tasks/Preprocessing/Longbow.wdl → wdl/tasks/Preprocessing/Longbow.wdl
diff --git a/tasks/Preprocessing/Medaka.wdl → wdl/tasks/Preprocessing/Medaka.wdl b/tasks/Preprocessing/Medaka.wdl → wdl/tasks/Preprocessing/Medaka.wdl
diff --git a/tasks/QC/AlignedMetrics.wdl → wdl/tasks/QC/AlignedMetrics.wdl b/tasks/QC/AlignedMetrics.wdl → wdl/tasks/QC/AlignedMetrics.wdl
diff --git a/tasks/QC/CollectPacBioAlignedMetrics.wdl → wdl/tasks/QC/CollectPacBioAlignedMetrics.wdl b/tasks/QC/CollectPacBioAlignedMetrics.wdl → wdl/tasks/QC/CollectPacBioAlignedMetrics.wdl
diff --git a/tasks/QC/CollectSMRTCellUnalignedMetrics.wdl → ...ks/QC/CollectSMRTCellUnalignedMetrics.wdl b/tasks/QC/CollectSMRTCellUnalignedMetrics.wdl → ...ks/QC/CollectSMRTCellUnalignedMetrics.wdl
diff --git a/tasks/QC/FPCheckAoU.wdl → wdl/tasks/QC/FPCheckAoU.wdl b/tasks/QC/FPCheckAoU.wdl → wdl/tasks/QC/FPCheckAoU.wdl
diff --git a/tasks/QC/Fingerprinting.wdl → wdl/tasks/QC/Fingerprinting.wdl b/tasks/QC/Fingerprinting.wdl → wdl/tasks/QC/Fingerprinting.wdl
diff --git a/tasks/QC/Quast.wdl → wdl/tasks/QC/Quast.wdl b/tasks/QC/Quast.wdl → wdl/tasks/QC/Quast.wdl
diff --git a/tasks/QC/SampleLevelAlignedMetrics.wdl → wdl/tasks/QC/SampleLevelAlignedMetrics.wdl b/tasks/QC/SampleLevelAlignedMetrics.wdl → wdl/tasks/QC/SampleLevelAlignedMetrics.wdl
diff --git a/tasks/Transcriptomics/MASSeq.wdl → wdl/tasks/Transcriptomics/MASSeq.wdl b/tasks/Transcriptomics/MASSeq.wdl → wdl/tasks/Transcriptomics/MASSeq.wdl
diff --git a/.../Transcriptomics/Postprocessing_Tasks.wdl → .../Transcriptomics/Postprocessing_Tasks.wdl b/.../Transcriptomics/Postprocessing_Tasks.wdl → .../Transcriptomics/Postprocessing_Tasks.wdl
diff --git a/...s/Transcriptomics/Preprocessing_Tasks.wdl → ...s/Transcriptomics/Preprocessing_Tasks.wdl b/...s/Transcriptomics/Preprocessing_Tasks.wdl → ...s/Transcriptomics/Preprocessing_Tasks.wdl
diff --git a/tasks/Transcriptomics/UMI_Tools.wdl → wdl/tasks/Transcriptomics/UMI_Tools.wdl b/tasks/Transcriptomics/UMI_Tools.wdl → wdl/tasks/Transcriptomics/UMI_Tools.wdl
diff --git a/tasks/Utility/AssignChildLongReads.wdl → wdl/tasks/Utility/AssignChildLongReads.wdl b/tasks/Utility/AssignChildLongReads.wdl → wdl/tasks/Utility/AssignChildLongReads.wdl
diff --git a/tasks/Utility/BAMutils.wdl → wdl/tasks/Utility/BAMutils.wdl b/tasks/Utility/BAMutils.wdl → wdl/tasks/Utility/BAMutils.wdl
diff --git a/tasks/Utility/Finalize.wdl → wdl/tasks/Utility/Finalize.wdl b/tasks/Utility/Finalize.wdl → wdl/tasks/Utility/Finalize.wdl
diff --git a/tasks/Utility/GeneralUtils.wdl → wdl/tasks/Utility/GeneralUtils.wdl b/tasks/Utility/GeneralUtils.wdl → wdl/tasks/Utility/GeneralUtils.wdl
diff --git a/tasks/Utility/Hail.wdl → wdl/tasks/Utility/Hail.wdl b/tasks/Utility/Hail.wdl → wdl/tasks/Utility/Hail.wdl
diff --git a/tasks/Utility/JupyterNotebooks.wdl → wdl/tasks/Utility/JupyterNotebooks.wdl b/tasks/Utility/JupyterNotebooks.wdl → wdl/tasks/Utility/JupyterNotebooks.wdl
diff --git a/tasks/Utility/ONTUtils.wdl → wdl/tasks/Utility/ONTUtils.wdl b/tasks/Utility/ONTUtils.wdl → wdl/tasks/Utility/ONTUtils.wdl
diff --git a/tasks/Utility/PBUtils.wdl → wdl/tasks/Utility/PBUtils.wdl b/tasks/Utility/PBUtils.wdl → wdl/tasks/Utility/PBUtils.wdl
diff --git a/tasks/Utility/SoftClipper.wdl → wdl/tasks/Utility/SoftClipper.wdl b/tasks/Utility/SoftClipper.wdl → wdl/tasks/Utility/SoftClipper.wdl
diff --git a/tasks/Utility/StringTie2.wdl → wdl/tasks/Utility/StringTie2.wdl b/tasks/Utility/StringTie2.wdl → wdl/tasks/Utility/StringTie2.wdl
diff --git a/tasks/Utility/Utils.wdl → wdl/tasks/Utility/Utils.wdl b/tasks/Utility/Utils.wdl → wdl/tasks/Utility/Utils.wdl
diff --git a/tasks/Utility/VariantUtils.wdl → wdl/tasks/Utility/VariantUtils.wdl b/tasks/Utility/VariantUtils.wdl → wdl/tasks/Utility/VariantUtils.wdl
diff --git a/tasks/Utility/cnv_common_tasks.wdl → wdl/tasks/Utility/cnv_common_tasks.wdl b/tasks/Utility/cnv_common_tasks.wdl → wdl/tasks/Utility/cnv_common_tasks.wdl
diff --git a/tasks/VariantCalling/CCSPepper.wdl → wdl/tasks/VariantCalling/CCSPepper.wdl b/tasks/VariantCalling/CCSPepper.wdl → wdl/tasks/VariantCalling/CCSPepper.wdl
diff --git a/...s/VariantCalling/CallAssemblyVariants.wdl → ...s/VariantCalling/CallAssemblyVariants.wdl b/...s/VariantCalling/CallAssemblyVariants.wdl → ...s/VariantCalling/CallAssemblyVariants.wdl
diff --git a/tasks/VariantCalling/CallVariantsONT.wdl → wdl/tasks/VariantCalling/CallVariantsONT.wdl b/tasks/VariantCalling/CallVariantsONT.wdl → wdl/tasks/VariantCalling/CallVariantsONT.wdl
diff --git a/tasks/VariantCalling/CallVariantsPBCCS.wdl → ...asks/VariantCalling/CallVariantsPBCCS.wdl b/tasks/VariantCalling/CallVariantsPBCCS.wdl → ...asks/VariantCalling/CallVariantsPBCCS.wdl
diff --git a/tasks/VariantCalling/CallVariantsPBCLR.wdl → ...asks/VariantCalling/CallVariantsPBCLR.wdl b/tasks/VariantCalling/CallVariantsPBCLR.wdl → ...asks/VariantCalling/CallVariantsPBCLR.wdl
diff --git a/tasks/VariantCalling/Clair.wdl → wdl/tasks/VariantCalling/Clair.wdl b/tasks/VariantCalling/Clair.wdl → wdl/tasks/VariantCalling/Clair.wdl
diff --git a/tasks/VariantCalling/GLNexus.wdl → wdl/tasks/VariantCalling/GLNexus.wdl b/tasks/VariantCalling/GLNexus.wdl → wdl/tasks/VariantCalling/GLNexus.wdl
diff --git a/tasks/VariantCalling/ONTPepper.wdl → wdl/tasks/VariantCalling/ONTPepper.wdl b/tasks/VariantCalling/ONTPepper.wdl → wdl/tasks/VariantCalling/ONTPepper.wdl
diff --git a/tasks/VariantCalling/PBSV.wdl → wdl/tasks/VariantCalling/PBSV.wdl b/tasks/VariantCalling/PBSV.wdl → wdl/tasks/VariantCalling/PBSV.wdl
diff --git a/tasks/VariantCalling/Sniffles.wdl → wdl/tasks/VariantCalling/Sniffles.wdl b/tasks/VariantCalling/Sniffles.wdl → wdl/tasks/VariantCalling/Sniffles.wdl
diff --git a/tasks/VariantCalling/Sniffles2.wdl → wdl/tasks/VariantCalling/Sniffles2.wdl b/tasks/VariantCalling/Sniffles2.wdl → wdl/tasks/VariantCalling/Sniffles2.wdl
diff --git a/tasks/Visualization/NanoPlot.wdl → wdl/tasks/Visualization/NanoPlot.wdl b/tasks/Visualization/NanoPlot.wdl → wdl/tasks/Visualization/NanoPlot.wdl