freeform-summary-to-galaxy-interface

name	freeform-summary-to-galaxy-interface
description	Map a free-form source summary into a Galaxy workflow interface design brief.

freeform-summary-to-galaxy-interface

Follow the procedure below and use the artifact/reference sections as the runtime contract.

When To Use

• Map a free-form source summary into a Galaxy workflow interface design brief.

Inputs

• Read artifact freeform-summary. Produced by interview-to-freeform-summary, summarize-paper. Free-form source summary emitted by summarize-paper or interview-to-freeform-summary; methods, tools, sample data, references, and workflow intent with explicit uncertainty.
• Read artifact open-requirements-ledger. Produced by advance-galaxy-draft-step, apply-galaxy-workflow-changeset, compare-against-iwc-exemplar, cwl-summary-to-galaxy-data-flow, cwl-summary-to-galaxy-interface, cwl-summary-to-galaxy-template, freeform-summary-to-galaxy-data-flow, freeform-summary-to-galaxy-interface, freeform-summary-to-galaxy-template, implement-galaxy-tool-step, interview-to-galaxy-workflow-changeset, nextflow-summary-to-galaxy-data-flow, nextflow-summary-to-galaxy-interface, nextflow-summary-to-galaxy-reference-data, nextflow-summary-to-galaxy-template, repair-galaxy-draft-topology. Carried obligations ledger open-requirements-ledger: read prior open entries; this design step appends new unmet needs and marks ones its decisions resolve.

Outputs

• Write artifact freeform-galaxy-interface as freeform-galaxy-interface.md. Format: markdown. Reviewable Markdown brief: Galaxy workflow inputs, outputs, labels, collection shapes, checkpoint outputs, source-summary provenance, confidence, open questions.
• Write artifact open-requirements-ledger as open-requirements.ledger.yml. Format: yaml. Updated obligations ledger: new unmet needs this step surfaces appended; prior entries its decisions close marked resolved.

Required Tools

• None declared. Procedure should not assume external CLIs are present.

Load Upfront

• references/notes/open-requirements-ledger.md: Research note copied verbatim into the bundle. Carry the open-requirements ledger: read open entries bearing on this step's decisions, mark resolved the ones it closes, and append any new unmet need it surfaces.

Load On Demand

• references/notes/galaxy-collection-semantics.md: Research note copied verbatim into the bundle. Choose Galaxy collection input shapes (File / list / paired / list:paired / record) from the source's per-sample, paired, grouped, or nested data descriptions. Use when: the free-form summary describes paired reads, per-sample groups, nested or grouped inputs, or any input that should become a Galaxy dataset collection.
• references/notes/galaxy-collection-semantics.upstream.myst: Companion file copied verbatim into the bundle. Sibling of references/notes/galaxy-collection-semantics.md; read it where that note directs.
• references/notes/galaxy-collection-semantics.yml: Companion file copied verbatim into the bundle. Sibling of references/notes/galaxy-collection-semantics.md; read it where that note directs.
• references/notes/galaxy-sample-sheet-collections.md: Research note copied verbatim into the bundle. Pick the right sample_sheet variant and translate described per-sample column metadata into Galaxy column_definitions when the source describes sample-sheet-shaped inputs. Use when: the free-form summary describes a sample sheet, a per-sample/per-record table, or any table mapping samples to files that should become a Galaxy collection or sample-sheet input.
• references/notes/galaxy-workflow-testability-design.md: Research note copied verbatim into the bundle. Choose stable workflow input/output labels and promoted checkpoint outputs that future tests can address. Use when: deciding labels, public outputs, checkpoint outputs, or fixture-compatible collection inputs.

Validation

• None declared.

Procedure

Read a free-form source summary and emit a reviewable Markdown interface brief for a Galaxy workflow. Capture workflow inputs, workflow outputs, labels, Galaxy collection shapes, checkpoint outputs worth exposing for tests, source-summary provenance, confidence, and open questions.

Free-form sources are narrative- or interview-derived and carry explicit uncertainty. Translate what the summary supports into interface decisions; carry unresolved interface choices forward as open questions rather than inventing precise inputs, outputs, or labels.

The output is not a gxformat2 skeleton and not a workflow schema. It is a design handoff consumed by freeform-summary-to-galaxy-data-flow, freeform-summary-to-galaxy-template, and later test-plan work.

Carry the open-requirements-ledger through this step: read the open entries that bear on the choices you make here, mark resolved any your decisions close, and append any new unmet need you surface — a declared output with no producer, an unpinned parameter, a tool with no corpus exemplar — so a later skill inherits it instead of re-deriving it.

Runtime Notes

• Do not read Foundry source files at runtime; use only files packaged in this skill bundle and user-supplied artifacts.
• Preserve declared artifact filenames unless the user or harness supplies explicit paths.
• Carry unresolved assumptions into the output artifact instead of silently inventing missing source evidence.