القائمة
Map a free-form source 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 | freeform-summary-to-galaxy-interface |
| description | Map a free-form source summary into a Galaxy workflow interface design brief. |
Follow the procedure below and use the artifact/reference sections as the runtime contract.
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.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.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.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/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/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.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.