Structured contract copied for validation or lookup.
- Purpose
- Carry the required implementation-contract shape into skeleton construction.
workflow-brief-to-galaxy-template
Build a gxformat2 skeleton from a reviewed Workflow Brief and its Galaxy design briefs, consulting retained source evidence.
Mold health
warn- Source layout
Every file beside index.md is one the mold kind declares.
- Axis fields
target-specific fields are coherent.
- Eval plan
Abstract oracle: the properties any cast of this Mold must satisfy.
eval.md declares properties and check type.
eval.md ↗ - Scenarios
Concrete cases bound to fixtures, run against the eval properties.
scenarios.md not written yet.
- Typed refs
14 typed references; 0 resolver issues.
- On-demand triggers
All on-demand references describe triggers.
- Evidence checks
Hypothesis references include verification.
- axis
- target-specific
- target
- galaxy
- name
- workflow-brief-to-galaxy-template
contract
Reference Loading
Typed references describe what casting consumes, and when the generated skill should load each artifact.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Keep the reviewed brief authoritative while using retained summaries as evidence rather than replacement intent.
- Verify
- Confirm a worked run preserves brief scope and bytes through topology construction.
Structured contract copied for validation or lookup.
- Purpose
- Output contract: the emitted gxformat2 draft conforms to [[galaxy-workflow-draft]]. Cast bundles the JSON Schema so the skill carries its output shape alongside the [[draft-validate]] CLI checks.
Command reference. Usually cast to a sidecar and loaded only when invoked.
- Purpose
- Validate the emitted draft against draft-contract rules (sentinel form, topology, _plan_* placement) before handing off.
- Trigger
- After writing or modifying the draft workflow file.
- Verify
- Cast the skill, run on a representative paper-derived summary, confirm draft-validate diagnostics route back.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Close the open entries the settled topology discharges, and append a blocking entry for any settled step whose declared output no wired input can supply — the computability gap gxwf validation cannot see, raised here rather than left for the per-step loop to hit.
- Verify
- Promote after a worked run shows entries this Mold appends or resolves are consumed downstream without re-derivation.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Emit the gxformat2 draft superset: TODO tool_id, optional state / tool_shed_repository, and per-step _plan_state / _plan_context planning fields.
- Verify
- Promote after a downstream per-step implementation Mold consumes _plan_state and _plan_context without re-deriving intent from source evidence.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Choose stable workflow input/output labels, testable checkpoint outputs, and fixture-compatible workflow interfaces while drafting the skeleton.
- Trigger
- When the template decides workflow inputs, workflow outputs, promoted checkpoints, or collection output identifiers that future tests will need to address.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Preserve Galaxy collection typing and map-over/reduction semantics in the gxformat2 skeleton.
- Trigger
- When creating workflow inputs, outputs, and placeholder connections involving collections.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Respect the handoff from the Workflow-Brief-to-Galaxy interface and data-flow briefs to the gxformat2 skeleton.
- Trigger
- When translating abstract nodes, unresolved tool needs, and placeholder transformations into template TODOs.
- Verify
- Promote after two worked brief-to-Galaxy templates preserve the design-brief/template split without schema changes.
Workflow-construction idiom. Copied verbatim.
- Purpose
- Use corpus-grounded collection pattern guidance for unresolved skeleton steps.
- Trigger
- When adding TODO steps for collection cleanup, reshaping, relabeling, identifier synchronization, or collection-tabular bridges.
Workflow-construction idiom. Copied verbatim.
- Purpose
- Use corpus-grounded tabular pattern guidance for unresolved skeleton steps.
- Trigger
- When adding TODO steps for tabular filtering, projection, joins, aggregation, text-processing recipes, or tabular-collection bridges.
Workflow-construction idiom. Copied verbatim.
- Purpose
- Use corpus-grounded conditional pattern guidance for unresolved skeleton steps.
- Trigger
- When adding TODO steps for optional steps, gating on non-empty results, routing between alternative outputs, or transform-or-pass-through branches.
Workflow-construction idiom. Copied verbatim.
- Purpose
- Use corpus-grounded genomic-interval pattern guidance for unresolved skeleton steps.
- Trigger
- When adding TODO steps for interval overlap, merge, coverage, windowing, masking, or set-algebra on coordinate features.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Group the settled step set into titled stage frames (the gxformat2 `comments:` array) so the skeleton carries the analysis-stage narrative IWC authors annotate by hand. Schema-legal and optional.
- Trigger
- After topology is settled and the skeleton can be partitioned into named analysis stages (inputs, per-stage step clusters, parameter-derivation knots, visualization/outputs).
Cast artifacts
- Claude skill workflow-brief-to-galaxy-template — Build a gxformat2 skeleton from a reviewed Workflow Brief and its Galaxy design briefs, consulting retained source evidence.
Artifact handoffs
/ pipeline contractProduces
-
gxformat2 draft (see [[galaxy-workflow-draft-format]]): topology fully resolved (workflow inputs, outputs, step set, edges); tool_id / 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.
-
Carried obligations ledger re-emitted by this step: entries it appended or closed updated, every other entry passed through with its provenance intact.
Consumes
Inputs sharing a role are alternatives — one producer satisfies it.
-
Expert-reviewed implementation contract governing scope and requirements.
- freeform-summary source-evidence
Optional narrative source evidence retained from brief production; consult it for source-backed detail within the selected scope.
- summary-nextflow source-evidence
Optional structured Nextflow source evidence; source processes and channels are evidence, not a Galaxy topology mandate.
-
Galaxy interface brief from [[workflow-brief-to-galaxy-interface]] that pins workflow inputs, outputs, labels.
-
Galaxy data-flow brief from [[workflow-brief-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]]: the run's open, resolved, and surrendered entries with their provenance. Absent on the first Mold of a run; start an empty one.
workflow-brief-to-galaxy-template
Read the unchanged Workflow Brief and its Galaxy interface and data-flow briefs. Consult the original source artifact and retained freeform-summary or summary-nextflow when present. Emit a gxformat2 skeleton with workflow inputs, workflow outputs, placeholder steps, rough connections, and TODO slots for later implementation Molds.
The Workflow Brief is the implementation contract. Source artifacts are an evidence dossier: use them to substantiate methods, formats, parameters, and named tools within the selected scope, never to reintroduce excluded work or override expert requirements. A hand-authored brief without a source summary remains a valid input; record consequential missing evidence in the ledger instead of inventing it.
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 Workflow-Brief-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 reviewed intent, 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.
Evidence tendency: narrative sources name tools less often than structured pipeline summaries, so their steps land in Deferred more often — but source evidence that names a specific tool/version can harden to the matching tier, and a corpus-confirmed utility wrapper is not deferred merely because the source is informal. When deferring a domain tool, cite the originating paper section, interview answer, pipeline location, figure, or supplementary table in _plan_context, and record vague intent in _plan_state 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:
- an output column or field that no wired input carries;
- an aggregate or summary whose grouping key isn’t present upstream;
- a filter or threshold whose criterion isn’t produced by any input;
- a join whose key doesn’t exist on both sides;
- a step whose
_plan_*promises more than itsin:ports can supply; - if classification step, is that classification/enumeration possible only from inputs.
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, record the vague intent in _plan_state and append a blocking entry to the open-requirements-ledger naming the step, the uncomputable output, and the missing evidence, so the per-step loop or repair-galaxy-draft-topology acts on it rather than discovering it late.
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.
Incoming References (13)
- repair-galaxy-draft-topology related mold — Re-wire a Galaxy draft region when a step's declared output can't be computed from its wired inputs.
- workflow-brief-to-galaxy-data-flow related note — Translate a reviewed Workflow Brief and its Galaxy interface into a Galaxy data-flow design brief.
- workflow-brief-to-galaxy-interface related note — Map a reviewed Workflow Brief into a Galaxy workflow interface design brief, consulting retained source evidence when available.
- Galaxy: collection patterns related mold — Choose a Galaxy collection operation or map-over recipe from the current and required data shapes.
- Galaxy: conditionals patterns related mold — Choose a Galaxy when gate, routed output, fallback, or collection cleanup by what must change downstream.
- Galaxy: genomic interval patterns related mold — Use this MOC to choose corpus-grounded Galaxy genomic interval operations and recipes on coordinate features.
- Galaxy: sequence patterns related mold — Use this MOC to choose corpus-grounded Galaxy operations on sequence records (FASTA) — interconvert, reformat, merge, length, extract/mask by region.
- Galaxy: tabular patterns related mold — Use this MOC to choose corpus-grounded Galaxy tabular transformation patterns.
- WORKFLOW BRIEF → GALAXY phase of pipeline — Consume an expert-reviewed, unchanged Workflow Brief directly through the Galaxy design and implementation chain.
- Galaxy data-flow draft contract related mold — Defines the proposed boundary between Galaxy data-flow drafts, gxformat2 templates, and concrete step implementation.
- Galaxy Workflow Comments related note — How to annotate a gxformat2 workflow with editor comments: one titled frame per analysis stage, populate contains_steps, color decorative.
- Galaxy workflow draft format related mold — gxformat2 draft superset: wrapper-tier TODOs (tool_id, state, port names) plus _plan_state / _plan_context / _plan_in / _plan_out per tool step.
- Galaxy workflow draft (gxformat2 superset) related mold — JSON Schema for `class: GalaxyWorkflowDraft` — gxformat2 with `TODO_*` sentinels and `_plan_*` planning fields per draft step.