ma/nextflow/docs/reference/stdlib-namespaces.md

(stdlib-namespaces)=

Namespaces

This page lists all of the available namespaces in the Nextflow standard library.

(stdlib-namespaces-global)=

Global namespace

The global namespace contains globally available constants and functions.

Constants

baseDir: Path

:::{deprecated} 20.04.0 :::

Alias of workflow.projectDir.

launchDir: Path

Alias of workflow.launchDir.

moduleDir: Path

Directory where a module script is located (equivalent to projectDir if used in the main script).

params

Map of workflow parameters specified in the config file or as command line options.

projectDir: Path

Alias of workflow.projectDir.

secrets: Map<String,String>

:::{versionadded} 24.02.0-edge :::

Map of pipeline secrets. See {ref}secrets-page for more information.

workDir: Path

Alias of workflow.workDir.

Functions

branchCriteria( criteria: Closure ) -> Closure

Create a branch criteria to use with the {ref}operator-branch operator.

env( name: String ) -> String

:::{versionadded} 25.04.0 :::

Get the value of the environment variable with the specified name in the Nextflow launch environment.

error( message: String = null )

Throw a script runtime error with an optional error message.

exit( exitCode: int = 0, message: String = null )

:::{deprecated} 22.06.0-edge Use error() instead :::

Stop the pipeline execution and return an exit code and optional error message.

file( filePattern: String, [options] ) -> Path

Get a file from a file name or glob pattern.

The following options are available:

checkIfExists: boolean

When true, throws an exception if the specified path does not exist in the file system (default: false)

followLinks: boolean

When true, follows symbolic links when traversing a directory tree, otherwise treats them as files (default: true)

glob: boolean

When true, interprets characters *, ?, [] and {} as glob wildcards, otherwise handles them as normal characters (default: true)

hidden: boolean

When true, includes hidden files in the resulting paths (default: false)

maxDepth: int

Maximum number of directory levels to visit (default: no limit)

type: String

Type of paths returned, can be 'file', 'dir' or 'any' (default: 'file')

:::{note} This function returns a collection if the glob pattern yields zero or multiple files. Use files() to get a collection of files. :::

files( filePattern: String, [options] ) -> Iterable<Path>

Get a collection of files from a file name or glob pattern. Supports the same options as file().

See also: {ref}channel.fromPath <channel-path>.

groupKey( key, size: int ) -> GroupKey

Create a grouping key to use with the {ref}operator-grouptuple operator.

multiMapCriteria( criteria: Closure ) -> Closure

Create a multi-map criteria to use with the {ref}operator-multiMap operator.

print( value )

Print a value to standard output.

printf( format: String, values... )

Print a formatted string with the given values to standard output.

println( value )

Print a value to standard output with a newline.

sendMail( [options] )

Send an email. See {ref}mail-page for more information.

sleep( milliseconds: long )

Sleep for the given number of milliseconds.

record( [options] ) -> Record

Create a record from the given named arguments.

tuple( args... ) -> Tuple

Create a tuple from the given arguments.

(stdlib-namespaces-channel)=

channel

The channel namespace contains the built-in channel factories. See {ref}channel-factory for details.

(stdlib-namespaces-nextflow)=

log

The log namepsace contains functions for logging messages to the console.

error( message: String )

Log an error message to the console.

This function does not terminate the pipeline -- use the global error() function instead.

info( message: String )

Log an info message to the console.

warn( message: String )

Log a warning message to the console.

nextflow

The nextflow namespace contains information about the current Nextflow runtime.

build: int

Nextflow runtime build number.

timestamp: String

Nextflow runtime compile timestamp.

version: VersionNumber

Nextflow runtime version number. See {ref}VersionNumber <stdlib-types-versionnumber> for more information.

(stdlib-namespaces-workflow)=

workflow

The workflow namespace contains information about the current workflow run.

Properties

commandLine: String

Command line as entered by the user to launch the workflow execution.

commitId: String

Git commit ID of the executed workflow repository.

When providing a Git tag, branch name, or commit hash using the -r CLI option, the associated workflow.commitId is also populated.

complete: OffsetDateTime

Available only in the workflow.onComplete handler

Timestamp of workflow when execution is completed.

configFiles: List<Path>

Configuration files used for the workflow execution.

container: String | Map<String,String>

Docker image used to run workflow tasks, or a map of process names to process containers when multiple images are used.

containerEngine: String

Returns the name of the container engine (e.g. docker or singularity) or null if no container engine is enabled.

duration: Duration

Available only in the workflow.onComplete handler

Time elapsed to complete workflow execution.

errorMessage: String

Available only in the workflow.onComplete and workflow.onError handlers

Error message of the task that caused the workflow execution to fail.

errorReport: String

Available only in the workflow.onComplete and workflow.onError handlers

Detailed error of the task that caused the workflow execution to fail.

exitStatus: int

Available only in the workflow.onComplete and workflow.onError handlers

Exit status of the task that caused the workflow execution to fail.

failOnIgnore: boolean

:::{versionadded} 24.05.0-edge :::

Whether the workflow.failOnIgnore config option was enabled.

See also: {ref}process-error-strategy

fusion

Namespace containing information about the current Fusion runtime. The following properties are available:

enabled: boolean

Whether Fusion is enabled.

version: String

The Fusion version being used.

homeDir: Path

User system home directory.

launchDir: Path

Directory where the workflow was launched.

manifest

Namespace corresponding to the {ref}config-manifest config scope.

outputDir: Path

:::{versionadded} 24.10.0 :::

Workflow output directory.

preview: boolean

:::{versionadded} 24.04.0 :::

Whether the current workflow run is a preview run.

profile: String

Comma-separated list of active configuration profiles.

projectDir: Path

Directory where the workflow project is located.

repository: String

Project repository Git remote URL.

resume: boolean

Returns true whenever the current instance is resumed from a previous execution.

revision: String

Git branch/tag of the executed workflow repository.

When providing a Git tag or branch name using the -r CLI option, the workflow.revision is also populated.

runName: String

Mnemonic name assigned to this execution instance.

scriptFile: Path

Project main script file path.

scriptId: String

Project main script unique hash ID.

scriptName: String

Project main script file name.

sessionId: UUID

Unique identifier (UUID) associated to current execution.

start: OffsetDateTime

Timestamp of workflow at execution start.

stubRun: boolean

Returns true whenever the current instance is a stub-run execution .

success: boolean

Available only in the workflow.onComplete and workflow.onError handlers

Reports if the execution completed successfully.

userName: String

User system account name.

wave

Namespace containing Wave runtime information. The following properties are available:

enabled: boolean

Whether Wave is enabled.

workDir: Path

The directory where task temporary files are stored.

Functions

onComplete( action: Closure )

Define an action to take when the workflow completes (whether successful or not).

onError( action: Closure )

Define an action to take if the workflow is terminated due to a runtime error or task failure.