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."
Casting — the compilation process that produces a cast artifact from a Mold: deterministic tooling first, LLM second, in that order of trust — and in this Foundry the deterministic half reaches all the way, so there is no second phase. Operates as per-kind dispatch over the Mold's typed references (see Reference): each kind's cast: block in reference_contract.yml declares how it resolves and which mode it defaults to, so schemas get copied from a package export, manpages get cast to JSON sidecars, examples, prompts and patterns get copied verbatim, evals get dropped. The integration boundary — artifacts come out condensed, isolated, and frozen. 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, advance-galaxy-draft-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- or Pipeline-owned content (eval.md): the abstract oracle for a cast artifact (Mold) or end-to-end journey (Pipeline). Fixture-independent property checks and guardrails — how you judge any output, never a specific input/expected pair. Like a checker that asserts "a sort returns the same elements in nondecreasing order," not the case "sort([3,1,2]) == [1,2,3]"; concrete cases live in the Scenario note. Strictly property-shaped: every check states a property 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 Scenario note (concrete cases) and Refinement note (design questions). See content/meta/eval-philosophy.md for the reasoning.
Feedback ledger — opt-in runtime artifact (foundry-feedback-ledger) carrying actionable observations about the Foundry assets used during a real cast-skill or Pipeline run. The feedback runtime mode initializes it; skills append entries keyed by canonical authored-source locator; the terminal report-foundry-run-feedback Mold checks current main and existing issues before producing local drafts. Observations whose root cause is a related project (Galaxy, a tool wrapper, IWC corpus, or harness CLI) are admissible and are filed against the Foundry with their analysis rather than redirected to another tracker. Unlike the open-requirements ledger, it describes the machinery building the workflow rather than durable knowledge about the workflow being built, and it never participates in a convergence invariant.
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. The substrate term for this source-of-truth artifact is Knowledge Base (KB).
Freeform summary — Markdown source-evidence handoff for narrative or interview-derived starts. Produced by summarize-paper and interview-to-freeform-summary; consumed authoritatively by freeform-summary-to-galaxy-interface, freeform-summary-to-galaxy-data-flow, freeform-summary-to-galaxy-template, freeform-summary-to-galaxy-test-plan, freeform-summary-to-workflow-brief, and freeform-summary-to-cwl-design, and optionally as supporting evidence by the Workflow-Brief-to-Galaxy Molds. Deliberately not a rigid workflow schema: it preserves uncertainty, open questions, methods, tools, sample data, parameters, and expected outputs.
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 content/meta/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 materialize in workflow-fixtures/iwc-format2/ in the Foundry checkout. Pattern pages cite exemplars; Molds reference them as ground truth; casting may inline references; evaluations exercise generated skills against them.
Knowledge Base (KB) — the inspectable, human-readable source of truth at the center of the instance: the standalone site where Pipelines, Molds, pattern pages, CLI manual pages, and IO schemas live and from which casting reads. Authored to be read and learned by a human, not merely stored for an agent to retrieve. The KB is the source; a skill artifact is the package. Colloquially the Foundry (see Foundry).
Lifecycle pipeline — a Pipeline that operates on an existing workflow or workflow submission after construction. Carries lifecycle/review for advisory assessment or lifecycle/publication for maturation and publication handoff. The facet is orthogonal to source/* and target/*; harness-owned approval, state, and external mutations remain outside its Mold phases.
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 orchestrator Molds that advance the workflow by one step (advance-galaxy-draft-step). 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 discover-shed-tool, run-workflow-test, validate-galaxy-workflow.
Open-requirements ledger — the carried workflow-run knowledge artifact (open-requirements-ledger) threaded through the source→Galaxy pipeline. Obligation entries record unmet needs and dropped work; separate collections preserve discoveries, authorized decisions, and proposed changes to an immutable Workflow Brief. Molds append obligations and mark resolved the ones their decisions close; an entry nothing can close is left open with a surrender note and marked surrendered by the terminal path. Entries carry a blocking grade: a plain obligation the chain can work around, versus a computability gap that drives topology-repair escalation and is what the convergence gate counts. Proposed brief changes can only be accepted by the separate expert editing step. The artifact does not carry ordinary harness progress or Foundry feedback. In the per-step loop it remains the countable substrate for the topology-repair convergence invariant. See content/research/open-requirements-ledger/index.md.
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 (copied verbatim; a pattern is a flat note, so nothing travels beside it). 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: [[...]], 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>/index.md). A directory note like Mold: index.md is the only frontmatter-bearing file, with optional eval.md (pipeline-level oracle) and scenarios.md (end-to-end journeys) siblings. 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. Machine-checked: every Mold-shaped phase resolves to a real Mold note. Molds need not belong to a pipeline — standalone and indirectly-invoked Molds are first-class, not coverage gaps.
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.
Provenance — a record (_provenance.json) emitted beside every cast artifact: which Mold revision, which model version, which references resolved, which checks ran. The durable, non-commodity asset — the answer to "which specific claim is real and where it came from." Present in every cast; never lightened.
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 Scenario note (concrete cases).
Reference (a.k.a. reference kind) — a typed dependency a Mold declares; the kind discriminator controls casting behavior (per-kind dispatch). Provisional kinds: pattern (markdown reference, copied verbatim), cli-command (manual page, cast to JSON sidecar), schema (JSON Schema file, copied verbatim from a package export), example (fixture, authored vocabulary the caster declines), prompt (markdown fragment, the kind's bundled companion copied 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.
Runtime-produced artifact — a declared artifact whose producer is the harness or a skill runtime mode rather than a Mold. Registered once in runtime_artifacts.yml with its stable id, format, filename, protocol note, and producer: a runtime-mode producer names the option that turns it on and its initializer; a harness producer (the run record) is written on every run and names no option. It satisfies ordinary Mold input_artifacts[] producer validation and appears in cast provenance as runtime:<option>, or runtime:harness for an always-on one; sharing an id with a Mold output is an error.
Scenario note — Mold- or Pipeline-owned content (scenarios.md): the concrete test cases the eval oracle is applied against (a Mold input, or a whole-journey input for a Pipeline). Each case binds a fixture/input and states its expected values or assertions as free text (e.g. "CalliNGS-NF → 11 processes from root modules.nf", "sort([3,1,2]) == [1,2,3]"). All fixture-specific concreteness lives here, keeping the Evaluation plan (eval.md) a pure abstract oracle. A run pairs a scenario's output with the eval oracle's property checks (driven by /test-drive). Foundry-maintainer infrastructure; never packaged into cast artifacts. Distinct from Evaluation plan (abstract checker) and Refinement note (design questions).
Schema (Mold IO) — a machine-checkable contract for a Mold artifact. Structured JSON/YAML artifacts use JSON Schema; a Workflow Brief uses a declarative Markdown section schema. Source declarations live in their packages, schema notes identify the package export and validator, and casting copies the declaration into the bundle. Distinct from the shared zod frontmatter contract for content notes.
Skill artifact (a.k.a. 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. SKILL.md (or any skill file) is therefore a compile target, never the authoring surface. May target Claude's skill format, a web-app-baked skill, a generic format, etc.
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 [...slug].astro via PipelineBody.astro + PhaseGraph.astro; the per-pipeline harness off-ramp lives at pipelines/[slug]/harness.astro.
Source-specific (Mold axis) — a Mold whose content depends on the input format. Examples: summarize-paper, interview-to-freeform-summary, summarize-nextflow, summarize-cwl. Structured sources emit their own schema by design; paper and interview starts share the freeform-summary handoff.
Target (a.k.a. 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; the KB stays the source of truth.
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.
Topology repair — bounded re-wiring of a settled draft by repair-galaxy-draft-topology, the escalation target the per-step loop reaches when implementation proves a declared step output can't be computed from its wired inputs. Distinct from settling (the template Mold decides topology from the design briefs): repair is narrow (one named region), reactive (only a detected computability gap triggers it), bounded (decreasing open-blocker count under a hard escalation cap), and never decided by the loop — the loop escalates the decision back to the template tier. New steps land at draft tier and are realized by the existing discover-or-author → implement machinery. See repair-galaxy-draft-topology and the Open-requirements ledger.
Generic (Mold axis) — a Mold whose content depends on neither source nor target nor a single tool. Rare in the current inventory.
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.
Workflow Brief — an expert-editable Markdown input carrying scientific intent and scope under Workflow, and tooling/operating conditions under Agent Environment. Most details are optional; nonempty Blockers under either parent prevent implementation. Agents producing it make no inferred Galaxy design choices. Design and implementation leave it unchanged and record durable workflow discoveries, decisions, obligations, and proposed changes in open-requirements.ledger.yml; ordinary progress remains harness state.