Issue with outputting string variables containing equal sign (=)

[HarryHung]

I am not sure whether it is a bug of Nextflow or I am doing it wrong.

If I use output type env and the string variable contains a equal sign =, only the part before the = will be output, even though the whole string is captured in .command.env

Example code:

process TEST {
    output:
    env OUTPUT_VAR

    shell:
    '''
    OUTPUT_VAR='PART1=PART2'
    '''
}


workflow {
    TEST().view()
}

Terminal output:

PART1

Expected output:

PART1=PART2

The .command.env is as following, showing that the whole variable was successfully captured. But without any quote, it seems the information after = is lost after further usage of this variable

OUTPUT_VAR=PART1=PART2

I don't think this is the expected behaviour, as standard bash can have string variables containing =

OUTPUT_VAR='PART1=PART2'
echo $OUTPUT_VAR

PART1=PART2

I am grateful for any idea or suggestion. Or let me know if I should submit an issue.

Thank you!

[pditommaso]

Likely is related to this

nextflow/modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy

Lines 1496 to 1504 in c492ad2

	protected Map collectOutEnvMap(Path workDir) {
	final env = workDir.resolve(TaskRun.CMD_ENV).text
	final result = new HashMap(50)
	for(String line : env.readLines() ) {
	def (k,v) = line.tokenize('=')
	result.put(k,v)
	}
	return result
	}

[HarryHung]

Thanks, looks like it.
It feels like a bug to me, should I report it?

[pditommaso]

Yes, please

[HarryHung]

Issue created:
#3553

[mribeirodantas]

Can't find this issue 🤔

[pditommaso]

This #3553 ?

[HarryHung]

It seems the issue disappear for me as well. I did not delete it though...

[HarryHung]

Somehow, it returned.

[mribeirodantas]

Yeah, I can see it now. That was weird 😅