Lint for correct publishDir specification in modules.config

[drpatelh]

There are various ways you can use the publishDIr directive in the native DSL2 implementation. One can only replace the entire publishDir directive which leads to a lot of repeated code in this config file. Along with checking if one of enabled: false, pattern: "<pattern>", or saveAs: { filename -> filename.equals('versions.yml') ? null : filename } is present (and that needs to account for the nested syntax too), otherwise the versions.yml gets output too.

Not sure how trivial it would be to lint for stuff like this...from what I have seen these directives can be used in loads of different ways so it is going to be a nightmare writing a parser for this. Also, NF configs aren't standard JSON / YAML we can just slurp up. I am not 💯 about having a custom function given that we have removed the need for almost all of them now but we do need to find a way to make these publishDir specifications clearer.

See nf-core/rnaseq#701 (comment)