Hi, I'm at the end of the nextflow linting cleaning of the nf-core/modules repository. I have remaining the modules using templates where arguments are called in the script but not in the main.nf. See the SRATOOLS_PREFETCH args2 argument for example. I was wondering if we had more guidelines about how to fix this. What I thought would be nice would be to pass the argument directly to the script either through an environment variable or a positional argument. This would make their usage explicit. What do you think ?

I think maybe summon @Ben Sherman for this question. Ben, how do we stop the linting from complaining that the

template

uses args, as it currently whinges about it.

A nice feature would be

template "detect_ncbi_settings.sh" "${args}"

We need to introduce a new way to call template where you pass in the args explicitly. Until then I wouldn't worry about it, it's just a warning

Louis is busy trying to eliminate all the warnings in the module repo 😉