القائمة
gxformat2 skeleton with per-step TODOs from a Nextflow summary and prior Galaxy design briefs.
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-template |
| description | gxformat2 skeleton with per-step TODOs from a Nextflow summary and prior Galaxy design briefs. |
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; consulted while emitting placeholder steps.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, optionality, datatype hints, and rebuild-on-absence behavior the skeleton must honor.nextflow-galaxy-interface. Produced by nextflow-summary-to-galaxy-interface. Galaxy interface brief from nextflow-summary-to-galaxy-interface that pins workflow inputs, outputs, labels.nextflow-galaxy-data-flow. Produced by nextflow-summary-to-galaxy-data-flow. Galaxy data-flow brief from nextflow-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 briefs); 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 abstract data-flow draft to 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/gxformat2-schema.md: Research note copied verbatim into the bundle. Use the gxformat2 structural vocabulary for workflow inputs, outputs, steps, and producer-side output actions while emitting the skeleton.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 when emitting placeholder steps and TODO context.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.references/notes/nextflow-conditional-to-galaxy-subworkflow-when.md: Research note copied verbatim into the bundle. Emit when: clauses on the right step type (subworkflow vs tool) and the right output fan-in primitive (pick_value, modes first_non_null / first_or_skip / the_only_non_null) when the data-flow brief carries a conditional disposition through to the skeleton. Use when: the upstream data-flow brief assigns a source conditional to a subworkflow when: or inline when: shape, or when emitting the merge step for two or more when:-gated branches that produce the same logical output.references/notes/nextflow-reference-data-classification.md: Research note copied verbatim into the bundle. Cross-check source-side reference-data classifications before committing reference assets, optional inputs, and rebuild behavior into the gxformat2 skeleton. Use when: emitting workflow inputs or input-connection wiring for reference assets and 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. Resolve reference-asset declarations into gxformat2 inputs with the right datatype, optionality, and rebuild-on-absence wiring; cross-check the upstream brief against the datatypes table and v1 posture when the brief is silent or low-confidence on a specific asset. Use when: emitting workflow inputs or input-connection wiring for any reference asset flagged in the reference-data brief (FASTA, fai, dict, indexes, dbsnp, known_indels, intervals, PoN, …), or when the source pipeline declares iGenomes-derived params, per-asset reference path params, or any compute-if-missing index-building branch.galaxy-workflow-draft.gxwf.yml for artifact galaxy-workflow-draft against the galaxy-workflow-draft schema when a validator is available.Read the original Nextflow source artifact, the summary-nextflow.json summary, the Nextflow-to-Galaxy reference-data brief, the Nextflow-to-Galaxy interface brief, and the Nextflow-to-Galaxy data-flow brief. Emit a gxformat2 skeleton with workflow inputs, workflow outputs, placeholder steps, rough connections, and TODO slots for later implementation skills.
The reference-data, interface, and data-flow briefs guide the skeleton, but they do not replace source evidence. Treat the prior-step index as the working context: Nextflow source, source summary, reference-data brief, interface brief, data-flow brief, 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 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: nf-core modules name their tool, pin a version, and carry the command: block, conda packages, and container tags — so steps reach Resolved when a pattern page or IWC exemplar covers the operation (fill tool_id, parameters, and port names from the worked example), and Identity-pinned when the module names the tool but its settings for this context stay open. Deferred is for domain-specific scientific tools with no covering pattern (alignment, variant calling, expression quantification, etc.) — pack _plan_context with the source command, conda specs, container tags, and pre/post conditions the per-step skill needs to pick a wrapper. Emitting TODO over a pattern-covered recipe discards real evidence the per-step skill cannot recover.
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.