Missing value declared as output parameter

[prmunn]

Bug report

(Please follow this template replacing the text between parentheses with the requested information)

Expected behavior and actual behavior

Val should be returned from a function

Steps to reproduce the problem

Calling the following function:

process haplotagging_padUMI {

output:
val include_stagger, emit: include_stagger_val

script:
    """
    include_stagger="Test value"

    echo \$include_stagger
    """

}

Program output

ERROR ~ Error executing process > 'haplotagging_create_bam_files:haplotagging_padUMI (1)'

Caused by:
Missing value declared as output parameter: include_stagger

Environment

• Nextflow version: latest version, using DSL2
• Java version: Not sure
• Operating system: Linux
• Bash version: (use the command $SHELL --version): GNU bash, version 5.1.8(1)-release (x86_64-redhat-linux-gnu)

Additional context

(Add any other context about the problem here)

[robsyme]

Hi

The val output type will emit a native Nextflow (Groovy) variable, and not a variable from the language in the script block (in your case, bash). If you would like to emit a bash variable, you would use the env type. See the documentation here: https://www.nextflow.io/docs/latest/process.html#output-type-env

[prmunn]

Ah... that appears to have fixed my problem. Thanks.