Make GENOME and GENOME_AND_ANNOTATION into workflows

[FernandoDuarteF]

We should make our two main subworflows (GENOME and GENOME_AND_ANNOTATION) into workflows, as it makes more sense for the structure and modularization of the pipeline (we cannot use subworkflows inside subworflows).

For example, as for now, we would not be able to import the BUSCO subworkflow from #77 inside GENOME_AND_ANNOTATION subworkflow.

[GallVp]

Hi @FernandoDuarteF

I like the idea of workflows.

However, I am a bit confused as to why subworkflows can not be imported into other subworkflows?

[FernandoDuarteF]

I now realise that it is possible to import subworkflows into other subworkflows. I should have said that we 'should not' or 'try to avoid', as I assume it's not good practice, but perhaps I'm wrong?

Either way I think in this case we should have two workflows.

[GallVp]

I now realise that it is possible to import subworkflows into other subworkflows. I should have said that we 'should not' or 'try to avoid', as I assume it's not good practice, but perhaps I'm wrong?

Either way I think in this case we should have two workflows.

Good point.

I can't think of a reason why sub-workflows within a local pipeline sub-workflow would be a problem.

For reusable sub-workflows, it is certainly a problem because of version slips. When a nested sub-workflow/module is modified, the only deterrent against breaking the dependent sub-workflow is nf-test tags.