Example changes how to stage inputs/output modules in a more 'nextflowy' way

[jfy133]

I have run out of time, but I worked a bit on updating the Checkm2 module (my local database is a different version and ID on't have time to donwload the new one down)

But essentially I switch the database input(s) to either be a user-supplied path, and if not supplied, then let the respective module download it.

Then in the module switch the two val inputs to simply just the database files themselves and using the path variable. E.g., CHECKM2 module won't start until the GTDBTK2 database is recieved. Nextflow will (by default) just symlink the database into without needing a separate value. But as you've used path instead of val or the use of a param the used database, Nextflow will have staged correctly the input files in a way it 'likes' - even if the files are on another file system.

You should also make sure not to use outdir in the module itself, and rely on publishDir as specify in modules.config, so Nextflow itself can correctly publish these!

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
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