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Integrate reciprocally retention workflow

Cecilia SENSALARI requested to merge dev into master

Main change:

  • Add function modules to perform the workflow to detect the top 2000 (lambda rank) reciprocally retained gene families (extend_orthogroups.py, fc_reciprocal_retention.py)
  • The Nextflow pipeline (main.nf) also takes into account the reciprocal retention workflow when scheduling the wgdParalog process
  • Other modules have been adapted to handle the new code

Note that the integration is still in progress in dev or feature branches.

Bugfix:

  • In the Nextflow pipeline (main.nf), the input config file for ksrates can now be located anywhere because all commands are using its absolute path, while before the configuration file had to be located in the folder from which the NF pipeline was run because of a wrong variable in main.nf.

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