move cromwell

AlekseiLitkovetc · Feb 25, 2018 · a40de67 · a40de67
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diff --git a/cromwell/.dockerignore → .dockerignore b/cromwell/.dockerignore → .dockerignore
diff --git a/cromwell/.gitattributes → .gitattributes b/cromwell/.gitattributes → .gitattributes
diff --git a/cromwell/.gitignore → .gitignore b/cromwell/.gitignore → .gitignore
diff --git a/...ea/inspectionProfiles/Project_Default.xml → .idea/inspectionProfiles/Project_Default.xml b/...ea/inspectionProfiles/Project_Default.xml → .idea/inspectionProfiles/Project_Default.xml
diff --git a/cromwell/.pullapprove.yml → .pullapprove.yml b/cromwell/.pullapprove.yml → .pullapprove.yml
diff --git a/cromwell/.travis.yml → .travis.yml b/cromwell/.travis.yml → .travis.yml
diff --git a/cromwell/AUTHORS → AUTHORS b/cromwell/AUTHORS → AUTHORS
diff --git a/cromwell/CHANGELOG.md → CHANGELOG.md b/cromwell/CHANGELOG.md → CHANGELOG.md
diff --git a/cromwell/LICENSE-ASL-2.0 → LICENSE-ASL-2.0 b/cromwell/LICENSE-ASL-2.0 → LICENSE-ASL-2.0
diff --git a/cromwell/LICENSE.txt → LICENSE.txt b/cromwell/LICENSE.txt → LICENSE.txt
diff --git a/cromwell/README.md → README.md b/cromwell/README.md → README.md
diff --git a/cromwell/backend/README.md → backend/README.md b/cromwell/backend/README.md → backend/README.md
diff --git a/...backend/BackendCacheHitCopyingActor.scala → ...backend/BackendCacheHitCopyingActor.scala b/...backend/BackendCacheHitCopyingActor.scala → ...backend/BackendCacheHitCopyingActor.scala
diff --git a/...l/backend/BackendInitializationData.scala → ...l/backend/BackendInitializationData.scala b/...l/backend/BackendInitializationData.scala → ...l/backend/BackendInitializationData.scala
diff --git a/...omwell/backend/BackendJobBreadCrumb.scala → ...omwell/backend/BackendJobBreadCrumb.scala b/...omwell/backend/BackendJobBreadCrumb.scala → ...omwell/backend/BackendJobBreadCrumb.scala
diff --git a/...ll/backend/BackendJobExecutionActor.scala → ...ll/backend/BackendJobExecutionActor.scala b/...ll/backend/BackendJobExecutionActor.scala → ...ll/backend/BackendJobExecutionActor.scala
diff --git a/...mwell/backend/BackendLifecycleActor.scala → ...mwell/backend/BackendLifecycleActor.scala b/...mwell/backend/BackendLifecycleActor.scala → ...mwell/backend/BackendLifecycleActor.scala
diff --git a/...ackend/BackendLifecycleActorFactory.scala → ...ackend/BackendLifecycleActorFactory.scala b/...ackend/BackendLifecycleActorFactory.scala → ...ackend/BackendLifecycleActorFactory.scala
diff --git a/.../BackendSingletonActorAbortWorkflow.scala → .../BackendSingletonActorAbortWorkflow.scala b/.../BackendSingletonActorAbortWorkflow.scala → .../BackendSingletonActorAbortWorkflow.scala
diff --git a/...nd/BackendWorkflowFinalizationActor.scala → ...nd/BackendWorkflowFinalizationActor.scala b/...nd/BackendWorkflowFinalizationActor.scala → ...nd/BackendWorkflowFinalizationActor.scala
diff --git a/.../BackendWorkflowInitializationActor.scala → .../BackendWorkflowInitializationActor.scala b/.../BackendWorkflowInitializationActor.scala → .../BackendWorkflowInitializationActor.scala
diff --git a/...n/scala/cromwell/backend/MemorySize.scala → ...n/scala/cromwell/backend/MemorySize.scala b/...n/scala/cromwell/backend/MemorySize.scala → ...n/scala/cromwell/backend/MemorySize.scala
diff --git a/.../backend/RuntimeAttributeDefinition.scala → .../backend/RuntimeAttributeDefinition.scala b/.../backend/RuntimeAttributeDefinition.scala → .../backend/RuntimeAttributeDefinition.scala
diff --git a/...cromwell/backend/RuntimeEnvironment.scala → ...cromwell/backend/RuntimeEnvironment.scala b/...cromwell/backend/RuntimeEnvironment.scala → ...cromwell/backend/RuntimeEnvironment.scala
diff --git a/...async/AsyncBackendJobExecutionActor.scala → ...async/AsyncBackendJobExecutionActor.scala b/...async/AsyncBackendJobExecutionActor.scala → ...async/AsyncBackendJobExecutionActor.scala
diff --git a/...mwell/backend/async/ExecutionHandle.scala → ...mwell/backend/async/ExecutionHandle.scala b/...mwell/backend/async/ExecutionHandle.scala → ...mwell/backend/async/ExecutionHandle.scala
diff --git a/...mwell/backend/async/ExecutionResult.scala → ...mwell/backend/async/ExecutionResult.scala b/...mwell/backend/async/ExecutionResult.scala → ...mwell/backend/async/ExecutionResult.scala
diff --git a/...kend/async/KnownJobFailureException.scala → ...kend/async/KnownJobFailureException.scala b/...kend/async/KnownJobFailureException.scala → ...kend/async/KnownJobFailureException.scala
diff --git a/...cala/cromwell/backend/async/package.scala → ...cala/cromwell/backend/async/package.scala b/...cala/cromwell/backend/async/package.scala → ...cala/cromwell/backend/async/package.scala
diff --git a/...main/scala/cromwell/backend/backend.scala → ...main/scala/cromwell/backend/backend.scala b/...main/scala/cromwell/backend/backend.scala → ...main/scala/cromwell/backend/backend.scala
diff --git a/...trumentation/BackendInstrumentation.scala → ...trumentation/BackendInstrumentation.scala b/...trumentation/BackendInstrumentation.scala → ...trumentation/BackendInstrumentation.scala
diff --git a/...mwell/backend/io/DirectoryFunctions.scala → ...mwell/backend/io/DirectoryFunctions.scala b/...mwell/backend/io/DirectoryFunctions.scala → ...mwell/backend/io/DirectoryFunctions.scala
diff --git a/...a/cromwell/backend/io/GlobFunctions.scala → ...a/cromwell/backend/io/GlobFunctions.scala b/...a/cromwell/backend/io/GlobFunctions.scala → ...a/cromwell/backend/io/GlobFunctions.scala
diff --git a/.../scala/cromwell/backend/io/JobPaths.scala → .../scala/cromwell/backend/io/JobPaths.scala b/.../scala/cromwell/backend/io/JobPaths.scala → .../scala/cromwell/backend/io/JobPaths.scala
diff --git a/...mwell/backend/io/JobPathsWithDocker.scala → ...mwell/backend/io/JobPathsWithDocker.scala b/...mwell/backend/io/JobPathsWithDocker.scala → ...mwell/backend/io/JobPathsWithDocker.scala
diff --git a/...a/cromwell/backend/io/WorkflowPaths.scala → ...a/cromwell/backend/io/WorkflowPaths.scala b/...a/cromwell/backend/io/WorkflowPaths.scala → ...a/cromwell/backend/io/WorkflowPaths.scala
diff --git a/.../backend/io/WorkflowPathsWithDocker.scala → .../backend/io/WorkflowPathsWithDocker.scala b/.../backend/io/WorkflowPathsWithDocker.scala → .../backend/io/WorkflowPathsWithDocker.scala
diff --git a/...main/scala/cromwell/backend/package.scala → ...main/scala/cromwell/backend/package.scala b/...main/scala/cromwell/backend/package.scala → ...main/scala/cromwell/backend/package.scala
diff --git a/...tandard/StandardAsyncExecutionActor.scala → ...tandard/StandardAsyncExecutionActor.scala b/...tandard/StandardAsyncExecutionActor.scala → ...tandard/StandardAsyncExecutionActor.scala
diff --git a/...standard/StandardCachingActorHelper.scala → ...standard/StandardCachingActorHelper.scala b/...standard/StandardCachingActorHelper.scala → ...standard/StandardCachingActorHelper.scala
diff --git a/...tandard/StandardExpressionFunctions.scala → ...tandard/StandardExpressionFunctions.scala b/...tandard/StandardExpressionFunctions.scala → ...tandard/StandardExpressionFunctions.scala
diff --git a/.../standard/StandardFinalizationActor.scala → .../standard/StandardFinalizationActor.scala b/.../standard/StandardFinalizationActor.scala → .../standard/StandardFinalizationActor.scala
diff --git a/...tandard/StandardInitializationActor.scala → ...tandard/StandardInitializationActor.scala b/...tandard/StandardInitializationActor.scala → ...tandard/StandardInitializationActor.scala
diff --git a/...standard/StandardInitializationData.scala → ...standard/StandardInitializationData.scala b/...standard/StandardInitializationData.scala → ...standard/StandardInitializationData.scala
diff --git a/...ard/StandardJobExecutionActorParams.scala → ...ard/StandardJobExecutionActorParams.scala b/...ard/StandardJobExecutionActorParams.scala → ...ard/StandardJobExecutionActorParams.scala
diff --git a/...ndard/StandardLifecycleActorFactory.scala → ...ndard/StandardLifecycleActorFactory.scala b/...ndard/StandardLifecycleActorFactory.scala → ...ndard/StandardLifecycleActorFactory.scala
diff --git a/...standard/StandardSyncExecutionActor.scala → ...standard/StandardSyncExecutionActor.scala b/...standard/StandardSyncExecutionActor.scala → ...standard/StandardSyncExecutionActor.scala
diff --git a/...rdValidatedRuntimeAttributesBuilder.scala → ...rdValidatedRuntimeAttributesBuilder.scala b/...rdValidatedRuntimeAttributesBuilder.scala → ...rdValidatedRuntimeAttributesBuilder.scala
diff --git a/...d/callcaching/JobCachingActorHelper.scala → ...d/callcaching/JobCachingActorHelper.scala b/...d/callcaching/JobCachingActorHelper.scala → ...d/callcaching/JobCachingActorHelper.scala
diff --git a/...aching/StandardCacheHitCopyingActor.scala → ...aching/StandardCacheHitCopyingActor.scala b/...aching/StandardCacheHitCopyingActor.scala → ...aching/StandardCacheHitCopyingActor.scala
diff --git a/...allcaching/StandardFileHashingActor.scala → ...allcaching/StandardFileHashingActor.scala b/...allcaching/StandardFileHashingActor.scala → ...allcaching/StandardFileHashingActor.scala
diff --git a/...end/validation/ContinueOnReturnCode.scala → ...end/validation/ContinueOnReturnCode.scala b/...end/validation/ContinueOnReturnCode.scala → ...end/validation/ContinueOnReturnCode.scala
diff --git a/...tion/ContinueOnReturnCodeValidation.scala → ...tion/ContinueOnReturnCodeValidation.scala b/...tion/ContinueOnReturnCodeValidation.scala → ...tion/ContinueOnReturnCodeValidation.scala
diff --git a/...ll/backend/validation/CpuValidation.scala → ...ll/backend/validation/CpuValidation.scala b/...ll/backend/validation/CpuValidation.scala → ...ll/backend/validation/CpuValidation.scala
diff --git a/...backend/validation/DockerValidation.scala → ...backend/validation/DockerValidation.scala b/...backend/validation/DockerValidation.scala → ...backend/validation/DockerValidation.scala
diff --git a/...d/validation/FailOnStderrValidation.scala → ...d/validation/FailOnStderrValidation.scala b/...d/validation/FailOnStderrValidation.scala → ...d/validation/FailOnStderrValidation.scala
diff --git a/...backend/validation/MemoryValidation.scala → ...backend/validation/MemoryValidation.scala b/...backend/validation/MemoryValidation.scala → ...backend/validation/MemoryValidation.scala
diff --git a/...rimitiveRuntimeAttributesValidation.scala → ...rimitiveRuntimeAttributesValidation.scala b/...rimitiveRuntimeAttributesValidation.scala → ...rimitiveRuntimeAttributesValidation.scala
diff --git a/...validation/RuntimeAttributesDefault.scala → ...validation/RuntimeAttributesDefault.scala b/...validation/RuntimeAttributesDefault.scala → ...validation/RuntimeAttributesDefault.scala
diff --git a/...idation/RuntimeAttributesValidation.scala → ...idation/RuntimeAttributesValidation.scala b/...idation/RuntimeAttributesValidation.scala → ...idation/RuntimeAttributesValidation.scala
diff --git a/...n/ValidatedRuntimeAttributesBuilder.scala → ...n/ValidatedRuntimeAttributesBuilder.scala b/...n/ValidatedRuntimeAttributesBuilder.scala → ...n/ValidatedRuntimeAttributesBuilder.scala
diff --git a/...ption/ValidationAggregatedException.scala → ...ption/ValidationAggregatedException.scala b/...ption/ValidationAggregatedException.scala → ...ption/ValidationAggregatedException.scala
diff --git a/.../scala/cromwell/backend/wdl/Command.scala → .../scala/cromwell/backend/wdl/Command.scala b/.../scala/cromwell/backend/wdl/Command.scala → .../scala/cromwell/backend/wdl/Command.scala
diff --git a/...ackend/wdl/FileSizeLimitationConfig.scala → ...ackend/wdl/FileSizeLimitationConfig.scala b/...ackend/wdl/FileSizeLimitationConfig.scala → ...ackend/wdl/FileSizeLimitationConfig.scala
diff --git a/...cromwell/backend/wdl/FileSizeTooBig.scala → ...cromwell/backend/wdl/FileSizeTooBig.scala b/...cromwell/backend/wdl/FileSizeTooBig.scala → ...cromwell/backend/wdl/FileSizeTooBig.scala
diff --git a/...romwell/backend/wdl/OutputEvaluator.scala → ...romwell/backend/wdl/OutputEvaluator.scala b/...romwell/backend/wdl/OutputEvaluator.scala → ...romwell/backend/wdl/OutputEvaluator.scala
diff --git a/...mwell/backend/wdl/ReadLikeFunctions.scala → ...mwell/backend/wdl/ReadLikeFunctions.scala b/...mwell/backend/wdl/ReadLikeFunctions.scala → ...mwell/backend/wdl/ReadLikeFunctions.scala
diff --git a/...cromwell/backend/wdl/WriteFunctions.scala → ...cromwell/backend/wdl/WriteFunctions.scala b/...cromwell/backend/wdl/WriteFunctions.scala → ...cromwell/backend/wdl/WriteFunctions.scala
diff --git a/...kend/wfs/DefaultWorkflowPathBuilder.scala → ...kend/wfs/DefaultWorkflowPathBuilder.scala b/...kend/wfs/DefaultWorkflowPathBuilder.scala → ...kend/wfs/DefaultWorkflowPathBuilder.scala
diff --git a/...ell/backend/wfs/WorkflowPathBuilder.scala → ...ell/backend/wfs/WorkflowPathBuilder.scala b/...ell/backend/wfs/WorkflowPathBuilder.scala → ...ell/backend/wfs/WorkflowPathBuilder.scala
diff --git a/.../scala/cromwell/backend/BackendSpec.scala → .../scala/cromwell/backend/BackendSpec.scala b/.../scala/cromwell/backend/BackendSpec.scala → .../scala/cromwell/backend/BackendSpec.scala
diff --git a/...kendWorkflowInitializationActorSpec.scala → ...kendWorkflowInitializationActorSpec.scala b/...kendWorkflowInitializationActorSpec.scala → ...kendWorkflowInitializationActorSpec.scala
diff --git a/...ala/cromwell/backend/MemorySizeSpec.scala → ...ala/cromwell/backend/MemorySizeSpec.scala b/...ala/cromwell/backend/MemorySizeSpec.scala → ...ala/cromwell/backend/MemorySizeSpec.scala
diff --git a/...kend/RuntimeAttributeValidationSpec.scala → ...kend/RuntimeAttributeValidationSpec.scala b/...kend/RuntimeAttributeValidationSpec.scala → ...kend/RuntimeAttributeValidationSpec.scala
diff --git a/...t/scala/cromwell/backend/TestConfig.scala → ...t/scala/cromwell/backend/TestConfig.scala b/...t/scala/cromwell/backend/TestConfig.scala → ...t/scala/cromwell/backend/TestConfig.scala
diff --git a/...la/cromwell/backend/io/JobPathsSpec.scala → ...la/cromwell/backend/io/JobPathsSpec.scala b/...la/cromwell/backend/io/JobPathsSpec.scala → ...la/cromwell/backend/io/JobPathsSpec.scala
diff --git a/...mwell/backend/io/JobPathsSpecHelper.scala → ...mwell/backend/io/JobPathsSpecHelper.scala b/...mwell/backend/io/JobPathsSpecHelper.scala → ...mwell/backend/io/JobPathsSpecHelper.scala
diff --git a/...a/cromwell/backend/io/TestWorkflows.scala → ...a/cromwell/backend/io/TestWorkflows.scala b/...a/cromwell/backend/io/TestWorkflows.scala → ...a/cromwell/backend/io/TestWorkflows.scala
diff --git a/...omwell/backend/io/WorkflowPathsSpec.scala → ...omwell/backend/io/WorkflowPathsSpec.scala b/...omwell/backend/io/WorkflowPathsSpec.scala → ...omwell/backend/io/WorkflowPathsSpec.scala
diff --git a/...lidatedRuntimeAttributesBuilderSpec.scala → ...lidatedRuntimeAttributesBuilderSpec.scala b/...lidatedRuntimeAttributesBuilderSpec.scala → ...lidatedRuntimeAttributesBuilderSpec.scala
diff --git a/...aching/StandardFileHashingActorSpec.scala → ...aching/StandardFileHashingActorSpec.scala b/...aching/StandardFileHashingActorSpec.scala → ...aching/StandardFileHashingActorSpec.scala
diff --git a/...validation/ContinueOnReturnCodeSpec.scala → ...validation/ContinueOnReturnCodeSpec.scala b/...validation/ContinueOnReturnCodeSpec.scala → ...validation/ContinueOnReturnCodeSpec.scala
diff --git a/...dation/RuntimeAttributesDefaultSpec.scala → ...dation/RuntimeAttributesDefaultSpec.scala b/...dation/RuntimeAttributesDefaultSpec.scala → ...dation/RuntimeAttributesDefaultSpec.scala
diff --git a/...ion/RuntimeAttributesValidationSpec.scala → ...ion/RuntimeAttributesValidationSpec.scala b/...ion/RuntimeAttributesValidationSpec.scala → ...ion/RuntimeAttributesValidationSpec.scala
diff --git a/...a/cromwell/backend/wdl/FileSizeSpec.scala → ...a/cromwell/backend/wdl/FileSizeSpec.scala b/...a/cromwell/backend/wdl/FileSizeSpec.scala → ...a/cromwell/backend/wdl/FileSizeSpec.scala
diff --git a/...ell/backend/wdl/OutputEvaluatorSpec.scala → ...ell/backend/wdl/OutputEvaluatorSpec.scala b/...ell/backend/wdl/OutputEvaluatorSpec.scala → ...ell/backend/wdl/OutputEvaluatorSpec.scala
diff --git a/...l/backend/wdl/ReadLikeFunctionsSpec.scala → ...l/backend/wdl/ReadLikeFunctionsSpec.scala b/...l/backend/wdl/ReadLikeFunctionsSpec.scala → ...l/backend/wdl/ReadLikeFunctionsSpec.scala
diff --git a/cromwell/build.sbt → build.sbt b/cromwell/build.sbt → build.sbt
diff --git a/cromwell/centaur/README.md → centaur/README.md b/cromwell/centaur/README.md → centaur/README.md
diff --git a/cromwell/centaur/centaur.sh → centaur/centaur.sh b/cromwell/centaur/centaur.sh → centaur/centaur.sh
diff --git a/cromwell/centaur/run_tests_parallel.sh → centaur/run_tests_parallel.sh b/cromwell/centaur/run_tests_parallel.sh → centaur/run_tests_parallel.sh
diff --git a/...centaur/src/it/resources/application.conf → centaur/src/it/resources/application.conf b/...centaur/src/it/resources/application.conf → centaur/src/it/resources/application.conf
diff --git a/...centaur/AbstractCentaurTestCaseSpec.scala → ...centaur/AbstractCentaurTestCaseSpec.scala b/...centaur/AbstractCentaurTestCaseSpec.scala → ...centaur/AbstractCentaurTestCaseSpec.scala
diff --git a/...c/it/scala/centaur/CentaurTestSuite.scala → ...c/it/scala/centaur/CentaurTestSuite.scala b/...c/it/scala/centaur/CentaurTestSuite.scala → ...c/it/scala/centaur/CentaurTestSuite.scala
diff --git a/...cala/centaur/SequentialTestCaseSpec.scala → ...cala/centaur/SequentialTestCaseSpec.scala b/...cala/centaur/SequentialTestCaseSpec.scala → ...cala/centaur/SequentialTestCaseSpec.scala
diff --git a/.../scala/centaur/StandardTestCaseSpec.scala → .../scala/centaur/StandardTestCaseSpec.scala b/.../scala/centaur/StandardTestCaseSpec.scala → .../scala/centaur/StandardTestCaseSpec.scala
diff --git a/...rc/main/config/cromwell-account.pem.ctmpl → ...rc/main/config/cromwell-account.pem.ctmpl b/...rc/main/config/cromwell-account.pem.ctmpl → ...rc/main/config/cromwell-account.pem.ctmpl
diff --git a/...aur/src/main/config/jes-compose.yml.ctmpl → ...aur/src/main/config/jes-compose.yml.ctmpl b/...aur/src/main/config/jes-compose.yml.ctmpl → ...aur/src/main/config/jes-compose.yml.ctmpl
diff --git a/...r/src/main/config/local-compose.yml.ctmpl → ...r/src/main/config/local-compose.yml.ctmpl b/...r/src/main/config/local-compose.yml.ctmpl → ...r/src/main/config/local-compose.yml.ctmpl
diff --git a/...ic/CNV-Pair/cnv_somatic_pair_workflow.wdl → ...ic/CNV-Pair/cnv_somatic_pair_workflow.wdl b/...ic/CNV-Pair/cnv_somatic_pair_workflow.wdl → ...ic/CNV-Pair/cnv_somatic_pair_workflow.wdl
diff --git a/...nv_somatic_pair_workflow_do_gc_wes.inputs → ...nv_somatic_pair_workflow_do_gc_wes.inputs b/...nv_somatic_pair_workflow_do_gc_wes.inputs → ...nv_somatic_pair_workflow_do_gc_wes.inputs
diff --git a/.../CNV-Panel/cnv_somatic_panel_workflow.wdl → .../CNV-Panel/cnv_somatic_panel_workflow.wdl b/.../CNV-Panel/cnv_somatic_panel_workflow.wdl → .../CNV-Panel/cnv_somatic_panel_workflow.wdl
diff --git a/...v_somatic_panel_workflow_do_gc_wes.inputs → ...v_somatic_panel_workflow_do_gc_wes.inputs b/...v_somatic_panel_workflow_do_gc_wes.inputs → ...v_somatic_panel_workflow_do_gc_wes.inputs
diff --git a/...nTestCases/Somatic/Mutect2/Mutect2.inputs → ...nTestCases/Somatic/Mutect2/Mutect2.inputs b/...nTestCases/Somatic/Mutect2/Mutect2.inputs → ...nTestCases/Somatic/Mutect2/Mutect2.inputs
diff --git a/...tionTestCases/Somatic/Mutect2/Mutect2.wdl → ...tionTestCases/Somatic/Mutect2/Mutect2.wdl b/...tionTestCases/Somatic/Mutect2/Mutect2.wdl → ...tionTestCases/Somatic/Mutect2/Mutect2.wdl
diff --git a/...ionTestCases/Somatic/cnv_common_tasks.wdl → ...ionTestCases/Somatic/cnv_common_tasks.wdl b/...ionTestCases/Somatic/cnv_common_tasks.wdl → ...ionTestCases/Somatic/cnv_common_tasks.wdl
diff --git a/...omatic/cnv_somatic_oncotator_workflow.wdl → ...omatic/cnv_somatic_oncotator_workflow.wdl b/...omatic/cnv_somatic_oncotator_workflow.wdl → ...omatic/cnv_somatic_oncotator_workflow.wdl
diff --git a/...esources/integrationTestCases/arrays.test → ...esources/integrationTestCases/arrays.test b/...esources/integrationTestCases/arrays.test → ...esources/integrationTestCases/arrays.test
diff --git a/...pe-caller-workflow/HaplotypeCallerWF.json → ...pe-caller-workflow/HaplotypeCallerWF.json b/...pe-caller-workflow/HaplotypeCallerWF.json → ...pe-caller-workflow/HaplotypeCallerWF.json
diff --git a/...ype-caller-workflow/HaplotypeCallerWF.wdl → ...ype-caller-workflow/HaplotypeCallerWF.wdl b/...ype-caller-workflow/HaplotypeCallerWF.wdl → ...ype-caller-workflow/HaplotypeCallerWF.wdl
diff --git a/...ery-gatk/generic.google-papi.options.json → ...ery-gatk/generic.google-papi.options.json b/...ery-gatk/generic.google-papi.options.json → ...ery-gatk/generic.google-papi.options.json
diff --git a/...oint-discovery-gatk4.hg38.wgs.inputs.json → ...oint-discovery-gatk4.hg38.wgs.inputs.json b/...oint-discovery-gatk4.hg38.wgs.inputs.json → ...oint-discovery-gatk4.hg38.wgs.inputs.json
diff --git a/...-discovery-gatk/joint-discovery-gatk4.wdl → ...-discovery-gatk/joint-discovery-gatk4.wdl b/...-discovery-gatk/joint-discovery-gatk4.wdl → ...-discovery-gatk/joint-discovery-gatk4.wdl
diff --git a/...kflow/PairedEndSingleSampleWf.inputs.json → ...kflow/PairedEndSingleSampleWf.inputs.json b/...kflow/PairedEndSingleSampleWf.inputs.json → ...kflow/PairedEndSingleSampleWf.inputs.json
diff --git a/...flow/PairedEndSingleSampleWf.options.json → ...flow/PairedEndSingleSampleWf.options.json b/...flow/PairedEndSingleSampleWf.options.json → ...flow/PairedEndSingleSampleWf.options.json
diff --git a/...tion-workflow/PairedEndSingleSampleWf.wdl → ...tion-workflow/PairedEndSingleSampleWf.wdl b/...tion-workflow/PairedEndSingleSampleWf.wdl → ...tion-workflow/PairedEndSingleSampleWf.wdl
diff --git a/...iant-discovery-gatk4.hg38.wgs.inputs.json → ...iant-discovery-gatk4.hg38.wgs.inputs.json b/...iant-discovery-gatk4.hg38.wgs.inputs.json → ...iant-discovery-gatk4.hg38.wgs.inputs.json
diff --git a/...rocessing-for-variant-discovery-gatk4.wdl → ...rocessing-for-variant-discovery-gatk4.wdl b/...rocessing-for-variant-discovery-gatk4.wdl → ...rocessing-for-variant-discovery-gatk4.wdl
diff --git a/...ationTestCases/green/arrays/arrays.inputs → ...ationTestCases/green/arrays/arrays.inputs b/...ationTestCases/green/arrays/arrays.inputs → ...ationTestCases/green/arrays/arrays.inputs
diff --git a/...tionTestCases/green/arrays/arrays.options → ...tionTestCases/green/arrays/arrays.options b/...tionTestCases/green/arrays/arrays.options → ...tionTestCases/green/arrays/arrays.options
diff --git a/...egrationTestCases/green/arrays/arrays.wdl → ...egrationTestCases/green/arrays/arrays.wdl b/...egrationTestCases/green/arrays/arrays.wdl → ...egrationTestCases/green/arrays/arrays.wdl
diff --git a/...es/green/singlesample/singlesample.inputs → ...es/green/singlesample/singlesample.inputs b/...es/green/singlesample/singlesample.inputs → ...es/green/singlesample/singlesample.inputs
diff --git a/...s/green/singlesample/singlesample.options → ...s/green/singlesample/singlesample.options b/...s/green/singlesample/singlesample.options → ...s/green/singlesample/singlesample.options
diff --git a/...Cases/green/singlesample/singlesample.wdl → ...Cases/green/singlesample/singlesample.wdl b/...Cases/green/singlesample/singlesample.wdl → ...Cases/green/singlesample/singlesample.wdl
diff --git a/...integrationTestCases/haplotypecaller.test → ...integrationTestCases/haplotypecaller.test b/...integrationTestCases/haplotypecaller.test → ...integrationTestCases/haplotypecaller.test
diff --git a/.../integrationTestCases/jointdiscovery.test → .../integrationTestCases/jointdiscovery.test b/.../integrationTestCases/jointdiscovery.test → .../integrationTestCases/jointdiscovery.test
diff --git a/...sources/integrationTestCases/mutect2.test → ...sources/integrationTestCases/mutect2.test b/...sources/integrationTestCases/mutect2.test → ...sources/integrationTestCases/mutect2.test
diff --git a/...es/integrationTestCases/singlesample.test → ...es/integrationTestCases/singlesample.test b/...es/integrationTestCases/singlesample.test → ...es/integrationTestCases/singlesample.test
diff --git a/...ionTestCases/singlesample_production.test → ...ionTestCases/singlesample_production.test b/...ionTestCases/singlesample_production.test → ...ionTestCases/singlesample_production.test
diff --git a/...ntegrationTestCases/somatic_cnv_pair.test → ...ntegrationTestCases/somatic_cnv_pair.test b/...ntegrationTestCases/somatic_cnv_pair.test → ...ntegrationTestCases/somatic_cnv_pair.test
diff --git a/...tegrationTestCases/somatic_cnv_panel.test → ...tegrationTestCases/somatic_cnv_panel.test b/...tegrationTestCases/somatic_cnv_panel.test → ...tegrationTestCases/somatic_cnv_panel.test
diff --git a/...centaur/src/main/resources/reference.conf → centaur/src/main/resources/reference.conf b/...centaur/src/main/resources/reference.conf → centaur/src/main/resources/reference.conf
diff --git a/...nitialWorkDirRequirement.inline_file.test → ...nitialWorkDirRequirement.inline_file.test b/...nitialWorkDirRequirement.inline_file.test → ...nitialWorkDirRequirement.inline_file.test
diff --git a/...irement.inline_file_custom_entryname.test → ...irement.inline_file_custom_entryname.test b/...irement.inline_file_custom_entryname.test → ...irement.inline_file_custom_entryname.test
diff --git a/...itialWorkDirRequirement.input_string.test → ...itialWorkDirRequirement.input_string.test b/...itialWorkDirRequirement.input_string.test → ...itialWorkDirRequirement.input_string.test
diff --git a/...DirRequirement.input_string_function.test → ...DirRequirement.input_string_function.test b/...DirRequirement.input_string_function.test → ...DirRequirement.input_string_function.test
diff --git a/...WorkDirRequirement/file_array_listing.cwl → ...WorkDirRequirement/file_array_listing.cwl b/...WorkDirRequirement/file_array_listing.cwl → ...WorkDirRequirement/file_array_listing.cwl
diff --git a/...InitialWorkDirRequirement/inline_file.cwl → ...InitialWorkDirRequirement/inline_file.cwl b/...InitialWorkDirRequirement/inline_file.cwl → ...InitialWorkDirRequirement/inline_file.cwl
diff --git a/...uirement/inline_file_custom_entryname.cwl → ...uirement/inline_file_custom_entryname.cwl b/...uirement/inline_file_custom_entryname.cwl → ...uirement/inline_file_custom_entryname.cwl
diff --git a/...nitialWorkDirRequirement/input_string.cwl → ...nitialWorkDirRequirement/input_string.cwl b/...nitialWorkDirRequirement/input_string.cwl → ...nitialWorkDirRequirement/input_string.cwl
diff --git a/...kDirRequirement/input_string_function.cwl → ...kDirRequirement/input_string_function.cwl b/...kDirRequirement/input_string_function.cwl → ...kDirRequirement/input_string_function.cwl
diff --git a/...tandardTestCases/abort.instant_abort.test → ...tandardTestCases/abort.instant_abort.test b/...tandardTestCases/abort.instant_abort.test → ...tandardTestCases/abort.instant_abort.test
diff --git a/...ardTestCases/abort.restart_abort_jes.test → ...ardTestCases/abort.restart_abort_jes.test b/...ardTestCases/abort.restart_abort_jes.test → ...ardTestCases/abort.restart_abort_jes.test
diff --git a/...dTestCases/abort.restart_abort_local.test → ...dTestCases/abort.restart_abort_local.test b/...dTestCases/abort.restart_abort_local.test → ...dTestCases/abort.restart_abort_local.test
diff --git a/...ardTestCases/abort.restart_abort_tes.test → ...ardTestCases/abort.restart_abort_tes.test b/...ardTestCases/abort.restart_abort_tes.test → ...ardTestCases/abort.restart_abort_tes.test
diff --git a/...ndardTestCases/abort.scheduled_abort.test → ...ndardTestCases/abort.scheduled_abort.test b/...ndardTestCases/abort.scheduled_abort.test → ...ndardTestCases/abort.scheduled_abort.test
diff --git a/...rdTestCases/abort.sub_workflow_abort.test → ...rdTestCases/abort.sub_workflow_abort.test b/...rdTestCases/abort.sub_workflow_abort.test → ...rdTestCases/abort.sub_workflow_abort.test
diff --git a/...standardTestCases/abort/instant_abort.wdl → ...standardTestCases/abort/instant_abort.wdl b/...standardTestCases/abort/instant_abort.wdl → ...standardTestCases/abort/instant_abort.wdl
diff --git a/...andardTestCases/abort/scheduled_abort.wdl → ...andardTestCases/abort/scheduled_abort.wdl b/...andardTestCases/abort/scheduled_abort.wdl → ...andardTestCases/abort/scheduled_abort.wdl
diff --git a/...ardTestCases/abort/sub_workflow_abort.wdl → ...ardTestCases/abort/sub_workflow_abort.wdl b/...ardTestCases/abort/sub_workflow_abort.wdl → ...ardTestCases/abort/sub_workflow_abort.wdl
diff --git a/...ses/abort/sub_workflow_aborted_import.wdl → ...ses/abort/sub_workflow_aborted_import.wdl b/...ses/abort/sub_workflow_aborted_import.wdl → ...ses/abort/sub_workflow_aborted_import.wdl
diff --git a/...andardTestCases/aliased_subworkflows.test → ...andardTestCases/aliased_subworkflows.test b/...andardTestCases/aliased_subworkflows.test → ...andardTestCases/aliased_subworkflows.test
diff --git a/...sed_subworkflows/aliased_subworkflows.wdl → ...sed_subworkflows/aliased_subworkflows.wdl b/...sed_subworkflows/aliased_subworkflows.wdl → ...sed_subworkflows/aliased_subworkflows.wdl
diff --git a/...ases/aliased_subworkflows/subworkflow.wdl → ...ases/aliased_subworkflows/subworkflow.wdl b/...ases/aliased_subworkflows/subworkflow.wdl → ...ases/aliased_subworkflows/subworkflow.wdl
diff --git a/...resources/standardTestCases/array_io.test → ...resources/standardTestCases/array_io.test b/...resources/standardTestCases/array_io.test → ...resources/standardTestCases/array_io.test
diff --git a/...s/standardTestCases/array_io/array_io.wdl → ...s/standardTestCases/array_io/array_io.wdl b/...s/standardTestCases/array_io/array_io.wdl → ...s/standardTestCases/array_io/array_io.wdl
diff --git a/...ardTestCases/array_literal_locations.test → ...ardTestCases/array_literal_locations.test b/...ardTestCases/array_literal_locations.test → ...ardTestCases/array_literal_locations.test
diff --git a/...ral_locations/array_literal_locations.wdl → ...ral_locations/array_literal_locations.wdl b/...ral_locations/array_literal_locations.wdl → ...ral_locations/array_literal_locations.wdl
diff --git a/...tandardTestCases/arrays_scatters_ifs.test → ...tandardTestCases/arrays_scatters_ifs.test b/...tandardTestCases/arrays_scatters_ifs.test → ...tandardTestCases/arrays_scatters_ifs.test
diff --git a/...rays_scatters_ifs/arrays_scatters_ifs.wdl → ...rays_scatters_ifs/arrays_scatters_ifs.wdl b/...rays_scatters_ifs/arrays_scatters_ifs.wdl → ...rays_scatters_ifs/arrays_scatters_ifs.wdl
diff --git a/...tandardTestCases/backendWithNoDocker.test → ...tandardTestCases/backendWithNoDocker.test b/...tandardTestCases/backendWithNoDocker.test → ...tandardTestCases/backendWithNoDocker.test
diff --git a/...ckendWithNoDocker/backendWithNoDocker.wdl → ...ckendWithNoDocker/backendWithNoDocker.wdl b/...ckendWithNoDocker/backendWithNoDocker.wdl → ...ckendWithNoDocker/backendWithNoDocker.wdl
diff --git a/...es/standardTestCases/bad_docker_name.test → ...es/standardTestCases/bad_docker_name.test b/...es/standardTestCases/bad_docker_name.test → ...es/standardTestCases/bad_docker_name.test
diff --git a/...Cases/bad_docker_name/bad_docker_name.wdl → ...Cases/bad_docker_name/bad_docker_name.wdl b/...Cases/bad_docker_name/bad_docker_name.wdl → ...Cases/bad_docker_name/bad_docker_name.wdl
diff --git a/...es/standardTestCases/bad_file_string.test → ...es/standardTestCases/bad_file_string.test b/...es/standardTestCases/bad_file_string.test → ...es/standardTestCases/bad_file_string.test
diff --git a/...Cases/bad_file_string/bad_file_string.wdl → ...Cases/bad_file_string/bad_file_string.wdl b/...Cases/bad_file_string/bad_file_string.wdl → ...Cases/bad_file_string/bad_file_string.wdl
diff --git a/...es/standardTestCases/bad_output_task.test → ...es/standardTestCases/bad_output_task.test b/...es/standardTestCases/bad_output_task.test → ...es/standardTestCases/bad_output_task.test
diff --git a/...Cases/bad_output_task/bad_output_task.wdl → ...Cases/bad_output_task/bad_output_task.wdl b/...Cases/bad_output_task/bad_output_task.wdl → ...Cases/bad_output_task/bad_output_task.wdl
diff --git a/...dTestCases/bad_workflow_failure_mode.test → ...dTestCases/bad_workflow_failure_mode.test b/...dTestCases/bad_workflow_failure_mode.test → ...dTestCases/bad_workflow_failure_mode.test
diff --git a/...re_mode/bad_workflow_failure_mode.options → ...re_mode/bad_workflow_failure_mode.options b/...re_mode/bad_workflow_failure_mode.options → ...re_mode/bad_workflow_failure_mode.options
diff --git a/...ailure_mode/bad_workflow_failure_mode.wdl → ...ailure_mode/bad_workflow_failure_mode.wdl b/...ailure_mode/bad_workflow_failure_mode.wdl → ...ailure_mode/bad_workflow_failure_mode.wdl
diff --git a/...ses/cacheBetweenWF/cacheBetweenWF.options → ...ses/cacheBetweenWF/cacheBetweenWF.options b/...ses/cacheBetweenWF/cacheBetweenWF.options → ...ses/cacheBetweenWF/cacheBetweenWF.options
diff --git a/...stCases/cacheBetweenWF/cacheBetweenWF.wdl → ...stCases/cacheBetweenWF/cacheBetweenWF.wdl b/...stCases/cacheBetweenWF/cacheBetweenWF.wdl → ...stCases/cacheBetweenWF/cacheBetweenWF.wdl
diff --git a/...ces/standardTestCases/cacheBetweenWf.test → ...ces/standardTestCases/cacheBetweenWf.test b/...ces/standardTestCases/cacheBetweenWf.test → ...ces/standardTestCases/cacheBetweenWf.test
diff --git a/...rces/standardTestCases/cacheWithinWF.test → ...rces/standardTestCases/cacheWithinWF.test b/...rces/standardTestCases/cacheWithinWF.test → ...rces/standardTestCases/cacheWithinWF.test
diff --git a/...TestCases/cacheWithinWF/cacheWithinWF.wdl → ...TestCases/cacheWithinWF/cacheWithinWF.wdl b/...TestCases/cacheWithinWF/cacheWithinWF.wdl → ...TestCases/cacheWithinWF/cacheWithinWF.wdl
diff --git a/...ache_capoeira/call_cache_capoeira_jes.wdl → ...ache_capoeira/call_cache_capoeira_jes.wdl b/...ache_capoeira/call_cache_capoeira_jes.wdl → ...ache_capoeira/call_cache_capoeira_jes.wdl
diff --git a/...he_capoeira/call_cache_capoeira_local.wdl → ...he_capoeira/call_cache_capoeira_local.wdl b/...he_capoeira/call_cache_capoeira_local.wdl → ...he_capoeira/call_cache_capoeira_local.wdl
diff --git a/...ache_capoeira/call_cache_capoeira_tes.wdl → ...ache_capoeira/call_cache_capoeira_tes.wdl b/...ache_capoeira/call_cache_capoeira_tes.wdl → ...ache_capoeira/call_cache_capoeira_tes.wdl
diff --git a/...ardTestCases/call_cache_capoeira_jes.test → ...ardTestCases/call_cache_capoeira_jes.test b/...ardTestCases/call_cache_capoeira_jes.test → ...ardTestCases/call_cache_capoeira_jes.test
diff --git a/...dTestCases/call_cache_capoeira_local.test → ...dTestCases/call_cache_capoeira_local.test b/...dTestCases/call_cache_capoeira_local.test → ...dTestCases/call_cache_capoeira_local.test
diff --git a/...ardTestCases/call_cache_capoeira_tes.test → ...ardTestCases/call_cache_capoeira_tes.test b/...ardTestCases/call_cache_capoeira_tes.test → ...ardTestCases/call_cache_capoeira_tes.test
diff --git a/...andardTestCases/chain_fail/chain_fail.wdl → ...andardTestCases/chain_fail/chain_fail.wdl b/...andardTestCases/chain_fail/chain_fail.wdl → ...andardTestCases/chain_fail/chain_fail.wdl
diff --git a/...estCases/chain_fail/chain_fail_import.wdl → ...estCases/chain_fail/chain_fail_import.wdl b/...estCases/chain_fail/chain_fail_import.wdl → ...estCases/chain_fail/chain_fail_import.wdl
diff --git a/...esources/standardTestCases/chainfail.test → ...esources/standardTestCases/chainfail.test b/...esources/standardTestCases/chainfail.test → ...esources/standardTestCases/chainfail.test
diff --git a/...ndardTestCases/circular_dependencies.test → ...ndardTestCases/circular_dependencies.test b/...ndardTestCases/circular_dependencies.test → ...ndardTestCases/circular_dependencies.test
diff --git a/...ar_dependencies/circular_dependencies.wdl → ...ar_dependencies/circular_dependencies.wdl b/...ar_dependencies/circular_dependencies.wdl → ...ar_dependencies/circular_dependencies.wdl
diff --git a/...tandardTestCases/complex_types_files.test → ...tandardTestCases/complex_types_files.test b/...tandardTestCases/complex_types_files.test → ...tandardTestCases/complex_types_files.test
diff --git a/...mplex_types_files/complex_types_files.wdl → ...mplex_types_files/complex_types_files.wdl b/...mplex_types_files/complex_types_files.wdl → ...mplex_types_files/complex_types_files.wdl
diff --git a/...ardTestCases/composedenginefunctions.test → ...ardTestCases/composedenginefunctions.test b/...ardTestCases/composedenginefunctions.test → ...ardTestCases/composedenginefunctions.test
diff --git a/...ginefunctions/composedenginefunctions.wdl → ...ginefunctions/composedenginefunctions.wdl b/...ginefunctions/composedenginefunctions.wdl → ...ginefunctions/composedenginefunctions.wdl
diff --git a/...ses/conditionals.declarations_in_ifs.test → ...ses/conditionals.declarations_in_ifs.test b/...ses/conditionals.declarations_in_ifs.test → ...ses/conditionals.declarations_in_ifs.test
diff --git a/...stCases/conditionals.ifs_in_scatters.test → ...stCases/conditionals.ifs_in_scatters.test b/...stCases/conditionals.ifs_in_scatters.test → ...stCases/conditionals.ifs_in_scatters.test
diff --git a/...itionals.ifs_upstream_and_downstream.test → ...itionals.ifs_upstream_and_downstream.test b/...itionals.ifs_upstream_and_downstream.test → ...itionals.ifs_upstream_and_downstream.test
diff --git a/...stCases/conditionals.lots_of_nesting.test → ...stCases/conditionals.lots_of_nesting.test b/...stCases/conditionals.lots_of_nesting.test → ...stCases/conditionals.lots_of_nesting.test
diff --git a/...estCases/conditionals.nested_lookups.test → ...estCases/conditionals.nested_lookups.test b/...estCases/conditionals.nested_lookups.test → ...estCases/conditionals.nested_lookups.test
diff --git a/...stCases/conditionals.scatters_in_ifs.test → ...stCases/conditionals.scatters_in_ifs.test b/...stCases/conditionals.scatters_in_ifs.test → ...stCases/conditionals.scatters_in_ifs.test
diff --git a/...dardTestCases/conditionals.simple_if.test → ...dardTestCases/conditionals.simple_if.test b/...dardTestCases/conditionals.simple_if.test → ...dardTestCases/conditionals.simple_if.test
diff --git a/...ditionals.simple_if_workflow_outputs.test → ...ditionals.simple_if_workflow_outputs.test b/...ditionals.simple_if_workflow_outputs.test → ...ditionals.simple_if_workflow_outputs.test
diff --git a/...ses/conditionals.subworkflows_in_ifs.test → ...ses/conditionals.subworkflows_in_ifs.test b/...ses/conditionals.subworkflows_in_ifs.test → ...ses/conditionals.subworkflows_in_ifs.test
diff --git a/...clarations_in_ifs/declarations_in_ifs.wdl → ...clarations_in_ifs/declarations_in_ifs.wdl b/...clarations_in_ifs/declarations_in_ifs.wdl → ...clarations_in_ifs/declarations_in_ifs.wdl
diff --git a/...tests/ifs_in_scatters/ifs_in_scatters.wdl → ...tests/ifs_in_scatters/ifs_in_scatters.wdl b/...tests/ifs_in_scatters/ifs_in_scatters.wdl → ...tests/ifs_in_scatters/ifs_in_scatters.wdl
diff --git a/...ownstream/ifs_upstream_and_downstream.wdl → ...ownstream/ifs_upstream_and_downstream.wdl b/...ownstream/ifs_upstream_and_downstream.wdl → ...ownstream/ifs_upstream_and_downstream.wdl
diff --git a/...tests/lots_of_nesting/lots_of_nesting.wdl → ...tests/lots_of_nesting/lots_of_nesting.wdl b/...tests/lots_of_nesting/lots_of_nesting.wdl → ...tests/lots_of_nesting/lots_of_nesting.wdl
diff --git a/...nested_lookups/nested_lookups.inputs.json → ...nested_lookups/nested_lookups.inputs.json b/...nested_lookups/nested_lookups.inputs.json → ...nested_lookups/nested_lookups.inputs.json
diff --git a/...s_tests/nested_lookups/nested_lookups.wdl → ...s_tests/nested_lookups/nested_lookups.wdl b/...s_tests/nested_lookups/nested_lookups.wdl → ...s_tests/nested_lookups/nested_lookups.wdl
diff --git a/...tests/scatters_in_ifs/scatters_in_ifs.wdl → ...tests/scatters_in_ifs/scatters_in_ifs.wdl b/...tests/scatters_in_ifs/scatters_in_ifs.wdl → ...tests/scatters_in_ifs/scatters_in_ifs.wdl
diff --git a/...onditionals_tests/simple_if/simple_if.wdl → ...onditionals_tests/simple_if/simple_if.wdl b/...onditionals_tests/simple_if/simple_if.wdl → ...onditionals_tests/simple_if/simple_if.wdl
diff --git a/...ow_outputs/simple_if_workflow_outputs.wdl → ...ow_outputs/simple_if_workflow_outputs.wdl b/...ow_outputs/simple_if_workflow_outputs.wdl → ...ow_outputs/simple_if_workflow_outputs.wdl
diff --git a/...tests/subworkflows_in_ifs/subworkflow.wdl → ...tests/subworkflows_in_ifs/subworkflow.wdl b/...tests/subworkflows_in_ifs/subworkflow.wdl → ...tests/subworkflows_in_ifs/subworkflow.wdl
diff --git a/...bworkflows_in_ifs/subworkflows_in_ifs.wdl → ...bworkflows_in_ifs/subworkflows_in_ifs.wdl b/...bworkflows_in_ifs/subworkflows_in_ifs.wdl → ...bworkflows_in_ifs/subworkflows_in_ifs.wdl
diff --git a/...tandardTestCases/confirm_preemptible.test → ...tandardTestCases/confirm_preemptible.test b/...tandardTestCases/confirm_preemptible.test → ...tandardTestCases/confirm_preemptible.test
diff --git a/...nfirm_preemptible/confirm_preemptible.wdl → ...nfirm_preemptible/confirm_preemptible.wdl b/...nfirm_preemptible/confirm_preemptible.wdl → ...nfirm_preemptible/confirm_preemptible.wdl
diff --git a/...tandardTestCases/cont_while_possible.test → ...tandardTestCases/cont_while_possible.test b/...tandardTestCases/cont_while_possible.test → ...tandardTestCases/cont_while_possible.test
diff --git a/...hile_possible/cont_while_possible.options → ...hile_possible/cont_while_possible.options b/...hile_possible/cont_while_possible.options → ...hile_possible/cont_while_possible.options
diff --git a/...nt_while_possible/cont_while_possible.wdl → ...nt_while_possible/cont_while_possible.wdl b/...nt_while_possible/cont_while_possible.wdl → ...nt_while_possible/cont_while_possible.wdl
diff --git a/..._possible/cont_while_possible_scatter.wdl → ..._possible/cont_while_possible_scatter.wdl b/..._possible/cont_while_possible_scatter.wdl → ..._possible/cont_while_possible_scatter.wdl
diff --git a/...estCases/cont_while_possible_scatter.test → ...estCases/cont_while_possible_scatter.test b/...estCases/cont_while_possible_scatter.test → ...estCases/cont_while_possible_scatter.test
diff --git a/...ardTestCases/continue_on_return_code.test → ...ardTestCases/continue_on_return_code.test b/...ardTestCases/continue_on_return_code.test → ...ardTestCases/continue_on_return_code.test
diff --git a/...n_return_code/continue_on_return_code.wdl → ...n_return_code/continue_on_return_code.wdl b/...n_return_code/continue_on_return_code.wdl → ...n_return_code/continue_on_return_code.wdl
diff --git a/...ses/cromwell_restart/cromwell_restart.wdl → ...ses/cromwell_restart/cromwell_restart.wdl b/...ses/cromwell_restart/cromwell_restart.wdl → ...ses/cromwell_restart/cromwell_restart.wdl
diff --git a/...ain/resources/standardTestCases/curl.test → ...ain/resources/standardTestCases/curl.test b/...ain/resources/standardTestCases/curl.test → ...ain/resources/standardTestCases/curl.test
diff --git a/...resources/standardTestCases/curl/curl.wdl → ...resources/standardTestCases/curl/curl.wdl b/...resources/standardTestCases/curl/curl.wdl → ...resources/standardTestCases/curl/curl.wdl
diff --git a/...standardTestCases/custom_mount_point.test → ...standardTestCases/custom_mount_point.test b/...standardTestCases/custom_mount_point.test → ...standardTestCases/custom_mount_point.test
diff --git a/...custom_mount_point/custom_mount_point.wdl → ...custom_mount_point/custom_mount_point.wdl b/...custom_mount_point/custom_mount_point.wdl → ...custom_mount_point/custom_mount_point.wdl
diff --git a/...rdTestCases/cwl_interpolated_strings.test → ...rdTestCases/cwl_interpolated_strings.test b/...rdTestCases/cwl_interpolated_strings.test → ...rdTestCases/cwl_interpolated_strings.test
diff --git a/...ated_strings/cwl_interpolated_strings.cwl → ...ated_strings/cwl_interpolated_strings.cwl b/...ated_strings/cwl_interpolated_strings.cwl → ...ated_strings/cwl_interpolated_strings.cwl
diff --git a/...ted_strings/cwl_interpolated_strings.json → ...ted_strings/cwl_interpolated_strings.json b/...ted_strings/cwl_interpolated_strings.json → ...ted_strings/cwl_interpolated_strings.json
diff --git a/...rces/standardTestCases/cwl_optionals.test → ...rces/standardTestCases/cwl_optionals.test b/...rces/standardTestCases/cwl_optionals.test → ...rces/standardTestCases/cwl_optionals.test
diff --git a/...TestCases/cwl_optionals/cwl_optionals.cwl → ...TestCases/cwl_optionals/cwl_optionals.cwl b/...TestCases/cwl_optionals/cwl_optionals.cwl → ...TestCases/cwl_optionals/cwl_optionals.cwl
diff --git a/...estCases/cwl_optionals/cwl_optionals.json → ...estCases/cwl_optionals/cwl_optionals.json b/...estCases/cwl_optionals/cwl_optionals.json → ...estCases/cwl_optionals/cwl_optionals.json
diff --git a/...Cases/cwl_output_json/cwl_output_json.cwl → ...Cases/cwl_output_json/cwl_output_json.cwl b/...Cases/cwl_output_json/cwl_output_json.cwl → ...Cases/cwl_output_json/cwl_output_json.cwl
diff --git a/...es/cwl_output_json/cwl_output_json.inputs → ...es/cwl_output_json/cwl_output_json.inputs b/...es/cwl_output_json/cwl_output_json.inputs → ...es/cwl_output_json/cwl_output_json.inputs
diff --git a/...tandardTestCases/cwl_output_json_jes.test → ...tandardTestCases/cwl_output_json_jes.test b/...tandardTestCases/cwl_output_json_jes.test → ...tandardTestCases/cwl_output_json_jes.test
diff --git a/...TestCases/cwl_resources/cwl_resources.cwl → ...TestCases/cwl_resources/cwl_resources.cwl b/...TestCases/cwl_resources/cwl_resources.cwl → ...TestCases/cwl_resources/cwl_resources.cwl
diff --git a/.../standardTestCases/cwl_resources_jes.test → .../standardTestCases/cwl_resources_jes.test b/.../standardTestCases/cwl_resources_jes.test → .../standardTestCases/cwl_resources_jes.test
diff --git a/...dout_expression/cwl_stdout_expression.cwl → ...dout_expression/cwl_stdout_expression.cwl b/...dout_expression/cwl_stdout_expression.cwl → ...dout_expression/cwl_stdout_expression.cwl
diff --git a/...out_expression/cwl_stdout_expression.json → ...out_expression/cwl_stdout_expression.json b/...out_expression/cwl_stdout_expression.json → ...out_expression/cwl_stdout_expression.json
diff --git a/...estCases/cwl_stdout_expression_local.test → ...estCases/cwl_stdout_expression_local.test b/...estCases/cwl_stdout_expression_local.test → ...estCases/cwl_stdout_expression_local.test
diff --git a/...TestCases/cwl_stdout_expression_papi.test → ...TestCases/cwl_stdout_expression_papi.test b/...TestCases/cwl_stdout_expression_papi.test → ...TestCases/cwl_stdout_expression_papi.test
diff --git a/.../standardTestCases/cwls/scatter-job1.json → .../standardTestCases/cwls/scatter-job1.json b/.../standardTestCases/cwls/scatter-job1.json → .../standardTestCases/cwls/scatter-job1.json
diff --git a/...es/standardTestCases/cwls/scatter-wf1.cwl → ...es/standardTestCases/cwls/scatter-wf1.cwl b/...es/standardTestCases/cwls/scatter-wf1.cwl → ...es/standardTestCases/cwls/scatter-wf1.cwl
diff --git a/...urces/standardTestCases/declarations.test → ...urces/standardTestCases/declarations.test b/...urces/standardTestCases/declarations.test → ...urces/standardTestCases/declarations.test
diff --git a/...estCases/declarations/declarations.inputs → ...estCases/declarations/declarations.inputs b/...estCases/declarations/declarations.inputs → ...estCases/declarations/declarations.inputs
diff --git a/...rdTestCases/declarations/declarations.wdl → ...rdTestCases/declarations/declarations.wdl b/...rdTestCases/declarations/declarations.wdl → ...rdTestCases/declarations/declarations.wdl
diff --git a/...ndardTestCases/declarations_as_nodes.test → ...ndardTestCases/declarations_as_nodes.test b/...ndardTestCases/declarations_as_nodes.test → ...ndardTestCases/declarations_as_nodes.test
diff --git a/...ations_as_nodes/declarations_as_nodes.wdl → ...ations_as_nodes/declarations_as_nodes.wdl b/...ations_as_nodes/declarations_as_nodes.wdl → ...ations_as_nodes/declarations_as_nodes.wdl
diff --git a/...TestCases/default_runtime_attributes.test → ...TestCases/default_runtime_attributes.test b/...TestCases/default_runtime_attributes.test → ...TestCases/default_runtime_attributes.test
diff --git a/...ibutes/default_runtime_attributes.options → ...ibutes/default_runtime_attributes.options b/...ibutes/default_runtime_attributes.options → ...ibutes/default_runtime_attributes.options
diff --git a/...attributes/default_runtime_attributes.wdl → ...attributes/default_runtime_attributes.wdl b/...attributes/default_runtime_attributes.wdl → ...attributes/default_runtime_attributes.wdl
diff --git a/...s/standardTestCases/defined_function.test → ...s/standardTestCases/defined_function.test b/...s/standardTestCases/defined_function.test → ...s/standardTestCases/defined_function.test
diff --git a/...ses/defined_function/defined_function.wdl → ...ses/defined_function/defined_function.wdl b/...ses/defined_function/defined_function.wdl → ...ses/defined_function/defined_function.wdl
diff --git a/...ses/docker_hash/docker_hash_dockerhub.wdl → ...ses/docker_hash/docker_hash_dockerhub.wdl b/...ses/docker_hash/docker_hash_dockerhub.wdl → ...ses/docker_hash/docker_hash_dockerhub.wdl
diff --git a/...er_hash/docker_hash_dockerhub_private.wdl → ...er_hash/docker_hash_dockerhub_private.wdl b/...er_hash/docker_hash_dockerhub_private.wdl → ...er_hash/docker_hash_dockerhub_private.wdl
diff --git a/...TestCases/docker_hash/docker_hash_gcr.wdl → ...TestCases/docker_hash/docker_hash_gcr.wdl b/...TestCases/docker_hash/docker_hash_gcr.wdl → ...TestCases/docker_hash/docker_hash_gcr.wdl
diff --git a/...s/docker_hash/docker_hash_gcr_private.wdl → ...s/docker_hash/docker_hash_gcr_private.wdl b/...s/docker_hash/docker_hash_gcr_private.wdl → ...s/docker_hash/docker_hash_gcr_private.wdl
diff --git a/...estCases/docker_hash/docker_hash_quay.wdl → ...estCases/docker_hash/docker_hash_quay.wdl b/...estCases/docker_hash/docker_hash_quay.wdl → ...estCases/docker_hash/docker_hash_quay.wdl
diff --git a/...ndardTestCases/docker_hash_dockerhub.test → ...ndardTestCases/docker_hash_dockerhub.test b/...ndardTestCases/docker_hash_dockerhub.test → ...ndardTestCases/docker_hash_dockerhub.test
diff --git a/...tCases/docker_hash_dockerhub_private.test → ...tCases/docker_hash_dockerhub_private.test b/...tCases/docker_hash_dockerhub_private.test → ...tCases/docker_hash_dockerhub_private.test
diff --git a/...es/standardTestCases/docker_hash_gcr.test → ...es/standardTestCases/docker_hash_gcr.test b/...es/standardTestCases/docker_hash_gcr.test → ...es/standardTestCases/docker_hash_gcr.test
diff --git a/...ardTestCases/docker_hash_gcr_private.test → ...ardTestCases/docker_hash_gcr_private.test b/...ardTestCases/docker_hash_gcr_private.test → ...ardTestCases/docker_hash_gcr_private.test
diff --git a/...s/standardTestCases/docker_hash_quay.test → ...s/standardTestCases/docker_hash_quay.test b/...s/standardTestCases/docker_hash_quay.test → ...s/standardTestCases/docker_hash_quay.test
diff --git a/...ndardTestCases/dontCacheToFailedJobs.test → ...ndardTestCases/dontCacheToFailedJobs.test b/...ndardTestCases/dontCacheToFailedJobs.test → ...ndardTestCases/dontCacheToFailedJobs.test
diff --git a/...failed_jobs/dont_cache_to_failed_jobs.wdl → ...failed_jobs/dont_cache_to_failed_jobs.wdl b/...failed_jobs/dont_cache_to_failed_jobs.wdl → ...failed_jobs/dont_cache_to_failed_jobs.wdl
diff --git a/...dardTestCases/dont_strip_line_prefix.test → ...dardTestCases/dont_strip_line_prefix.test b/...dardTestCases/dont_strip_line_prefix.test → ...dardTestCases/dont_strip_line_prefix.test
diff --git a/...ip_line_prefix/dont_strip_line_prefix.wdl → ...ip_line_prefix/dont_strip_line_prefix.wdl b/...ip_line_prefix/dont_strip_line_prefix.wdl → ...ip_line_prefix/dont_strip_line_prefix.wdl
diff --git a/...ces/standardTestCases/dontglobinputs.test → ...ces/standardTestCases/dontglobinputs.test b/...ces/standardTestCases/dontglobinputs.test → ...ces/standardTestCases/dontglobinputs.test
diff --git a/...stCases/dontglobinputs/dontglobinputs.wdl → ...stCases/dontglobinputs/dontglobinputs.wdl b/...stCases/dontglobinputs/dontglobinputs.wdl → ...stCases/dontglobinputs/dontglobinputs.wdl
diff --git a/...ndardTestCases/dot_dir_stuck_running.test → ...ndardTestCases/dot_dir_stuck_running.test b/...ndardTestCases/dot_dir_stuck_running.test → ...ndardTestCases/dot_dir_stuck_running.test
diff --git a/...r_stuck_running/dot_dir_stuck_running.wdl → ...r_stuck_running/dot_dir_stuck_running.wdl b/...r_stuck_running/dot_dir_stuck_running.wdl → ...r_stuck_running/dot_dir_stuck_running.wdl
diff --git a/...urces/standardTestCases/draft3_empty.test → ...urces/standardTestCases/draft3_empty.test b/...urces/standardTestCases/draft3_empty.test → ...urces/standardTestCases/draft3_empty.test
diff --git a/...rces/standardTestCases/empty_scatter.test → ...rces/standardTestCases/empty_scatter.test b/...rces/standardTestCases/empty_scatter.test → ...rces/standardTestCases/empty_scatter.test
diff --git a/...TestCases/empty_scatter/empty_scatter.wdl → ...TestCases/empty_scatter/empty_scatter.wdl b/...TestCases/empty_scatter/empty_scatter.wdl → ...TestCases/empty_scatter/empty_scatter.wdl
diff --git a/...urces/standardTestCases/empty_string.test → ...urces/standardTestCases/empty_string.test b/...urces/standardTestCases/empty_string.test → ...urces/standardTestCases/empty_string.test
diff --git a/...rdTestCases/empty_string/empty_string.wdl → ...rdTestCases/empty_string/empty_string.wdl b/...rdTestCases/empty_string/empty_string.wdl → ...rdTestCases/empty_string/empty_string.wdl
diff --git a/...ain/resources/standardTestCases/exit.test → ...ain/resources/standardTestCases/exit.test b/...ain/resources/standardTestCases/exit.test → ...ain/resources/standardTestCases/exit.test
diff --git a/...resources/standardTestCases/exit/exit.wdl → ...resources/standardTestCases/exit/exit.wdl b/...resources/standardTestCases/exit/exit.wdl → ...resources/standardTestCases/exit/exit.wdl
diff --git a/...rces/standardTestCases/expressionLib.test → ...rces/standardTestCases/expressionLib.test b/...rces/standardTestCases/expressionLib.test → ...rces/standardTestCases/expressionLib.test
diff --git a/...TestCases/expressionLib/expressionLib.cwl → ...TestCases/expressionLib/expressionLib.cwl b/...TestCases/expressionLib/expressionLib.cwl → ...TestCases/expressionLib/expressionLib.cwl
diff --git a/...ases/failing_continue_on_return_code.test → ...ases/failing_continue_on_return_code.test b/...ases/failing_continue_on_return_code.test → ...ases/failing_continue_on_return_code.test
diff --git a/..._code/failing_continue_on_return_code.wdl → ..._code/failing_continue_on_return_code.wdl b/..._code/failing_continue_on_return_code.wdl → ..._code/failing_continue_on_return_code.wdl
diff --git a/...s/failures.restart_while_failing_jes.test → ...s/failures.restart_while_failing_jes.test b/...s/failures.restart_while_failing_jes.test → ...s/failures.restart_while_failing_jes.test
diff --git a/...failures.restart_while_failing_local.test → ...failures.restart_while_failing_local.test b/...failures.restart_while_failing_local.test → ...failures.restart_while_failing_local.test
diff --git a/...s/failures.restart_while_failing_tes.test → ...s/failures.restart_while_failing_tes.test b/...s/failures.restart_while_failing_tes.test → ...s/failures.restart_while_failing_tes.test
diff --git a/...rdTestCases/failures.terminal_status.test → ...rdTestCases/failures.terminal_status.test b/...rdTestCases/failures.terminal_status.test → ...rdTestCases/failures.terminal_status.test
diff --git a/...ases/failures/invalid_wdl/invalid_wdl.wdl → ...ases/failures/invalid_wdl/invalid_wdl.wdl b/...ases/failures/invalid_wdl/invalid_wdl.wdl → ...ases/failures/invalid_wdl/invalid_wdl.wdl
diff --git a/...t_while_failing/restart_while_failing.wdl → ...t_while_failing/restart_while_failing.wdl b/...t_while_failing/restart_while_failing.wdl → ...t_while_failing/restart_while_failing.wdl
diff --git a/...lures/terminal_status/terminal_status.wdl → ...lures/terminal_status/terminal_status.wdl b/...lures/terminal_status/terminal_status.wdl → ...lures/terminal_status/terminal_status.wdl
diff --git a/...ardTestCases/file_outputs_from_input.test → ...ardTestCases/file_outputs_from_input.test b/...ardTestCases/file_outputs_from_input.test → ...ardTestCases/file_outputs_from_input.test
diff --git a/...ts_from_input/file_outputs_from_input.wdl → ...ts_from_input/file_outputs_from_input.wdl b/...ts_from_input/file_outputs_from_input.wdl → ...ts_from_input/file_outputs_from_input.wdl
diff --git a/...es/standardTestCases/filearrayoutput.test → ...es/standardTestCases/filearrayoutput.test b/...es/standardTestCases/filearrayoutput.test → ...es/standardTestCases/filearrayoutput.test
diff --git a/...Cases/filearrayoutput/filearrayoutput.wdl → ...Cases/filearrayoutput/filearrayoutput.wdl b/...Cases/filearrayoutput/filearrayoutput.wdl → ...Cases/filearrayoutput/filearrayoutput.wdl
diff --git a/...nal_call_logs_dir/final_call_logs_dir.wdl → ...nal_call_logs_dir/final_call_logs_dir.wdl b/...nal_call_logs_dir/final_call_logs_dir.wdl → ...nal_call_logs_dir/final_call_logs_dir.wdl
diff --git a/..._logs_dir/final_call_logs_dir_jes.options → ..._logs_dir/final_call_logs_dir_jes.options b/..._logs_dir/final_call_logs_dir_jes.options → ..._logs_dir/final_call_logs_dir_jes.options
diff --git a/...ogs_dir/final_call_logs_dir_local.options → ...ogs_dir/final_call_logs_dir_local.options b/...ogs_dir/final_call_logs_dir_local.options → ...ogs_dir/final_call_logs_dir_local.options
diff --git a/...ardTestCases/final_call_logs_dir_jes.test → ...ardTestCases/final_call_logs_dir_jes.test b/...ardTestCases/final_call_logs_dir_jes.test → ...ardTestCases/final_call_logs_dir_jes.test
diff --git a/...dTestCases/final_call_logs_dir_local.test → ...dTestCases/final_call_logs_dir_local.test b/...dTestCases/final_call_logs_dir_local.test → ...dTestCases/final_call_logs_dir_local.test
diff --git a/...ardTestCases/final_call_logs_dir_tes.test → ...ardTestCases/final_call_logs_dir_tes.test b/...ardTestCases/final_call_logs_dir_tes.test → ...ardTestCases/final_call_logs_dir_tes.test
diff --git a/...rces/standardTestCases/floating_tags.test → ...rces/standardTestCases/floating_tags.test b/...rces/standardTestCases/floating_tags.test → ...rces/standardTestCases/floating_tags.test
diff --git a/...Cases/floating_tags/floating_tags.options → ...Cases/floating_tags/floating_tags.options b/...Cases/floating_tags/floating_tags.options → ...Cases/floating_tags/floating_tags.options