Fix ARTIC data table declaration and protocol URL - #8255
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July 30, 2026 19:07
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What changed
modeltoclair3_models, matching the name consumed byartic_minion.xml.tool-data/clair3_models.loc.models.loc.sampletoclair3_models.loc.sampleso the shipped sample initializes the configured location file.Why
artic_minion.xmlconsumesclair3_models, but ARTIC's sample and test table configurations declared an unused table namedmodel. The production configuration also referred tomodel.loc, while the shipped sample used the plural filenamemodels.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.htmlpage. 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_modelstable 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.testfrom_data_tablereference has a matching declaration.git diff --checkplanemo lint --urls --fail_level error tools/artic/artic_minion.xml