- Now the Nextflow pipeline takes into account
  the reciprocally retained gene families, by
  starting their workflow if required.
- Bug fix: the configuration file can now be
  located in any directory because the ksrates
  commands use its absolute path and not
  anymore its basename, as it was already
  supposed to be.

- These functions used to be in a separate file
  ("make_orthogroup_database.py"), and now are
  migrated to the ksrates pipeline.
- Still not sure whether we should provide the
  orthogroups database and other needed files
  ourselves of let them be computed by the user
  through these new functions the first time
  they run the rec.ret. pipeline; probably
  the second option to avoid that the GitHub
  repository becomes too heavy.
- In this case the function will have to be
  called in extend_orthogroups.py

- All the workflow to identify rec. ret. gene
  families is now called inside fc_wgd, at the
  same place where the standard pipeline calls
  blast and mcl, and replaces their use.
- The workflow code is still stored in a module
  aside, extend_orthogroups.py

"plot-paralogs" command generates the "rate_adjustment/species" directory if the directory doesn't exist (i.e. it has been deleted), avoiding that the code crashes.