From e3089f0e617e5808bacbaafa8e8bdc39c1534d5b Mon Sep 17 00:00:00 2001 From: Paolo Di Tommaso Date: Sat, 10 Feb 2024 18:20:00 +0100 Subject: [PATCH] Update copyright info Signed-off-by: Paolo Di Tommaso --- Makefile | 2 +- NOTICE | 4 ++-- build.gradle | 2 +- .../groovy/io/nextflow/gradle/tasks/GithubUploader.groovy | 2 +- config/codenarc/codenarc.groovy | 2 +- config/codenarc/codenarc.xml | 2 +- docker/Makefile | 2 +- docker/entry.sh | 2 +- launch.sh | 2 +- modules/nextflow/src/main/groovy/nextflow/Channel.groovy | 2 +- modules/nextflow/src/main/groovy/nextflow/NF.groovy | 2 +- modules/nextflow/src/main/groovy/nextflow/Nextflow.groovy | 2 +- modules/nextflow/src/main/groovy/nextflow/Session.groovy | 2 +- .../nextflow/src/main/groovy/nextflow/ast/ASTHelpers.groovy | 2 +- .../src/main/groovy/nextflow/ast/GStringToLazyVisitor.groovy | 2 +- .../nextflow/src/main/groovy/nextflow/ast/LangHelpers.java | 2 +- .../nextflow/src/main/groovy/nextflow/ast/NextflowDSL.groovy | 2 +- 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| 2 +- .../main/groovy/nextflow/splitter/AbstractTextSplitter.groovy | 2 +- .../src/main/groovy/nextflow/splitter/BytesSplitter.groovy | 2 +- .../main/groovy/nextflow/splitter/CacheableCollector.groovy | 2 +- .../groovy/nextflow/splitter/CharSequenceCollector.groovy | 2 +- .../main/groovy/nextflow/splitter/CollectorStrategy.groovy | 2 +- .../src/main/groovy/nextflow/splitter/CsvSplitter.groovy | 2 +- .../src/main/groovy/nextflow/splitter/EntryCounter.groovy | 2 +- .../src/main/groovy/nextflow/splitter/FastaSplitter.groovy | 2 +- .../src/main/groovy/nextflow/splitter/FastqSplitter.groovy | 2 +- .../src/main/groovy/nextflow/splitter/HeaderCollector.groovy | 2 +- .../src/main/groovy/nextflow/splitter/JsonSplitter.groovy | 2 +- .../main/groovy/nextflow/splitter/ObjectListCollector.groovy | 2 +- .../src/main/groovy/nextflow/splitter/SplitterEx.groovy | 2 +- .../src/main/groovy/nextflow/splitter/SplitterFactory.groovy | 2 +- .../src/main/groovy/nextflow/splitter/SplitterStrategy.groovy | 2 +- .../src/main/groovy/nextflow/splitter/StringSplitter.groovy | 2 +- .../main/groovy/nextflow/splitter/TextFileCollector.groovy | 2 +- .../src/main/groovy/nextflow/splitter/TextSplitter.groovy | 2 +- .../src/main/groovy/nextflow/trace/AnsiLogObserver.groovy | 2 +- .../src/main/groovy/nextflow/trace/GraphObserver.groovy | 2 +- .../src/main/groovy/nextflow/trace/ProgressRecord.groovy | 2 +- .../src/main/groovy/nextflow/trace/ProgressState.groovy | 2 +- .../src/main/groovy/nextflow/trace/ReportObserver.groovy | 2 +- .../src/main/groovy/nextflow/trace/ReportSummary.groovy | 2 +- .../src/main/groovy/nextflow/trace/TimelineObserver.groovy | 2 +- .../src/main/groovy/nextflow/trace/TraceFileObserver.groovy | 2 +- .../src/main/groovy/nextflow/trace/TraceHelper.groovy | 2 +- .../src/main/groovy/nextflow/trace/TraceObserver.groovy | 2 +- .../src/main/groovy/nextflow/trace/TraceRecord.groovy | 2 +- .../src/main/groovy/nextflow/trace/WorkflowStats.groovy | 2 +- .../main/groovy/nextflow/trace/WorkflowStatsObserver.groovy | 2 +- .../nextflow/src/main/groovy/nextflow/util/ArrayBag.groovy | 2 +- modules/nextflow/src/main/groovy/nextflow/util/Barrier.groovy | 2 +- .../src/main/groovy/nextflow/util/BlankSeparatedList.groovy | 2 +- .../main/groovy/nextflow/util/BlockingBlockingQueue.groovy | 2 +- .../groovy/nextflow/util/BlockingThreadExecutorFactory.groovy | 2 +- .../src/main/groovy/nextflow/util/ClientProxyThrottler.groovy | 2 +- .../src/main/groovy/nextflow/util/ClusterConfig.groovy | 2 +- .../src/main/groovy/nextflow/util/ConfigHelper.groovy | 2 +- .../src/main/groovy/nextflow/util/CustomPoolFactory.groovy | 2 +- .../src/main/groovy/nextflow/util/CustomThreadFactory.groovy | 2 +- .../src/main/groovy/nextflow/util/CustomThreadPool.java | 2 +- .../nextflow/src/main/groovy/nextflow/util/HexIdentity.groovy | 2 +- .../nextflow/src/main/groovy/nextflow/util/HistoryFile.groovy | 2 +- .../nextflow/src/main/groovy/nextflow/util/LockManager.groovy | 2 +- .../src/main/groovy/nextflow/util/LoggerHelper.groovy | 2 +- .../main/groovy/nextflow/util/MustacheTemplateEngine.groovy | 2 +- .../src/main/groovy/nextflow/util/NameGenerator.groovy | 2 +- .../src/main/groovy/nextflow/util/PathEscapeAware.groovy | 2 +- .../src/main/groovy/nextflow/util/PathSplitter.groovy | 2 +- .../nextflow/src/main/groovy/nextflow/util/PathTrie.groovy | 2 +- .../nextflow/src/main/groovy/nextflow/util/ProxyConfig.groovy | 2 +- .../src/main/groovy/nextflow/util/RemoteSession.groovy | 2 +- .../src/main/groovy/nextflow/util/SerializationHelper.groovy | 2 +- .../nextflow/src/main/groovy/nextflow/util/ServiceName.groovy | 2 +- .../nextflow/src/main/groovy/nextflow/util/SimpleAgent.groovy | 2 +- .../src/main/groovy/nextflow/util/SimpleHttpClient.groovy | 2 +- .../src/main/groovy/nextflow/util/SpuriousDeps.groovy | 2 +- .../src/main/groovy/nextflow/util/ThreadPoolBuilder.groovy | 2 +- .../src/main/groovy/nextflow/util/ThreadPoolHelper.groovy | 2 +- .../src/main/groovy/nextflow/util/ThreadPoolManager.groovy | 2 +- .../src/main/groovy/nextflow/util/ThrottlingExecutor.groovy | 2 +- modules/nextflow/src/main/groovy/nextflow/util/Trie.groovy | 2 +- .../nextflow/src/main/groovy/nextflow/util/TupleHelper.groovy | 2 +- .../src/main/groovy/nextflow/util/VirtualThreadPool.groovy | 2 +- .../src/main/java/com/esotericsoftware/minlog/Log.java | 2 +- .../runtime/metaclass/CustomMetaClassCreationHandle.java | 2 +- .../main/java/groovy/runtime/metaclass/ExtensionProvider.java | 2 +- .../groovy/runtime/metaclass/NextflowDelegatingMetaClass.java | 2 +- .../groovy/runtime/metaclass/NumberDelegatingMetaClass.java | 2 +- modules/nextflow/src/main/resources/META-INF/extensions.idx | 2 +- .../services/org.codehaus.groovy.runtime.ExtensionModule | 2 +- .../src/main/resources/nextflow/dag/mermaid.dag.template.html | 2 +- .../src/main/resources/nextflow/executor/command-run.txt | 2 +- .../src/main/resources/nextflow/executor/command-trace.txt | 2 +- .../src/main/resources/nextflow/executor/modules-env.txt | 2 +- .../src/main/resources/nextflow/mail/notification.html | 2 +- .../src/main/resources/nextflow/trace/ReportTemplate.html | 2 +- .../src/main/resources/nextflow/trace/TimelineTemplate.html | 2 +- modules/nextflow/src/test/groovy/FunctionalTests.groovy | 2 +- .../runtime/metaclass/NextflowDelegatingMetaClassTest.groovy | 2 +- .../runtime/metaclass/NumberDelegatingMetaClassTest.groovy | 2 +- modules/nextflow/src/test/groovy/misc/ScriptEnv.groovy | 2 +- .../src/test/groovy/misc/ScriptNoInputNoOutput.groovy | 2 +- .../nextflow/src/test/groovy/misc/ScriptProcessorTest.groovy | 2 +- modules/nextflow/src/test/groovy/nextflow/ChannelTest.groovy | 2 +- modules/nextflow/src/test/groovy/nextflow/NextflowTest.groovy | 2 +- modules/nextflow/src/test/groovy/nextflow/SessionTest.groovy | 2 +- .../src/test/groovy/nextflow/ast/NextflowXformImplTest.groovy | 2 +- .../nextflow/src/test/groovy/nextflow/ast/OpXformTest.groovy | 2 +- .../test/groovy/nextflow/ast/TaskCmdXformVisitorTest.groovy | 2 +- .../src/test/groovy/nextflow/cache/CacheDBTest.groovy | 2 +- .../test/groovy/nextflow/cache/DefaultCacheStoreTest.groovy | 2 +- .../nextflow/src/test/groovy/nextflow/cli/CmdCleanTest.groovy | 2 +- .../nextflow/src/test/groovy/nextflow/cli/CmdCloneTest.groovy | 2 +- .../src/test/groovy/nextflow/cli/CmdConfigTest.groovy | 2 +- .../src/test/groovy/nextflow/cli/CmdHelperTest.groovy | 2 +- .../nextflow/src/test/groovy/nextflow/cli/CmdInfoTest.groovy | 2 +- .../src/test/groovy/nextflow/cli/CmdInspectTest.groovy | 2 +- .../nextflow/src/test/groovy/nextflow/cli/CmdLogTest.groovy | 2 +- .../nextflow/src/test/groovy/nextflow/cli/CmdPullTest.groovy | 2 +- .../nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy | 2 +- .../src/test/groovy/nextflow/cli/CmdSecretTest.groovy | 2 +- .../nextflow/src/test/groovy/nextflow/cli/LauncherTest.groovy | 2 +- .../src/test/groovy/nextflow/conda/CondaCacheTest.groovy | 2 +- .../src/test/groovy/nextflow/conda/CondaConfigTest.groovy | 2 +- .../test/groovy/nextflow/config/CascadingConfigTest.groovy | 2 +- .../src/test/groovy/nextflow/config/ConfigBuilderTest.groovy | 2 +- .../src/test/groovy/nextflow/config/ConfigParserTest.groovy | 2 +- .../src/test/groovy/nextflow/config/ManifestTest.groovy | 2 +- .../groovy/nextflow/container/ApptainerBuilderTest.groovy | 2 +- .../test/groovy/nextflow/container/ApptainerCacheTest.groovy | 2 +- .../groovy/nextflow/container/CharliecloudBuilderTest.groovy | 2 +- .../groovy/nextflow/container/CharliecloudCacheTest.groovy | 2 +- .../groovy/nextflow/container/ContainerBuilderTest.groovy | 2 +- .../test/groovy/nextflow/container/ContainerConfigTest.groovy | 2 +- .../groovy/nextflow/container/ContainerHandlerTest.groovy | 2 +- .../nextflow/container/ContainerNameValidatorTest.groovy | 2 +- .../test/groovy/nextflow/container/DockerBuilderTest.groovy | 2 +- .../test/groovy/nextflow/container/PodmanBuilderTest.groovy | 2 +- .../test/groovy/nextflow/container/ShifterBuilderTest.groovy | 2 +- .../groovy/nextflow/container/SingularityBuilderTest.groovy | 2 +- .../groovy/nextflow/container/SingularityCacheTest.groovy | 2 +- .../test/groovy/nextflow/container/UdockerBuilderTest.groovy | 2 +- .../nextflow/container/inspect/ContainersInspectorTest.groovy | 2 +- .../nextflow/container/resolver/ContainerInfoTest.groovy | 2 +- .../container/resolver/DefaultContainerResolverTest.groovy | 2 +- modules/nextflow/src/test/groovy/nextflow/dag/DAGTest.groovy | 2 +- .../src/test/groovy/nextflow/dag/DotRendererTest.groovy | 2 +- .../src/test/groovy/nextflow/dag/MermaidRendererTest.groovy | 2 +- .../nextflow/dag/MultipleInputChannelExceptionTest.groovy | 2 +- .../nextflow/dag/MultipleOutputChannelExceptionTest.groovy | 2 +- .../test/groovy/nextflow/datasource/SraExplorerTest.groovy | 2 +- .../groovy/nextflow/executor/AbstractGridExecutorTest.groovy | 2 +- .../groovy/nextflow/executor/BashTemplateEngineTest.groovy | 2 +- .../groovy/nextflow/executor/BashWrapperBuilderTest.groovy | 2 +- .../src/test/groovy/nextflow/executor/BatchCleanupTest.groovy | 2 +- .../test/groovy/nextflow/executor/BridgeExecutorTest.groovy | 2 +- .../test/groovy/nextflow/executor/CondorExecutorTest.groovy | 2 +- .../src/test/groovy/nextflow/executor/CrgExecutorTest.groovy | 2 +- .../src/test/groovy/nextflow/executor/FluxExecutorTest.groovy | 2 +- .../src/test/groovy/nextflow/executor/GridExecutorTest.groovy | 2 +- .../test/groovy/nextflow/executor/GridTaskHandlerTest.groovy | 2 +- .../groovy/nextflow/executor/HyperQueueExecutorTest.groovy | 2 +- .../src/test/groovy/nextflow/executor/LsfExecutorTest.groovy | 2 +- .../src/test/groovy/nextflow/executor/MoabExecutorTest.groovy | 2 +- .../test/groovy/nextflow/executor/NqsiiExecutorTest.groovy | 2 +- .../src/test/groovy/nextflow/executor/PbsExecutorTest.groovy | 2 +- .../test/groovy/nextflow/executor/PbsProExecutorTest.groovy | 2 +- .../src/test/groovy/nextflow/executor/SgeExecutorTest.groovy | 2 +- .../nextflow/executor/SimpleFileCopyStrategyTest.groovy | 2 +- .../test/groovy/nextflow/executor/SlurmExecutorTest.groovy | 2 +- .../groovy/nextflow/executor/fusion/FusionHelperTest.groovy | 2 +- .../nextflow/executor/fusion/FusionScriptLauncherTest.groovy | 2 +- .../nextflow/executor/local/LocalTaskHandlerTest.groovy | 2 +- .../nextflow/executor/res/AcceleratorResourceTest.groovy | 2 +- .../test/groovy/nextflow/executor/res/DiskResourceTest.groovy | 4 ++-- .../src/test/groovy/nextflow/extension/BranchOpTest.groovy | 2 +- .../src/test/groovy/nextflow/extension/BufferOpTest.groovy | 2 +- .../groovy/nextflow/extension/CapturePropertiesTest.groovy | 2 +- .../groovy/nextflow/extension/CollectFileOperatorTest.groovy | 2 +- .../src/test/groovy/nextflow/extension/CollectOpTest.groovy | 2 +- .../src/test/groovy/nextflow/extension/CombineOpTest.groovy | 2 +- .../src/test/groovy/nextflow/extension/ConcatOpTest.groovy | 2 +- .../test/groovy/nextflow/extension/CountFastaOpTest.groovy | 2 +- .../test/groovy/nextflow/extension/CountFastqOpTest.groovy | 2 +- .../test/groovy/nextflow/extension/CountLinesOpTest.groovy | 2 +- .../test/groovy/nextflow/extension/DataflowHelperTest.groovy | 2 +- .../nextflow/extension/DataflowMathExtensionTest.groovy | 2 +- .../nextflow/extension/DataflowMergeExtensionTest.groovy | 2 +- .../groovy/nextflow/extension/DataflowTapExtensionTest.groovy | 2 +- .../src/test/groovy/nextflow/extension/DumpOpTest.groovy | 2 +- .../src/test/groovy/nextflow/extension/GroupKeyTest.groovy | 2 +- .../test/groovy/nextflow/extension/GroupTupleOpTest.groovy | 2 +- .../src/test/groovy/nextflow/extension/JoinOpTest.groovy | 2 +- .../src/test/groovy/nextflow/extension/LoggerTest.groovy | 2 +- .../src/test/groovy/nextflow/extension/MixOpTest.groovy | 2 +- .../src/test/groovy/nextflow/extension/MultiMapOpTest.groovy | 2 +- .../test/groovy/nextflow/extension/OperatorImplTest.groovy | 2 +- .../src/test/groovy/nextflow/extension/PhaseOpTest.groovy | 2 +- .../src/test/groovy/nextflow/extension/PublishOpTest.groovy | 2 +- .../test/groovy/nextflow/extension/RandomSampleTest.groovy | 2 +- .../src/test/groovy/nextflow/extension/SetOpTest.groovy | 2 +- .../groovy/nextflow/extension/SplitFastaOperatorTest.groovy | 2 +- .../test/groovy/nextflow/extension/SplitFastqOp2Test.groovy | 2 +- .../groovy/nextflow/extension/SplitFastqOperatorTest.groovy | 2 +- .../src/test/groovy/nextflow/extension/SplitOpTest.groovy | 2 +- .../groovy/nextflow/extension/SplitterMergeClosureTest.groovy | 2 +- .../src/test/groovy/nextflow/extension/TransposeOpTest.groovy | 2 +- .../src/test/groovy/nextflow/extension/UntilManyOpTest.groovy | 2 +- .../test/groovy/nextflow/extension/ViewOperatorTest.groovy | 2 +- .../extension/plugin/ChannelFactoryInstanceTest.groovy | 2 +- .../extension/plugin/PluginExtensionProviderTest.groovy | 2 +- .../src/test/groovy/nextflow/file/DirWatcherTest.groovy | 2 +- .../src/test/groovy/nextflow/file/DirWatcherV2Test.groovy | 2 +- .../src/test/groovy/nextflow/file/FilePorterTest.groovy | 2 +- .../src/test/groovy/nextflow/file/PathVisitorTest.groovy | 2 +- .../test/groovy/nextflow/file/SequentialFileStoreTest.groovy | 2 +- .../test/groovy/nextflow/file/SimpleFileCollectorTest.groovy | 2 +- .../src/test/groovy/nextflow/file/SlurperExTest.groovy | 2 +- .../test/groovy/nextflow/file/SortFileCollectorTest.groovy | 2 +- .../src/test/groovy/nextflow/fusion/FusionConfigTest.groovy | 2 +- .../src/test/groovy/nextflow/k8s/K8sConfigTest.groovy | 2 +- .../src/test/groovy/nextflow/k8s/K8sDriverLauncherTest.groovy | 2 +- .../src/test/groovy/nextflow/k8s/K8sTaskHandlerTest.groovy | 2 +- .../src/test/groovy/nextflow/k8s/K8sWrapperBuilderTest.groovy | 2 +- .../test/groovy/nextflow/k8s/client/ClientConfigTest.groovy | 2 +- .../groovy/nextflow/k8s/client/ConfigDiscoveryTest.groovy | 2 +- .../src/test/groovy/nextflow/k8s/client/K8sClientTest.groovy | 2 +- .../nextflow/k8s/client/K8sResponseExceptionTest.groovy | 2 +- .../groovy/nextflow/k8s/client/K8sResponseJsonTest.groovy | 2 +- .../src/test/groovy/nextflow/k8s/model/PodEnvTest.groovy | 2 +- .../test/groovy/nextflow/k8s/model/PodMountConfigTest.groovy | 2 +- .../test/groovy/nextflow/k8s/model/PodMountSecretTest.groovy | 2 +- .../test/groovy/nextflow/k8s/model/PodNodeSelectorTest.groovy | 2 +- .../src/test/groovy/nextflow/k8s/model/PodOptionsTest.groovy | 2 +- .../test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy | 2 +- .../test/groovy/nextflow/k8s/model/PodVolumeClaimTest.groovy | 2 +- .../src/test/groovy/nextflow/mail/AttachmentTest.groovy | 2 +- .../nextflow/src/test/groovy/nextflow/mail/MailTest.groovy | 2 +- .../nextflow/src/test/groovy/nextflow/mail/MailerTest.groovy | 2 +- .../test/groovy/nextflow/processor/BatchContextTest.groovy | 2 +- .../test/groovy/nextflow/processor/ErrorStrategyTest.groovy | 2 +- .../groovy/nextflow/processor/LocalPollingMonitorTest.groovy | 2 +- .../nextflow/processor/ParallelPollingMonitorTest.groovy | 2 +- .../src/test/groovy/nextflow/processor/PublishDirTest.groovy | 2 +- .../src/test/groovy/nextflow/processor/TaskBeanTest.groovy | 2 +- .../src/test/groovy/nextflow/processor/TaskConfigTest.groovy | 2 +- .../src/test/groovy/nextflow/processor/TaskContextTest.groovy | 2 +- .../src/test/groovy/nextflow/processor/TaskHandlerTest.groovy | 2 +- .../src/test/groovy/nextflow/processor/TaskIdTest.groovy | 2 +- .../src/test/groovy/nextflow/processor/TaskPathTest.groovy | 2 +- .../groovy/nextflow/processor/TaskPollingMonitorTest.groovy | 2 +- .../test/groovy/nextflow/processor/TaskProcessorTest.groovy | 2 +- .../src/test/groovy/nextflow/processor/TaskRunTest.groovy | 2 +- .../groovy/nextflow/processor/TaskTemplateEngineTest.groovy | 2 +- .../src/test/groovy/nextflow/scm/AssetManagerTest.groovy | 2 +- .../groovy/nextflow/scm/AzureRepositoryProviderTest.groovy | 2 +- .../nextflow/scm/BitbucketRepositoryProviderTest.groovy | 2 +- .../nextflow/scm/BitbucketServerRepositoryProviderTest.groovy | 2 +- .../nextflow/src/test/groovy/nextflow/scm/GitUrlTest.groovy | 2 +- .../groovy/nextflow/scm/GiteaRepositoryProviderTest.groovy | 2 +- .../groovy/nextflow/scm/GithubRepositoryProviderTest.groovy | 2 +- .../groovy/nextflow/scm/GitlabRepositoryProviderTest.groovy | 2 +- .../src/test/groovy/nextflow/scm/HubOptionsTest.groovy | 2 +- .../groovy/nextflow/scm/LocalRepositoryProviderTest.groovy | 2 +- .../src/test/groovy/nextflow/scm/ProviderConfigTest.groovy | 2 +- .../src/test/groovy/nextflow/scm/ProviderPathTest.groovy | 2 +- .../test/groovy/nextflow/scm/RepositoryProviderTest.groovy | 2 +- .../src/test/groovy/nextflow/scm/UpdateModuleTest.groovy | 2 +- .../src/test/groovy/nextflow/script/BaseScriptTest.groovy | 2 +- .../src/test/groovy/nextflow/script/BodyDefTest.groovy | 2 +- .../src/test/groovy/nextflow/script/IterableDefTest.groovy | 2 +- .../src/test/groovy/nextflow/script/ProcessConfigTest.groovy | 2 +- .../src/test/groovy/nextflow/script/ScriptBindingTest.groovy | 2 +- .../src/test/groovy/nextflow/script/ScriptMetaTest.groovy | 2 +- .../src/test/groovy/nextflow/script/ScriptRecurseTest.groovy | 2 +- .../src/test/groovy/nextflow/script/ScriptRunnerTest.groovy | 2 +- .../src/test/groovy/nextflow/script/TaskClosureTest.groovy | 2 +- .../test/groovy/nextflow/script/WorkflowBindingTest.groovy | 2 +- .../test/groovy/nextflow/script/WorkflowMetadataTest.groovy | 2 +- .../test/groovy/nextflow/script/WorkflowNotifierTest.groovy | 2 +- .../groovy/nextflow/script/bundle/ResourcesBundleTest.groovy | 2 +- .../test/groovy/nextflow/script/params/EachInParamTest.groovy | 2 +- .../test/groovy/nextflow/script/params/EnvOutParamTest.groovy | 2 +- .../test/groovy/nextflow/script/params/FileInParamTest.groovy | 2 +- .../groovy/nextflow/script/params/FileOutParamTest.groovy | 2 +- .../test/groovy/nextflow/script/params/ParamsInTest.groovy | 2 +- .../test/groovy/nextflow/script/params/ParamsOutTest.groovy | 2 +- .../groovy/nextflow/script/params/TupleInParamTest.groovy | 2 +- .../groovy/nextflow/script/params/TupleOutParamTest.groovy | 2 +- .../src/test/groovy/nextflow/secret/SecretHelperTest.groovy | 2 +- .../nextflow/src/test/groovy/nextflow/sort/BigSortTest.groovy | 2 +- .../test/groovy/nextflow/splitter/AbstractSplitterTest.groovy | 2 +- .../groovy/nextflow/splitter/AbstractTextSplitterTest.groovy | 2 +- .../test/groovy/nextflow/splitter/BytesSplitterTest.groovy | 2 +- .../groovy/nextflow/splitter/CharSequenceCollectorTest.groovy | 2 +- .../src/test/groovy/nextflow/splitter/CsvSplitterTest.groovy | 2 +- .../test/groovy/nextflow/splitter/FastaSplitterTest.groovy | 2 +- .../test/groovy/nextflow/splitter/FastqSplitterTest.groovy | 2 +- .../src/test/groovy/nextflow/splitter/JsonSplitterTest.groovy | 2 +- .../groovy/nextflow/splitter/ObjectListCollectorTest.groovy | 2 +- .../src/test/groovy/nextflow/splitter/SplitterExTest.groovy | 2 +- 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.../src/main/nextflow/file/http/FtpFileSystemProvider.groovy | 2 +- .../src/main/nextflow/file/http/HttpFileSystemProvider.groovy | 2 +- .../main/nextflow/file/http/HttpsFileSystemProvider.groovy | 2 +- .../src/main/nextflow/file/http/XAuthProvider.groovy | 2 +- .../src/main/nextflow/file/http/XAuthRegistry.groovy | 2 +- .../src/main/nextflow/file/http/XFileAttributes.groovy | 2 +- .../nf-httpfs/src/main/nextflow/file/http/XFileSystem.groovy | 2 +- .../src/main/nextflow/file/http/XFileSystemProvider.groovy | 2 +- modules/nf-httpfs/src/main/nextflow/file/http/XPath.groovy | 2 +- .../src/main/nextflow/file/http/XPathRegistrant.groovy | 2 +- .../src/main/nextflow/file/http/XPathSerializer.groovy | 2 +- modules/nf-httpfs/src/resources/META-INF/extensions.idx | 2 +- .../META-INF/services/java.nio.file.spi.FileSystemProvider | 2 +- .../src/test/nextflow/file/http/HttpFilesTests.groovy | 2 +- .../src/test/nextflow/file/http/XAuthRegistryTest.groovy | 2 +- 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.../src/main/nextflow/cloud/aws/util/AwsHelper.groovy | 2 +- .../src/main/nextflow/cloud/aws/util/S3BashLib.groovy | 2 +- .../main/nextflow/cloud/aws/util/S3CredentialsProvider.groovy | 2 +- .../src/main/nextflow/cloud/aws/util/S3PathFactory.groovy | 2 +- .../src/main/nextflow/cloud/aws/util/S3PathSerializer.groovy | 2 +- .../nextflow/cloud/aws/util/SsoCredentialsProviderV1.groovy | 2 +- plugins/nf-amazon/src/resources/META-INF/extensions.idx | 2 +- .../META-INF/services/java.nio.file.spi.FileSystemProvider | 2 +- plugins/nf-amazon/src/test/nextflow/S3ChannelTest.groovy | 2 +- plugins/nf-amazon/src/test/nextflow/S3SessionTest.groovy | 2 +- .../cloud/aws/batch/AwsBatchFileCopyStrategyTest.groovy | 2 +- .../test/nextflow/cloud/aws/batch/AwsBatchProxyTest.groovy | 2 +- .../cloud/aws/batch/AwsBatchScriptLauncherTest.groovy | 2 +- .../nextflow/cloud/aws/batch/AwsBatchTaskHandlerTest.groovy | 2 +- .../src/test/nextflow/cloud/aws/batch/AwsOptionsTest.groovy | 2 +- 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2 +- .../src/main/nextflow/cache/CloudCacheStore.groovy | 2 +- plugins/nf-cloudcache/src/resources/META-INF/extensions.idx | 2 +- plugins/nf-codecommit/build.gradle | 2 +- .../aws/codecommit/AwsCodeCommitCredentialProvider.groovy | 2 +- .../nextflow/cloud/aws/codecommit/AwsCodeCommitFactory.groovy | 2 +- .../nextflow/cloud/aws/codecommit/AwsCodeCommitPlugin.groovy | 2 +- .../cloud/aws/codecommit/AwsCodeCommitProviderConfig.groovy | 2 +- .../aws/codecommit/AwsCodeCommitRepositoryProvider.groovy | 2 +- plugins/nf-codecommit/src/resources/META-INF/extensions.idx | 2 +- .../cloud/aws/codecommit/AwsCodeCommitFactoryTest.groovy | 2 +- .../aws/codecommit/AwsCodeCommitProviderConfigTest.groovy | 2 +- .../aws/codecommit/AwsCodeCommitRepositoryProviderTest.groovy | 2 +- plugins/nf-console/build.gradle | 2 +- .../src/main/nextflow/ui/console/ConsolePlugin.groovy | 2 +- .../src/main/nextflow/ui/console/ConsoleRunner.groovy | 2 +- .../nf-console/src/main/nextflow/ui/console/Nextflow.groovy | 2 +- 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.../main/nextflow/ga4gh/tes/client/model/TesServiceInfo.java | 2 +- .../src/main/nextflow/ga4gh/tes/client/model/TesState.java | 2 +- .../src/main/nextflow/ga4gh/tes/client/model/TesTask.java | 2 +- .../src/main/nextflow/ga4gh/tes/client/model/TesTaskLog.java | 2 +- .../main/nextflow/ga4gh/tes/executor/TesBashBuilder.groovy | 2 +- .../src/main/nextflow/ga4gh/tes/executor/TesExecutor.groovy | 2 +- .../nextflow/ga4gh/tes/executor/TesFileCopyStrategy.groovy | 2 +- .../main/nextflow/ga4gh/tes/executor/TesTaskHandler.groovy | 2 +- plugins/nf-ga4gh/src/resources/META-INF/extensions.idx | 2 +- .../nextflow/ga4gh/tes/executor/TesBashBuilderTest.groovy | 2 +- .../test/nextflow/ga4gh/tes/executor/TesExecutorTest.groovy | 2 +- .../ga4gh/tes/executor/TesFileCopyStrategyTest.groovy | 2 +- .../nextflow/ga4gh/tes/executor/TesTaskHandlerTest.groovy | 2 +- .../src/main/nextflow/cloud/google/GoogleCloudPlugin.groovy | 2 +- .../src/main/nextflow/cloud/google/GoogleOpts.groovy | 2 +- .../main/nextflow/cloud/google/config/GoogleRetryOpts.groovy | 2 +- .../nextflow/cloud/google/config/GoogleStorageOpts.groovy | 2 +- .../src/main/nextflow/cloud/google/util/GsBashLib.groovy | 2 +- .../main/nextflow/cloud/google/util/GsPathSerializer.groovy | 2 +- plugins/nf-google/src/resources/META-INF/extensions.idx | 2 +- .../src/test/nextflow/cloud/google/GoogleSpecification.groovy | 2 +- .../cloud/google/batch/GoogleBatchLauncherSpecMock.groovy | 2 +- .../cloud/google/batch/logging/BatchLoggingTest.groovy | 2 +- .../nextflow/cloud/google/config/GoogleRetryOptsTest.groovy | 2 +- .../google/lifesciences/GoogleLifeSciencesConfigTest.groovy | 2 +- .../google/lifesciences/GoogleLifeSciencesExecutorTest.groovy | 2 +- .../GoogleLifeSciencesFileCopyStrategyTest.groovy | 2 +- .../google/lifesciences/GoogleLifeSciencesHelperTest.groovy | 2 +- .../lifesciences/GoogleLifeSciencesScriptLauncherTest.groovy | 2 +- .../lifesciences/GoogleLifeSciencesTaskHandlerTest.groovy | 2 +- .../test/nextflow/cloud/google/util/GsPathFactoryTest.groovy | 2 +- .../nextflow/cloud/google/util/GsPathSerializerTest.groovy | 2 +- .../nf-google/src/test/nextflow/extension/EscapeTest2.groovy | 2 +- .../nf-google/src/test/nextflow/extension/FilesExTest2.groovy | 2 +- .../nf-google/src/test/nextflow/file/FileHelperGsTest.groovy | 2 +- plugins/nf-google/src/test/nextflow/file/GsPathTest.groovy | 2 +- .../src/main/io/seqera/tower/plugin/CacheCommand.groovy | 2 +- .../src/main/io/seqera/tower/plugin/CacheManager.groovy | 2 +- .../src/main/io/seqera/tower/plugin/LogsCheckpoint.groovy | 2 +- .../src/main/io/seqera/tower/plugin/LogsHandler.groovy | 2 +- .../src/main/io/seqera/tower/plugin/TowerClient.groovy | 2 +- .../src/main/io/seqera/tower/plugin/TowerFactory.groovy | 2 +- .../src/main/io/seqera/tower/plugin/TowerJsonGenerator.groovy | 2 +- .../src/main/io/seqera/tower/plugin/TowerPlugin.groovy | 2 +- .../src/main/io/seqera/tower/plugin/TowerReports.groovy | 2 +- .../src/main/io/seqera/tower/plugin/TowerXAuth.groovy | 2 +- .../src/main/io/seqera/tower/plugin/WorkflowProgress.groovy | 2 +- plugins/nf-tower/src/resources/META-INF/extensions.idx | 2 +- .../META-INF/services/nextflow.trace.TraceObserverFactory | 2 +- plugins/nf-tower/src/resources/tower-schema.properties | 2 +- .../src/test/io/seqera/tower/plugin/CacheManagerTest.groovy | 2 +- .../src/test/io/seqera/tower/plugin/LogsCheckpointTest.groovy | 2 +- .../src/test/io/seqera/tower/plugin/LogsHandlerTest.groovy | 2 +- .../src/test/io/seqera/tower/plugin/TowerClientTest.groovy | 2 +- .../src/test/io/seqera/tower/plugin/TowerFactoryTest.groovy | 2 +- .../test/io/seqera/tower/plugin/TowerJsonGeneratorTest.groovy | 2 +- .../src/test/io/seqera/tower/plugin/TowerReportsTest.groovy | 2 +- .../src/main/io/seqera/wave/plugin/ContainerConfig.groovy | 2 +- .../src/main/io/seqera/wave/plugin/ContainerLayer.groovy | 2 +- .../io/seqera/wave/plugin/DescribeContainerResponse.groovy | 2 +- .../io/seqera/wave/plugin/SubmitContainerTokenRequest.groovy | 2 +- .../io/seqera/wave/plugin/SubmitContainerTokenResponse.groovy | 2 +- .../nf-wave/src/main/io/seqera/wave/plugin/WaveAssets.groovy | 2 +- .../nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy | 2 +- .../nf-wave/src/main/io/seqera/wave/plugin/WaveFactory.groovy | 2 +- .../nf-wave/src/main/io/seqera/wave/plugin/WavePlugin.groovy | 2 +- .../main/io/seqera/wave/plugin/adapter/InstantAdapter.groovy | 2 +- .../src/main/io/seqera/wave/plugin/cli/WaveCmdEntry.groovy | 2 +- .../src/main/io/seqera/wave/plugin/cli/WaveDebugCmd.groovy | 2 +- .../src/main/io/seqera/wave/plugin/cli/WaveRunCmd.groovy | 2 +- .../src/main/io/seqera/wave/plugin/config/HttpOpts.groovy | 2 +- .../src/main/io/seqera/wave/plugin/config/ReportOpts.groovy | 2 +- .../src/main/io/seqera/wave/plugin/config/RetryOpts.groovy | 2 +- .../src/main/io/seqera/wave/plugin/config/TowerConfig.groovy | 2 +- .../src/main/io/seqera/wave/plugin/config/WaveConfig.groovy | 2 +- .../seqera/wave/plugin/exception/BadResponseException.groovy | 2 +- .../seqera/wave/plugin/exception/UnauthorizedException.groovy | 2 +- .../src/main/io/seqera/wave/plugin/packer/Packer.groovy | 2 +- .../seqera/wave/plugin/resolver/WaveContainerResolver.groovy | 2 +- .../src/main/io/seqera/wave/plugin/util/BasicCliOpts.groovy | 2 +- .../src/main/io/seqera/wave/plugin/util/CliOpts.groovy | 2 +- .../src/main/io/seqera/wave/plugin/util/DigestFunctions.java | 2 +- .../src/main/io/seqera/wave/plugin/util/GnuCliOpts.groovy | 2 +- .../src/test/io/seqera/wave/plugin/ContainerConfigTest.groovy | 2 +- .../src/test/io/seqera/wave/plugin/ContainerLayerTest.groovy | 2 +- .../src/test/io/seqera/wave/plugin/WaveAssetsTest.groovy | 2 +- .../src/test/io/seqera/wave/plugin/WaveClientTest.groovy | 2 +- .../src/test/io/seqera/wave/plugin/WaveFactoryTest.groovy | 2 +- .../test/io/seqera/wave/plugin/cli/WaveDebugCmdTest.groovy | 2 +- .../src/test/io/seqera/wave/plugin/config/HttpOptsTest.groovy | 2 +- .../test/io/seqera/wave/plugin/config/RetryOptsTest.groovy | 2 +- .../test/io/seqera/wave/plugin/config/TowerConfigTest.groovy | 2 +- .../test/io/seqera/wave/plugin/config/WaveConfigTest.groovy | 2 +- .../src/test/io/seqera/wave/plugin/packer/PackerTest.groovy | 2 +- .../src/test/io/seqera/wave/plugin/packer/TarHelper.groovy | 2 +- .../test/io/seqera/wave/plugin/packer/WaveCmdEntryTest.groovy | 2 +- .../wave/plugin/resolver/WaveContainerResolverTest.groovy | 2 +- .../test/io/seqera/wave/plugin/util/BasicCliOptsTest.groovy | 2 +- .../src/test/io/seqera/wave/plugin/util/GnuCliOptsTest.groovy | 2 +- settings.gradle | 2 +- tests/cli-args.nf | 2 +- tests/collect-file.nf | 2 +- tests/collect_and_merge.nf | 2 +- tests/config-labels.nf | 2 +- tests/config-vars.config | 2 +- tests/config-vars.nf | 2 +- tests/copy-no-follow.nf | 2 +- tests/dyn-mem.nf | 2 +- tests/dynamic-filename.nf | 2 +- tests/dynamic-storedir.nf | 2 +- tests/each-file-dsl2.nf | 2 +- tests/env-container-with(special)chars.nf | 2 +- tests/env-out.nf | 2 +- tests/env2.nf | 2 +- tests/error-finish.nf | 2 +- tests/error-message.nf | 2 +- tests/error.nf | 2 +- tests/exit-if-empty.nf | 2 +- tests/exitstatus-fail.nf | 2 +- tests/file-with-blanks.nf | 2 +- tests/file-with-quote.nf | 2 +- tests/files.nf | 2 +- tests/fusion-symlink.nf | 2 +- tests/glob.nf | 2 +- tests/hello.nf | 2 +- tests/input.nf | 2 +- tests/mixing-langs.nf | 2 +- tests/modules.nf | 2 +- tests/nativeCode.nf | 2 +- tests/nextflow.config | 2 +- tests/omega.config | 2 +- tests/opt-file.nf | 2 +- tests/output-file.nf | 2 +- tests/output-links.nf | 2 +- tests/print-http-file.nf | 2 +- tests/profiles.config | 2 +- tests/profiles.nf | 2 +- tests/property-out-vals.nf | 2 +- tests/publish-dir.nf | 2 +- tests/publish-nested.nf | 2 +- tests/publish-saveas.nf | 2 +- tests/race.nf | 2 +- tests/repeaters.nf | 2 +- tests/resume-retried-task.nf | 2 +- tests/retry-ignore.nf | 2 +- tests/s3-files.nf | 2 +- tests/sets.nf | 2 +- tests/shell-script.nf | 2 +- tests/singleton.nf | 2 +- tests/splitLetters.nf | 2 +- tests/storeCache.nf | 2 +- tests/subdirs.nf | 2 +- tests/tag-resume.config | 2 +- tests/tag-resume.nf | 2 +- tests/tagging-lazy.nf | 2 +- tests/tagging.nf | 2 +- tests/task-attempts.nf | 2 +- tests/task-retry.nf | 2 +- tests/task-vars.nf | 2 +- tests/template-dyn.nf | 2 +- tests/template-shell.nf | 2 +- tests/template-simple.nf | 2 +- tests/template.config | 2 +- tests/when-block.nf | 2 +- tests/workdir-with-blank.nf | 2 +- tests/workflow-oncomplete.nf | 2 +- tests/yesOrNo.nf | 2 +- 1070 files changed, 1072 insertions(+), 1072 deletions(-) diff --git a/Makefile b/Makefile index bf55192bd3..2479a1cd19 100644 --- a/Makefile +++ b/Makefile @@ -1,5 +1,5 @@ # -# Copyright 2013-2023, Seqera Labs +# Copyright 2013-2024, Seqera Labs # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/NOTICE b/NOTICE index 27fc4d0513..6fcf7e0b8b 100644 --- a/NOTICE +++ b/NOTICE @@ -1,6 +1,6 @@ NEXTFLOW -Copyright 2013-2023, Seqera Labs +Copyright 2013-2024, Seqera Labs This software includes source code and libraries developed by: @@ -142,7 +142,7 @@ This software includes source code and libraries developed by: Spack https://github.com/spack/spack - Copyright 2013-2023 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. + Copyright 2013-2024 Lawrence Livermore National Security, LLC and other Spack Project Developers. See the top-level COPYRIGHT file for details. Licensed under Apache License, Version 2.0 Nextflow is a registered trademark of Seqera Labs, Spain. diff --git a/build.gradle b/build.gradle index dc6afae452..cf98246ebb 100644 --- a/build.gradle +++ b/build.gradle @@ -1,5 +1,5 @@ /* - * Copyright 2013-2023, Seqera Labs + * Copyright 2013-2024, Seqera Labs * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/buildSrc/src/main/groovy/io/nextflow/gradle/tasks/GithubUploader.groovy b/buildSrc/src/main/groovy/io/nextflow/gradle/tasks/GithubUploader.groovy index b81657cc3a..34d4049c41 100644 --- a/buildSrc/src/main/groovy/io/nextflow/gradle/tasks/GithubUploader.groovy +++ b/buildSrc/src/main/groovy/io/nextflow/gradle/tasks/GithubUploader.groovy @@ -1,5 +1,5 @@ /* - * Copyright 2013-2023, Seqera Labs + * Copyright 2013-2024, Seqera Labs * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/config/codenarc/codenarc.groovy b/config/codenarc/codenarc.groovy index 366a4062e0..bd082baef6 100644 --- a/config/codenarc/codenarc.groovy +++ b/config/codenarc/codenarc.groovy @@ -1,5 +1,5 @@ /* - * Copyright 2013-2023, Seqera Labs + * Copyright 2013-2024, Seqera Labs * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/config/codenarc/codenarc.xml b/config/codenarc/codenarc.xml index f82c0be0bd..aeffe439b9 100644 --- a/config/codenarc/codenarc.xml +++ b/config/codenarc/codenarc.xml @@ -1,5 +1,5 @@