Inputs and outputs (typed)

Added in version 25.10

note

Typed processes require the nextflow.enable.types feature flag to be enabled in every script that uses them.

Stage directives

The following directives can be used in the stage: section of a typed process:

env( name: String, String value )

Declares an environment variable with the specified name and value in the task environment.

stageAs( value: Path, filePattern: String )

Stages a file into the task directory under the given alias.

stageAs( value: Iterable<Path>, filePattern: String )

Stages a collection of files into the task directory under the given alias.

stdin( value: String )

Stages the given value as the standard input (i.e., stdin) to the task script.

Outputs

The following functions are available in the output: and topic: sections of a typed process:

env( name: String ) -> String

Returns the value of an environment variable from the task environment.

eval( command: String ) -> String

Returns the standard output of the specified command, which is executed in the task environment after the task script completes.

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

Returns a file from the task environment that matches the specified pattern.

Available options:

followLinks: Boolean

When true, target files are returned in place of any matching symlink (default: true).

glob: Boolean

When true, the file name is interpreted as a glob pattern (default: true).

hidden: Boolean

When true, hidden files are included in the matching output files (default: false).

includeInputs: Boolean

When true and the file name is a glob pattern, any input files matching the pattern are also included in the output (default: false).

maxDepth: Integer

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

optional: Boolean

When true, the task will not fail if the given file is missing (default: false).

type: String

Type of paths returned, either file, dir or any (default: any, or file if the given file name contains a double star (**)).

files( pattern: String, [options] ) -> Set<Path>

Returns files from the task environment that match the given pattern.

Supports the same options as file() (except for optional).

stdout() -> String

Returns the standard output of the task script.