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nf-core

on blacklists: I have a question on how to pass them on modules, i.e. <https://nf-co.re/modules/deeptools_bamcoverage/|bamcoverage> has an optional parameter but it is not present in the <https://github.com/nf-core/modules/blob/master/modules/nf-core/deeptools/bamcoverage/main.nf|module code>:
```        bamCoverage \\
            --bam $input_out \\
            $args \\
            --numberOfProcessors ${task.cpus} \\
            --outFileName ${prefix}.${extension}```

should I open an issue to add it? or is there another way? if passed with ext.args the file is not staged properly as the path is taken as string

Yes, it'll need to be added as a separate input to be staged

Thank you <@U016SFULDB8>, so I'd proceed to propose to modify the relevant modules... would it be ok to open a single issue for all of them?

depends on how many it is. 2 or 3 is probably fine in one PR.