القائمة
Translate a Nextflow summary into a Galaxy data-flow 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-data-flow |
| description | Translate a Nextflow summary into a Galaxy data-flow 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 JSON the data-flow translation reads.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.nextflow-galaxy-interface. Produced by nextflow-summary-to-galaxy-interface. Preceding Galaxy interface brief from nextflow-summary-to-galaxy-interface that pins inputs, outputs, and labels.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-data-flow as nextflow-galaxy-data-flow.md. Format: markdown. Reviewable Markdown brief: abstract operations, collection map/reduce choices, shape-changing placeholder steps, unresolved Galaxy tool needs, 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/galaxy-data-flow-draft-contract.md: Research note copied verbatim into the bundle. Keep the data-flow brief separate from gxformat2 templating and concrete step implementation.references/notes/nextflow-operators-to-galaxy-collection-recipes.md: Research note copied verbatim into the bundle. Classify Nextflow operators as Galaxy wiring, collection semantics, explicit steps, or review triggers.references/notes/nextflow-to-galaxy-channel-shape-mapping.md: Research note copied verbatim into the bundle. Translate Nextflow channel, tuple, and path shapes into Galaxy dataset and collection 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 process, channel, operator, and fixture structure while drafting Galaxy-facing abstract data flow.references/patterns/galaxy-collection-patterns.md: Pattern note copied verbatim into the bundle. Ground collection-shape choices in curated, corpus-observed operation and recipe patterns. Use when: selecting collection cleanup, reshape, identifier, or collection-tabular bridge patterns.references/patterns/galaxy-conditionals-patterns.md: Pattern note copied verbatim into the bundle. Ground conditional-branch and optional-step choices in curated, corpus-observed Galaxy when/pick_value patterns. Use when: data-flow translation needs optional steps, gating on non-empty results, routing between alternative outputs, or transform-or-pass-through branches.references/patterns/galaxy-interval-patterns.md: Pattern note copied verbatim into the bundle. Ground genomic-interval operation choices in curated, corpus-observed Galaxy interval recipes. Use when: the workflow operates on genomic intervals (BED/GFF/VCF coordinate features) and data-flow translation needs overlap, merge, coverage, windowing, masking, or set-algebra steps.references/patterns/galaxy-tabular-patterns.md: Pattern note copied verbatim into the bundle. Ground tabular bridge and table-operation choices in curated, corpus-observed operation patterns. Use when: data-flow translation needs filtering, joining, aggregation, pivoting, or tabular-collection bridges.references/notes/galaxy-sample-sheet-collections.md: Research note copied verbatim into the bundle. Preserve per-row metadata on the data-flow side: keep sample_sheet column_definitions wired through identifier-keyed steps instead of dropping into parallel parameter inputs, and re-attach metadata after map-over steps that lose it. Use when: the upstream interface brief carries a sample_sheet[:paired|:paired_or_unpaired|:record] input, or when the Nextflow summary shows tuple(meta, path...) channel shape originating from samplesheetToList or splitCsv(header: true).references/notes/nextflow-conditional-to-galaxy-subworkflow-when.md: Research note copied verbatim into the bundle. Decide between subworkflow when: and inline tool-step when: for each source conditional, and pick the right output fan-in primitive (pick_value vs twin-cascade) so the data-flow brief carries a coherent conditional disposition forward. Use when: the Nextflow summary's workflow.conditionals[] is non-empty, or when subworkflow boundaries in the source align with parameter-driven branches (step, aligner, wes, tools, skip_, use_).references/notes/nextflow-path-glob-to-galaxy-datatype.md: Research note copied verbatim into the bundle. Preserve datatype confidence while translating path-like data-flow edges, process output patterns, and published outputs. Use when: choosing or reviewing Galaxy datatype extensions for data-flow edges, collection elements, or output datasets.references/notes/nextflow-reference-data-classification.md: Research note copied verbatim into the bundle. Cross-check source-side reference-data classifications before deciding how reference assets and optional rebuild branches flow through the Galaxy data-flow draft. Use when: the reference-data or interface 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. Decide how reference assets and their indexes flow through the Galaxy data-flow draft (preserving dbkey through map-overs, deferring index-building to wrappers vs surfacing as workflow steps). Use when: the upstream interface brief carries reference-data inputs (FASTA, fai, dict, indexes, known sites, intervals, PoN) or when the source pipeline's compute-if-missing branches imply rebuild semantics the data flow has to honor.Read a Nextflow summary plus the preceding Galaxy interface brief and emit a reviewable Markdown data-flow brief. Capture abstract operations, collection map/reduce choices, shape-changing placeholder transformations, unresolved Galaxy tool needs, confidence, and open questions.
The output is not gxformat2 and should not resolve exact Tool Shed tools. nextflow-summary-to-galaxy-template turns this handoff and the interface brief into a skeleton.
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.