القائمة
Map a CWL summary into a Galaxy workflow interface design brief.
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
Carry an existing Galaxy workflow's tests forward as a regression baseline and augment them for a change-set's deltas, emitting a Galaxy test plan.
Triage failing Galaxy run outputs; classify the failure surface and capture evidence before recommending repairs.
Synthesize a Galaxy workflow test plan from a free-form summary and the Galaxy design briefs.
Assemble Galaxy workflow test fixtures and assertions.
Execute a workflow's tests via Planemo; emit structured pass/fail and outputs.
Convert one nf-core module dir into a Galaxy tool wrapper (tool.xml + macros.xml + _provenance.yml + remote-URL <test> blocks).
| name | cwl-summary-to-galaxy-interface |
| description | Map a CWL summary into a Galaxy workflow interface design brief. |
Follow the procedure below and use the artifact/reference sections as the runtime contract.
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.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.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.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.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.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.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.