utils_nfcore_pipeline: Positional args warning is misleading

[awgymer]

Description of the bug

The new-ish positional args warning in nf-core pipelines has some misleading behaviour in at least one edge-case.

Using -stub-run/-stub will produce the following:

  WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected.
        Hint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`.

It seems that nextflow sets -stub to have a value of "true" when it normalises args which for whatever reason is later treated as an unattached positional arg?

This might be both an nf-core issue in that the check is rathe blunt, but also a nextflow issue because it seems weird to inject a normalised arg value into the positional args?

Command used and terminal output

No response

System information

nextflow 23.10.1