nextflow-summary-to-galaxy-reference-data

name	nextflow-summary-to-galaxy-reference-data
description	Decide the Galaxy-side shape of external reference data declared by a Nextflow pipeline.

nextflow-summary-to-galaxy-reference-data

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

When To Use

• Decide the Galaxy-side shape of external reference data declared by a Nextflow pipeline.

Inputs

• Read artifact summary-nextflow. Schema: summary-nextflow. Produced by summarize-nextflow. Structured Nextflow pipeline summary emitted by summarize-nextflow; the source for reference-data param evidence.
• 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 nextflow-galaxy-reference-data as nextflow-galaxy-reference-data.md. Format: markdown. Reviewable Markdown brief: per-asset reference inputs, requiredness, rebuild-on-absence behavior, iGenomes key disposition, open questions.
• 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

• None declared. Procedure should not assume external CLIs are present.

Load Upfront

• references/notes/nextflow-reference-data-classification.md: Research note copied verbatim into the bundle. Classify the source pipeline's reference-data usage against the eight Nextflow-side classifications (none, reference-producing, single asset, coordinated bundle, key-expanded bundle, compute-if-missing, multi-DB pick-list, parallel bundles plus cohort data).
• references/notes/nextflow-to-galaxy-reference-data-mapping.md: Research note copied verbatim into the bundle. Apply the v1 Galaxy posture (explicit optional inputs + in-tool rebuild) and datatype defaults when translating each classified asset into the brief.
• 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 reference_assets[] (curated path-typed inputs with used_by attribution to consuming subworkflows), reference_rebuilds[] (compute-if-missing rebuild rules with builder process and guard), and params[] provenance (source_kind, including getGenomeAttribute for nf-core key-expanded bundles) to determine which reference assets the source pipeline consumes and how it rebuilds them when absent.

Load On Demand

• references/notes/nextflow-params-to-galaxy-inputs.md: Research note copied verbatim into the bundle. Cross-check reference selectors against the broader params translation rules — curated string enums, do-not-introduce-new-data-tables, runtime-control exclusion. Use when: a reference param looks like a curated selector (closed enum, .loc-keyed) rather than a data-bearing path.

Validation

• None declared.

Procedure

Classify the ways the Nextflow pipeline uses reference data using nextflow-reference-data-classification, then use nextflow-to-galaxy-reference-data-mapping to determine and describe how each classified asset maps onto the target Galaxy workflow. Output is a reviewable Markdown brief consumed by nextflow-summary-to-galaxy-interface, nextflow-summary-to-galaxy-data-flow, and nextflow-summary-to-galaxy-template before they pin workflow inputs, data-flow edges, and the gxformat2 skeleton.

Reading the summary

The summary-nextflow schema surfaces reference-data evidence directly — read these fields before falling back to raw workflow.conditionals[] or guard-text inference:

• reference_assets[] — the curated asset inventory. Each entry has param (FK into params[]), asset_kind (fasta, fasta_index, sequence_dictionary, bwa_index, tabix_index, gtf, gff, bed, vcf, database, other), required, source_kind, used_by (consuming subworkflow/process names), and evidence.confidence. Use this as the primary input to classification — it already filters out non-asset path params and attributes callers.
• reference_rebuilds[] — detected compute-if-missing branches. Each entry binds asset_param to a builder process plus its builder_outputs, the verbatim guard, resolved guard_params, and fallback_for (the <asset>_in-style take when paired). When reference_rebuilds[] is non-empty, the compute-if-missing classification applies to those asset_param values. Empty reference_rebuilds[] does NOT mean "no compute-if-missing" — some pipelines use positive-form idioms (if (<asset>) { unpack } else { build }) that the detector does not yet match (see galaxyproject/foundry#229 follow-ups).
• params[].source_kind == "getGenomeAttribute" plus params[].source_expression — the key-expanded bundle signal. A pipeline that synthesizes many path params via getGenomeAttribute('attr') is using the iGenomes pattern; classify the bundle accordingly.
• subworkflows[].invocations[] — caller-side argument binding onto take: names. Use when reference_assets[].used_by is ambiguous or when verifying that the same param threads into multiple subworkflows.

If a needed signal is missing from the summary (e.g. RNA-seq's positive-form rebuild idiom is not yet detected), say so in the brief and flag the asset as rebuild-unverified rather than re-parsing source files.

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.

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.