Galaxy Workflow Foundry
Instance #1. The first and more-built Foundry — the one the pattern was abstracted from.
Read the instance’s own site: https://galaxyproject.github.io/foundry/
Domain
Convert workflows authored in other systems — papers describing a computational analysis, Nextflow pipelines, CWL workflows — into validated Galaxy workflows in the gxformat2 format. An LLM can read a paper and propose a Galaxy workflow, and then fail the same boring, detectable ways every time: hallucinated tool IDs, dropped +galaxyN revisions, fabricated parameter names, gxformat2 the parser rejects on line one. The Foundry decomposes the conversion into atomic, schema-validated steps an agent can execute reliably — a Pipeline of Molds, each casting into a self-contained skill artifact.
Corpus
Grounded in the IWC workflow corpus of curated, working gxformat2 exemplars. Patterns and Molds are derived from observed structure in that corpus, not invented top-down; every reference traces back to one or more real exemplars, and the same exemplars double as evaluation material for cast skills.
The check — a deterministic CLI (“the rails”)
This instance’s external check is mechanical: gxwf parses and validates gxformat2 and tool steps inline as each step is authored. The failure modes that defeat hand-written conversion skills — UUID validity, tool-ID and +galaxyN revision suffixes, input_connections parameter-name mismatches, conditional-selector branches in tool_state — are caught deterministically, not papered over with enumerated prose caveats. Fast, cheap, non-self-certifying because the parser is external to the model. These are the rails: the LLM can propose freely, but nothing certifies until the CLI accepts it.
This is the simpler end of the external check‘s range: where a deterministic tool can decide validity, the check is just that tool. (Workflow construction is also where this instance reaches for pipelines — ordered Mold sequences for an inherently sequential task; see the-diff.)
Targets
Casts to skill artifacts (Anthropic Agent Skill / generic skill targets). Cast skills are condensed, isolated, and frozen against the Foundry revision they came from — no runtime dependency on the Foundry, no wiki-links to chase from inside a skill. Casting is the integration boundary, with provenance recorded beside every artifact.
Status
The more mature instance. The spine is in place — content types, validator with cross-file resolution, pipeline lifting, Mold-inventory invariants — with real Mold authoring, pattern pages, CLI manual pages, casting tooling, and the Astro site as active forward work. Skeleton plus scaffolding, but the scaffolding is load-bearing.
Compare against instance #2 in the-diff — where this domain’s deterministic CLI check gives way to a constructed empirical referee, a different domain solving the same role its own way. For the shared substrate beneath both, see anatomy-of-an-instance.