Glossary
Pinned definitions for the Galaxy Workflow Foundry. Used by the PRD, design docs, and the eventual MOLD_SPEC. If two docs disagree on a term, this file wins; resolve drift by updating here first.
Alphabetical.
Branch ([branch] annotation, phase kind) — a Pipeline phase that encodes harness-level routing/fallback rather than wrapping a Mold. Carries a named routing pattern (discover-or-author, test-data-resolution, …) and either branches: (binary with fallthrough) or chain: (N-step sequential fallback) of Mold wiki-links plus optional terminal sentinels (e.g. user-supplied). Inner wiki-links resolve to Molds and are validator-checked. Renders on a subway map as a decision diamond. Replaces the prior [harness] annotation umbrella.
Cast (verb) — produce a self-contained artifact from a Mold via the casting process. (noun) — a single casting result for one Mold and target. Example: "the cast of implement-galaxy-tool-step for the Claude target."
Cast artifact — the compiled output produced by casting a Mold. Self-contained, condensed, no links back to the Foundry, no runtime dependency on it. Frozen against the Foundry version it was cast from. May target Claude's skill format, a web-app-baked skill, a generic format, etc.
Cast target — an output format that casting can produce. Examples: Claude skill directory, skill baked into a web application, generic (non-Claude) skill format. A single Mold may cast to several targets.
Casting — the LLM-driven process that produces a cast artifact from a Mold. Operates as per-kind dispatch over the Mold's typed references (see Reference kind): patterns get LLM-condensed, schemas get copied verbatim, manpages get cast to JSON sidecars, examples get copied, prompts get inlined, evals get dropped. The casting process is non-deterministic by design and expected to evolve as models improve.
Casting skill — the producer skill or tool that reads a Mold and emits a cast artifact. Distinct from a generated skill, which is one possible kind of cast artifact.
CLI reference content — per-command CLI documentation under content/cli/<tool>/<command>.md. Action Molds (discover-shed-tool, validate-galaxy-step, validate-galaxy-workflow, run-workflow-test) reference individual manual pages directly; whole-CLI reference surfaces are not Molds unless a real action emerges.
CLI manual page — a Foundry content note describing a single CLI command or subcommand (install/source, synopsis, args, flags, examples, exit codes, output shape, error patterns, gotchas). Lives at content/cli/<tool>/<cmd>.md. Hand-authored or seeded from --help then humanized. Wiki-linked from action Molds. Cast to a structured sidecar by the casting pipeline; not inlined as prose.
Composed path — a harness pipeline that uses CWL as a structured intermediate target before reaching Galaxy. Examples: PAPER → CWL → GALAXY, NEXTFLOW → CWL → GALAXY. Contrasts with direct path. Both are first-class options.
Corpus-first — the principle that everything in the Foundry (patterns, Molds, design guidance) is grounded in observed structure of real IWC workflows, not invented top-down. Anything in the Foundry should be traceable back to one or more IWC exemplars.
Direct path — a harness pipeline that targets Galaxy without going through a CWL intermediate. Examples: NEXTFLOW → GALAXY, PAPER → GALAXY. Contrasts with composed path.
Evaluation plan — Mold-owned content (eval.md) that describes how a generated skill or other cast artifact is exercised: which IWC exemplars it should reproduce or align with, pass/fail or qualitative criteria. Strictly assertion-shaped: every case has a fixture and something that could fail. Lives alongside the Mold in the Foundry. Not packaged into cast artifacts — evals are Foundry-maintainer infrastructure, not consumer-facing. Distinct from Usage note (illustration) and Refinement note (design questions).
Foundry (short for Galaxy Workflow Foundry) — the standalone knowledge base where Pipelines, Molds, pattern pages, CLI manual pages, IO schemas, and IWC-citing content live. Renders as a navigable site; serves as the source of truth that casting reads.
Gate ([gate] annotation, phase kind — future) — placeholder for a phase-level annotation marking an inline approval / scope-confirmation checkpoint. Coined when a real pipeline first needs an inline pause for user input; not used by any current pipeline. The phase-kind set is open and not pre-enumerated — [branch] and [gate] are unrelated behaviors and don't share an umbrella tag.
Galaxy Workflow Foundry — the project's full name. See Foundry. Subtitle of choice for documents and presentations.
Generated skill — a skill-shaped cast artifact, such as a Claude skill produced from a Mold. Generated skills are consumed by harnesses; they are not the same thing as the casting skill that produced them.
gxformat2 — Galaxy's Format-2 workflow format. The target format for Galaxy-targeting authoring Molds.
gxwf — the design-time CLI tool. Workflow validation, tool discovery / search / revisions, schema, conversion, lint. Available in TypeScript and Python; both share an interface. Inside the Foundry, gxwf's CLI surface is captured as CLI manual pages (content/cli/gxwf/*) referenced by action Molds; the existing ~/.claude/skills/gxwf-cli (a help-text dump) is prior art being replaced. Contrasts with Planemo.
Harness — hand-authored orchestration glue that sequences Molds, manages user-approval gates, maintains run state, handles routing decisions (e.g., the discover-or-author branch). Not cast from a Mold; not in the Foundry's casting pipeline. May be heavyweight (Archon-style) or a lightweight orchestration skill.
Harness-level concern — a recurring pipeline activity that belongs to the harness, not to any individual Mold. Examples: approval gates, scope confirmation, plan presentation, tool-discovery routing, test-data fallback chains, state and resumption. These are not Molds. Some of them surface inline in pipelines as non-Mold phase kinds ([branch] for routing, the future [gate] for checkpoints); others (state, resumption, autonomy posture) are off-pipeline harness-internal concerns. See docs/HARNESS_PIPELINES.md.
IWC — Intergalactic Workflow Commission. Curates the canonical set of high-quality Galaxy workflows. The Foundry's foundational corpus.
IWC exemplar — one workflow from the IWC corpus. The cleaned gxformat2 versions live in /Users/jxc755/projects/repositories/workflow-fixtures/iwc-format2/. Pattern pages cite exemplars; Molds reference them as ground truth; casting may inline references; evaluations exercise generated skills against them.
Loop ([loop] annotation) — a phase-level flag (loop: true in frontmatter) marking a phase that runs once per step in the workflow being constructed. Applied to per-step authoring phases (implement-galaxy-tool-step, validate-galaxy-step, …) and to [branch] phases that route per-step (discover-or-author). Renders on a subway map as a decorated station.
Mold — an abstract, structured template inside the Foundry that describes a workflow-construction action. Authored as a typed reference manifest with a presentation layer: a .md file whose frontmatter declares typed references to heterogeneous artifacts (pattern pages, CLI manual pages, IO schemas, prompt fragments, examples), and whose body is a procedural skeleton that ties them together. Rendered as a navigable Foundry page; cast into one or more cast artifacts via casting's per-kind dispatch over those references.
Mold (atomic, phase-sized) — the granularity rule: each Mold is roughly the size of one Mold-shaped phase in a Pipeline. Not necessarily small; summarize-nextflow and implement-galaxy-tool-step are both atomic at this tier even though they differ in content size.
Not a Mold — explicit boundary marker for things that are not cast from the Foundry. Includes harnesses, harness-level concerns (state, resumption, autonomy posture), Pipelines themselves, non-Mold phase kinds ([branch], future [gate] — these reference Molds via embedded wiki-links but are not Molds), and pure reference content (pattern pages, CLI manual pages, IO schemas — these are referenced by Molds, not Molds themselves). Wrapping a CLI is not a disqualifier: see validate-galaxy-step, discover-shed-tool, run-workflow-test.
Pattern page — a Foundry reference page describing a Galaxy workflow construction pattern (collection manipulation, tabular manipulation, conditional handling, custom-tool authoring, …). Wiki-linked from action Molds; pulled into cast artifacts via casting's pattern-kind dispatch (LLM-condensed, mixed verbatim and summarization). Different from a Mold: a pattern page is reference, a Mold is action. Some patterns have a companion action Mold (e.g., custom-tool-authoring pattern + author-galaxy-tool-wrapper Mold).
Phase — one atomic unit of a Pipeline's ordered phases array. Either Mold-shaped (mold: [...](/foundry/pipelines/cwl-to-galaxy/), optionally loop: true) or a non-Mold annotation kind: [branch] today, future [gate] when needed. Open set — new phase kinds are coined when first surfaced inline rather than pre-enumerated. Validator resolves embedded wiki-links per kind (Mold-shaped phases must resolve to type: mold; [branch] inner items resolve to Molds or are terminal sentinels like user-supplied).
Pipeline — first-class Foundry note type (type: pipeline, content/pipelines/<slug>.md). An ordered sequence of phases that compose into a harness journey (paper-to-galaxy, nextflow-to-galaxy, cwl-to-galaxy, paper-to-cwl, nextflow-to-cwl). Dual purpose: (a) build artifact — names the Molds a harness will orchestrate; (b) navigation primitive — the journey-surface IA over the KB, rendered as a subway map. phases frontmatter is the machine-readable spine; the body is the human-readable view. Pipelines are referenced content, not cast. The Mold-inventory invariant ("Molds = union of pipeline phases") is machine-checked: every Mold-shaped phase resolves to a real Mold note, and non-draft Molds with no pipeline membership surface as inventory-coverage warnings.
Planemo — the runtime CLI tool. Executes Galaxy and CWL workflows. Used by run-workflow-test, debug-galaxy-workflow-output, debug-cwl-workflow-output. Inside the Foundry, Planemo's CLI surface is captured as CLI manual pages (content/cli/planemo/*) referenced by action Molds. Contrasts with gxwf.
Refinement journal — append-only sequence of entries under content/molds/<slug>/refinements/<date>-<slug>.md, one per /refine-mold run. Each entry carries small structured frontmatter (mold, date, intent, decision) and free-form body. Entries are superseded rather than edited; the decision field (keep | schema-change | reference-change | eval-add | open-question | other) supports cross-Mold rollups.
Refinement note — Mold-owned content (refinement.md) that parks open design questions about the Mold itself: schema fields under suspicion, references whose value isn't clear, scope edges. Free-form; not assertion-shaped. Read by the /refine-mold skill as part of context-loading. Never packaged into cast artifacts. Distinct from Evaluation plan (assertions) and Usage note (illustration).
Reference kind — the type discriminator on a Mold's typed references; controls casting behavior. Provisional kinds: pattern (markdown reference, LLM-condensed), cli-command (manual page, cast to JSON sidecar), schema (JSON Schema file, copied verbatim), example (fixture, copied verbatim), prompt (markdown fragment, inlined verbatim), eval (Foundry-only, never in cast). Per-kind dispatch is what makes casting more than "resolve all wiki links the same way."
Routing pattern — the named-pattern value inside a [branch] phase that determines its inner shape and rendering. Initial vocabulary: discover-or-author (binary with branches: and a fallthrough: step) and test-data-resolution (sequential chain: of Mold wiki-links ending in a terminal sentinel like user-supplied). Open question whether the set graduates into a closed schema enum or stays open with validator coverage of embedded wiki-links only.
Schema (Mold IO) — a JSON Schema file declaring the input or output shape of a Mold (e.g., the per-source summary schemas, the Galaxy tool summary schema). Lives in schemas/ (a non-content directory; not a vault note). Referenced by Molds via typed-path frontmatter fields; copied verbatim into cast bundles by casting. Distinct from meta_schema.yml, which is the frontmatter contract for content notes.
Subway map — informal name for the visual rendering of a Pipeline as a vertical line of stops: Mold-shaped phases are linked stations, [loop] decorates per-step stations, [branch] stops are decision diamonds with their inner branches/chains expanded, future [gate] stops would render as checkpoint markers. Off-ramps per stop point to the patterns / CLI manpages / schemas the Mold references — the reference-surface drill-downs from a journey-surface point. Rendered by pipelines/[slug].astro (deferred until off-ramp content density justifies the visual).
Source-specific (Mold axis) — a Mold whose content depends on the input format. Examples: summarize-paper, summarize-nextflow, summarize-cwl. Each emits its own schema by design — no shared summary schema.
Target-specific (Mold axis) — a Mold whose content depends on the output target. Examples: summary-to-cwl-template, summarize-galaxy-tool, validate-cwl.
Tool-specific (Mold axis) — a provisional Mold axis for actions whose behavior depends on one external tool. Whole-CLI reference surfaces are reference content, not Molds.
Generic (Mold axis) — a Mold whose content depends on neither source nor target nor a single tool. Rare in the current inventory.
Usage note — Mold-owned content (usage.md) illustrating representative invocations of a Mold. Author-facing narrative; no assertions, no expectation: lines. Lives alongside eval.md and refinement.md to keep illustrative content out of evaluation. Never packaged into cast artifacts in v1; may later be cast as examples/-shaped content.
Validation posture (schema, not caveats) — the Foundry's stance on failure modes: gxwf static schema validation catches the failure modes prior-art skills had to enumerate as prose caveats (UUID validity, tool-ID/owner/+galaxyN, parameter-name mismatches, etc.). The Foundry does not maintain a parallel caveat catalog; the validation loop (author → validate → fix) is the enforcement mechanism, run inline per step.