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Fix ARTIC data table declaration and protocol URL - #8255

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agent/fix-artic-clair3-data-table
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Fix ARTIC data table declaration and protocol URL#8255
jmchilton wants to merge 2 commits into
mainfrom
agent/fix-artic-clair3-data-table

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@jmchilton

@jmchilton jmchilton commented Jul 30, 2026

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What changed

  • Rename ARTIC's Clair3 model table declaration from model to clair3_models, matching the name consumed by artic_minion.xml.
  • Point the production table configuration at tool-data/clair3_models.loc.
  • Rename models.loc.sample to clair3_models.loc.sample so the shipped sample initializes the configured location file.
  • Replace the removed MPXV bioinformatics SOP URL with ARTIC's current fieldbioinformatics SOP.

Why

artic_minion.xml consumes clair3_models, but ARTIC's sample and test table configurations declared an unused table named model. The production configuration also referred to model.loc, while the shipped sample used the plural filename models.loc.sample. As a result, ARTIC's local declaration could not provide data to its cached-model selector.

The wrapper also linked to the removed https://artic.network/mpxv/mpxv-bioinformatics-sop.html page. ARTIC now publishes the relevant MPXV example in its current fieldbioinformatics SOP.

These inconsistencies were discovered using linting built for planemo#1672.

Impact

ARTIC now consistently declares and ships the same clair3_models table consumed by the wrapper, and its help links to a live, authoritative protocol. The table schema remains unchanged and aligned with the Clair3 model data manager.

Validation

  • xmllint --noout tools/artic/artic_minion.xml tools/artic/tool_data_table_conf.xml.sample tools/artic/tool_data_table_conf.xml.test
  • Verified every ARTIC from_data_table reference has a matching declaration.
  • git diff --check
  • planemo lint --urls --fail_level error tools/artic/artic_minion.xml

@jmchilton
jmchilton marked this pull request as ready for review July 30, 2026 19:07
@jmchilton jmchilton changed the title Fix ARTIC Clair3 data table declaration Fix ARTIC data table declaration and protocol URL Jul 30, 2026
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