nextflow-summary-to-galaxy-template

name	nextflow-summary-to-galaxy-template
description	gxformat2 skeleton with per-step TODOs from a Nextflow summary and prior Galaxy design briefs.

nextflow-summary-to-galaxy-template

Follow the procedure below and use the artifact/reference sections as the runtime contract.

When To Use

• gxformat2 skeleton with per-step TODOs from a Nextflow summary and prior Galaxy design briefs.

Inputs

• Read artifact summary-nextflow. Schema: summary-nextflow. Produced by summarize-nextflow. Structured Nextflow pipeline summary emitted by summarize-nextflow; consulted while emitting placeholder steps.
• Read artifact 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.
• Read artifact 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.
• Read artifact 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.
• Read artifact 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.
• Read artifact 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.
• Read artifact 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.

Outputs

• Write artifact 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.
• Write artifact 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.

Required Tools

• 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/cli

Load Upfront

• references/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.

Load On Demand

• 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.

Validation

• Validate galaxy-workflow-draft.gxwf.yml for artifact galaxy-workflow-draft against the galaxy-workflow-draft schema when a validator is available.

Procedure

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.

Runtime Notes

• Do not read Foundry source files at runtime; use only files packaged in this skill bundle and user-supplied artifacts.
• Preserve declared artifact filenames unless the user or harness supplies explicit paths.
• Carry unresolved assumptions into the output artifact instead of silently inventing missing source evidence.