Reference sets configuration for microbes

[manuelcarbajo]

Updated microbial reference genomes for the upcoming release. This update includes Archaea, Bacteria, Fungi, and Protists.

Note: As “Protists” is no longer a formal or searchable taxonomic group in NCBI Taxonomy, a base_collection named "shared_protists" has been introduced. This base collection aggregates all genomes used for comparative analyses across protist lineages.

Nine protist collections names have been defined: sar, amoebozoa, excavata, discoba, opisthokonta, haptophyta, viridiplantae, rhodophyta, and cryptophyceae. These collections correspond to higher-level eukaryotic clades that are explicitly represented and queryable in NCBI Taxonomy and together provide comprehensive coverage of protist diversity with genome-scale representation. These groups were selected using as criteria NCBI Taxonomy Browser (defining which higher-level eukaryotic clades are explicitly represented and queryable) and Adl SM et al. (2019) "Revisions to the classification, nomenclature, and diversity of eukaryotes." Journal of Eukaryotic Microbiology 66:4–119

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 59.07%. Comparing base (69393a7) to head (2d222ea).
⚠️ Report is 1 commits behind head on feature/mvp-rapid.

Additional details and impacted files

@@                Coverage Diff                 @@
##           feature/mvp-rapid    #1004   +/-   ##
==================================================
  Coverage              59.07%   59.07%           
==================================================
  Files                    213      213           
  Lines                  22671    22671           
  Branches                3527     3527           
==================================================
  Hits                   13394    13394           
  Misses                  8150     8150           
  Partials                1127     1127           

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

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
• 📦 JS Bundle Analysis: Save yourself from yourself by tracking and limiting bundle sizes in JS merges.

[manuelcarbajo]

Thank you very much for flagging these typos Thomas. If everything else is good and Travis passes all checks I'm happy to go ahead with the merge.

[twalsh-ebi]

Hi @manuelcarbajo .. Would it be possible to remove the Protists taxonomic_group elements, and replace each of the base_collection elements with a composable_collection, as I've suggested in this case?

Suggested change

	<base_collection name="shared_protists"/>
	<taxonomic_group taxon_name="SAR"/>
	<composable_collection name="shared_protists"/>

[manuelcarbajo]

Thanks @twalsh-ebi . If Travis is happy with this configuration, it works for me.

The taxonomic_group elements were originally added to satisfy the RNG validation requirements for the collections definition, so I’m glad to see a cleaner approach using composable_collection instead.