Split the modules out into separate files

[andersgs]

It would be useful to have the modules in separate files, you can then build a catalogue of modules (perhaps in its own repo) that you can use across workflows and pipelines.

[dfornika]

Good suggestion. If we followed this approach, we might also be able to take advantage of the library of modules from nf-core project.

We've taken this approach to some extent in other pipelines, such as our BCCDC-PHL/routine-sequence-qc pipeline. But in order to make the modules truly re-usable we'd need to think carefully about how to isolate them from the specific details of how they're used in the context of any given pipeline. I've been meaning to look more closely at the standards used in the nf-core/modules project to achieve that isolation.

We might also look at MDU-PHL/kovid-trees-nf for ideas on how to better isolate our modules within a single pipeline.