Galaxy Workflow Foundry

Knowledge base + casting pipeline for building Galaxy workflows with gxwf.

An LLM can read a paper or a Nextflow pipeline and propose a Galaxy workflow — and fail the same boring, detectable ways every time: hallucinated tool IDs, dropped +galaxyN revisions, fabricated parameter names, gxformat2 the parser rejects on line one. Hand-authored "convert a workflow" skills paper over these with prose caveats that don't compose and rot on the next regression. The Foundry's bet: a knowledge base becomes useful when its structure makes it executable, and a skill becomes trustworthy when its source stays inspectable.

Site: https://galaxyproject.github.io/foundry/

Goal

Convert workflows authored in other systems — papers describing computational analyses, Nextflow pipelines, CWL workflows — into validated Galaxy workflows in the gxformat2 format. The Foundry decomposes that conversion into atomic, schema-validated steps that an LLM agent can execute reliably, grounded in gxwf's static validation of gxformat2 and tool steps.

Why

Hand-authored, monolithic conversion skills are brittle, hard to test, and don't compose. The Foundry takes a different shape:

• Principled. The Foundry keeps upstream systems authoritative, records provenance for derived artifacts, uses deterministic tooling for deterministic checks, and keeps source knowledge portable across agent runtimes. See docs/GUIDING_PRINCIPLES.md.
• Decomposed. Each conversion step is its own Mold — a typed reference manifest that casts into a self-contained skill artifact. The full conversion is an ordered Pipeline of Molds.
• Schema-driven. gxwf validates every authored step inline. The validation loop catches failure modes deterministically — UUID validity, tool-ID and +galaxyN revision suffixes, input_connections parameter-name mismatches, conditional-selector branches in tool_state — rather than relying on enumerated prose caveats.
• Corpus-grounded. Patterns and Molds are derived from observed structure in the IWC workflow corpus, not invented top-down. Every reference is traceable back to one or more curated, working gxformat2 exemplars; the same exemplars double as evaluation material for cast skills.
• Agent-friendly. Cast skills are condensed, isolated, and frozen against the Foundry version they were cast from. No runtime dependency on the Foundry, no chasing wiki-links from inside a skill. Casting is the integration boundary.

What's here

• Pipelines (content/pipelines/) — ordered Mold sequences composing into an end-to-end conversion (paper-to-galaxy, nextflow-to-galaxy, cwl-to-galaxy, interview-to-galaxy, update-interview-to-galaxy, paper-to-cwl, nextflow-to-cwl). Build artifact and primary navigation surface.
• Molds (content/molds/) — abstract templates describing a workflow-construction action. Each Mold is a typed reference manifest: it declares the patterns, CLI manual pages, schemas, prompts, and examples it depends on, and casts into one or more skill artifacts.
• Patterns (content/patterns/) — Galaxy workflow construction reference (collection manipulation, tabular manipulation, conditional handling, custom-tool authoring). Wiki-linked from action Molds; pulled into cast skills via casting's pattern-kind dispatch.
• CLI manual pages (content/cli/<tool>/) — one note per command or subcommand, covering gxwf, planemo, cwltool, cwl-utils, foundry, and galaxy-tool-cache. Cast to JSON sidecars by action Molds that reference exact commands.
• Schemas (content/schemas/) — <name>.md schema notes only; the JSON Schema itself lives in its TypeScript package at packages/<name>-schema/src/<name>.schema.json (Foundry-authored) or is synced there from an upstream npm package (vendored). The note's frontmatter declares package + package_export. site/src/lib/schema-registry.ts imports each schema directly from the package; Mold frontmatter cites schemas via [[wiki-link]] and cast imports the named runtime export at build time, serializing it verbatim into cast bundles.
• Casts (casts/<target>/<name>/) — generated artifacts, one per (Mold, target) pair. Frozen, condensed, no links back.

Authoring

Two flows feed the Foundry:

• Slash commands (.claude/commands/) — agent-driven scaffold-prompt-validate. Primary.
• Hand edits + npm run validate — small fixes.

Casting produces skill artifacts: npm run cast -- --mold=<slug> --target=<target>.

Frontmatter is contract-enforced by the shared zod schema in @galaxy-foundry/note-schema (used by both the validator and the site); every note carries a registered tag from meta_tags.yml. Validate before commit.

Tooling

npm run validate          # schema + cross-file checks
npm run test              # vitest suite
npm run typecheck         # tsc --noEmit
npm run dashboard         # generate content/Dashboard.md
npm run index             # generate content/Index.md
npm run cast              # cast a Mold (see above)
npm run site:dev          # Astro dev server

--check variants on the generators detect drift; CI runs them before deploy.

Design docs

Long-form design narrative under docs/:

• GUIDING_PRINCIPLES.md — why the Foundry prioritizes upstream authority, provenance, deterministic tooling, portability, actionable knowledge, and corpus grounding.
• ARCHITECTURE.md — directory layout, types, validation pipeline, site rendering.
• HARNESS_PIPELINES.md — pipeline narrative behind content/pipelines/.
• MOLDS.md — Mold inventory rationale and bucketing axes.
• COMPILATION_PIPELINE.md — casting design.
• CORPUS_INGESTION.md — IWC grounding; URL-not-mirror principle.
• SCHEMA_PACKAGES.md — standard package shape for Foundry-authored JSON Schemas and CLI validators.
• COMPARISONS.md — positioning vs wikis/skill bundles plus a dated KB-to-skill landscape snapshot.

Status

Working system, pre-review. All seven pipelines cast end-to-end into Claude skills: 45 Molds, 54 pattern pages, CLI manual pages for six tools, foundry-build cast + assemble-pipeline, and the live Astro site.

Forward work is quality and reach rather than existence. Every Mold is still status: draft — none have passed a review gate. The generic and web cast targets are scaffolded but empty; only Claude casts today. Eval coverage is partial: 33 of 45 Molds have an eval.md, 27 have scenarios.md.