Secrets cannot contain `\n`

[long-matt-r]

Bug report

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

Expected behavior and actual behavior

If a multi-line secret is set, I would expect a multi-line secret to be passed as an envirnoment variable when specified in a process. Instead it seems to silently skip the step with no errors thrown?

Steps to reproduce the problem

And here's a basic script

process test_connection {
    container = 'ubuntu'
    secret 'SNOWFLAKE_PRIVATE_KEY_RAW'

    input:
    val markerid

    script:
    """
    echo \$SNOWFLAKE_PRIVATE_KEY_RAW
    """
}


workflow {
    markerid = channel.of(1, 2)

    test_connection(markerid)
}

Program output

For the sake of this example, I am deleting the ubuntu Docker image between runs.

If I have nextflow secrets set SNOWFLAKE_PRIVATE_KEY_RAW 'test' then:

<> % nextflow run snowflake.nf -with-docker

 N E X T F L O W   ~  version 25.04.1

Launching `snowflake.nf` [soggy_bhaskara] DSL2 - revision: c95f04129e

executor >  local (2)
[c6/264bb8] process > test_connection (2) [100%] 2 of 2 ✔
test

test

<> % docker image ls | grep ubuntu                        
ubuntu                                                          latest             57c587f9225f   2 weeks ago         101MB

If instead I have:

<> % nextflow secrets set SNOWFLAKE_PRIVATE_KEY_RAW "test  
result" 

then:

<> % nextflow run snowflake.nf -with-docker                       

 N E X T F L O W   ~  version 25.04.1

Launching `snowflake.nf` [cheesy_magritte] DSL2 - revision: c95f04129e

executor >  local (2)
[14/e2c67b] process > test_connection (1) [100%] 2 of 2 ✔

<> % docker image ls | grep ubuntu
# no results

And it doesn't actually execute anything because it hasn't even pulled the docker image.

(Copy and paste the output produced by the failing execution. Please highlight it as a code block. Whenever possible upload the .nextflow.log file.)

Environment

• Nextflow version: 25.04.1.5946
• Java version: openjdk 23.0.2 2025-01-21
• Operating system: macOS
• Bash version: zsh 5.9 (arm64-apple-darwin24.0)

Additional context

(Add any other context about the problem here)