Check for comma-separated profiles with whitespace

[ewels]

Description of feature

A common user error is to have spaces in config profiles on the command line, for example:

-profile test, singularity

This gives an unintuitive error about not having required software available etc.

It would be nice if we could automatically detect suspected cases of this:

• Trailing comma in the profile
• 1 or more positional arguments

Could then throw a warning, or even exit with an error if we're feeling confident.

[mashehu]

How would we catch that in the template? Nextflow should check the parameters, not sure where nf-core/tools can interfere with that?

[maxulysse]

yeah, shouldn't this be handled on the Nextflow side?

[ewels]

Having positional arguments in the command is valid for Nextflow, but we never do it with nf-core. So if we use that as the main detection method it should be nf-core specific.

I'm suggesting that we put this into a function that sits in lib in the template and is called for every pipeline launch.

The trailing comma in the profile string is an optional extra, if we want to make the check more specific. I'm not 100% certain that we can get the raw profile string or not.

[ewels]

See here

${args[0]}