القائمة
gxformat2 skeleton with per-step TODOs from a free-form summary and Galaxy 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-template |
| description | gxformat2 skeleton with per-step TODOs from a free-form summary and Galaxy 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; consulted while emitting placeholder steps.freeform-galaxy-interface. Produced by freeform-summary-to-galaxy-interface. Galaxy interface brief from freeform-summary-to-galaxy-interface that pins workflow inputs, outputs, labels.freeform-galaxy-data-flow. Produced by freeform-summary-to-galaxy-data-flow. Galaxy data-flow brief from freeform-summary-to-galaxy-data-flow that pins abstract operations and collection choices.iwc-comparison-notes. Produced by compare-against-iwc-exemplar. Structural diff guidance from compare-against-iwc-exemplar (run on the design brief); steers the skeleton toward IWC-aligned structure before per-step authoring. Carries an inline gxformat2 excerpt of the nearest exemplar.iwc-exemplar-gxformat2. Produced by compare-against-iwc-exemplar. Cleaned gxformat2 view of the nearest IWC exemplar's relevant subgraph from compare-against-iwc-exemplar; pattern-match the draft's input/collection shapes, map-over wiring, output promotion, and post-job actions against this concrete idiom. Absent when no nearest exemplar was found.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.galaxy-workflow-draft as galaxy-workflow-draft.gxwf.yml. Format: yaml. Schema: galaxy-workflow-draft. gxformat2 draft (see galaxy-workflow-draft-format): topology fully resolved (workflow inputs, outputs, step set, edges); tool_id / tool_state / tool_shed_repository and wrapper-determined port names may be TODO with free-text _plan_state / _plan_context / _plan_in / _plan_out per step for later implementation Molds.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/galaxy-data-flow-draft-contract.md: Research note copied verbatim into the bundle. Respect the handoff from the freeform-to-Galaxy interface and data-flow briefs to the gxformat2 skeleton. Use when: translating abstract nodes, unresolved tool needs, and placeholder transformations into template TODOs.references/notes/galaxy-workflow-draft-format.md: Research note copied verbatim into the bundle. Emit the gxformat2 draft superset: TODO tool_id, optional tool_state / tool_shed_repository, and per-step _plan_state / _plan_context planning fields.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/galaxy-workflow-draft.schema.json: Schema file copied verbatim into the bundle. Output contract: the emitted gxformat2 draft conforms to galaxy-workflow-draft. Cast bundles the JSON Schema so the skill carries its output shape alongside the draft-validate CLI checks.references/cli/draft-validate.json: CLI command reference packaged as a sidecar. Validate the emitted draft against draft-contract rules (sentinel form, topology, plan* placement) before handing off. Use when: after writing or modifying the draft workflow file.references/patterns/galaxy-collection-patterns.md: Pattern note copied verbatim into the bundle. Use corpus-grounded collection pattern guidance for unresolved skeleton steps. Use when: adding TODO steps for collection cleanup, reshaping, relabeling, identifier synchronization, or collection-tabular bridges.references/patterns/galaxy-conditionals-patterns.md: Pattern note copied verbatim into the bundle. Use corpus-grounded conditional pattern guidance for unresolved skeleton steps. Use when: adding TODO steps for 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. Use corpus-grounded genomic-interval pattern guidance for unresolved skeleton steps. Use when: adding TODO steps for interval overlap, merge, coverage, windowing, masking, or set-algebra on coordinate features.references/patterns/galaxy-tabular-patterns.md: Pattern note copied verbatim into the bundle. Use corpus-grounded tabular pattern guidance for unresolved skeleton steps. Use when: adding TODO steps for tabular filtering, projection, joins, aggregation, text-processing recipes, or tabular-collection bridges.references/notes/galaxy-collection-semantics.md: Research note copied verbatim into the bundle. Preserve Galaxy collection typing and map-over/reduction semantics in the gxformat2 skeleton. Use when: creating workflow inputs, outputs, and placeholder connections involving collections.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-workflow-comments.md: Research note copied verbatim into the bundle. Group the settled step set into titled stage frames (the gxformat2 comments: array) so the skeleton carries the analysis-stage narrative IWC authors annotate by hand. Schema-legal and optional. Use when: after topology is settled and the skeleton can be partitioned into named analysis stages (inputs, per-stage step clusters, parameter-derivation knots, visualization/outputs).references/notes/galaxy-workflow-testability-design.md: Research note copied verbatim into the bundle. Choose stable workflow input/output labels, testable checkpoint outputs, and fixture-compatible workflow interfaces while drafting the skeleton. Use when: the template decides workflow inputs, workflow outputs, promoted checkpoints, or collection output identifiers that future tests will need to address.galaxy-workflow-draft.gxwf.yml for artifact galaxy-workflow-draft against the galaxy-workflow-draft schema when a validator is available.Read the original free-form source artifact if present, the free-form summary Markdown document, and the freeform-to-Galaxy interface and data-flow briefs. Emit a gxformat2 skeleton with workflow inputs, workflow outputs, placeholder steps, rough connections, and TODO slots for later implementation skills.
The free-form summary does not have a concrete schema yet; treat it as Markdown. Treat the prior-step index as the working context: source transcript or paper, free-form summary, freeform-to-Galaxy interface and data-flow briefs, and any open questions carried forward.
Topology is this skill's job to settle. The output must be concrete gxformat2: workflow inputs with their final collection shapes and formats, workflow outputs, the step set, the producer→consumer edge graph, branches, and when: guards are all decided here. The upstream freeform-to-Galaxy interface and data-flow briefs guide those decisions, but if they hedge or leave a topology choice open, this skill makes the call from source evidence, IWC exemplars, and pattern pages — never emit a topology TODO. Wrapper resolution, by contrast, is evidence-gated, not source-gated: resolve each tool step to the tier its evidence supports — Resolved (fully concrete, no _plan_*), Identity-pinned (concrete tool_id, parameters and changeset left to the per-step skill), or Deferred (tool_id: TODO) — as defined in galaxy-workflow-draft-format. Capture whatever you defer in the _plan_* family (_plan_state, _plan_context, _plan_in, _plan_out) so the per-step skill has the source evidence and constraints it needs.
Source tendency: free-form sources rarely name tools, so steps land in Deferred more often than nf-core or CWL — but a free-form source that does name a specific tool/version with evidence hardens to the matching tier, and a corpus-confirmed utility wrapper (interval/tabular/collection op) is not deferred just because the surrounding prose is informal. When deferring a domain tool, cite the originating paper section, interview answer, figure, or supplementary table in _plan_context, and record vague intent in _plan_state ("default settings", "stranded reverse if mentioned, else unstranded") so the per-step skill knows the evidence ceiling.
Before handing off, sanity-check that each step is computable from what feeds it. Once the step set is settled, re-read it and ask, for each step, whether the operation its intent implies can actually be produced from the inputs you wired. The connection graph only knows that ports connect — not what each port is supposed to contain — so an output that needs evidence no input carries will validate fine and still be impossible to implement. Where you spot that gap, don't leave it implicit: wire (or add) the step that supplies the missing input, or record the unmet need plainly in _plan_state so the per-step skill or a reviewer can act on it rather than discover it late.
Things worth a second look:
_plan_* promises more than its in: ports can supply;Optionally, once topology is settled, group the step set into titled stage frames via the gxformat2 comments: array (one frame per analysis stage, contains_steps: populated, color decorative) — see galaxy-workflow-comments for the convention.
Before handing off, check each settled step is computable from what feeds it. The connection graph knows that ports connect, not what they carry — so a declared output that needs evidence no wired input supplies will validate yet can't be implemented. Where you find that gap, wire (or add) the producer; if you can't, append a blocking entry to the open-requirements-ledger naming the step, the uncomputable output, and the missing evidence (and record vague intent in _plan_state) so the per-step loop or repair-galaxy-draft-topology acts on it rather than discovering it late. More generally, carry the ledger: read the entries bearing on your topology decisions and mark resolved the ones you close.
Output shape is gxformat2 with wrapper-tier relaxations and _plan_state / _plan_context / _plan_in / _plan_out per tool step — see galaxy-workflow-draft-format. Refinement open work for those planning fields lives in refinement.md.