Global namespace

The global namespace contains globally available constants and functions.

Constants

baseDir: Path

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>

Added in version 24.04

Map of pipeline secrets. See Secrets for more information.

workDir: Path

Alias of workflow.workDir.

Functions

branchCriteria( criteria: Closure ) -> Closure

Create a branch criteria to use with the branch operator.

env( name: String ) -> String

Added in version 25.04

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 in version 22.10

Use error() instead

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

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

Get a file from a file name or glob pattern. Returns a collection of files if the glob pattern yields zero or multiple files.

Available options:

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').

See also: channel.fromPath.

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

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

groupKey( key, size: int ) -> GroupKey

Create a grouping key to use with the groupTuple operator.

multiMapCriteria( criteria: Closure ) -> Closure

Create a multi-map criteria to use with the 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 Notifications for more information.

Available options:

to

The mail target recipients. Specify multiple addresses as a comma-separated list.

cc

The mail CC recipients. Specify multiple addresses as a comma-separated list.

bcc

The mail BCC recipients. Specify multiple addresses as a comma-separated list.

from

The mail sender address.

subject

The mail subject.

charset

The mail content charset (default: UTF-8).

text

The mail plain text content.

body

The mail body content. Can be either plain text or HTML content.

To send an email that includes both plain text and HTML content, use both the text and body attributes: text is used for the plain text content, while body is used for the rich HTML content.

type

The mail body mime type (default: automatically detected).

attach

List of file attachments. Each attachment may specify the following options:

• contentId: The Content-ID header field
• disposition: The Content-Disposition header field
• fileName: The filename parameter of the Content-Disposition header field
• description: The Content-Description header field

sleep( milliseconds: long )

Sleep for the given number of milliseconds.

record( [options] ) -> Record

Create a record from the given named arguments.

tuple( collection: List ) -> ArrayTuple

Create a tuple from the given arguments.