القائمة
Find nearest IWC exemplar(s) and surface a structural diff against the upstream Galaxy design briefs to guide template authoring.
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 | compare-against-iwc-exemplar |
| description | Find nearest IWC exemplar(s) and surface a structural diff against the upstream Galaxy design briefs to guide template authoring. |
Follow the procedure below and use the artifact/reference sections as the runtime contract.
nextflow-galaxy-interface. Produced by nextflow-summary-to-galaxy-interface. Galaxy interface brief from nextflow-summary-to-galaxy-interface when running the NEXTFLOW → GALAXY pipeline.nextflow-galaxy-data-flow. Produced by nextflow-summary-to-galaxy-data-flow. Galaxy data-flow brief from nextflow-summary-to-galaxy-data-flow when running the NEXTFLOW → GALAXY pipeline.cwl-galaxy-interface. Produced by cwl-summary-to-galaxy-interface. Galaxy interface brief from cwl-summary-to-galaxy-interface when running the CWL → GALAXY pipeline.cwl-galaxy-data-flow. Produced by cwl-summary-to-galaxy-data-flow. Galaxy data-flow brief from cwl-summary-to-galaxy-data-flow when running the CWL → GALAXY pipeline.freeform-galaxy-interface. Produced by freeform-summary-to-galaxy-interface. Galaxy interface brief from freeform-summary-to-galaxy-interface when running the PAPER → GALAXY or INTERVIEW → GALAXY pipelines.freeform-galaxy-data-flow. Produced by freeform-summary-to-galaxy-data-flow. Galaxy data-flow brief from freeform-summary-to-galaxy-data-flow when running the PAPER → GALAXY or INTERVIEW → GALAXY pipelines.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.iwc-comparison-notes as iwc-comparison-notes.md. Format: markdown. Structural diff against the nearest IWC exemplar(s); guidance for the downstream *-summary-to-galaxy-template Mold before per-step authoring. Carries an inline, bounded gxformat2 excerpt of the nearest exemplar's relevant subgraph under a labeled section, cross-referencing the iwc-exemplar-gxformat2 sibling file.iwc-exemplar-gxformat2 as iwc-exemplar.gxwf.yml. Format: yaml. Cleaned gxformat2 conversion (via convert --to format2 --compact) of the nearest IWC exemplar's relevant subgraph — the concrete idiom the downstream template draft pattern-matches against. Bounded to the relevant subgraph, not the whole workflow. Absent when no nearest exemplar is found.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.gxwf (gxwf). npm install -g @galaxy-tool-util/cli@^1.8.1.
Ephemeral run: npx --yes --package @galaxy-tool-util/cli@1.8.1 gxwf.
Check: gxwf --help | grep -q draft-validate.
Docs: https://github.com/jmchilton/galaxy-tool-util-ts/tree/main/packages/clireferences/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/cli/convert.json: CLI command reference packaged as a sidecar. Normalize fetched IWC workflows into a consistent representation for structural comparison, and surface the nearest exemplar forward as a cleaned gxformat2 view (sibling file plus inline excerpt) for the downstream template Mold. Use when: after fetching a candidate IWC workflow file and before structural comparison; and again on the nearest exemplar after ranking to emit the iwc-exemplar-gxformat2 view.references/notes/galaxy-data-flow-draft-contract.md: Research note copied verbatim into the bundle. Compare against the design briefs' abstract intent without turning exemplar comparison into tool resolution. Use when: deciding whether to compare abstract data-flow shape, interface structure, or speculative implementation details.references/notes/iwc-shortcuts-anti-patterns.md: Research note copied verbatim into the bundle. Flag proposed shortcuts that are accepted in IWC versus shortcuts that should be treated as smells. Use when: the design briefs propose tests, assertions, labels, or expected-output comparisons.references/notes/iwc-test-data-conventions.md: Research note copied verbatim into the bundle. Compare proposed test-data placement and fixture shapes against IWC conventions. Use when: the design briefs hint at workflow tests or input fixture organization.Find the nearest IWC exemplar workflow(s) for the upstream Galaxy design briefs and emit a structural diff that guides the downstream *-summary-to-galaxy-template skill before per-step authoring effort is spent.
This skill is the corpus-first check in Galaxy-targeting pipelines. It runs after the source-specific interface and data-flow briefs and before the gxformat2 template skill. Discovery, ranking, and comparison are one action — there is no separate retrieval skill.
https://github.com/galaxyproject/iwc) to ~/.foundry/iwc.Domain comes first so a structurally similar workflow in the wrong science area does not become a misleading exemplar. Topology comes second because collection shape is one of the most important Galaxy-specific design decisions. Test style is useful after a workflow match, but should not drive initial retrieval. Briefs with no domain signal should not produce a high-confidence exemplar even if they share generic tools.
| Level | Meaning |
|---|---|
| High | Same domain/subdomain, same input topology, same primary tool families, same major DAG motifs, and matching test fixture shape. |
| Medium | Same domain and topology, but partial tool-family or output match. Useful exemplar, not canonical. |
| Low | Cross-domain structural match only. Useful for a pattern comparison, not a nearest domain exemplar. |
| No nearest exemplar | Candidate lacks domain or topology alignment, or only shares generic tools such as MultiQC. |
Each finding should name the authoring surface most likely to own the fix:
*-summary-to-galaxy-template skill to apply.*-test-to-galaxy-test-plan or implement-galaxy-workflow-test.Do not block downstream authoring on low-confidence exemplar mismatches. Report them as review guidance for the template skill and the user.
The schema tells the template skill what is legal gxformat2; it does not show idiom. A real, domain-adjacent gxformat2 workflow is high-value signal for constructing the draft — input/collection shapes, map-over wiring, output promotion, post-job actions. Agents have seen far more legacy .ga JSON than gxformat2 YAML in training, so surface the converted view rather than leaving it as prose.
Once the nearest exemplar is chosen (High or Medium confidence):
--to format2 --compact).iwc-exemplar.gxwf.yml sibling artifact — the slice that matches the briefs' structure, not the whole workflow.iwc-comparison-notes.md, and cite the abstract IWC workflow ID (e.g. transcriptomics/rnaseq-pe/rnaseq-pe) plus the step labels it covers. Cross-reference the sibling file for the fuller view.Keep it size-bounded — a whole large workflow is noise; the relevant subgraph is the signal. When the result is "no nearest exemplar," emit neither the sibling file nor the excerpt. A Low-confidence cross-domain match may surface a short excerpt for pattern comparison but should be labeled as such, not as a domain exemplar.
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.