Remove ortholog and topup clustering modes

[twalsh-ebi]

Description

This draft PR would remove the ortholog and topup clustering modes from the gene-tree pipelines.

Neither mode has been used in production for quite some time. Furthermore, topup mode has been broken since release/110, since it uses a runnable (CopyTreesFromDB) which calls the obsolete method MemberAdaptor::fetch_by_stable_id.

Related JIRA tickets:

• ENSCOMPARASW-4179
• ENSCOMPARASW-7053
• ENSCOMPARASW-7055

Overview of changes

This draft PR would:

• remove the option to configure ortholog or topup clustering mode from the protein-trees pipeline, and remove the ortholog clustering mode from the ncRNA-trees pipeline;
• remove all pipeline analyses related to the ortholog and topup clustering modes;
• remove related pipeline parameters, including the copy and raxml_update clusterset_ids;
• add deprecation information to each of the runnables involved in the ortholog and topup clustering modes, and to the seq_member_id_current_reused_map table in pipeline-tables.sql; and
• add a treebreak_decision pipeline step to simplify the pipeline in the vicinity of the QuickTreeBreak loop.

This image shows a section of the pipeline following these changes:

Testing

These changes were tested during a run of the Pan Compara protein-trees pipeline as part of release/114 production.

(Some minor changes to documentation and parameters were made after the pipeline run.)

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For code reviewers: code review SOP

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 60.36%. Comparing base (78ab7e1) to head (d303272).

Additional details and impacted files

@@               Coverage Diff               @@
##           release/114     #872      +/-   ##
===============================================
- Coverage        60.37%   60.36%   -0.01%     
===============================================
  Files              197      197              
  Lines            22452    22452              
  Branches          3627     3627              
===============================================
- Hits             13555    13554       -1     
  Misses            7681     7681              
- Partials          1216     1217       +1     

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[twalsh-ebi]

My apologies, this was submitted against the wrong branch.

I've resubmitted this draft PR against the main branch (see ensembl-compara draft PR 873)