القائمة
Map a Nextflow 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 | nextflow-summary-to-galaxy-interface |
| description | Map a Nextflow summary into a Galaxy workflow interface design brief. |
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-of-truth JSON for interface choices.nextflow-galaxy-reference-data. Produced by nextflow-summary-to-galaxy-reference-data. Reference-data shape brief from nextflow-summary-to-galaxy-reference-data that pins per-asset reference inputs and rebuild-on-absence behavior.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-interface as nextflow-galaxy-interface.md. Format: markdown. Reviewable Markdown brief: Galaxy workflow inputs, outputs, labels, collection shapes, checkpoint outputs, source provenance.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-params-to-galaxy-inputs.md: Research note copied verbatim into the bundle. Translate Nextflow launch params, materialized inputs, sample sheets, and control flags into gxformat2-compatible Galaxy workflow inputs.references/notes/nextflow-path-glob-to-galaxy-datatype.md: Research note copied verbatim into the bundle. Choose Galaxy datatype extensions and confidence notes for data inputs, collection elements, and exposed outputs.references/notes/nextflow-to-galaxy-channel-shape-mapping.md: Research note copied verbatim into the bundle. Choose Galaxy File/list/paired/list:paired/list:list interface shapes from Nextflow channel shapes.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 source-level channel, parameter, process, and test-fixture evidence before choosing Galaxy workflow inputs and outputs.references/notes/galaxy-sample-sheet-collections.md: Research note copied verbatim into the bundle. Pick the right sample_sheet variant and translate nf-schema column metadata into Galaxy column_definitions when the source pipeline uses sample-sheet-shaped inputs. Use when: the Nextflow summary reports a samplesheetToList materialization, a parameter whose nf-schema entry sets schema: assets/schema_*.json, or a channel built from splitCsv(header: true) over a tabular params 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.references/notes/nextflow-reference-data-classification.md: Research note copied verbatim into the bundle. Cross-check source-side reference-data classifications before translating the reference-data brief into Galaxy workflow inputs. Use when: the reference-data brief is silent, low-confidence, or conflicts with source evidence for iGenomes-derived params, coordinated bundles, compute-if-missing branches, multi-DB pick-lists, or cohort-specific assets.references/notes/nextflow-to-galaxy-reference-data-mapping.md: Research note copied verbatim into the bundle. Translate iGenomes-style and per-asset reference-data params into Galaxy inputs without inheriting nf-core's reference-resolution magic; v1 posture is explicit optional inputs with in-tool rebuild on absence. Use when: the source pipeline declares iGenomes-derived params (params.genome with getGenomeAttribute), per-asset reference path params (fasta, fasta_fai, dict, bwa_index, dbsnp, known_indels, intervals, pon), or any compute-if-missing index-building branch in the source.Read a Nextflow 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.
The output is not a gxformat2 skeleton and not a workflow schema. It is a design handoff consumed by nextflow-summary-to-galaxy-data-flow, nextflow-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.