Hello nf-core training part 4: ext.args is not taking the defined option

Training
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1

Hey everyone,

I’m following the Hello nf-core training tutorial and am now on Part 4: Make an Nf-core module (working in the provided GitHub codespace).

After implementing ext.args in the COWPY module and in the HELLO workflow, like the tutorial demanded, the kosh option isn’t being identified when I try to run the pipeline in step 1.3.4.

This is what I wrote on the COWPY module:

script:
def args = task.ext.args ?: ‘’
"""
cat $input_file | cowpy $args > cowpy-${input_file}
"""

This is what I wrote in modules.config :

withName: 'COWPY' {
        ext.args = { "-c ${params.character}" }
    }

As you can I see, I think it’s identical to the tutorial material…

When I try to run with nextflow run . --outdir core-hello-results -profile test,docker --validate_params false --character kosh, and inspect the output cowpy-test.txt file, it shows the default result instead of the one with the kosh character.

This is what I get when I run cat on the command.sh file:

#!/usr/bin/env bash -C -e -u -o pipefail
cat test.txt | cowpy > cowpy-test.txt

Can anyone help me debug this?