gxformat2 skeleton with per-step TODOs from a free-form summary and Galaxy design brief.
Directory Mold with only index.md frontmatter.
source-specific fields are coherent.
Abstract oracle: fixture-independent property checks any run must satisfy.
eval.md declares properties and check type.
eval.md ↗Concrete cases: fixtures bound to expected values, run against the eval properties.
scenarios.md not written yet.
12 typed references; 0 resolver issues.
All on-demand references describe triggers.
Hypothesis references include verification.
Typed Mold references describe what casting consumes and when the generated skill should load each artifact.
Structured contract copied for validation or lookup.
Command reference. Usually cast to a sidecar and loaded only when invoked.
Background synthesis loaded by explicit progressive-disclosure metadata.
Background synthesis loaded by explicit progressive-disclosure metadata.
Background synthesis loaded by explicit progressive-disclosure metadata.
Background synthesis loaded by explicit progressive-disclosure metadata.
Background synthesis loaded by explicit progressive-disclosure metadata.
Workflow-construction idiom. Usually condensed during casting.
Workflow-construction idiom. Usually condensed during casting.
Workflow-construction idiom. Usually condensed during casting.
Workflow-construction idiom. Usually condensed during casting.
Background synthesis loaded by explicit progressive-disclosure metadata.
gxformat2 draft (see [[galaxy-workflow-draft-format]]): topology fully resolved (workflow inputs, outputs, step set, edges); tool_id / tool_state / tool_shed_repository and wrapper-determined port names may be TODO with free-text _plan_state / _plan_context / _plan_in / _plan_out per step for later implementation Molds.
Updated obligations ledger: new unmet needs this step surfaces appended; prior entries its decisions close marked resolved.
Free-form source summary emitted by [[summarize-paper]] or [[interview-to-freeform-summary]]; consulted while emitting placeholder steps.
Galaxy interface brief from [[freeform-summary-to-galaxy-interface]] that pins workflow inputs, outputs, labels.
Galaxy data-flow brief from [[freeform-summary-to-galaxy-data-flow]] that pins abstract operations and collection choices.
Structural diff guidance from [[compare-against-iwc-exemplar]] (run on the design brief); steers the skeleton toward IWC-aligned structure before per-step authoring. Carries an inline gxformat2 excerpt of the nearest exemplar.
Cleaned gxformat2 view of the nearest IWC exemplar's relevant subgraph from [[compare-against-iwc-exemplar]]; pattern-match the draft's input/collection shapes, map-over wiring, output promotion, and post-job actions against this concrete idiom. Absent when no nearest exemplar was found.
Carried obligations ledger [[open-requirements-ledger]]: read prior open entries; this design step appends new unmet needs and marks ones its decisions resolve.
Read the original free-form source artifact if present, the free-form summary Markdown document, and the freeform-to-Galaxy interface and data-flow briefs. Emit a gxformat2 skeleton with workflow inputs, workflow outputs, placeholder steps, rough connections, and TODO slots for later implementation Molds.
The free-form summary does not have a concrete schema yet; treat it as Markdown. Treat the prior-step index as the working context: source transcript or paper, free-form summary, freeform-to-Galaxy interface and data-flow briefs, and any open questions carried forward.
Topology is this Mold’s job to settle. The output must be concrete gxformat2: workflow inputs with their final collection shapes and formats, workflow outputs, the step set, the producer→consumer edge graph, branches, and when: guards are all decided here. The upstream freeform-to-Galaxy interface and data-flow briefs guide those decisions, but if they hedge or leave a topology choice open, this Mold makes the call from source evidence, IWC exemplars, and pattern pages — never emit a topology TODO. Wrapper resolution, by contrast, is evidence-gated, not source-gated: resolve each tool step to the tier its evidence supports — Resolved (fully concrete, no _plan_*), Identity-pinned (concrete tool_id, parameters and changeset left to the per-step Mold), or Deferred (tool_id: TODO) — as defined in galaxy-workflow-draft-format. Capture whatever you defer in the _plan_* family (_plan_state, _plan_context, _plan_in, _plan_out) so the per-step Mold has the source evidence and constraints it needs.
Source tendency: free-form sources rarely name tools, so steps land in Deferred more often than nf-core or CWL — but a free-form source that does name a specific tool/version with evidence hardens to the matching tier, and a corpus-confirmed utility wrapper (interval/tabular/collection op) is not deferred just because the surrounding prose is informal. When deferring a domain tool, cite the originating paper section, interview answer, figure, or supplementary table in _plan_context, and record vague intent in _plan_state (“default settings”, “stranded reverse if mentioned, else unstranded”) so the per-step Mold knows the evidence ceiling.
Before handing off, sanity-check that each step is computable from what feeds it. Once the step set is settled, re-read it and ask, for each step, whether the operation its intent implies can actually be produced from the inputs you wired. The connection graph only knows that ports connect — not what each port is supposed to contain — so an output that needs evidence no input carries will validate fine and still be impossible to implement. Where you spot that gap, don’t leave it implicit: wire (or add) the step that supplies the missing input, or record the unmet need plainly in _plan_state so the per-step Mold or a reviewer can act on it rather than discover it late.
Things worth a second look:
_plan_* promises more than its in: ports can supply;Optionally, once topology is settled, group the step set into titled stage frames via the gxformat2 comments: array (one frame per analysis stage, contains_steps: populated, color decorative) — see galaxy-workflow-comments for the convention.
Before handing off, check each settled step is computable from what feeds it. The connection graph knows that ports connect, not what they carry — so a declared output that needs evidence no wired input supplies will validate yet can’t be implemented. Where you find that gap, wire (or add) the producer; if you can’t, append a blocking entry to the open-requirements-ledger naming the step, the uncomputable output, and the missing evidence (and record vague intent in _plan_state) so the per-step loop or repair-galaxy-draft-topology acts on it rather than discovering it late. More generally, carry the ledger: read the entries bearing on your topology decisions and mark resolved the ones you close.
Output shape is gxformat2 with wrapper-tier relaxations and _plan_state / _plan_context / _plan_in / _plan_out per tool step — see galaxy-workflow-draft-format. Refinement open work for those planning fields lives in refinement.md.