Create new entries for the pipeline

[jvfe]

• [x] Phylogenomics
• [x] rSPR
• [x] evolCCM
• [x] Recombination
• [x] Gene Order

[rbeiko]

Would it make sense to have entries for all subworkflows? I'm thinking additionally of pan-genomics at the moment but we will eventually want to consider dynamics and gene order.

Similarly we might allow the user to exit the pipeline at a given point in the pipeline.

[jvfe]

Would it make sense to have entries for all subworkflows? I'm thinking additionally of pan-genomics at the moment but we will eventually want to consider dynamics and gene order.

Similarly we might allow the user to exit the pipeline at a given point in the pipeline.

So, currently phylogenomics/pangenomics is in the same subworkflow, since that's how it was first implemented. They'll both be present in the phylogenomics entry, or should that be refacotred?

[rbeiko]

Let's leave it like that for now. Separating them can be for V2 or V6.