Add PR-driven reference-data workflow-bundle pipeline (MetaPhlAn, mOTUs, SameStr)#89

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mvdbeek wants to merge 20 commits into

galaxyproject:mainfrom

mvdbeek:reference-data-workflow-bundles

Commits on Jul 9, 2026

Add PR-driven reference-data workflow-bundle pipeline (schema, lint, generator)
mvdbeek
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Validate generated workflows with gxformat2 and declare bundle outputs
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Add Stage 3 bundle import (invocation resolver + CVMFS importer + tests)
mvdbeek
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Wire Stage 2 (build.yml) and Stage 3 (CVMFS import driver)
mvdbeek
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Splice reference-data (Stage 3) import into .ci/jenkins.sh
mvdbeek
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Document the versioned reference-data (workflow-bundle) contribution flow
mvdbeek
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Verify reference data doesn't already exist via the Galaxy tool data table API
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Reference an existing upstream database instead of rebuilding it
mvdbeek
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Document reference-existing behavior for chained requests
mvdbeek
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Commits on Jul 11, 2026

Commits on Jul 12, 2026

Pin motus_db request to data_manager_motus 3.1.0+galaxy1
mvdbeek
committed

Commits on Jul 13, 2026