add updateReferencesFile()

[maxulysse]

updateReferencesFile() is a new function to help with references.
It replaces a given basepath within a datasheet yaml file into any other given basepath.

[nvnieuwk]

LGTM

[edmundmiller]

Can you add end to end Nextflow example workflows for these?

The one's in the docs look good, they're just in the docs so they're not going to run in the tests. 😅

[edmundmiller]

I'm looking at this further. I don't love the concept of letting people rewrite the YAML files on the fly or changing this path; I would rather that die.

I think we can provide them with a YAML script to adjust the YAML to their use case, but I believe that would just end up breaking so many things if we change these as an ad hoc approach.

Do users really want a full mirror of igenomes, or did they just copy a genome or two?

If it's the latter, then I think they should just write their tiny YAML file and move on.