Structured contract copied for validation or lookup.
- Purpose
- Carry the required implementation-contract shape into this design step.
workflow-brief-to-galaxy-data-flow
Translate a reviewed Workflow Brief and its Galaxy interface into a Galaxy data-flow design brief.
Mold health
ok- 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 declares cases bound to fixtures.
scenarios.md ↗ - Typed refs
9 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-data-flow
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 reviewed intent authoritative while using source summaries only as supporting evidence.
- Verify
- Confirm a worked run preserves scope and the brief's bytes while resolving Galaxy data-flow choices.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Inherit open entries rather than re-deriving them, close the ones this brief's wiring and collection decisions settle, and append data-flow obligations the narrative leaves open — a described transformation with no named tool, an implied intermediate the source never states, an ordering the prose doesn't fix.
- 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
- Keep the data-flow brief separate from gxformat2 templating and concrete step implementation.
- Verify
- Promote after two worked brief-to-Galaxy translations preserve this Mold boundary without moving fields.
Workflow-construction idiom. Copied verbatim.
- Purpose
- Ground collection-shape choices in curated, corpus-observed operation and recipe patterns.
- Trigger
- When selecting collection cleanup, reshape, identifier, or collection-tabular bridge patterns.
Workflow-construction idiom. Copied verbatim.
- Purpose
- Ground tabular bridge and table-operation choices in curated, corpus-observed operation patterns.
- Trigger
- When data-flow translation needs filtering, joining, aggregation, pivoting, or tabular-collection bridges.
Workflow-construction idiom. Copied verbatim.
- Purpose
- Ground conditional-branch and optional-step choices in curated, corpus-observed Galaxy when/pick_value patterns.
- Trigger
- When data-flow translation needs optional steps, gating on non-empty results, routing between alternative outputs, or transform-or-pass-through branches.
Workflow-construction idiom. Copied verbatim.
- Purpose
- Ground genomic-interval operation choices in curated, corpus-observed Galaxy interval recipes.
- Trigger
- When the workflow operates on genomic intervals (BED/GFF/VCF coordinate features) and data-flow translation needs overlap, merge, coverage, windowing, masking, or set-algebra steps.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Preserve per-row metadata on the data-flow side: keep sample_sheet column_definitions wired through identifier-keyed steps instead of dropping into parallel parameter inputs, and re-attach metadata after map-over steps that lose it.
- Trigger
- When the interface brief carries a sample_sheet[:paired|:paired_or_unpaired|:record] input, or supporting evidence describes per-sample/per-record metadata that must survive map-over steps.
Cast artifacts
- Claude skill workflow-brief-to-galaxy-data-flow — Translate a reviewed Workflow Brief and its Galaxy interface into a Galaxy data-flow design brief.
Artifact handoffs
/ pipeline contractProduces
-
Reviewable Markdown brief: abstract operations, collection map/reduce choices, shape-changing placeholder steps, unresolved Galaxy tool needs, confidence, open questions.
-
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 scientific scope, requirements, and acceptance criteria.
- freeform-summary source-evidence
Optional narrative source evidence retained from brief production; consult it for details within the selected scope.
- summary-nextflow source-evidence
Optional structured Nextflow source evidence; consult it without treating source implementation as Galaxy design.
-
Preceding Galaxy interface brief from [[workflow-brief-to-galaxy-interface]] that pins inputs, outputs, and labels.
-
Carried workflow-run knowledge [[open-requirements-ledger]] initialized by the interface Mold.
workflow-brief-to-galaxy-data-flow
Read the reviewed Workflow Brief plus the preceding Galaxy interface brief and emit a reviewable Markdown data-flow brief. Consult retained source evidence when available. Capture abstract operations, collection map/reduce choices, shape-changing placeholder transformations, unresolved Galaxy tool needs, confidence, and open questions.
The Workflow Brief governs scope and requirements. A freeform-summary or summary-nextflow can substantiate details within that scope but cannot broaden it or turn source implementation into assumed Galaxy wiring. Translate what the brief, interface, and evidence support; classify the rest as unresolved tool needs or ledger obligations. If correct implementation requires changing reviewed intent, propose a brief change and stop rather than silently applying it.
The output is not gxformat2 and should not resolve exact Tool Shed tools. workflow-brief-to-galaxy-template turns this handoff and the interface brief into a skeleton.
Incoming References (4)
- 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.
- workflow-brief-to-galaxy-template related note — Build a gxformat2 skeleton from a reviewed Workflow Brief and its Galaxy design briefs, consulting retained source evidence.
- 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.