القائمة
Decide the Galaxy-side shape of external reference data declared by a Nextflow pipeline.
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 | nextflow-summary-to-galaxy-reference-data |
| description | Decide the Galaxy-side shape of external reference data declared by a Nextflow pipeline. |
Follow the procedure below and use the artifact/reference sections as the runtime contract.
summary-nextflow. Schema: summary-nextflow. Produced by summarize-nextflow. Structured Nextflow pipeline summary emitted by summarize-nextflow; the source for reference-data param evidence.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.nextflow-galaxy-reference-data as nextflow-galaxy-reference-data.md. Format: markdown. Reviewable Markdown brief: per-asset reference inputs, requiredness, rebuild-on-absence behavior, iGenomes key disposition, 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/nextflow-reference-data-classification.md: Research note copied verbatim into the bundle. Classify the source pipeline's reference-data usage against the eight Nextflow-side classifications (none, reference-producing, single asset, coordinated bundle, key-expanded bundle, compute-if-missing, multi-DB pick-list, parallel bundles plus cohort data).references/notes/nextflow-to-galaxy-reference-data-mapping.md: Research note copied verbatim into the bundle. Apply the v1 Galaxy posture (explicit optional inputs + in-tool rebuild) and datatype defaults when translating each classified asset into the brief.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-nextflow.schema.json: Schema file copied verbatim into the bundle. Read reference_assets[] (curated path-typed inputs with used_by attribution to consuming subworkflows), reference_rebuilds[] (compute-if-missing rebuild rules with builder process and guard), and params[] provenance (source_kind, including getGenomeAttribute for nf-core key-expanded bundles) to determine which reference assets the source pipeline consumes and how it rebuilds them when absent.references/notes/nextflow-params-to-galaxy-inputs.md: Research note copied verbatim into the bundle. Cross-check reference selectors against the broader params translation rules — curated string enums, do-not-introduce-new-data-tables, runtime-control exclusion. Use when: a reference param looks like a curated selector (closed enum, .loc-keyed) rather than a data-bearing path.Classify the ways the Nextflow pipeline uses reference data using nextflow-reference-data-classification, then use nextflow-to-galaxy-reference-data-mapping to determine and describe how each classified asset maps onto the target Galaxy workflow. Output is a reviewable Markdown brief consumed by nextflow-summary-to-galaxy-interface, nextflow-summary-to-galaxy-data-flow, and nextflow-summary-to-galaxy-template before they pin workflow inputs, data-flow edges, and the gxformat2 skeleton.
The summary-nextflow schema surfaces reference-data evidence directly — read these fields before falling back to raw workflow.conditionals[] or guard-text inference:
reference_assets[] — the curated asset inventory. Each entry has param (FK into params[]), asset_kind (fasta, fasta_index, sequence_dictionary, bwa_index, tabix_index, gtf, gff, bed, vcf, database, other), required, source_kind, used_by (consuming subworkflow/process names), and evidence.confidence. Use this as the primary input to classification — it already filters out non-asset path params and attributes callers.reference_rebuilds[] — detected compute-if-missing branches. Each entry binds asset_param to a builder process plus its builder_outputs, the verbatim guard, resolved guard_params, and fallback_for (the <asset>_in-style take when paired). When reference_rebuilds[] is non-empty, the compute-if-missing classification applies to those asset_param values. Empty reference_rebuilds[] does NOT mean "no compute-if-missing" — some pipelines use positive-form idioms (if (<asset>) { unpack } else { build }) that the detector does not yet match (see galaxyproject/foundry#229 follow-ups).params[].source_kind == "getGenomeAttribute" plus params[].source_expression — the key-expanded bundle signal. A pipeline that synthesizes many path params via getGenomeAttribute('attr') is using the iGenomes pattern; classify the bundle accordingly.subworkflows[].invocations[] — caller-side argument binding onto take: names. Use when reference_assets[].used_by is ambiguous or when verifying that the same param threads into multiple subworkflows.If a needed signal is missing from the summary (e.g. RNA-seq's positive-form rebuild idiom is not yet detected), say so in the brief and flag the asset as rebuild-unverified rather than re-parsing source files.
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.