290 lines
8.3 KiB
Markdown
290 lines
8.3 KiB
Markdown
(stdlib-namespaces)=
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# Namespaces
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This page lists all of the available namespaces in the Nextflow standard library.
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(stdlib-namespaces-global)=
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## Global namespace
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The global namespace contains globally available constants and functions.
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**Constants**
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`baseDir: Path`
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: :::{deprecated} 20.04.0
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:::
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: Alias of `workflow.projectDir`.
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`launchDir: Path`
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: Alias of `workflow.launchDir`.
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`moduleDir: Path`
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: Directory where a module script is located (equivalent to `projectDir` if used in the main script).
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`params`
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: Map of workflow parameters specified in the config file or as command line options.
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`projectDir: Path`
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: Alias of `workflow.projectDir`.
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`secrets: Map<String,String>`
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: :::{versionadded} 24.02.0-edge
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:::
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: Map of pipeline secrets. See {ref}`secrets-page` for more information.
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`workDir: Path`
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: Alias of `workflow.workDir`.
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**Functions**
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`branchCriteria( criteria: Closure ) -> Closure`
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: Create a branch criteria to use with the {ref}`operator-branch` operator.
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`env( name: String ) -> String`
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: :::{versionadded} 25.04.0
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:::
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: Get the value of the environment variable with the specified name in the Nextflow launch environment.
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`error( message: String = null )`
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: Throw a script runtime error with an optional error message.
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`exit( exitCode: int = 0, message: String = null )`
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: :::{deprecated} 22.06.0-edge
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Use `error()` instead
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:::
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: Stop the pipeline execution and return an exit code and optional error message.
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`file( filePattern: String, [options] ) -> Path`
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: Get a file from a file name or glob pattern.
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: The following options are available:
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`checkIfExists: boolean`
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: When `true`, throws an exception if the specified path does not exist in the file system (default: `false`)
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`followLinks: boolean`
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: When `true`, follows symbolic links when traversing a directory tree, otherwise treats them as files (default: `true`)
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`glob: boolean`
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: When `true`, interprets characters `*`, `?`, `[]` and `{}` as glob wildcards, otherwise handles them as normal characters (default: `true`)
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`hidden: boolean`
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: When `true`, includes hidden files in the resulting paths (default: `false`)
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`maxDepth: int`
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: Maximum number of directory levels to visit (default: *no limit*)
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`type: String`
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: Type of paths returned, can be `'file'`, `'dir'` or `'any'` (default: `'file'`)
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: :::{note}
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This function returns a collection if the glob pattern yields zero or multiple files. Use `files()` to get a collection of files.
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:::
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`files( filePattern: String, [options] ) -> Iterable<Path>`
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: Get a collection of files from a file name or glob pattern. Supports the same options as `file()`.
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: See also: {ref}`channel.fromPath <channel-path>`.
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`groupKey( key, size: int ) -> GroupKey`
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: Create a grouping key to use with the {ref}`operator-grouptuple` operator.
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`multiMapCriteria( criteria: Closure ) -> Closure`
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: Create a multi-map criteria to use with the {ref}`operator-multiMap` operator.
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`print( value )`
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: Print a value to standard output.
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`printf( format: String, values... )`
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: Print a formatted string with the given values to standard output.
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`println( value )`
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: Print a value to standard output with a newline.
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`sendMail( [options] )`
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: Send an email. See {ref}`mail-page` for more information.
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`sleep( milliseconds: long )`
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: Sleep for the given number of milliseconds.
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`record( [options] ) -> Record`
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: Create a record from the given named arguments.
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`tuple( args... ) -> Tuple`
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: Create a tuple from the given arguments.
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(stdlib-namespaces-channel)=
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## `channel`
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The `channel` namespace contains the built-in channel factories. See {ref}`channel-factory` for details.
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(stdlib-namespaces-nextflow)=
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## `log`
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The `log` namepsace contains functions for logging messages to the console.
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`error( message: String )`
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: Log an error message to the console.
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: This function does not terminate the pipeline -- use the global `error()` function instead.
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`info( message: String )`
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: Log an info message to the console.
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`warn( message: String )`
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: Log a warning message to the console.
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## `nextflow`
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The `nextflow` namespace contains information about the current Nextflow runtime.
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`build: int`
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: Nextflow runtime build number.
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`timestamp: String`
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: Nextflow runtime compile timestamp.
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`version: VersionNumber`
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: Nextflow runtime version number. See {ref}`VersionNumber <stdlib-types-versionnumber>` for more information.
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(stdlib-namespaces-workflow)=
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## `workflow`
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The `workflow` namespace contains information about the current workflow run.
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**Properties**
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`commandLine: String`
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: Command line as entered by the user to launch the workflow execution.
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`commitId: String`
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: Git commit ID of the executed workflow repository.
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: When providing a Git tag, branch name, or commit hash using the `-r` CLI option, the associated `workflow.commitId` is also populated.
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`complete: OffsetDateTime`
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: *Available only in the `workflow.onComplete` handler*
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: Timestamp of workflow when execution is completed.
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`configFiles: List<Path>`
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: Configuration files used for the workflow execution.
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`container: String | Map<String,String>`
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: Docker image used to run workflow tasks, or a map of process names to process containers when multiple images are used.
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`containerEngine: String`
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: Returns the name of the container engine (e.g. docker or singularity) or null if no container engine is enabled.
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`duration: Duration`
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: *Available only in the `workflow.onComplete` handler*
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: Time elapsed to complete workflow execution.
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`errorMessage: String`
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: *Available only in the `workflow.onComplete` and `workflow.onError` handlers*
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: Error message of the task that caused the workflow execution to fail.
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`errorReport: String`
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: *Available only in the `workflow.onComplete` and `workflow.onError` handlers*
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: Detailed error of the task that caused the workflow execution to fail.
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`exitStatus: int`
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: *Available only in the `workflow.onComplete` and `workflow.onError` handlers*
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: Exit status of the task that caused the workflow execution to fail.
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`failOnIgnore: boolean`
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: :::{versionadded} 24.05.0-edge
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: Whether the `workflow.failOnIgnore` config option was enabled.
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: See also: {ref}`process-error-strategy`
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`fusion`
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: Namespace containing information about the current Fusion runtime. The following properties are available:
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: `enabled: boolean`
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: Whether Fusion is enabled.
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: `version: String`
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: The Fusion version being used.
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`homeDir: Path`
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: User system home directory.
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`launchDir: Path`
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: Directory where the workflow was launched.
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`manifest`
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: Namespace corresponding to the {ref}`config-manifest` config scope.
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`outputDir: Path`
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: :::{versionadded} 24.10.0
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: Workflow output directory.
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`preview: boolean`
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: :::{versionadded} 24.04.0
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: Whether the current workflow run is a preview run.
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`profile: String`
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: Comma-separated list of active configuration profiles.
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`projectDir: Path`
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: Directory where the workflow project is located.
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`repository: String`
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: Project repository Git remote URL.
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`resume: boolean`
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: Returns `true` whenever the current instance is resumed from a previous execution.
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`revision: String`
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: Git branch/tag of the executed workflow repository.
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: When providing a Git tag or branch name using the `-r` CLI option, the `workflow.revision` is also populated.
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`runName: String`
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: Mnemonic name assigned to this execution instance.
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`scriptFile: Path`
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: Project main script file path.
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`scriptId: String`
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: Project main script unique hash ID.
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`scriptName: String`
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: Project main script file name.
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`sessionId: UUID`
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: Unique identifier (UUID) associated to current execution.
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`start: OffsetDateTime`
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: Timestamp of workflow at execution start.
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`stubRun: boolean`
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: Returns `true` whenever the current instance is a stub-run execution .
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`success: boolean`
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: *Available only in the `workflow.onComplete` and `workflow.onError` handlers*
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: Reports if the execution completed successfully.
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`userName: String`
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: User system account name.
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`wave`
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: Namespace containing Wave runtime information. The following properties are available:
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: `enabled: boolean`
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: Whether Wave is enabled.
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`workDir: Path`
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: The directory where task temporary files are stored.
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**Functions**
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`onComplete( action: Closure )`
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: Define an action to take when the workflow completes (whether successful or not).
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`onError( action: Closure )`
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: Define an action to take if the workflow is terminated due to a runtime error or task failure.
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