Use tree refinement and constraint topology in species tree pipeline

[ens-sb]

Description

There is a need for specifying a topology constraint in the pipeline in order to allow adding new genomes to an existing topology while keeping it fixed.

Related JIRA tickets:

• ENSCOMPARASW-7374

Overview of changes

Change 1

Using the astral tree as starting topology instead of constraint in the protein branch length calculation step.

Change 2

Added option to specify constraining topology as a newick file.

Testing

The pipeline was tested on the vertebrates 112 division. The run finished in 5 hours.

---

For code reviewers: code review SOP

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 60.25%. Comparing base (3b6ba42) to head (18f0e66).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #784      +/-   ##
==========================================
- Coverage   60.27%   60.25%   -0.02%     
==========================================
  Files         195      195              
  Lines       22412    22412              
  Branches     3618     3618              
==========================================
- Hits        13509    13505       -4     
- Misses       7698     7699       +1     
- Partials     1205     1208       +3     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.