Foundry
Home Research

Galaxy native workflow (.ga) structural JSON Schema

Vendored structural JSON Schema for Galaxy native workflow (.ga) format: vocabulary for the JSON shape Galaxy emits and consumes.

draft research/componenttarget/galaxy
Raw
Revised
2026-05-05
Rev
1
Sources
https://github.com/jmchilton/galaxy-tool-util-ts/blob/7ae4ecd0ba8d492225f58a6d455c4cc5317298f0/packages/schema/src/native-galaxy-workflow.ts
Related
component

Vendored from upstream, pinned at SHA 7ae4ecd. One file lives next to this note:

  • native-galaxy-workflow.schema.json — Draft-07 JSON Schema generated from @galaxy-tool-util/schema’s NativeGalaxyWorkflowSchema via gxwf structural-schema --format native. Agents and casting should consume this when reasoning about the JSON shape Galaxy actually exports/imports (the .ga format), as opposed to the human-authoring gxformat2 YAML.

Re-sync: pnpm sync:vendored --update. Sync builds galaxy-tool-util-ts and re-runs the generator before copy.

Boundary vs gxformat2

gxformat2-schema covers the human-authoring YAML format (*.gxwf.yml, class: GalaxyWorkflow). This schema covers the JSON format Galaxy server emits/consumes (*.ga, a_galaxy_workflow: "true"). gxformat2 transpiles into native; the two are not interchangeable line-by-line.

Top-level shape

The schema declares required [class, a_galaxy_workflow, format-version] with class: enum["NativeGalaxyWorkflow"]. Optional: uuid, name, annotation, tags, version, license, release, creator, report, readme, help, logo_url, doi, source_metadata, comments, steps, subworkflows.

Caveat: schema is stricter than reality

Real .ga files do not carry a class field. Tested against $IWC/workflows/repeatmasking/RepeatMasking-Workflow.ga: top keys are a_galaxy_workflow, annotation, format-version, license, release, name, creator, steps, tags, uuid, version. The schema’s required: ["class", ...] rejects every real workflow Galaxy currently produces. Treat the schema as vocabulary reference, not a runtime validator for in-the-wild .ga files, until upstream relaxes the requirement or Galaxy starts emitting class. Worth filing on galaxy-tool-util-ts.

Caveats

  • Doc strings dropped. Same Effect-TS JSONSchema.make limitation as gxformat2-schema.
  • Repeated $id: "/schemas/unknown" markers appear 4× in this schema. Strict Ajv refuses to compile; pass { strict: false } or strip duplicates before compile.