Remove ortholog and topup clustering modes

[twalsh-ebi]

Description

This 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 73.04%. Comparing base (cd1e53c) to head (9cefb09).

Additional details and impacted files

@@             Coverage Diff             @@
##             main     #873       +/-   ##
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+ Coverage   60.67%   73.04%   +12.37%     
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  Files         212       15      -197     
  Lines       23016      564    -22452     
  Branches     3627        0     -3627     
===========================================
- Hits        13966      412    -13554     
+ Misses       7833      152     -7681     
+ Partials     1217        0     -1217     

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