And generate gene sets per species in main.nf:

- All genes in the species.
- For each GO term, all genes having the GO term.

TODO When done, edit off the partial and capitalise

Sometimes it worked without, sometimes it didn't, I suppose due to some
jobs running on the cluster which may reset the env and some locally
which apparently keep the env. It's no longer necessary to run nextflow
itself with the venv active.

Keep as species names, do not map to species objects. Make it easy to
map a name to a species obj anywhere.

Join removed as it's no longer used, use phase or cross in the future.
Plus, Nextflow has recently added a join operator of its own (not
equivalent).

- Use --options instead of arguments
- Output CSV instead of TSV as empty fields are difficult to spot
  otherwise (try to spot the difference between 	 and 		)

Value channels can be reused without tapping.

I.e. Add --col-species to cedalion-clime-matrix

orthofinder, phyml, interproscan, blast2go boolean input columns allow
controlling what species to include in what part of the run.

More explicit input allows having the proteome files elsewhere without
using symlinks.

tsv instead of txt, fix typo

+ tidy whitespace

and add cedalion-best-hit-defs script.

- Replace blast2go-convert-decypher with split-blast-hits + sedding.
  This is more flexible.

- Our RefSeq Decypher db used to have Hit_def and/or Hit_id formatted as
  gi|{ncbi GI number}|ref|{refseq id}| description. Now it just has a
  refseq id and description. The BLAST2GO script was updated to reflect
  this.

by making it streaming instead of reading whole file to memory

Not used in pipeline, but needed to serve a request for a manual CLIME
run

Unused because we assume PhyML outputs a bifurcating tree

- Rename $parameters variable so it doesn't name clash
- Give more memory
- A couple more fixes

and:

- Use pytil instead of chicken_turtle_util
- Remove unnecessary @UnresolvedImport

Only use core genes with gap positions removed. Use SPR
search. Assume resulting tree is bifurcating.