Add procedural tree and profile support to workflow

[cerebis]

Now that both are supported by the underlying tools, we need to add the support into the workflow. issues #31 and #35

This will require developing a definition syntax for sweeps and should also achieve multiple ancestral genomes. An initial concept for the definition is shown in issue #28.

YAML or JSON would make things portable. We would then add a Groovy class which reads this and initialises a field within the Nextflow params structure. Hanging the entire sweep of a single field would be result in deeper referencing, but would also leave everything pertinent to the sweep under a single hierarchy and touch-down within the params object at only a single spot -- minimising potential namespace clashes.

[cerebis]

In attempting to implement the workflow, it was determined that writing a profile to disk once generated was simpler than passing seeds and parameters to each dependent process.

What has been implemented:

• yaml definition of a sweep
• io and basic methods for using loaded definition
• generation of communities from multiple ancestral phylogenetic lineages.

This issue is therefore closed.