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nf-core

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Can someone suggest if im moving in the right direction - i've found a module with a hardcoded parameter that isnt adjustable via `task.ext.args`
<https://github.com/nf-core/modules/issues/10308> I can open a PR to fix this but im wondering how we communicate these changes, that a commandline option that was previously applied, will now no longer be used.

Is it up to the consumer of the module to carefully vet incoming changes when they update their modules?

It looks like this parameter is required for the tool to run, but has been hardcoded to one option yes.
See <https://nf-co.re/docs/guidelines/components/modules#required-val-channel-inputs>

If that is the case, it'll just fail if you remove it

But yes, it is up to the consumer of the module to check the incoming changes

Ok, if understand correctly
```regtools junctions extract \\
        $args \\
        -s XS \\                   <-- existing hard-coded option to remove
        -o ${prefix}.junc \\
        $bam```
add a channel input
```val(strand_specificity) // XS, use XS tags provided by aligner; RF, first-strand; FR, second-strand;```
and a default value
```def strand = strand_specificity ?: 'XS'```
and use the value
```regtools junctions extract \\
        $args \\
        -s ${strand} \\                   <-- add this
        -o ${prefix}.junc \\
        $bam```