cwl-summary-to-galaxy-interface

name	cwl-summary-to-galaxy-interface
description	Map a CWL summary into a Galaxy workflow interface design brief.

cwl-summary-to-galaxy-interface

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

When To Use

• Map a CWL summary into a Galaxy workflow interface design brief.

Inputs

• Read artifact summary-cwl. Schema: summary-cwl. Produced by summarize-cwl. Structured CWL summary emitted by summarize-cwl; the source-of-truth JSON for Galaxy interface choices.
• 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 cwl-galaxy-interface as cwl-galaxy-interface.md. Format: markdown. Reviewable Markdown brief: Galaxy workflow inputs, outputs, labels, exposed and checkpoint outputs, source provenance, confidence.
• 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/component-cwl-workflow-anatomy.md: Research note copied verbatim into the bundle. Keep source-faithful CWL facts separate from Galaxy-facing interface choices.
• 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.
• references/schemas/summary-cwl.schema.json: Schema file copied verbatim into the bundle. Read CWL workflow inputs, outputs, types, formats, secondary files, scatter, and requirement evidence before choosing the Galaxy interface.

Load On Demand

• references/notes/cwl-when-pickvalue-to-galaxy-branching.md: Research note copied verbatim into the bundle. Pick among the three honest Galaxy branching translations (paired_or_unpaired input, native pick_value step, sibling workflows) before drafting the interface. Use when: summary-cwl has any steps[].when non-null OR any workflow output uses pickValue.
• references/notes/galaxy-collection-semantics.md: Research note copied verbatim into the bundle. Choose Galaxy collection input shapes from CWL arrays, scatter inputs, records, Directory values, and secondary-file contracts. Use when: cWL types include arrays, records, Directory, secondaryFiles, or scatter over File-like inputs.
• 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-paired-or-unpaired-collections.md: Research note copied verbatim into the bundle. Choose paired_or_unpaired (or list:paired_or_unpaired) shape when the CWL discriminator is paired-vs-single reads, instead of inventing a workflow-level reads_mode select parameter. Use when: summary-cwl declares 2+ optional File? read-like inputs whose step bindings are gated by complementary when: predicates, OR workflow outputs use pickValue over branches keyed on input presence, OR an upstream meta.single_end-style discriminator surfaces in the summary.
• references/notes/galaxy-workflow-testability-design.md: Research note copied verbatim into the bundle. Choose stable Galaxy workflow input/output labels and promoted checkpoint outputs. Use when: deciding labels, public outputs, checkpoint outputs, or fixture-compatible collection inputs.

Validation

• None declared.

Procedure

Read a CWL summary and emit a reviewable Markdown interface brief for a Galaxy workflow. Preserve CWL input/output intent while choosing Galaxy-facing labels, data shapes, exposed outputs, checkpoint outputs, provenance, confidence, and open questions.

The output is a design handoff, not gxformat2 and not a rich workflow schema.

Prefer direct mappings when they are honest: CWL scalar inputs become Galaxy parameter inputs, File inputs become dataset inputs, File[] plus scatter commonly becomes a list collection, and declared formats seed Galaxy datatype choices. Surface Directory, records, expression-shaped defaults, and secondary-file-heavy outputs as review notes rather than flattening them silently.

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.