Agent Skill · cast

nextflow-summary-to-galaxy-reference-data

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

Install with Claude Code

/plugin marketplace add galaxyproject/foundry
/plugin install foundry-skills@galaxy-workflow-foundry

Then invoke as:

/foundry-skills:nextflow-summary-to-galaxy-reference-data

Install with Codex

codex plugin marketplace add galaxyproject/foundry
codex plugin add foundry-skills@galaxy-workflow-foundry

Then select with /skills or invoke explicitly as:

$nextflow-summary-to-galaxy-reference-data

Skill Bundle

/ packaged cast

attached files: 5
upfront: 4
on demand: 1
cast rev: n/a
validated: 0

Produces: 2 artifacts.

Consumes: 2 artifacts.

Artifact Contract

/ skill handoff

Produces

nextflow-galaxy-reference-data

Reviewable Markdown brief: per-asset reference inputs, requiredness, rebuild-on-absence behavior, iGenomes key disposition, open questions.

markdownnextflow-galaxy-reference-data.md

Raw artifact contract

{
  "id": "nextflow-galaxy-reference-data",
  "kind": "markdown",
  "default_filename": "nextflow-galaxy-reference-data.md",
  "description": "Reviewable Markdown brief: per-asset reference inputs, requiredness, rebuild-on-absence behavior, iGenomes key disposition, open questions."
}

open-requirements-ledger

Updated obligations ledger: new unmet needs this step surfaces appended; prior entries its decisions close marked resolved.

yamlopen-requirements.ledger.yml

Raw artifact contract

{
  "id": "open-requirements-ledger",
  "kind": "yaml",
  "default_filename": "open-requirements.ledger.yml",
  "description": "Updated obligations ledger: new unmet needs this step surfaces appended; prior entries its decisions close marked resolved."
}

Consumes

summary-nextflow

Structured Nextflow pipeline summary emitted by [[summarize-nextflow]]; the source for reference-data param evidence.

Raw artifact contract

{
  "id": "summary-nextflow",
  "description": "Structured Nextflow pipeline summary emitted by [[summarize-nextflow]]; the source for reference-data param evidence.",
  "inherited_schema": "[[summary-nextflow]]",
  "producers": [
    "summarize-nextflow"
  ]
}

open-requirements-ledger

Carried obligations ledger [[open-requirements-ledger]]: read prior open entries; this design step appends new unmet needs and marks ones its decisions resolve.

Raw artifact contract

{
  "id": "open-requirements-ledger",
  "description": "Carried obligations ledger [[open-requirements-ledger]]: read prior open entries; this design step appends new unmet needs and marks ones its decisions resolve.",
  "producers": [
    "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"
  ]
}

Attached Files

/ runtime references

Load upfront

research

nextflow-reference-data-classification

packaged

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).

upfront runtime verbatim corpus-observed deterministic 7.9 KB

bundle: references/notes/nextflow-reference-data-classification.md
source: content/research/nextflow-reference-data-classification.md

Preview md

---
type: research
subtype: component
title: "Nextflow reference-data classification"
tags:
  - research/component
  - source/nextflow
status: draft
created: 2026-05-10
revised: 2026-05-10
revision: 3
ai_generated: true
related_notes:
  - "[[summary-nextflow]]"
  - "[[nextflow-to-galaxy-reference-data-mapping]]"
  - "[[nextflow-summary-to-galaxy-reference-data]]"
  - "[[nextflow-summary-to-galaxy-interface]]"
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[nextflow-summary-to-galaxy-template]]"
related_molds:
  - "[[summarize-nextflow]]"
  - "[[nextflow-summary-to-galaxy-reference-data]]"
  - "[[nextflow-summary-to-galaxy-interface]]"
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[nextflow-summary-to-galaxy-template]]"
sources:
  - "https://nf-co.re/docs/usage/reference_genomes"
  - "https://github.com/nf-core/sarek/blob/master/conf/igenomes.config"
  - "https://github.com/nf-core/configs"
  - "https://github.com/galaxyproject/foundry/issues/221"
summary: "Source-side taxonomy of how Nextflow pipelines use reference data — eight classifications detectable from a summary-nextflow artifact."
---

# Nextflow reference-data classification

Reference-data shape varies along several roughly orthogonal dimensions: whether the pipeline consumes or produces reference data, the cardinality of the assets, whether they're keyed or per-asset, whether rebuild fallback exists, and whether multiple bundles run in parallel. The classifications below are flags an LLM can detect from a `summary-nextflow` artifact; a single pipeline often matches more than one. Grounded in the complexity bridge fixtures from galaxyproject/foundry#221.

For the Galaxy-side translation of these classifications, see [[nextflow-to-galaxy-reference-data-mapping]].

## None

Pipeline consumes no ref
...

research

nextflow-to-galaxy-reference-data-mapping

packaged

Apply the v1 Galaxy posture (explicit optional inputs + in-tool rebuild) and datatype defaults when translating each classified asset into the brief.

upfront runtime verbatim corpus-observed deterministic 12.4 KB

bundle: references/notes/nextflow-to-galaxy-reference-data-mapping.md
source: content/research/nextflow-to-galaxy-reference-data-mapping.md

Preview md

---
type: research
subtype: component
title: "Nextflow to Galaxy reference-data mapping"
tags:
  - research/component
  - source/nextflow
  - target/galaxy
status: draft
created: 2026-05-08
revised: 2026-05-10
revision: 5
ai_generated: true
related_notes:
  - "[[nextflow-reference-data-classification]]"
  - "[[nextflow-params-to-galaxy-inputs]]"
  - "[[nextflow-path-glob-to-galaxy-datatype]]"
  - "[[summary-nextflow]]"
  - "[[nextflow-summary-to-galaxy-reference-data]]"
  - "[[nextflow-summary-to-galaxy-template]]"
  - "[[galaxy-sample-sheet-collections]]"
  - "[[galaxy-datatypes-conf]]"
related_molds:
  - "[[summarize-nextflow]]"
  - "[[nextflow-summary-to-galaxy-reference-data]]"
  - "[[nextflow-summary-to-galaxy-interface]]"
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[nextflow-summary-to-galaxy-template]]"
sources:
  - "https://github.com/galaxyproject/foundry/issues/221"
summary: "Galaxy-side translation of Nextflow reference-data classifications: idioms available, the v1 posture, datatype defaults, and the in-tool rebuild trade-off."
---

# Nextflow to Galaxy reference-data mapping

Mapping research for [[nextflow-summary-to-galaxy-reference-data]]. Once a Nextflow pipeline's reference-data usage is classified per [[nextflow-reference-data-classification]], this note pins the Galaxy-side translation: idioms available, the v1 posture, datatype defaults, the in-tool rebuild trade-off, and known representation gaps the brief should flag.

## Galaxy side

Galaxy has multiple idioms for surfacing reference data. The bullets below are presented as available shapes; the recommendations that follow narrow them to the v1 posture.

- **`dbkey`-keyed cached lookups.** Workflow inputs carry a `dbkey` annotation; tools consume an admin-pre-loaded data table indexed by
...

research

open-requirements-ledger

packaged

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.

upfront runtime verbatim hypothesis deterministic 7.8 KB

bundle: references/notes/open-requirements-ledger.md
source: content/research/open-requirements-ledger.md

Preview md

---
type: research
subtype: design-spec
title: "Open-requirements ledger"
tags:
  - research/design-spec
  - target/galaxy
status: draft
created: 2026-06-16
revised: 2026-06-16
revision: 1
ai_generated: true
related_notes:
  - "[[galaxy-workflow-draft-format]]"
related_molds:
  - "[[advance-galaxy-draft-step]]"
  - "[[repair-galaxy-draft-topology]]"
  - "[[implement-galaxy-tool-step]]"
summary: "Carried unresolved-requirements artifact the source→Galaxy pipeline discharges or explicitly surrenders, autonomously."
---

# Open-requirements ledger

The `open-requirements-ledger` is a single artifact threaded through the source→Galaxy pipeline that records **obligations the pipeline has taken on but not yet met** — a declared output with no producer, a parameter whose value the source never pinned, a tool with no corpus exemplar. Each Mold that surfaces one **appends** it; each Mold whose decision closes one **marks it resolved**; the terminal path **surrenders** whatever remains open, explicitly, into the final artifact.

## Framing: obligations the pipeline discharges, not questions a human answers

This is deliberately *not* an "open questions for the user" list. The pipeline is autonomous — no human-in-the-loop gate is assumed. The ledger's consumers are **Molds and the loop's convergence gate**, with human readout a secondary affordance. An entry is closed by a downstream Mold doing work (wiring a producer, picking a wrapper, settling a value), or — when nothing can close it — surrendered: written into the final draft as a known, labelled gap rather than silently dropped or fabricated around.

The distinction matters because a "questions for a human" framing leaks an operator's personal interaction style into a tool meant to run inside anyone's harness. The ledger must
...

schema

summary-nextflow

packaged

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.

upfront runtime verbatim corpus-observed deterministic 58.7 KB

bundle: references/schemas/summary-nextflow.schema.json
source: package://@galaxy-foundry/summarize-nextflow#summaryNextflowSchema

Preview json

{
  "$schema": "http://json-schema.org/draft-07/schema#",
  "$id": "https://galaxyproject.org/foundry/schemas/summary-nextflow.schema.json",
  "$comment": "Canonical source: packages/summarize-nextflow/src/schema/summary-nextflow.schema.json in galaxyproject/foundry. Mold frontmatter cites this schema via [[summary-nextflow]] wiki-links; the cast pipeline imports the `summaryNextflowSchema` runtime export and serializes it into cast bundles.",
  "title": "Nextflow Pipeline Summary",
  "description": "Structured per-source summary emitted by the summarize-nextflow Mold.\n\nPer-source schema by design — paper, Nextflow, and CWL each have their own summary shape; downstream Molds (data flow, templates, tool wrappers) consume any source's summary and handle the polymorphism.\n\nField names mirror gxy-sketches' SketchSource / ToolSpec / TestDataRef / ExpectedOutputRef where parity exists; see content/research/gxy-sketches-alignment.md.",
  "$ref": "#/$defs/Summary",
  "$defs": {
    "Summary": {
      "title": "Summary",
      "description": "Top-level shape. Every Nextflow summary is exactly this object.",
      "type": "object",
      "additionalProperties": false,
      "required": [
        "source",
        "params",
        "sample_sheets",
        "profiles",
        "tools",
        "processes",
        "subworkflows",
        "workflow",
        "reference_assets",
        "reference_rebuilds",
        "test_fixtures",
        "nf_tests"
      ],
      "properties": {
        "source": {
          "$ref": "#/$defs/SourceRecord"
        },
        "params": {
          "type": "array",
          "items": {
            "$ref": "#/$defs/Param"
          }
        },
        "sample_sheets": {
          "type": "array",
          "items": {
            "$ref": "#/$defs/SampleSheet"
          },
          "description": "Structured sample-sheet inputs. Each entry binds one `params[]` parameter to a row schema (column names, types, path-vs-meta classification, required flags, enums, patterns). Promoted from prose inside `params[].description` so downstream target translations (Galaxy `sample_sheet*` collections, CWL records-of-arrays) can choose collection variants without re-parsing the source pipeline. Empty array when no sample-sheet idiom is detected. Discovery sources: nf-schema `schema:` references, `samplesheetToList()` calls, and `splitCsv(header: true
...

Load on demand

research

nextflow-params-to-galaxy-inputs

packaged

Cross-check reference selectors against the broader params translation rules — curated string enums, do-not-introduce-new-data-tables, runtime-control exclusion.

Trigger: When a reference param looks like a curated selector (closed enum, .loc-keyed) rather than a data-bearing path.

on-demand runtime verbatim corpus-observed deterministic 17.7 KB

bundle: references/notes/nextflow-params-to-galaxy-inputs.md
source: content/research/nextflow-params-to-galaxy-inputs.md

Preview md

---
type: research
subtype: component
title: "Nextflow params to Galaxy workflow inputs"
tags:
  - research/component
  - source/nextflow
  - target/galaxy
status: draft
created: 2026-05-06
revised: 2026-05-08
revision: 4
ai_generated: true
related_notes:
  - "[[nextflow-workflow-io-semantics]]"
  - "[[gxformat2-workflow-inputs]]"
  - "[[galaxy-sample-sheet-collections]]"
  - "[[nextflow-path-glob-to-galaxy-datatype]]"
  - "[[nextflow-to-galaxy-channel-shape-mapping]]"
  - "[[galaxy-workflow-testability-design]]"
  - "[[galaxy-collection-semantics]]"
  - "[[summary-nextflow]]"
  - "[[nextflow-summary-to-galaxy-interface]]"
  - "[[nextflow-summary-to-galaxy-data-flow]]"
related_molds:
  - "[[summarize-nextflow]]"
  - "[[nextflow-summary-to-galaxy-interface]]"
  - "[[nextflow-summary-to-galaxy-data-flow]]"
sources:
  - "https://www.nextflow.io/docs/latest/cli.html#pipeline-parameters"
  - "https://nextflow-io.github.io/nf-schema/latest/nextflow_schema/nextflow_schema_specification/"
  - "https://nextflow-io.github.io/nf-schema/latest/samplesheets/samplesheetToList/"
  - "https://github.com/galaxyproject/gxformat2/blob/main/schema/v19_09/workflow.yml"
  - "https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/workflow/modules.py"
summary: "Rules for translating Nextflow params, sample sheets, channels, and control flags into gxformat2 inputs."
---

# Nextflow params to Galaxy workflow inputs

Use this note when [[nextflow-summary-to-galaxy-interface]] turns a [[summary-nextflow]] artifact into Galaxy workflow inputs. [[nextflow-workflow-io-semantics]] defines what counts as a Nextflow interface surface; this note narrows that into gxformat2 input decisions.

Evidence quality:

- **Corpus-observed** claims cite pinned fixtures under `$NEXTFLOW_FIXTURES`, the shared cl
...

SKILL.md


# 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.