I recovered the help text and "solved" the monochrome logs warning in this PR (with @Maxime Garcia helping). So if you want to do that for your pipeline you can just follow my steps. https://github.com/nf-core/bamtofastq/pull/137

It's either that, if it's never going to be used in the future and gets removed from the template, or prefixing it with _ (if the template is going to use it in the future somewhere)