From 1b57bd616c411dc1fab34532d0a57e749ac22aee Mon Sep 17 00:00:00 2001 From: Ben Sherman Date: Mon, 18 Nov 2024 16:59:24 -0600 Subject: [PATCH] Remove groovy gradle plugin Signed-off-by: Ben Sherman --- build.gradle | 1 - src/main/{groovy => java}/nextflow/config/dsl/ConfigOption.java | 0 src/main/{groovy => java}/nextflow/config/dsl/ConfigSchema.java | 0 src/main/{groovy => java}/nextflow/config/dsl/ConfigScope.java | 0 .../{groovy => java}/nextflow/config/scopes/ApptainerConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/AwsBatchConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/AwsClientConfig.java | 0 src/main/{groovy => java}/nextflow/config/scopes/AwsConfig.java | 0 .../nextflow/config/scopes/AzureActiveDirectoryConfig.java | 0 .../nextflow/config/scopes/AzureBatchConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/AzureConfig.java | 0 .../nextflow/config/scopes/AzureManagedIdentityConfig.java | 0 .../nextflow/config/scopes/AzureRegistryConfig.java | 0 .../nextflow/config/scopes/AzureRetryConfig.java | 0 .../nextflow/config/scopes/AzureStorageConfig.java | 0 .../nextflow/config/scopes/CharliecloudConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/CondaConfig.java | 0 src/main/{groovy => java}/nextflow/config/scopes/DagConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/DockerConfig.java | 0 src/main/{groovy => java}/nextflow/config/scopes/EnvConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/ExecutorConfig.java | 0 .../nextflow/config/scopes/ExecutorRetryConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/FusionConfig.java | 0 .../nextflow/config/scopes/GoogleBatchConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/GoogleConfig.java | 0 src/main/{groovy => java}/nextflow/config/scopes/K8sConfig.java | 0 src/main/{groovy => java}/nextflow/config/scopes/MailConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/MailSmtpConfig.java | 0 src/main/{groovy => java}/nextflow/config/scopes/Manifest.java | 0 .../{groovy => java}/nextflow/config/scopes/ParamsConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/PluginsConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/PodmanConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/ProcessConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/ProfilesConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/ReportConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/ShifterConfig.java | 0 .../nextflow/config/scopes/SingularityConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/SpackConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/TimelineConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/TowerConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/TraceConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/UnscopedConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/WaveBuildConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/WaveCondaConfig.java | 0 src/main/{groovy => java}/nextflow/config/scopes/WaveConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/WaveHttpConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/WaveRetryConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/WaveScanConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/WaveSpackConfig.java | 0 .../{groovy => java}/nextflow/config/scopes/WorkflowConfig.java | 0 .../nextflow/config/scopes/WorkflowOutputConfig.java | 0 .../{groovy => java}/nextflow/config/v2/ConfigAppendNode.java | 0 .../{groovy => java}/nextflow/config/v2/ConfigAssignNode.java | 0 .../{groovy => java}/nextflow/config/v2/ConfigAstBuilder.java | 0 .../{groovy => java}/nextflow/config/v2/ConfigBlockNode.java | 0 .../{groovy => java}/nextflow/config/v2/ConfigIncludeNode.java | 0 .../nextflow/config/v2/ConfigIncompleteNode.java | 0 src/main/{groovy => java}/nextflow/config/v2/ConfigNode.java | 0 .../{groovy => java}/nextflow/config/v2/ConfigParserPlugin.java | 0 .../nextflow/config/v2/ConfigParserPluginFactory.java | 0 .../{groovy => java}/nextflow/config/v2/ConfigStatement.java | 0 src/main/{groovy => java}/nextflow/config/v2/ConfigVisitor.java | 0 .../nextflow/config/v2/ConfigVisitorSupport.java | 0 .../{groovy => java}/nextflow/lsp/NextflowLanguageServer.java | 0 src/main/{groovy => java}/nextflow/lsp/ast/ASTNodeCache.java | 0 .../{groovy => java}/nextflow/lsp/ast/ASTNodeStringUtils.java | 0 src/main/{groovy => java}/nextflow/lsp/ast/ASTParentVisitor.java | 0 src/main/{groovy => java}/nextflow/lsp/ast/ASTUtils.java | 0 src/main/{groovy => java}/nextflow/lsp/compiler/Compiler.java | 0 .../{groovy => java}/nextflow/lsp/compiler/FutureWarning.java | 0 .../nextflow/lsp/compiler/LanguageServerErrorCollector.java | 0 src/main/{groovy => java}/nextflow/lsp/compiler/PhaseAware.java | 0 src/main/{groovy => java}/nextflow/lsp/compiler/Phases.java | 0 .../nextflow/lsp/compiler/RelatedInformationAware.java | 0 .../nextflow/lsp/compiler/StringReaderSourceWithURI.java | 0 src/main/{groovy => java}/nextflow/lsp/file/FileCache.java | 0 src/main/{groovy => java}/nextflow/lsp/file/PathUtils.java | 0 .../nextflow/lsp/services/CallHierarchyProvider.java | 0 .../{groovy => java}/nextflow/lsp/services/CodeLensProvider.java | 0 .../nextflow/lsp/services/CompletionProvider.java | 0 .../nextflow/lsp/services/DefinitionProvider.java | 0 .../nextflow/lsp/services/FormattingProvider.java | 0 .../{groovy => java}/nextflow/lsp/services/HoverProvider.java | 0 .../{groovy => java}/nextflow/lsp/services/LanguageService.java | 0 .../{groovy => java}/nextflow/lsp/services/LinkProvider.java | 0 .../nextflow/lsp/services/ReferenceProvider.java | 0 .../{groovy => java}/nextflow/lsp/services/RenameProvider.java | 0 .../{groovy => java}/nextflow/lsp/services/SymbolProvider.java | 0 .../nextflow/lsp/services/config/ConfigAstCache.java | 0 .../nextflow/lsp/services/config/ConfigCompletionProvider.java | 0 .../nextflow/lsp/services/config/ConfigFormattingProvider.java | 0 .../nextflow/lsp/services/config/ConfigHoverProvider.java | 0 .../nextflow/lsp/services/config/ConfigLinkProvider.java | 0 .../nextflow/lsp/services/config/ConfigSchemaVisitor.java | 0 .../nextflow/lsp/services/config/ConfigService.java | 0 .../nextflow/lsp/services/config/ConfigToGroovyVisitor.java | 0 .../nextflow/lsp/services/config/ResolveIncludeVisitor.java | 0 .../nextflow/lsp/services/script/MethodCallVisitor.java | 0 .../nextflow/lsp/services/script/ResolveIncludeVisitor.java | 0 .../nextflow/lsp/services/script/ResolveVisitor.java | 0 .../nextflow/lsp/services/script/ScriptAstCache.java | 0 .../lsp/services/script/ScriptCallHierarchyProvider.java | 0 .../nextflow/lsp/services/script/ScriptCodeLensProvider.java | 0 .../nextflow/lsp/services/script/ScriptCompletionProvider.java | 0 .../nextflow/lsp/services/script/ScriptDefinitionProvider.java | 0 .../nextflow/lsp/services/script/ScriptFormattingProvider.java | 0 .../nextflow/lsp/services/script/ScriptHoverProvider.java | 0 .../nextflow/lsp/services/script/ScriptLinkProvider.java | 0 .../nextflow/lsp/services/script/ScriptReferenceProvider.java | 0 .../nextflow/lsp/services/script/ScriptService.java | 0 .../nextflow/lsp/services/script/ScriptSymbolProvider.java | 0 .../nextflow/lsp/services/script/ScriptToGroovyVisitor.java | 0 .../nextflow/lsp/services/script/VariableScopeVisitor.java | 0 .../nextflow/lsp/services/script/dag/DataflowVisitor.java | 0 .../nextflow/lsp/services/script/dag/MermaidRenderer.java | 0 .../{groovy => java}/nextflow/lsp/services/util/Formatter.java | 0 .../nextflow/lsp/services/util/FormattingOptions.java | 0 .../{groovy => java}/nextflow/lsp/util/DebouncingExecutor.java | 0 .../{groovy => java}/nextflow/lsp/util/LanguageServerUtils.java | 0 src/main/{groovy => java}/nextflow/lsp/util/Logger.java | 0 src/main/{groovy => java}/nextflow/lsp/util/Positions.java | 0 src/main/{groovy => java}/nextflow/script/dsl/Constant.java | 0 src/main/{groovy => java}/nextflow/script/dsl/Description.java | 0 src/main/{groovy => java}/nextflow/script/dsl/DslScope.java | 0 .../{groovy => java}/nextflow/script/dsl/EntryWorkflowDsl.java | 0 src/main/{groovy => java}/nextflow/script/dsl/FeatureFlag.java | 0 .../{groovy => java}/nextflow/script/dsl/FeatureFlagDsl.java | 0 src/main/{groovy => java}/nextflow/script/dsl/Operator.java | 0 src/main/{groovy => java}/nextflow/script/dsl/OutputDsl.java | 0 src/main/{groovy => java}/nextflow/script/dsl/ProcessDsl.java | 0 src/main/{groovy => java}/nextflow/script/dsl/ScriptDsl.java | 0 src/main/{groovy => java}/nextflow/script/dsl/WorkflowDsl.java | 0 src/main/{groovy => java}/nextflow/script/types/Channel.java | 0 .../{groovy => java}/nextflow/script/types/ChannelFactory.java | 0 src/main/{groovy => java}/nextflow/script/types/Duration.java | 0 src/main/{groovy => java}/nextflow/script/types/Manifest.java | 0 src/main/{groovy => java}/nextflow/script/types/MemoryUnit.java | 0 .../{groovy => java}/nextflow/script/types/NextflowMetadata.java | 0 src/main/{groovy => java}/nextflow/script/types/ParamsMap.java | 0 src/main/{groovy => java}/nextflow/script/types/TaskConfig.java | 0 src/main/{groovy => java}/nextflow/script/types/Types.java | 0 .../{groovy => java}/nextflow/script/types/VersionNumber.java | 0 .../{groovy => java}/nextflow/script/types/WorkflowMetadata.java | 0 src/main/{groovy => java}/nextflow/script/v2/ASTHelpers.java | 0 .../nextflow/script/v2/AssignmentExpression.java | 0 .../{groovy => java}/nextflow/script/v2/FeatureFlagNode.java | 0 src/main/{groovy => java}/nextflow/script/v2/FunctionNode.java | 0 .../{groovy => java}/nextflow/script/v2/GroovydocManager.java | 0 src/main/{groovy => java}/nextflow/script/v2/IncludeNode.java | 0 .../{groovy => java}/nextflow/script/v2/IncludeVariable.java | 0 src/main/{groovy => java}/nextflow/script/v2/IncompleteNode.java | 0 .../{groovy => java}/nextflow/script/v2/InvalidDeclaration.java | 0 src/main/{groovy => java}/nextflow/script/v2/OutputNode.java | 0 src/main/{groovy => java}/nextflow/script/v2/ParamNode.java | 0 src/main/{groovy => java}/nextflow/script/v2/ProcessNode.java | 0 .../{groovy => java}/nextflow/script/v2/ScriptAstBuilder.java | 0 .../nextflow/script/v2/ScriptExpressionTransformer.java | 0 src/main/{groovy => java}/nextflow/script/v2/ScriptNode.java | 0 .../{groovy => java}/nextflow/script/v2/ScriptParserPlugin.java | 0 .../nextflow/script/v2/ScriptParserPluginFactory.java | 0 src/main/{groovy => java}/nextflow/script/v2/ScriptVisitor.java | 0 .../nextflow/script/v2/ScriptVisitorSupport.java | 0 src/main/{groovy => java}/nextflow/script/v2/WorkflowNode.java | 0 163 files changed, 1 deletion(-) rename src/main/{groovy => java}/nextflow/config/dsl/ConfigOption.java (100%) rename src/main/{groovy => java}/nextflow/config/dsl/ConfigSchema.java (100%) rename src/main/{groovy => java}/nextflow/config/dsl/ConfigScope.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/ApptainerConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/AwsBatchConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/AwsClientConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/AwsConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/AzureActiveDirectoryConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/AzureBatchConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/AzureConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/AzureManagedIdentityConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/AzureRegistryConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/AzureRetryConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/AzureStorageConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/CharliecloudConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/CondaConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/DagConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/DockerConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/EnvConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/ExecutorConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/ExecutorRetryConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/FusionConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/GoogleBatchConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/GoogleConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/K8sConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/MailConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/MailSmtpConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/Manifest.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/ParamsConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/PluginsConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/PodmanConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/ProcessConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/ProfilesConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/ReportConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/ShifterConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/SingularityConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/SpackConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/TimelineConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/TowerConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/TraceConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/UnscopedConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/WaveBuildConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/WaveCondaConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/WaveConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/WaveHttpConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/WaveRetryConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/WaveScanConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/WaveSpackConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/WorkflowConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/scopes/WorkflowOutputConfig.java (100%) rename src/main/{groovy => java}/nextflow/config/v2/ConfigAppendNode.java (100%) rename src/main/{groovy => java}/nextflow/config/v2/ConfigAssignNode.java (100%) rename src/main/{groovy => java}/nextflow/config/v2/ConfigAstBuilder.java (100%) rename src/main/{groovy => java}/nextflow/config/v2/ConfigBlockNode.java (100%) rename src/main/{groovy => java}/nextflow/config/v2/ConfigIncludeNode.java (100%) rename src/main/{groovy => java}/nextflow/config/v2/ConfigIncompleteNode.java (100%) rename src/main/{groovy => java}/nextflow/config/v2/ConfigNode.java (100%) rename src/main/{groovy => java}/nextflow/config/v2/ConfigParserPlugin.java (100%) rename src/main/{groovy => java}/nextflow/config/v2/ConfigParserPluginFactory.java (100%) rename src/main/{groovy => java}/nextflow/config/v2/ConfigStatement.java (100%) rename src/main/{groovy => java}/nextflow/config/v2/ConfigVisitor.java (100%) rename src/main/{groovy => java}/nextflow/config/v2/ConfigVisitorSupport.java (100%) rename src/main/{groovy => java}/nextflow/lsp/NextflowLanguageServer.java (100%) rename src/main/{groovy => java}/nextflow/lsp/ast/ASTNodeCache.java (100%) rename src/main/{groovy => java}/nextflow/lsp/ast/ASTNodeStringUtils.java (100%) rename src/main/{groovy => java}/nextflow/lsp/ast/ASTParentVisitor.java (100%) rename src/main/{groovy => java}/nextflow/lsp/ast/ASTUtils.java (100%) rename src/main/{groovy => java}/nextflow/lsp/compiler/Compiler.java (100%) rename src/main/{groovy => java}/nextflow/lsp/compiler/FutureWarning.java (100%) rename src/main/{groovy => java}/nextflow/lsp/compiler/LanguageServerErrorCollector.java (100%) rename src/main/{groovy => java}/nextflow/lsp/compiler/PhaseAware.java (100%) rename src/main/{groovy => java}/nextflow/lsp/compiler/Phases.java (100%) rename src/main/{groovy => java}/nextflow/lsp/compiler/RelatedInformationAware.java (100%) rename src/main/{groovy => java}/nextflow/lsp/compiler/StringReaderSourceWithURI.java (100%) rename src/main/{groovy => java}/nextflow/lsp/file/FileCache.java (100%) rename src/main/{groovy => java}/nextflow/lsp/file/PathUtils.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/CallHierarchyProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/CodeLensProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/CompletionProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/DefinitionProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/FormattingProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/HoverProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/LanguageService.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/LinkProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/ReferenceProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/RenameProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/SymbolProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/config/ConfigAstCache.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/config/ConfigCompletionProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/config/ConfigFormattingProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/config/ConfigHoverProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/config/ConfigLinkProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/config/ConfigSchemaVisitor.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/config/ConfigService.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/config/ConfigToGroovyVisitor.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/config/ResolveIncludeVisitor.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/script/MethodCallVisitor.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/script/ResolveIncludeVisitor.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/script/ResolveVisitor.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/script/ScriptAstCache.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/script/ScriptCallHierarchyProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/script/ScriptCodeLensProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/script/ScriptCompletionProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/script/ScriptDefinitionProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/script/ScriptFormattingProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/script/ScriptHoverProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/script/ScriptLinkProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/script/ScriptReferenceProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/script/ScriptService.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/script/ScriptSymbolProvider.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/script/ScriptToGroovyVisitor.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/script/VariableScopeVisitor.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/script/dag/DataflowVisitor.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/script/dag/MermaidRenderer.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/util/Formatter.java (100%) rename src/main/{groovy => java}/nextflow/lsp/services/util/FormattingOptions.java (100%) rename src/main/{groovy => java}/nextflow/lsp/util/DebouncingExecutor.java (100%) rename src/main/{groovy => java}/nextflow/lsp/util/LanguageServerUtils.java (100%) rename src/main/{groovy => java}/nextflow/lsp/util/Logger.java (100%) rename src/main/{groovy => java}/nextflow/lsp/util/Positions.java (100%) rename src/main/{groovy => java}/nextflow/script/dsl/Constant.java (100%) rename src/main/{groovy => java}/nextflow/script/dsl/Description.java (100%) rename src/main/{groovy => java}/nextflow/script/dsl/DslScope.java (100%) rename src/main/{groovy => java}/nextflow/script/dsl/EntryWorkflowDsl.java (100%) rename src/main/{groovy => java}/nextflow/script/dsl/FeatureFlag.java (100%) rename src/main/{groovy => java}/nextflow/script/dsl/FeatureFlagDsl.java (100%) rename src/main/{groovy => java}/nextflow/script/dsl/Operator.java (100%) rename src/main/{groovy => java}/nextflow/script/dsl/OutputDsl.java (100%) rename src/main/{groovy => java}/nextflow/script/dsl/ProcessDsl.java (100%) rename src/main/{groovy => java}/nextflow/script/dsl/ScriptDsl.java (100%) rename src/main/{groovy => java}/nextflow/script/dsl/WorkflowDsl.java (100%) rename src/main/{groovy => java}/nextflow/script/types/Channel.java (100%) rename src/main/{groovy => java}/nextflow/script/types/ChannelFactory.java (100%) rename src/main/{groovy => java}/nextflow/script/types/Duration.java (100%) rename src/main/{groovy => java}/nextflow/script/types/Manifest.java (100%) rename src/main/{groovy => java}/nextflow/script/types/MemoryUnit.java (100%) rename src/main/{groovy => java}/nextflow/script/types/NextflowMetadata.java (100%) rename src/main/{groovy => java}/nextflow/script/types/ParamsMap.java (100%) rename src/main/{groovy => java}/nextflow/script/types/TaskConfig.java (100%) rename src/main/{groovy => java}/nextflow/script/types/Types.java (100%) rename src/main/{groovy => java}/nextflow/script/types/VersionNumber.java (100%) rename src/main/{groovy => java}/nextflow/script/types/WorkflowMetadata.java (100%) rename src/main/{groovy => java}/nextflow/script/v2/ASTHelpers.java (100%) rename src/main/{groovy => java}/nextflow/script/v2/AssignmentExpression.java (100%) rename src/main/{groovy => java}/nextflow/script/v2/FeatureFlagNode.java (100%) rename src/main/{groovy => java}/nextflow/script/v2/FunctionNode.java (100%) rename src/main/{groovy => java}/nextflow/script/v2/GroovydocManager.java (100%) rename src/main/{groovy => java}/nextflow/script/v2/IncludeNode.java (100%) rename src/main/{groovy => java}/nextflow/script/v2/IncludeVariable.java (100%) rename src/main/{groovy => java}/nextflow/script/v2/IncompleteNode.java (100%) rename src/main/{groovy => java}/nextflow/script/v2/InvalidDeclaration.java (100%) rename src/main/{groovy => java}/nextflow/script/v2/OutputNode.java (100%) rename src/main/{groovy => java}/nextflow/script/v2/ParamNode.java (100%) rename src/main/{groovy => java}/nextflow/script/v2/ProcessNode.java (100%) rename src/main/{groovy => java}/nextflow/script/v2/ScriptAstBuilder.java (100%) rename src/main/{groovy => java}/nextflow/script/v2/ScriptExpressionTransformer.java (100%) rename src/main/{groovy => java}/nextflow/script/v2/ScriptNode.java (100%) rename src/main/{groovy => java}/nextflow/script/v2/ScriptParserPlugin.java (100%) rename src/main/{groovy => java}/nextflow/script/v2/ScriptParserPluginFactory.java (100%) rename src/main/{groovy => java}/nextflow/script/v2/ScriptVisitor.java (100%) rename src/main/{groovy => java}/nextflow/script/v2/ScriptVisitorSupport.java (100%) rename src/main/{groovy => java}/nextflow/script/v2/WorkflowNode.java (100%) diff --git a/build.gradle b/build.gradle index ef878c0..31d6e85 100644 --- a/build.gradle +++ b/build.gradle @@ -1,7 +1,6 @@ plugins { id 'com.gradleup.shadow' version '8.3.5' id 'application' - id 'groovy' id 'antlr' } diff --git a/src/main/groovy/nextflow/config/dsl/ConfigOption.java b/src/main/java/nextflow/config/dsl/ConfigOption.java similarity index 100% rename from src/main/groovy/nextflow/config/dsl/ConfigOption.java rename to src/main/java/nextflow/config/dsl/ConfigOption.java diff --git a/src/main/groovy/nextflow/config/dsl/ConfigSchema.java b/src/main/java/nextflow/config/dsl/ConfigSchema.java similarity index 100% rename from src/main/groovy/nextflow/config/dsl/ConfigSchema.java rename to src/main/java/nextflow/config/dsl/ConfigSchema.java diff --git a/src/main/groovy/nextflow/config/dsl/ConfigScope.java b/src/main/java/nextflow/config/dsl/ConfigScope.java similarity index 100% rename from src/main/groovy/nextflow/config/dsl/ConfigScope.java rename to src/main/java/nextflow/config/dsl/ConfigScope.java diff --git a/src/main/groovy/nextflow/config/scopes/ApptainerConfig.java b/src/main/java/nextflow/config/scopes/ApptainerConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/ApptainerConfig.java rename to src/main/java/nextflow/config/scopes/ApptainerConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/AwsBatchConfig.java b/src/main/java/nextflow/config/scopes/AwsBatchConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/AwsBatchConfig.java rename to src/main/java/nextflow/config/scopes/AwsBatchConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/AwsClientConfig.java b/src/main/java/nextflow/config/scopes/AwsClientConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/AwsClientConfig.java rename to src/main/java/nextflow/config/scopes/AwsClientConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/AwsConfig.java b/src/main/java/nextflow/config/scopes/AwsConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/AwsConfig.java rename to src/main/java/nextflow/config/scopes/AwsConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/AzureActiveDirectoryConfig.java b/src/main/java/nextflow/config/scopes/AzureActiveDirectoryConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/AzureActiveDirectoryConfig.java rename to src/main/java/nextflow/config/scopes/AzureActiveDirectoryConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/AzureBatchConfig.java b/src/main/java/nextflow/config/scopes/AzureBatchConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/AzureBatchConfig.java rename to src/main/java/nextflow/config/scopes/AzureBatchConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/AzureConfig.java b/src/main/java/nextflow/config/scopes/AzureConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/AzureConfig.java rename to src/main/java/nextflow/config/scopes/AzureConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/AzureManagedIdentityConfig.java b/src/main/java/nextflow/config/scopes/AzureManagedIdentityConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/AzureManagedIdentityConfig.java rename to src/main/java/nextflow/config/scopes/AzureManagedIdentityConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/AzureRegistryConfig.java b/src/main/java/nextflow/config/scopes/AzureRegistryConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/AzureRegistryConfig.java rename to src/main/java/nextflow/config/scopes/AzureRegistryConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/AzureRetryConfig.java b/src/main/java/nextflow/config/scopes/AzureRetryConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/AzureRetryConfig.java rename to src/main/java/nextflow/config/scopes/AzureRetryConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/AzureStorageConfig.java b/src/main/java/nextflow/config/scopes/AzureStorageConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/AzureStorageConfig.java rename to src/main/java/nextflow/config/scopes/AzureStorageConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/CharliecloudConfig.java b/src/main/java/nextflow/config/scopes/CharliecloudConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/CharliecloudConfig.java rename to src/main/java/nextflow/config/scopes/CharliecloudConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/CondaConfig.java b/src/main/java/nextflow/config/scopes/CondaConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/CondaConfig.java rename to src/main/java/nextflow/config/scopes/CondaConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/DagConfig.java b/src/main/java/nextflow/config/scopes/DagConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/DagConfig.java rename to src/main/java/nextflow/config/scopes/DagConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/DockerConfig.java b/src/main/java/nextflow/config/scopes/DockerConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/DockerConfig.java rename to src/main/java/nextflow/config/scopes/DockerConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/EnvConfig.java b/src/main/java/nextflow/config/scopes/EnvConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/EnvConfig.java rename to src/main/java/nextflow/config/scopes/EnvConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/ExecutorConfig.java b/src/main/java/nextflow/config/scopes/ExecutorConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/ExecutorConfig.java rename to src/main/java/nextflow/config/scopes/ExecutorConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/ExecutorRetryConfig.java b/src/main/java/nextflow/config/scopes/ExecutorRetryConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/ExecutorRetryConfig.java rename to src/main/java/nextflow/config/scopes/ExecutorRetryConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/FusionConfig.java b/src/main/java/nextflow/config/scopes/FusionConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/FusionConfig.java rename to src/main/java/nextflow/config/scopes/FusionConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/GoogleBatchConfig.java b/src/main/java/nextflow/config/scopes/GoogleBatchConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/GoogleBatchConfig.java rename to src/main/java/nextflow/config/scopes/GoogleBatchConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/GoogleConfig.java b/src/main/java/nextflow/config/scopes/GoogleConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/GoogleConfig.java rename to src/main/java/nextflow/config/scopes/GoogleConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/K8sConfig.java b/src/main/java/nextflow/config/scopes/K8sConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/K8sConfig.java rename to src/main/java/nextflow/config/scopes/K8sConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/MailConfig.java b/src/main/java/nextflow/config/scopes/MailConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/MailConfig.java rename to src/main/java/nextflow/config/scopes/MailConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/MailSmtpConfig.java b/src/main/java/nextflow/config/scopes/MailSmtpConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/MailSmtpConfig.java rename to src/main/java/nextflow/config/scopes/MailSmtpConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/Manifest.java b/src/main/java/nextflow/config/scopes/Manifest.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/Manifest.java rename to src/main/java/nextflow/config/scopes/Manifest.java diff --git a/src/main/groovy/nextflow/config/scopes/ParamsConfig.java b/src/main/java/nextflow/config/scopes/ParamsConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/ParamsConfig.java rename to src/main/java/nextflow/config/scopes/ParamsConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/PluginsConfig.java b/src/main/java/nextflow/config/scopes/PluginsConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/PluginsConfig.java rename to src/main/java/nextflow/config/scopes/PluginsConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/PodmanConfig.java b/src/main/java/nextflow/config/scopes/PodmanConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/PodmanConfig.java rename to src/main/java/nextflow/config/scopes/PodmanConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/ProcessConfig.java b/src/main/java/nextflow/config/scopes/ProcessConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/ProcessConfig.java rename to src/main/java/nextflow/config/scopes/ProcessConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/ProfilesConfig.java b/src/main/java/nextflow/config/scopes/ProfilesConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/ProfilesConfig.java rename to src/main/java/nextflow/config/scopes/ProfilesConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/ReportConfig.java b/src/main/java/nextflow/config/scopes/ReportConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/ReportConfig.java rename to src/main/java/nextflow/config/scopes/ReportConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/ShifterConfig.java b/src/main/java/nextflow/config/scopes/ShifterConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/ShifterConfig.java rename to src/main/java/nextflow/config/scopes/ShifterConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/SingularityConfig.java b/src/main/java/nextflow/config/scopes/SingularityConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/SingularityConfig.java rename to src/main/java/nextflow/config/scopes/SingularityConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/SpackConfig.java b/src/main/java/nextflow/config/scopes/SpackConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/SpackConfig.java rename to src/main/java/nextflow/config/scopes/SpackConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/TimelineConfig.java b/src/main/java/nextflow/config/scopes/TimelineConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/TimelineConfig.java rename to src/main/java/nextflow/config/scopes/TimelineConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/TowerConfig.java b/src/main/java/nextflow/config/scopes/TowerConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/TowerConfig.java rename to src/main/java/nextflow/config/scopes/TowerConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/TraceConfig.java b/src/main/java/nextflow/config/scopes/TraceConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/TraceConfig.java rename to src/main/java/nextflow/config/scopes/TraceConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/UnscopedConfig.java b/src/main/java/nextflow/config/scopes/UnscopedConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/UnscopedConfig.java rename to src/main/java/nextflow/config/scopes/UnscopedConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/WaveBuildConfig.java b/src/main/java/nextflow/config/scopes/WaveBuildConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/WaveBuildConfig.java rename to src/main/java/nextflow/config/scopes/WaveBuildConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/WaveCondaConfig.java b/src/main/java/nextflow/config/scopes/WaveCondaConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/WaveCondaConfig.java rename to src/main/java/nextflow/config/scopes/WaveCondaConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/WaveConfig.java b/src/main/java/nextflow/config/scopes/WaveConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/WaveConfig.java rename to src/main/java/nextflow/config/scopes/WaveConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/WaveHttpConfig.java b/src/main/java/nextflow/config/scopes/WaveHttpConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/WaveHttpConfig.java rename to src/main/java/nextflow/config/scopes/WaveHttpConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/WaveRetryConfig.java b/src/main/java/nextflow/config/scopes/WaveRetryConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/WaveRetryConfig.java rename to src/main/java/nextflow/config/scopes/WaveRetryConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/WaveScanConfig.java b/src/main/java/nextflow/config/scopes/WaveScanConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/WaveScanConfig.java rename to src/main/java/nextflow/config/scopes/WaveScanConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/WaveSpackConfig.java b/src/main/java/nextflow/config/scopes/WaveSpackConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/WaveSpackConfig.java rename to src/main/java/nextflow/config/scopes/WaveSpackConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/WorkflowConfig.java b/src/main/java/nextflow/config/scopes/WorkflowConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/WorkflowConfig.java rename to src/main/java/nextflow/config/scopes/WorkflowConfig.java diff --git a/src/main/groovy/nextflow/config/scopes/WorkflowOutputConfig.java b/src/main/java/nextflow/config/scopes/WorkflowOutputConfig.java similarity index 100% rename from src/main/groovy/nextflow/config/scopes/WorkflowOutputConfig.java rename to src/main/java/nextflow/config/scopes/WorkflowOutputConfig.java diff --git a/src/main/groovy/nextflow/config/v2/ConfigAppendNode.java b/src/main/java/nextflow/config/v2/ConfigAppendNode.java similarity index 100% rename from src/main/groovy/nextflow/config/v2/ConfigAppendNode.java rename to src/main/java/nextflow/config/v2/ConfigAppendNode.java diff --git a/src/main/groovy/nextflow/config/v2/ConfigAssignNode.java b/src/main/java/nextflow/config/v2/ConfigAssignNode.java similarity index 100% rename from src/main/groovy/nextflow/config/v2/ConfigAssignNode.java rename to src/main/java/nextflow/config/v2/ConfigAssignNode.java diff --git a/src/main/groovy/nextflow/config/v2/ConfigAstBuilder.java b/src/main/java/nextflow/config/v2/ConfigAstBuilder.java similarity index 100% rename from src/main/groovy/nextflow/config/v2/ConfigAstBuilder.java rename to src/main/java/nextflow/config/v2/ConfigAstBuilder.java diff --git a/src/main/groovy/nextflow/config/v2/ConfigBlockNode.java b/src/main/java/nextflow/config/v2/ConfigBlockNode.java similarity index 100% rename from src/main/groovy/nextflow/config/v2/ConfigBlockNode.java rename to src/main/java/nextflow/config/v2/ConfigBlockNode.java diff --git a/src/main/groovy/nextflow/config/v2/ConfigIncludeNode.java b/src/main/java/nextflow/config/v2/ConfigIncludeNode.java similarity index 100% rename from src/main/groovy/nextflow/config/v2/ConfigIncludeNode.java rename to src/main/java/nextflow/config/v2/ConfigIncludeNode.java diff --git a/src/main/groovy/nextflow/config/v2/ConfigIncompleteNode.java b/src/main/java/nextflow/config/v2/ConfigIncompleteNode.java similarity index 100% rename from src/main/groovy/nextflow/config/v2/ConfigIncompleteNode.java rename to src/main/java/nextflow/config/v2/ConfigIncompleteNode.java diff --git a/src/main/groovy/nextflow/config/v2/ConfigNode.java b/src/main/java/nextflow/config/v2/ConfigNode.java similarity index 100% rename from src/main/groovy/nextflow/config/v2/ConfigNode.java rename to src/main/java/nextflow/config/v2/ConfigNode.java diff --git a/src/main/groovy/nextflow/config/v2/ConfigParserPlugin.java b/src/main/java/nextflow/config/v2/ConfigParserPlugin.java similarity index 100% rename from src/main/groovy/nextflow/config/v2/ConfigParserPlugin.java rename to src/main/java/nextflow/config/v2/ConfigParserPlugin.java diff --git a/src/main/groovy/nextflow/config/v2/ConfigParserPluginFactory.java b/src/main/java/nextflow/config/v2/ConfigParserPluginFactory.java similarity index 100% rename from src/main/groovy/nextflow/config/v2/ConfigParserPluginFactory.java rename to src/main/java/nextflow/config/v2/ConfigParserPluginFactory.java diff --git a/src/main/groovy/nextflow/config/v2/ConfigStatement.java b/src/main/java/nextflow/config/v2/ConfigStatement.java similarity index 100% rename from src/main/groovy/nextflow/config/v2/ConfigStatement.java rename to src/main/java/nextflow/config/v2/ConfigStatement.java diff --git a/src/main/groovy/nextflow/config/v2/ConfigVisitor.java b/src/main/java/nextflow/config/v2/ConfigVisitor.java similarity index 100% rename from src/main/groovy/nextflow/config/v2/ConfigVisitor.java rename to src/main/java/nextflow/config/v2/ConfigVisitor.java diff --git a/src/main/groovy/nextflow/config/v2/ConfigVisitorSupport.java b/src/main/java/nextflow/config/v2/ConfigVisitorSupport.java similarity index 100% rename from src/main/groovy/nextflow/config/v2/ConfigVisitorSupport.java rename to src/main/java/nextflow/config/v2/ConfigVisitorSupport.java diff --git a/src/main/groovy/nextflow/lsp/NextflowLanguageServer.java b/src/main/java/nextflow/lsp/NextflowLanguageServer.java similarity index 100% rename from src/main/groovy/nextflow/lsp/NextflowLanguageServer.java rename to src/main/java/nextflow/lsp/NextflowLanguageServer.java diff --git a/src/main/groovy/nextflow/lsp/ast/ASTNodeCache.java b/src/main/java/nextflow/lsp/ast/ASTNodeCache.java similarity index 100% rename from src/main/groovy/nextflow/lsp/ast/ASTNodeCache.java rename to src/main/java/nextflow/lsp/ast/ASTNodeCache.java diff --git a/src/main/groovy/nextflow/lsp/ast/ASTNodeStringUtils.java b/src/main/java/nextflow/lsp/ast/ASTNodeStringUtils.java similarity index 100% rename from src/main/groovy/nextflow/lsp/ast/ASTNodeStringUtils.java rename to src/main/java/nextflow/lsp/ast/ASTNodeStringUtils.java diff --git a/src/main/groovy/nextflow/lsp/ast/ASTParentVisitor.java b/src/main/java/nextflow/lsp/ast/ASTParentVisitor.java similarity index 100% rename from src/main/groovy/nextflow/lsp/ast/ASTParentVisitor.java rename to src/main/java/nextflow/lsp/ast/ASTParentVisitor.java diff --git a/src/main/groovy/nextflow/lsp/ast/ASTUtils.java b/src/main/java/nextflow/lsp/ast/ASTUtils.java similarity index 100% rename from src/main/groovy/nextflow/lsp/ast/ASTUtils.java rename to src/main/java/nextflow/lsp/ast/ASTUtils.java diff --git a/src/main/groovy/nextflow/lsp/compiler/Compiler.java b/src/main/java/nextflow/lsp/compiler/Compiler.java similarity index 100% rename from src/main/groovy/nextflow/lsp/compiler/Compiler.java rename to src/main/java/nextflow/lsp/compiler/Compiler.java diff --git a/src/main/groovy/nextflow/lsp/compiler/FutureWarning.java b/src/main/java/nextflow/lsp/compiler/FutureWarning.java similarity index 100% rename from src/main/groovy/nextflow/lsp/compiler/FutureWarning.java rename to src/main/java/nextflow/lsp/compiler/FutureWarning.java diff --git a/src/main/groovy/nextflow/lsp/compiler/LanguageServerErrorCollector.java b/src/main/java/nextflow/lsp/compiler/LanguageServerErrorCollector.java similarity index 100% rename from src/main/groovy/nextflow/lsp/compiler/LanguageServerErrorCollector.java rename to src/main/java/nextflow/lsp/compiler/LanguageServerErrorCollector.java diff --git a/src/main/groovy/nextflow/lsp/compiler/PhaseAware.java b/src/main/java/nextflow/lsp/compiler/PhaseAware.java similarity index 100% rename from src/main/groovy/nextflow/lsp/compiler/PhaseAware.java rename to src/main/java/nextflow/lsp/compiler/PhaseAware.java diff --git a/src/main/groovy/nextflow/lsp/compiler/Phases.java b/src/main/java/nextflow/lsp/compiler/Phases.java similarity index 100% rename from src/main/groovy/nextflow/lsp/compiler/Phases.java rename to src/main/java/nextflow/lsp/compiler/Phases.java diff --git a/src/main/groovy/nextflow/lsp/compiler/RelatedInformationAware.java b/src/main/java/nextflow/lsp/compiler/RelatedInformationAware.java similarity index 100% rename from src/main/groovy/nextflow/lsp/compiler/RelatedInformationAware.java rename to src/main/java/nextflow/lsp/compiler/RelatedInformationAware.java diff --git a/src/main/groovy/nextflow/lsp/compiler/StringReaderSourceWithURI.java b/src/main/java/nextflow/lsp/compiler/StringReaderSourceWithURI.java similarity index 100% rename from src/main/groovy/nextflow/lsp/compiler/StringReaderSourceWithURI.java rename to src/main/java/nextflow/lsp/compiler/StringReaderSourceWithURI.java diff --git a/src/main/groovy/nextflow/lsp/file/FileCache.java b/src/main/java/nextflow/lsp/file/FileCache.java similarity index 100% rename from src/main/groovy/nextflow/lsp/file/FileCache.java rename to src/main/java/nextflow/lsp/file/FileCache.java diff --git a/src/main/groovy/nextflow/lsp/file/PathUtils.java b/src/main/java/nextflow/lsp/file/PathUtils.java similarity index 100% rename from src/main/groovy/nextflow/lsp/file/PathUtils.java rename to src/main/java/nextflow/lsp/file/PathUtils.java diff --git a/src/main/groovy/nextflow/lsp/services/CallHierarchyProvider.java b/src/main/java/nextflow/lsp/services/CallHierarchyProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/CallHierarchyProvider.java rename to src/main/java/nextflow/lsp/services/CallHierarchyProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/CodeLensProvider.java b/src/main/java/nextflow/lsp/services/CodeLensProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/CodeLensProvider.java rename to src/main/java/nextflow/lsp/services/CodeLensProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/CompletionProvider.java b/src/main/java/nextflow/lsp/services/CompletionProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/CompletionProvider.java rename to src/main/java/nextflow/lsp/services/CompletionProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/DefinitionProvider.java b/src/main/java/nextflow/lsp/services/DefinitionProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/DefinitionProvider.java rename to src/main/java/nextflow/lsp/services/DefinitionProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/FormattingProvider.java b/src/main/java/nextflow/lsp/services/FormattingProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/FormattingProvider.java rename to src/main/java/nextflow/lsp/services/FormattingProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/HoverProvider.java b/src/main/java/nextflow/lsp/services/HoverProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/HoverProvider.java rename to src/main/java/nextflow/lsp/services/HoverProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/LanguageService.java b/src/main/java/nextflow/lsp/services/LanguageService.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/LanguageService.java rename to src/main/java/nextflow/lsp/services/LanguageService.java diff --git a/src/main/groovy/nextflow/lsp/services/LinkProvider.java b/src/main/java/nextflow/lsp/services/LinkProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/LinkProvider.java rename to src/main/java/nextflow/lsp/services/LinkProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/ReferenceProvider.java b/src/main/java/nextflow/lsp/services/ReferenceProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/ReferenceProvider.java rename to src/main/java/nextflow/lsp/services/ReferenceProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/RenameProvider.java b/src/main/java/nextflow/lsp/services/RenameProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/RenameProvider.java rename to src/main/java/nextflow/lsp/services/RenameProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/SymbolProvider.java b/src/main/java/nextflow/lsp/services/SymbolProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/SymbolProvider.java rename to src/main/java/nextflow/lsp/services/SymbolProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/config/ConfigAstCache.java b/src/main/java/nextflow/lsp/services/config/ConfigAstCache.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/config/ConfigAstCache.java rename to src/main/java/nextflow/lsp/services/config/ConfigAstCache.java diff --git a/src/main/groovy/nextflow/lsp/services/config/ConfigCompletionProvider.java b/src/main/java/nextflow/lsp/services/config/ConfigCompletionProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/config/ConfigCompletionProvider.java rename to src/main/java/nextflow/lsp/services/config/ConfigCompletionProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/config/ConfigFormattingProvider.java b/src/main/java/nextflow/lsp/services/config/ConfigFormattingProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/config/ConfigFormattingProvider.java rename to src/main/java/nextflow/lsp/services/config/ConfigFormattingProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/config/ConfigHoverProvider.java b/src/main/java/nextflow/lsp/services/config/ConfigHoverProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/config/ConfigHoverProvider.java rename to src/main/java/nextflow/lsp/services/config/ConfigHoverProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/config/ConfigLinkProvider.java b/src/main/java/nextflow/lsp/services/config/ConfigLinkProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/config/ConfigLinkProvider.java rename to src/main/java/nextflow/lsp/services/config/ConfigLinkProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/config/ConfigSchemaVisitor.java b/src/main/java/nextflow/lsp/services/config/ConfigSchemaVisitor.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/config/ConfigSchemaVisitor.java rename to src/main/java/nextflow/lsp/services/config/ConfigSchemaVisitor.java diff --git a/src/main/groovy/nextflow/lsp/services/config/ConfigService.java b/src/main/java/nextflow/lsp/services/config/ConfigService.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/config/ConfigService.java rename to src/main/java/nextflow/lsp/services/config/ConfigService.java diff --git a/src/main/groovy/nextflow/lsp/services/config/ConfigToGroovyVisitor.java b/src/main/java/nextflow/lsp/services/config/ConfigToGroovyVisitor.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/config/ConfigToGroovyVisitor.java rename to src/main/java/nextflow/lsp/services/config/ConfigToGroovyVisitor.java diff --git a/src/main/groovy/nextflow/lsp/services/config/ResolveIncludeVisitor.java b/src/main/java/nextflow/lsp/services/config/ResolveIncludeVisitor.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/config/ResolveIncludeVisitor.java rename to src/main/java/nextflow/lsp/services/config/ResolveIncludeVisitor.java diff --git a/src/main/groovy/nextflow/lsp/services/script/MethodCallVisitor.java b/src/main/java/nextflow/lsp/services/script/MethodCallVisitor.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/script/MethodCallVisitor.java rename to src/main/java/nextflow/lsp/services/script/MethodCallVisitor.java diff --git a/src/main/groovy/nextflow/lsp/services/script/ResolveIncludeVisitor.java b/src/main/java/nextflow/lsp/services/script/ResolveIncludeVisitor.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/script/ResolveIncludeVisitor.java rename to src/main/java/nextflow/lsp/services/script/ResolveIncludeVisitor.java diff --git a/src/main/groovy/nextflow/lsp/services/script/ResolveVisitor.java b/src/main/java/nextflow/lsp/services/script/ResolveVisitor.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/script/ResolveVisitor.java rename to src/main/java/nextflow/lsp/services/script/ResolveVisitor.java diff --git a/src/main/groovy/nextflow/lsp/services/script/ScriptAstCache.java b/src/main/java/nextflow/lsp/services/script/ScriptAstCache.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/script/ScriptAstCache.java rename to src/main/java/nextflow/lsp/services/script/ScriptAstCache.java diff --git a/src/main/groovy/nextflow/lsp/services/script/ScriptCallHierarchyProvider.java b/src/main/java/nextflow/lsp/services/script/ScriptCallHierarchyProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/script/ScriptCallHierarchyProvider.java rename to src/main/java/nextflow/lsp/services/script/ScriptCallHierarchyProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/script/ScriptCodeLensProvider.java b/src/main/java/nextflow/lsp/services/script/ScriptCodeLensProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/script/ScriptCodeLensProvider.java rename to src/main/java/nextflow/lsp/services/script/ScriptCodeLensProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/script/ScriptCompletionProvider.java b/src/main/java/nextflow/lsp/services/script/ScriptCompletionProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/script/ScriptCompletionProvider.java rename to src/main/java/nextflow/lsp/services/script/ScriptCompletionProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/script/ScriptDefinitionProvider.java b/src/main/java/nextflow/lsp/services/script/ScriptDefinitionProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/script/ScriptDefinitionProvider.java rename to src/main/java/nextflow/lsp/services/script/ScriptDefinitionProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/script/ScriptFormattingProvider.java b/src/main/java/nextflow/lsp/services/script/ScriptFormattingProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/script/ScriptFormattingProvider.java rename to src/main/java/nextflow/lsp/services/script/ScriptFormattingProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/script/ScriptHoverProvider.java b/src/main/java/nextflow/lsp/services/script/ScriptHoverProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/script/ScriptHoverProvider.java rename to src/main/java/nextflow/lsp/services/script/ScriptHoverProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/script/ScriptLinkProvider.java b/src/main/java/nextflow/lsp/services/script/ScriptLinkProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/script/ScriptLinkProvider.java rename to src/main/java/nextflow/lsp/services/script/ScriptLinkProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/script/ScriptReferenceProvider.java b/src/main/java/nextflow/lsp/services/script/ScriptReferenceProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/script/ScriptReferenceProvider.java rename to src/main/java/nextflow/lsp/services/script/ScriptReferenceProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/script/ScriptService.java b/src/main/java/nextflow/lsp/services/script/ScriptService.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/script/ScriptService.java rename to src/main/java/nextflow/lsp/services/script/ScriptService.java diff --git a/src/main/groovy/nextflow/lsp/services/script/ScriptSymbolProvider.java b/src/main/java/nextflow/lsp/services/script/ScriptSymbolProvider.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/script/ScriptSymbolProvider.java rename to src/main/java/nextflow/lsp/services/script/ScriptSymbolProvider.java diff --git a/src/main/groovy/nextflow/lsp/services/script/ScriptToGroovyVisitor.java b/src/main/java/nextflow/lsp/services/script/ScriptToGroovyVisitor.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/script/ScriptToGroovyVisitor.java rename to src/main/java/nextflow/lsp/services/script/ScriptToGroovyVisitor.java diff --git a/src/main/groovy/nextflow/lsp/services/script/VariableScopeVisitor.java b/src/main/java/nextflow/lsp/services/script/VariableScopeVisitor.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/script/VariableScopeVisitor.java rename to src/main/java/nextflow/lsp/services/script/VariableScopeVisitor.java diff --git a/src/main/groovy/nextflow/lsp/services/script/dag/DataflowVisitor.java b/src/main/java/nextflow/lsp/services/script/dag/DataflowVisitor.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/script/dag/DataflowVisitor.java rename to src/main/java/nextflow/lsp/services/script/dag/DataflowVisitor.java diff --git a/src/main/groovy/nextflow/lsp/services/script/dag/MermaidRenderer.java b/src/main/java/nextflow/lsp/services/script/dag/MermaidRenderer.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/script/dag/MermaidRenderer.java rename to src/main/java/nextflow/lsp/services/script/dag/MermaidRenderer.java diff --git a/src/main/groovy/nextflow/lsp/services/util/Formatter.java b/src/main/java/nextflow/lsp/services/util/Formatter.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/util/Formatter.java rename to src/main/java/nextflow/lsp/services/util/Formatter.java diff --git a/src/main/groovy/nextflow/lsp/services/util/FormattingOptions.java b/src/main/java/nextflow/lsp/services/util/FormattingOptions.java similarity index 100% rename from src/main/groovy/nextflow/lsp/services/util/FormattingOptions.java rename to src/main/java/nextflow/lsp/services/util/FormattingOptions.java diff --git a/src/main/groovy/nextflow/lsp/util/DebouncingExecutor.java b/src/main/java/nextflow/lsp/util/DebouncingExecutor.java similarity index 100% rename from src/main/groovy/nextflow/lsp/util/DebouncingExecutor.java rename to src/main/java/nextflow/lsp/util/DebouncingExecutor.java diff --git a/src/main/groovy/nextflow/lsp/util/LanguageServerUtils.java b/src/main/java/nextflow/lsp/util/LanguageServerUtils.java similarity index 100% rename from src/main/groovy/nextflow/lsp/util/LanguageServerUtils.java rename to src/main/java/nextflow/lsp/util/LanguageServerUtils.java diff --git a/src/main/groovy/nextflow/lsp/util/Logger.java b/src/main/java/nextflow/lsp/util/Logger.java similarity index 100% rename from src/main/groovy/nextflow/lsp/util/Logger.java rename to src/main/java/nextflow/lsp/util/Logger.java diff --git a/src/main/groovy/nextflow/lsp/util/Positions.java b/src/main/java/nextflow/lsp/util/Positions.java similarity index 100% rename from src/main/groovy/nextflow/lsp/util/Positions.java rename to src/main/java/nextflow/lsp/util/Positions.java diff --git a/src/main/groovy/nextflow/script/dsl/Constant.java b/src/main/java/nextflow/script/dsl/Constant.java similarity index 100% rename from src/main/groovy/nextflow/script/dsl/Constant.java rename to src/main/java/nextflow/script/dsl/Constant.java diff --git a/src/main/groovy/nextflow/script/dsl/Description.java b/src/main/java/nextflow/script/dsl/Description.java similarity index 100% rename from src/main/groovy/nextflow/script/dsl/Description.java rename to src/main/java/nextflow/script/dsl/Description.java diff --git a/src/main/groovy/nextflow/script/dsl/DslScope.java b/src/main/java/nextflow/script/dsl/DslScope.java similarity index 100% rename from src/main/groovy/nextflow/script/dsl/DslScope.java rename to src/main/java/nextflow/script/dsl/DslScope.java diff --git a/src/main/groovy/nextflow/script/dsl/EntryWorkflowDsl.java b/src/main/java/nextflow/script/dsl/EntryWorkflowDsl.java similarity index 100% rename from src/main/groovy/nextflow/script/dsl/EntryWorkflowDsl.java rename to src/main/java/nextflow/script/dsl/EntryWorkflowDsl.java diff --git a/src/main/groovy/nextflow/script/dsl/FeatureFlag.java b/src/main/java/nextflow/script/dsl/FeatureFlag.java similarity index 100% rename from src/main/groovy/nextflow/script/dsl/FeatureFlag.java rename to src/main/java/nextflow/script/dsl/FeatureFlag.java diff --git a/src/main/groovy/nextflow/script/dsl/FeatureFlagDsl.java b/src/main/java/nextflow/script/dsl/FeatureFlagDsl.java similarity index 100% rename from src/main/groovy/nextflow/script/dsl/FeatureFlagDsl.java rename to src/main/java/nextflow/script/dsl/FeatureFlagDsl.java diff --git a/src/main/groovy/nextflow/script/dsl/Operator.java b/src/main/java/nextflow/script/dsl/Operator.java similarity index 100% rename from src/main/groovy/nextflow/script/dsl/Operator.java rename to src/main/java/nextflow/script/dsl/Operator.java diff --git a/src/main/groovy/nextflow/script/dsl/OutputDsl.java b/src/main/java/nextflow/script/dsl/OutputDsl.java similarity index 100% rename from src/main/groovy/nextflow/script/dsl/OutputDsl.java rename to src/main/java/nextflow/script/dsl/OutputDsl.java diff --git a/src/main/groovy/nextflow/script/dsl/ProcessDsl.java b/src/main/java/nextflow/script/dsl/ProcessDsl.java similarity index 100% rename from src/main/groovy/nextflow/script/dsl/ProcessDsl.java rename to src/main/java/nextflow/script/dsl/ProcessDsl.java diff --git a/src/main/groovy/nextflow/script/dsl/ScriptDsl.java b/src/main/java/nextflow/script/dsl/ScriptDsl.java similarity index 100% rename from src/main/groovy/nextflow/script/dsl/ScriptDsl.java rename to src/main/java/nextflow/script/dsl/ScriptDsl.java diff --git a/src/main/groovy/nextflow/script/dsl/WorkflowDsl.java b/src/main/java/nextflow/script/dsl/WorkflowDsl.java similarity index 100% rename from src/main/groovy/nextflow/script/dsl/WorkflowDsl.java rename to src/main/java/nextflow/script/dsl/WorkflowDsl.java diff --git a/src/main/groovy/nextflow/script/types/Channel.java b/src/main/java/nextflow/script/types/Channel.java similarity index 100% rename from src/main/groovy/nextflow/script/types/Channel.java rename to src/main/java/nextflow/script/types/Channel.java diff --git a/src/main/groovy/nextflow/script/types/ChannelFactory.java b/src/main/java/nextflow/script/types/ChannelFactory.java similarity index 100% rename from src/main/groovy/nextflow/script/types/ChannelFactory.java rename to src/main/java/nextflow/script/types/ChannelFactory.java diff --git a/src/main/groovy/nextflow/script/types/Duration.java b/src/main/java/nextflow/script/types/Duration.java similarity index 100% rename from src/main/groovy/nextflow/script/types/Duration.java rename to src/main/java/nextflow/script/types/Duration.java diff --git a/src/main/groovy/nextflow/script/types/Manifest.java b/src/main/java/nextflow/script/types/Manifest.java similarity index 100% rename from src/main/groovy/nextflow/script/types/Manifest.java rename to src/main/java/nextflow/script/types/Manifest.java diff --git a/src/main/groovy/nextflow/script/types/MemoryUnit.java b/src/main/java/nextflow/script/types/MemoryUnit.java similarity index 100% rename from src/main/groovy/nextflow/script/types/MemoryUnit.java rename to src/main/java/nextflow/script/types/MemoryUnit.java diff --git a/src/main/groovy/nextflow/script/types/NextflowMetadata.java b/src/main/java/nextflow/script/types/NextflowMetadata.java similarity index 100% rename from src/main/groovy/nextflow/script/types/NextflowMetadata.java rename to src/main/java/nextflow/script/types/NextflowMetadata.java diff --git a/src/main/groovy/nextflow/script/types/ParamsMap.java b/src/main/java/nextflow/script/types/ParamsMap.java similarity index 100% rename from src/main/groovy/nextflow/script/types/ParamsMap.java rename to src/main/java/nextflow/script/types/ParamsMap.java diff --git a/src/main/groovy/nextflow/script/types/TaskConfig.java b/src/main/java/nextflow/script/types/TaskConfig.java similarity index 100% rename from src/main/groovy/nextflow/script/types/TaskConfig.java rename to src/main/java/nextflow/script/types/TaskConfig.java diff --git a/src/main/groovy/nextflow/script/types/Types.java b/src/main/java/nextflow/script/types/Types.java similarity index 100% rename from src/main/groovy/nextflow/script/types/Types.java rename to src/main/java/nextflow/script/types/Types.java diff --git a/src/main/groovy/nextflow/script/types/VersionNumber.java b/src/main/java/nextflow/script/types/VersionNumber.java similarity index 100% rename from src/main/groovy/nextflow/script/types/VersionNumber.java rename to src/main/java/nextflow/script/types/VersionNumber.java diff --git a/src/main/groovy/nextflow/script/types/WorkflowMetadata.java b/src/main/java/nextflow/script/types/WorkflowMetadata.java similarity index 100% rename from src/main/groovy/nextflow/script/types/WorkflowMetadata.java rename to src/main/java/nextflow/script/types/WorkflowMetadata.java diff --git a/src/main/groovy/nextflow/script/v2/ASTHelpers.java b/src/main/java/nextflow/script/v2/ASTHelpers.java similarity index 100% rename from src/main/groovy/nextflow/script/v2/ASTHelpers.java rename to src/main/java/nextflow/script/v2/ASTHelpers.java diff --git a/src/main/groovy/nextflow/script/v2/AssignmentExpression.java b/src/main/java/nextflow/script/v2/AssignmentExpression.java similarity index 100% rename from src/main/groovy/nextflow/script/v2/AssignmentExpression.java rename to src/main/java/nextflow/script/v2/AssignmentExpression.java diff --git a/src/main/groovy/nextflow/script/v2/FeatureFlagNode.java b/src/main/java/nextflow/script/v2/FeatureFlagNode.java similarity index 100% rename from src/main/groovy/nextflow/script/v2/FeatureFlagNode.java rename to src/main/java/nextflow/script/v2/FeatureFlagNode.java diff --git a/src/main/groovy/nextflow/script/v2/FunctionNode.java b/src/main/java/nextflow/script/v2/FunctionNode.java similarity index 100% rename from src/main/groovy/nextflow/script/v2/FunctionNode.java rename to src/main/java/nextflow/script/v2/FunctionNode.java diff --git a/src/main/groovy/nextflow/script/v2/GroovydocManager.java b/src/main/java/nextflow/script/v2/GroovydocManager.java similarity index 100% rename from src/main/groovy/nextflow/script/v2/GroovydocManager.java rename to src/main/java/nextflow/script/v2/GroovydocManager.java diff --git a/src/main/groovy/nextflow/script/v2/IncludeNode.java b/src/main/java/nextflow/script/v2/IncludeNode.java similarity index 100% rename from src/main/groovy/nextflow/script/v2/IncludeNode.java rename to src/main/java/nextflow/script/v2/IncludeNode.java diff --git a/src/main/groovy/nextflow/script/v2/IncludeVariable.java b/src/main/java/nextflow/script/v2/IncludeVariable.java similarity index 100% rename from src/main/groovy/nextflow/script/v2/IncludeVariable.java rename to src/main/java/nextflow/script/v2/IncludeVariable.java diff --git a/src/main/groovy/nextflow/script/v2/IncompleteNode.java b/src/main/java/nextflow/script/v2/IncompleteNode.java similarity index 100% rename from src/main/groovy/nextflow/script/v2/IncompleteNode.java rename to src/main/java/nextflow/script/v2/IncompleteNode.java diff --git a/src/main/groovy/nextflow/script/v2/InvalidDeclaration.java b/src/main/java/nextflow/script/v2/InvalidDeclaration.java similarity index 100% rename from src/main/groovy/nextflow/script/v2/InvalidDeclaration.java rename to src/main/java/nextflow/script/v2/InvalidDeclaration.java diff --git a/src/main/groovy/nextflow/script/v2/OutputNode.java b/src/main/java/nextflow/script/v2/OutputNode.java similarity index 100% rename from src/main/groovy/nextflow/script/v2/OutputNode.java rename to src/main/java/nextflow/script/v2/OutputNode.java diff --git a/src/main/groovy/nextflow/script/v2/ParamNode.java b/src/main/java/nextflow/script/v2/ParamNode.java similarity index 100% rename from src/main/groovy/nextflow/script/v2/ParamNode.java rename to src/main/java/nextflow/script/v2/ParamNode.java diff --git a/src/main/groovy/nextflow/script/v2/ProcessNode.java b/src/main/java/nextflow/script/v2/ProcessNode.java similarity index 100% rename from src/main/groovy/nextflow/script/v2/ProcessNode.java rename to src/main/java/nextflow/script/v2/ProcessNode.java diff --git a/src/main/groovy/nextflow/script/v2/ScriptAstBuilder.java b/src/main/java/nextflow/script/v2/ScriptAstBuilder.java similarity index 100% rename from src/main/groovy/nextflow/script/v2/ScriptAstBuilder.java rename to src/main/java/nextflow/script/v2/ScriptAstBuilder.java diff --git a/src/main/groovy/nextflow/script/v2/ScriptExpressionTransformer.java b/src/main/java/nextflow/script/v2/ScriptExpressionTransformer.java similarity index 100% rename from src/main/groovy/nextflow/script/v2/ScriptExpressionTransformer.java rename to src/main/java/nextflow/script/v2/ScriptExpressionTransformer.java diff --git a/src/main/groovy/nextflow/script/v2/ScriptNode.java b/src/main/java/nextflow/script/v2/ScriptNode.java similarity index 100% rename from src/main/groovy/nextflow/script/v2/ScriptNode.java rename to src/main/java/nextflow/script/v2/ScriptNode.java diff --git a/src/main/groovy/nextflow/script/v2/ScriptParserPlugin.java b/src/main/java/nextflow/script/v2/ScriptParserPlugin.java similarity index 100% rename from src/main/groovy/nextflow/script/v2/ScriptParserPlugin.java rename to src/main/java/nextflow/script/v2/ScriptParserPlugin.java diff --git a/src/main/groovy/nextflow/script/v2/ScriptParserPluginFactory.java b/src/main/java/nextflow/script/v2/ScriptParserPluginFactory.java similarity index 100% rename from src/main/groovy/nextflow/script/v2/ScriptParserPluginFactory.java rename to src/main/java/nextflow/script/v2/ScriptParserPluginFactory.java diff --git a/src/main/groovy/nextflow/script/v2/ScriptVisitor.java b/src/main/java/nextflow/script/v2/ScriptVisitor.java similarity index 100% rename from src/main/groovy/nextflow/script/v2/ScriptVisitor.java rename to src/main/java/nextflow/script/v2/ScriptVisitor.java diff --git a/src/main/groovy/nextflow/script/v2/ScriptVisitorSupport.java b/src/main/java/nextflow/script/v2/ScriptVisitorSupport.java similarity index 100% rename from src/main/groovy/nextflow/script/v2/ScriptVisitorSupport.java rename to src/main/java/nextflow/script/v2/ScriptVisitorSupport.java diff --git a/src/main/groovy/nextflow/script/v2/WorkflowNode.java b/src/main/java/nextflow/script/v2/WorkflowNode.java similarity index 100% rename from src/main/groovy/nextflow/script/v2/WorkflowNode.java rename to src/main/java/nextflow/script/v2/WorkflowNode.java