Claude skill · cast

nextflow-summary-to-galaxy-template

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

Install

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

Then invoke as:

/foundry-skills:nextflow-summary-to-galaxy-template

Skill Bundle

/ packaged cast

attached files: 19
upfront: 6
on demand: 13
cast rev: 3
validated: 0

Produces: 2 artifacts.

Consumes: 7 artifacts.

Artifact Contract

/ skill handoff

Produces

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.

yamlgalaxy-workflow-draft.gxwf.yml[[galaxy-workflow-draft]]

Raw artifact contract

{
  "id": "galaxy-workflow-draft",
  "kind": "yaml",
  "default_filename": "galaxy-workflow-draft.gxwf.yml",
  "schema": "[[galaxy-workflow-draft]]",
  "description": "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

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]]; consulted while emitting placeholder steps.

Raw artifact contract

{
  "id": "summary-nextflow",
  "description": "Structured Nextflow pipeline summary emitted by [[summarize-nextflow]]; consulted while emitting placeholder steps.",
  "inherited_schema": "[[summary-nextflow]]",
  "producers": [
    "summarize-nextflow"
  ]
}

nextflow-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.

Raw artifact contract

{
  "id": "nextflow-galaxy-reference-data",
  "description": "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.",
  "producers": [
    "nextflow-summary-to-galaxy-reference-data"
  ]
}

nextflow-galaxy-interface

Galaxy interface brief from [[nextflow-summary-to-galaxy-interface]] that pins workflow inputs, outputs, labels.

Raw artifact contract

{
  "id": "nextflow-galaxy-interface",
  "description": "Galaxy interface brief from [[nextflow-summary-to-galaxy-interface]] that pins workflow inputs, outputs, labels.",
  "producers": [
    "nextflow-summary-to-galaxy-interface"
  ]
}

nextflow-galaxy-data-flow

Galaxy data-flow brief from [[nextflow-summary-to-galaxy-data-flow]] that pins abstract operations and collection choices.

Raw artifact contract

{
  "id": "nextflow-galaxy-data-flow",
  "description": "Galaxy data-flow brief from [[nextflow-summary-to-galaxy-data-flow]] that pins abstract operations and collection choices.",
  "producers": [
    "nextflow-summary-to-galaxy-data-flow"
  ]
}

iwc-comparison-notes

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.

Raw artifact contract

{
  "id": "iwc-comparison-notes",
  "description": "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.",
  "producers": [
    "compare-against-iwc-exemplar"
  ]
}

iwc-exemplar-gxformat2

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.

Raw artifact contract

{
  "id": "iwc-exemplar-gxformat2",
  "description": "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.",
  "producers": [
    "compare-against-iwc-exemplar"
  ]
}

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",
    "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",
    "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

galaxy-data-flow-draft-contract

packaged

Respect the handoff from abstract data-flow draft to gxformat2 skeleton.

Trigger: When translating abstract nodes, unresolved tool needs, and placeholder transformations into template TODOs.

upfront runtime verbatim hypothesis deterministic 7.4 KB

bundle: references/notes/galaxy-data-flow-draft-contract.md
source: content/research/galaxy-data-flow-draft-contract.md

Preview md

---
type: research
subtype: design-spec
title: "Galaxy data-flow draft contract"
tags:
  - research/design-spec
  - target/galaxy
status: draft
created: 2026-05-02
revised: 2026-05-03
revision: 2
ai_generated: true
related_notes:
  - "[[nextflow-to-galaxy-channel-shape-mapping]]"
  - "[[nextflow-operators-to-galaxy-collection-recipes]]"
  - "[[galaxy-workflow-draft]]"
related_molds:
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[cwl-summary-to-galaxy-data-flow]]"
  - "[[freeform-summary-to-galaxy-data-flow]]"
  - "[[nextflow-summary-to-galaxy-template]]"
  - "[[cwl-summary-to-galaxy-template]]"
  - "[[freeform-summary-to-galaxy-template]]"
  - "[[compare-against-iwc-exemplar]]"
  - "[[advance-galaxy-draft-step]]"
sources:
  - "https://github.com/galaxyproject/foundry/issues/54"
summary: "Defines the proposed boundary between Galaxy data-flow drafts, gxformat2 templates, and concrete step implementation."
---

# Galaxy Data-Flow Draft Contract

This is an architectural contract, not a schema. Evidence is strongest for Mold and Pipeline boundaries. Proposed fields are speculative until exercised by two or three worked translations.

## Boundary

The data-flow draft owns a target-shaped abstract DAG for Galaxy. It should not be valid `gxformat2` and should not resolve exact Tool Shed tools.

Data-flow draft owns:

- Galaxy-facing workflow inputs and outputs.
- Abstract nodes, edges, branches, collection mapping, collection reduction, and placeholder transformations.
- Input/output shape decisions such as `File`, `list`, `paired`, `list:paired`, or `list:list`.
- Conceptual Galaxy idioms: map-over, reduction, Apply Rules, collection cleanup, identifier synchronization, tabular bridge, fan-in / combine (concatenate, merge, or union N sources into one — a distinct node
...

research

galaxy-workflow-draft-format

packaged

Emit the gxformat2 draft superset: TODO tool_id, optional tool_state / tool_shed_repository, and per-step _plan_state / _plan_context planning fields.

upfront runtime verbatim hypothesis deterministic 12.5 KB

bundle: references/notes/galaxy-workflow-draft-format.md
source: content/research/galaxy-workflow-draft-format.md

Preview md

---
type: research
subtype: design-spec
title: "Galaxy workflow draft format"
tags:
  - research/design-spec
  - target/galaxy
status: draft
created: 2026-05-06
revised: 2026-05-10
revision: 2
ai_generated: true
related_notes:
  - "[[gxformat2-schema]]"
  - "[[galaxy-data-flow-draft-contract]]"
  - "[[discover-shed-tool]]"
  - "[[galaxy-workflow-draft]]"
  - "[[open-requirements-ledger]]"
related_molds:
  - "[[nextflow-summary-to-galaxy-template]]"
  - "[[cwl-summary-to-galaxy-template]]"
  - "[[freeform-summary-to-galaxy-template]]"
  - "[[compare-against-iwc-exemplar]]"
  - "[[implement-galaxy-tool-step]]"
  - "[[advance-galaxy-draft-step]]"
  - "[[repair-galaxy-draft-topology]]"
summary: "gxformat2 draft superset: wrapper-tier TODOs (tool_id, tool_state, port names) plus _plan_state / _plan_context / _plan_in / _plan_out per tool step."
---

# Galaxy workflow draft format

The output artifact `galaxy-workflow-draft` produced by the `*-summary-to-galaxy-template` Molds is **gxformat2 with wrapper-tier relaxations and free-text planning fields**, sized to the gap between data-flow design and tool-resolved implementation.

Topology — workflow inputs and their collection shapes, workflow outputs, the step set, the producer→consumer edge graph, branches, and `when:` guards — is **settled by the template Mold itself**, drawing on the upstream interface and data-flow briefs (see [[galaxy-data-flow-draft-contract]]). The output is concrete gxformat2 with no topology TODOs. Wrapper-tier resolution — which Tool Shed wrapper, what parameters, the wrapper-determined port names that populate `in:` / `out:` / `outputSource` — is **evidence-gated per step** (see Resolution tiers below): a step resolves fully when the evidence pins wrapper and parameters together, pins identity alon
...

research

gxformat2-schema

packaged

Use the gxformat2 structural vocabulary for workflow inputs, outputs, steps, and producer-side output actions while emitting the skeleton.

upfront runtime verbatim corpus-observed deterministic 3.9 KB

bundle: references/notes/gxformat2-schema.md
source: content/research/gxformat2-schema.md

Preview md

---
type: research
subtype: component
title: "gxformat2 structural JSON Schema"
tags:
  - research/component
  - target/galaxy
status: draft
created: 2026-05-05
revised: 2026-05-06
revision: 2
ai_generated: true
related_notes:
  - "[[galaxy-collection-semantics]]"
  - "[[galaxy-datatypes-conf]]"
  - "[[galaxy-workflow-testability-design]]"
  - "[[gxformat2-workflow-inputs]]"
  - "[[galaxy-workflow-draft]]"
sources:
  - "https://github.com/jmchilton/galaxy-tool-util-ts/blob/7ae4ecd0ba8d492225f58a6d455c4cc5317298f0/packages/schema/src/galaxy-workflow.ts"
summary: "Vendored structural JSON Schema for gxformat2 workflows: vocabulary for inputs, outputs, steps, and step subtypes."
---

> **Vendored from upstream**, pinned at SHA `7ae4ecd`. One file lives next to this note:
>
> - `gxformat2.schema.json` — Draft-07 JSON Schema generated from the `@galaxy-tool-util/schema` Effect-TS schema via `gxwf structural-schema --format format2`. **Agents and casting should consume this** when validating gxformat2 workflows or reasoning about the closed vocabulary of input/step types.
>
> **Re-sync:** `pnpm sync:vendored --update`. Sync builds galaxy-tool-util-ts and re-runs the generator before copy.

## Top-level shape

A gxformat2 document is an object with required `inputs`, `outputs`, `class` (`enum: ["GalaxyWorkflow"]`), and `steps`. Optional: `id`, `label`, `doc`, `uuid`, `report`, `tags`, `comments`, `creator`, `license`, `release`.

## Workflow input vocabulary

Each entry under `inputs` carries:

- `type` — closed enum: `null | boolean | int | long | float | double | string | integer | text | File | data | collection`. Drives whether the input is a parameter, a single dataset, or a collection.
- `format` — Galaxy datatype extension when `type ∈ {File, data}`. See [[galaxy-dataty
...

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 process, channel, operator, and fixture structure when emitting placeholder steps and TODO context.

upfront runtime verbatim corpus-observed deterministic 56.7 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
...

schema

galaxy-workflow-draft

packaged

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.

upfront runtime verbatim cast-validated deterministic 58.6 KB

bundle: references/schemas/galaxy-workflow-draft.schema.json
source: package://@galaxy-tool-util/schema#galaxyWorkflowDraftJsonSchema

Preview json

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$defs": {
    "WorkflowStepSchema": {
      "type": "object",
      "required": [],
      "properties": {
        "id": {
          "anyOf": [
            {
              "type": "null"
            },
            {
              "type": "string"
            }
          ]
        },
        "label": {
          "anyOf": [
            {
              "type": "null"
            },
            {
              "type": "string"
            }
          ]
        },
        "doc": {
          "anyOf": [
            {
              "type": "null"
            },
            {
              "type": "string"
            },
            {
              "type": "array",
              "items": {
                "type": "string"
              }
            }
          ]
        },
        "position": {
          "anyOf": [
            {
              "type": "null"
            },
            {
              "type": "object",
              "required": [
                "top",
                "left"
              ],
              "properties": {
                "top": {
                  "type": "number"
                },
                "left": {
                  "type": "number"
                }
              },
              "additionalProperties": false
            }
          ]
        },
        "tool_id": {
          "anyOf": [
            {
              "type": "null"
            },
            {
              "type": "string"
            }
          ]
        },
        "tool_shed_repository": {
          "$ref": "#/$defs/Shared15"
        },
        "tool_version": {
          "anyOf": [
            {
              "type": "null"
            },
            {
              "type": "string"
            }
          ]
        },
        "errors": {
          "anyOf": [
            {
              "type": "null"
            },
            {
              "type": "string"
            }
          ]
        },
        "uuid": {
          "anyOf": [
            {
              "type": "null"
            },
            {
              "type": "string"
            }
          ]
        },
        "in": {
          "$ref": "#/$defs/Shared16"
        },
        "out": {
          "anyOf": [
            {
              "type": "array",
              "items": {
                "$ref": "#/$defs/Shared4"
          
...

Load on demand

cli-command

draft-validate

packaged

Validate the emitted draft against draft-contract rules (sentinel form, topology, _plan_* placement) before handing off.

Trigger: After writing or modifying the draft workflow file.

on-demand runtime sidecar hypothesis deterministic 8.1 KB

bundle: references/cli/draft-validate.json
source: content/cli/gxwf/draft-validate.md

Preview json

{
  "type": "cli-command",
  "tool": "gxwf",
  "command": "draft-validate",
  "summary": "Validate a `class: GalaxyWorkflowDraft` workflow against draft-contract rules; with --concrete, also validate the extracted concrete subset.",
  "source_path": "content/cli/gxwf/draft-validate.md",
  "source_revision": 1,
  "package": "@galaxy-tool-util/cli",
  "description": "Validate a draft Galaxy workflow (class: GalaxyWorkflowDraft)",
  "synopsis": "gxwf draft-validate [options] <file>",
  "args": [
    {
      "raw": "file",
      "name": "file",
      "required": true,
      "variadic": false,
      "description": "Draft workflow file (.gxwf.yml)"
    }
  ],
  "options": [
    {
      "flags": "--format <fmt>",
      "name": "format",
      "description": "Force format: format2 (native is rejected for drafts)",
      "takesArgument": true,
      "argumentPlaceholder": "<fmt>",
      "optionalArgument": false,
      "negatable": false
    },
    {
      "flags": "--json",
      "name": "json",
      "description": "Output structured JSON report",
      "takesArgument": false,
      "optionalArgument": false,
      "negatable": false
    },
    {
      "flags": "--report-html [file]",
      "name": "reportHtml",
      "description": "Write HTML report to file (or stdout if omitted)",
      "takesArgument": true,
      "argumentPlaceholder": "[file]",
      "optionalArgument": true,
      "negatable": false
    },
    {
      "flags": "--report-markdown [file]",
      "name": "reportMarkdown",
      "description": "Write Markdown report to file (or stdout if omitted)",
      "takesArgument": true,
      "argumentPlaceholder": "[file]",
      "optionalArgument": true,
      "negatable": false
    },
    {
      "flags": "--concrete",
      "name": "concrete",
      "description": "Additionally extract the concrete subset and run the regular `gxwf validate` checks on it",
      "takesArgument": false,
      "optionalArgument": false,
      "negatable": false
    },
    {
      "flags": "--cache-dir <dir>",
      "name": "cacheDir",
      "description": "Tool cache directory (for --concrete tool-state validation)",
      "takesArgument": true,
      "argumentPlaceholder": "<dir>",
      "optionalArgument": false,
      "negatable": false
    },
    {
      "flags": "--no-tool-state",
      "name": "toolState",
      "description": "Skip tool-state validation in the --c
...

pattern

galaxy-collection-patterns

packaged

Use corpus-grounded collection pattern guidance for unresolved skeleton steps.

Trigger: When adding TODO steps for collection cleanup, reshaping, relabeling, identifier synchronization, or collection-tabular bridges.

on-demand runtime verbatim corpus-observed deterministic 4.6 KB

bundle: references/patterns/galaxy-collection-patterns.md
source: content/patterns/galaxy-collection-patterns.md

Preview md

---
type: pattern
pattern_kind: moc
evidence: corpus-observed
title: "Galaxy: collection patterns"
aliases:
  - "Galaxy collection pattern MOC"
  - "collection transformation patterns"
  - "IWC collection pattern map"
tags:
  - pattern
  - target/galaxy
  - topic/galaxy-transform
  - topic/collection-transform
status: draft
created: 2026-05-02
revised: 2026-05-02
revision: 1
ai_generated: true
summary: "Use this MOC to choose corpus-grounded Galaxy collection transformation patterns."
related_notes:
  - "[[iwc-transformations-survey]]"
  - "[[iwc-conditionals-survey]]"
related_patterns:
  - "[[manifest-to-mapped-collection-lifecycle]]"
  - "[[cleanup-sync-and-publish-nonempty-results]]"
  - "[[reshape-relabel-remap-by-collection-axis]]"
  - "[[fan-in-bundle-consume-and-flatten]]"
  - "[[collection-cleanup-after-mapover-failure]]"
  - "[[sync-collections-by-identifier]]"
  - "[[harmonize-by-sortlist-from-identifiers]]"
  - "[[regex-relabel-via-tabular]]"
  - "[[relabel-via-rules-and-find-replace]]"
  - "[[collection-swap-nesting-with-apply-rules]]"
  - "[[collection-split-identifier-via-rules]]"
  - "[[collection-build-list-paired-with-apply-rules]]"
  - "[[tabular-to-collection-by-row]]"
  - "[[tabular-concatenate-collection-to-table]]"
  - "[[tabular-pivot-collection-to-wide]]"
related_molds:
  - "[[implement-galaxy-tool-step]]"
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[cwl-summary-to-galaxy-data-flow]]"
  - "[[nextflow-summary-to-galaxy-template]]"
  - "[[cwl-summary-to-galaxy-template]]"
  - "[[freeform-summary-to-galaxy-template]]"
  - "[[compare-against-iwc-exemplar]]"
---

# Galaxy: collection patterns

This is the runtime-facing map for Galaxy collection transformation choices. Use it before loading raw survey notes. The survey remains evidence backin
...

pattern

galaxy-conditionals-patterns

packaged

Use corpus-grounded conditional pattern guidance for unresolved skeleton steps.

Trigger: When adding TODO steps for optional steps, gating on non-empty results, routing between alternative outputs, or transform-or-pass-through branches.

on-demand runtime verbatim corpus-observed deterministic 2.6 KB

bundle: references/patterns/galaxy-conditionals-patterns.md
source: content/patterns/galaxy-conditionals-patterns.md

Preview md

---
type: pattern
pattern_kind: moc
evidence: corpus-observed
title: "Galaxy: conditionals patterns"
aliases:
  - "Galaxy conditional pattern MOC"
  - "Galaxy when patterns"
  - "conditional workflow patterns"
tags:
  - pattern
  - target/galaxy
  - topic/galaxy-transform
status: draft
created: 2026-05-02
revised: 2026-05-02
revision: 1
ai_generated: true
summary: "Use this MOC to choose corpus-grounded Galaxy when and pick_value conditional patterns."
related_notes:
  - "[[iwc-conditionals-survey]]"
related_patterns:
  - "[[conditional-run-optional-step]]"
  - "[[conditional-route-between-alternative-outputs]]"
  - "[[conditional-gate-on-nonempty-result]]"
  - "[[conditional-transform-or-pass-through]]"
  - "[[collection-cleanup-after-mapover-failure]]"
related_molds:
  - "[[implement-galaxy-tool-step]]"
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[cwl-summary-to-galaxy-data-flow]]"
  - "[[nextflow-summary-to-galaxy-template]]"
  - "[[cwl-summary-to-galaxy-template]]"
  - "[[freeform-summary-to-galaxy-template]]"
  - "[[compare-against-iwc-exemplar]]"
---

# Galaxy: conditionals patterns

This is the runtime-facing map for Galaxy conditional workflow choices. Use it before loading raw survey notes. The survey remains evidence backing; the operation and recipe pages are the actionable references.

## Direct Gates

- [[conditional-run-optional-step]] — expose or derive a boolean, connect it as `inputs.when`, and use `when: $(inputs.when)` to skip optional steps.
- [[conditional-gate-on-nonempty-result]] — compute a boolean from empty/non-empty dataset or collection state before gating downstream reporting/export. The MGnify recipe is corpus-backed but clunky pending verified-pattern workflow work.

## Routes and Fallbacks

- [[conditional-route-between-alternati
...

pattern

galaxy-interval-patterns

packaged

Use corpus-grounded genomic-interval pattern guidance for unresolved skeleton steps.

Trigger: When adding TODO steps for interval overlap, merge, coverage, windowing, masking, or set-algebra on coordinate features.

on-demand runtime verbatim corpus-observed deterministic 5.5 KB

bundle: references/patterns/galaxy-interval-patterns.md
source: content/patterns/galaxy-interval-patterns.md

Preview md

---
type: pattern
pattern_kind: moc
evidence: corpus-observed
title: "Galaxy: genomic interval patterns"
aliases:
  - "Galaxy interval pattern MOC"
  - "genomic interval transformation patterns"
  - "IWC interval pattern map"
tags:
  - pattern
  - target/galaxy
  - topic/galaxy-transform
  - topic/interval-transform
status: draft
created: 2026-06-10
revised: 2026-06-10
revision: 1
ai_generated: true
summary: "Use this MOC to choose corpus-grounded Galaxy genomic interval operations and recipes on coordinate features."
related_notes:
  - "[[iwc-interval-operations-survey]]"
related_patterns:
  - "[[interval-overlap-filter]]"
  - "[[interval-coverage]]"
  - "[[interval-merge-overlapping]]"
  - "[[interval-window-flank]]"
  - "[[interval-consensus-by-multi-intersect]]"
  - "[[interval-mask-by-set-algebra]]"
  - "[[interval-windowed-coverage]]"
  - "[[tabular-synthesize-bed-from-3col]]"
related_molds:
  - "[[implement-galaxy-tool-step]]"
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[cwl-summary-to-galaxy-data-flow]]"
  - "[[nextflow-summary-to-galaxy-template]]"
  - "[[cwl-summary-to-galaxy-template]]"
  - "[[paper-summary-to-galaxy-template]]"
  - "[[compare-against-iwc-exemplar]]"
---

# Galaxy: genomic interval patterns

The runtime-facing map for Galaxy **coordinate-feature** choices — operations that understand `chrom/start/end/strand`, as opposed to opaque-column [[galaxy-tabular-patterns]] or container-shaped [[galaxy-collection-patterns]]. Use it before loading raw survey notes; [[iwc-interval-operations-survey]] is the evidence backing, these pages are the actionable references.

This is the smallest of the three data-shape MOCs by design. Interval algebra is a real but moderate cluster in IWC — concentrated in epigenetics peak-consensus and SARS-CoV-2 mask
...

pattern

galaxy-tabular-patterns

packaged

Use corpus-grounded tabular pattern guidance for unresolved skeleton steps.

Trigger: When adding TODO steps for tabular filtering, projection, joins, aggregation, text-processing recipes, or tabular-collection bridges.

on-demand runtime verbatim corpus-observed deterministic 3.3 KB

bundle: references/patterns/galaxy-tabular-patterns.md
source: content/patterns/galaxy-tabular-patterns.md

Preview md

---
type: pattern
pattern_kind: moc
evidence: corpus-observed
title: "Galaxy: tabular patterns"
aliases:
  - "Galaxy tabular pattern MOC"
  - "tabular transformation patterns"
  - "IWC tabular pattern map"
tags:
  - pattern
  - target/galaxy
  - topic/galaxy-transform
  - topic/tabular-transform
status: draft
created: 2026-05-02
revised: 2026-05-02
revision: 1
ai_generated: true
summary: "Use this MOC to choose corpus-grounded Galaxy tabular transformation patterns."
related_notes:
  - "[[iwc-tabular-operations-survey]]"
related_patterns:
  - "[[tabular-filter-by-column-value]]"
  - "[[tabular-filter-by-regex]]"
  - "[[tabular-cut-and-reorder-columns]]"
  - "[[tabular-compute-new-column]]"
  - "[[tabular-join-on-key]]"
  - "[[tabular-group-and-aggregate-with-datamash]]"
  - "[[tabular-sql-query]]"
  - "[[tabular-prepend-header]]"
  - "[[tabular-synthesize-bed-from-3col]]"
  - "[[tabular-split-taxonomy-string]]"
  - "[[tabular-relabel-by-row-counter]]"
  - "[[tabular-to-collection-by-row]]"
  - "[[tabular-concatenate-collection-to-table]]"
  - "[[tabular-pivot-collection-to-wide]]"
related_molds:
  - "[[implement-galaxy-tool-step]]"
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[cwl-summary-to-galaxy-data-flow]]"
  - "[[nextflow-summary-to-galaxy-template]]"
  - "[[cwl-summary-to-galaxy-template]]"
  - "[[freeform-summary-to-galaxy-template]]"
  - "[[compare-against-iwc-exemplar]]"
---

# Galaxy: tabular patterns

This is the runtime-facing map for Galaxy tabular transformation choices. Use it before loading raw survey notes. The survey remains evidence backing; the operation pages are the actionable references.

## Row And Column Operations

- [[tabular-filter-by-column-value]] — keep/drop rows by string column value with `Filter1`.
- [[tabular-filter-by-regex]] 
...

research

galaxy-collection-semantics

packaged

Preserve Galaxy collection typing and map-over/reduction semantics in the gxformat2 skeleton.

Trigger: When creating workflow inputs, outputs, and placeholder connections involving collections.

on-demand runtime verbatim corpus-observed deterministic 1.9 KB

bundle: references/notes/galaxy-collection-semantics.md
source: content/research/galaxy-collection-semantics.md

Preview md

---
type: research
subtype: component
title: "Galaxy collection semantics"
tags:
  - research/component
  - target/galaxy
status: draft
created: 2026-04-30
revised: 2026-05-05
revision: 3
ai_generated: false
related_notes:
  - "[[galaxy-xsd]]"
  - "[[galaxy-collection-tools]]"
  - "[[galaxy-apply-rules-dsl]]"
  - "[[nextflow-to-galaxy-channel-shape-mapping]]"
  - "[[nextflow-operators-to-galaxy-collection-recipes]]"
  - "[[galaxy-tool-job-failure-reference]]"
  - "[[galaxy-workflow-invocation-failure-reference]]"
  - "[[iwc-transformations-survey]]"
  - "[[galaxy-discover-datasets]]"
sources:
  - "https://github.com/galaxyproject/galaxy/blob/7765fae934fbfdee77e3be5f5b235e43735273ae/lib/galaxy/model/dataset_collections/types/collection_semantics.yml"
companions:
  - "galaxy-collection-semantics.yml"
  - "galaxy-collection-semantics.upstream.myst"
summary: "Vendored formal spec of Galaxy dataset-collection mapping/reduction semantics, with labeled examples and pinned test references."
---

> **Vendored from upstream**, pinned at SHA `7765fae`. Two files live next to this note:
>
> - `galaxy-collection-semantics.yml` — the structured source. **Agents and casting should consume this.** It carries the `tests:` blocks that pin concrete Galaxy test names; the rendered upstream view drops them.
> - `galaxy-collection-semantics.upstream.myst` — Galaxy's auto-generated MyST/LaTeX rendering of the YAML, vendored only so the human view below has something to render. Sync is manual.
>
> **When to consult:** authoring or reasoning about Molds and patterns that touch `data_collection` inputs, map-over / reduction shape changes, sub-collection mapping, `paired_or_unpaired`, or `sample_sheet`.

```vendored-myst
file: galaxy-collection-semantics.upstream.myst
source: https://github.com/g
...

research

galaxy-collection-semantics

packaged

Preserve Galaxy collection typing and map-over/reduction semantics in the gxformat2 skeleton.

Trigger: When creating workflow inputs, outputs, and placeholder connections involving collections.

on-demand runtime verbatim corpus-observed deterministic 33.4 KB

bundle: references/notes/galaxy-collection-semantics.upstream.myst
source: content/research/galaxy-collection-semantics.upstream.myst

Preview myst

# Collection Semantics

This document describes the semantics around working with Galaxy dataset collections.
In particular it describes how they operate within Galaxy tools and workflows.

:::{admonition} You Probably Don't Need to Read This
:class: caution

Any significantly sophisticated workflow language will have ways to collect data
into arrays or vectors or dictionaries and apply operations across this data (mapping)
or reduce the dimensionality of this data (reductions). Typically, this is explicitly
annotated with map functions or for loops. Galaxy however is designed to be a point
and click interface for connecting steps and running tools. It is important that steps
just connect and just do the most natural thing - and this is what Galaxy does.
This document just provides a mathematical formalism to that "what should just
intuitively work" that can be used to document test cases and help with implementation.
This is reference documentation not user documentation, Galaxy should just work.
:::

## Mapping

If a tool consumes a simple dataset parameter and produces a simple dataset parameter,
then any collection type may be "mapped over" the data input to that tool. The result of
that is the tool being applied to each element of the collection and "implicit collections"
being created from the outputs that are produced from those operations. Those implicit
collections have the same element identifiers in the same order as the input collection that is
mapped over. Each element of the implicit collections correspond to their own job and
Galaxy very naturally and intuitively parallelizes jobs without extra work from the user
and without any knowledge of the tool.


(BASIC_MAPPING_PAIRED)=
(BASIC_MAPPING_PAIRED_OR_UNPAIRED_PAIRED)=
(BASIC_MAPPING_PAIRED_OR_UNPAIRED_UN
...

research

galaxy-collection-semantics

packaged

Preserve Galaxy collection typing and map-over/reduction semantics in the gxformat2 skeleton.

Trigger: When creating workflow inputs, outputs, and placeholder connections involving collections.

on-demand runtime verbatim corpus-observed deterministic 43.8 KB

bundle: references/notes/galaxy-collection-semantics.yml
source: content/research/galaxy-collection-semantics.yml

Preview yml

- doc: |
    # Collection Semantics

    This document describes the semantics around working with Galaxy dataset collections.
    In particular it describes how they operate within Galaxy tools and workflows.

    :::{admonition} You Probably Don't Need to Read This
    :class: caution

    Any significantly sophisticated workflow language will have ways to collect data
    into arrays or vectors or dictionaries and apply operations across this data (mapping)
    or reduce the dimensionality of this data (reductions). Typically, this is explicitly
    annotated with map functions or for loops. Galaxy however is designed to be a point
    and click interface for connecting steps and running tools. It is important that steps
    just connect and just do the most natural thing - and this is what Galaxy does.
    This document just provides a mathematical formalism to that "what should just
    intuitively work" that can be used to document test cases and help with implementation.
    This is reference documentation not user documentation, Galaxy should just work.
    :::

    ## Mapping

    If a tool consumes a simple dataset parameter and produces a simple dataset parameter,
    then any collection type may be "mapped over" the data input to that tool. The result of
    that is the tool being applied to each element of the collection and "implicit collections"
    being created from the outputs that are produced from those operations. Those implicit
    collections have the same element identifiers in the same order as the input collection that is
    mapped over. Each element of the implicit collections correspond to their own job and
    Galaxy very naturally and intuitively parallelizes jobs without extra work from the user
    and without any knowledge of the tool.

...

research

galaxy-workflow-comments

packaged

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.

Trigger: After topology is settled and the skeleton can be partitioned into named analysis stages (inputs, per-stage step clusters, parameter-derivation knots, visualization/outputs).

on-demand runtime verbatim corpus-observed deterministic 4.8 KB

bundle: references/notes/galaxy-workflow-comments.md
source: content/research/galaxy-workflow-comments.md

Preview md

---
type: research
subtype: component
tags:
  - research/component
  - target/galaxy
status: draft
created: 2026-06-12
revised: 2026-06-12
revision: 1
ai_generated: true
related_notes:
  - "[[iwc-comments-survey]]"
  - "[[gxformat2-schema]]"
  - "[[freeform-summary-to-galaxy-template]]"
  - "[[nextflow-summary-to-galaxy-template]]"
  - "[[cwl-summary-to-galaxy-template]]"
summary: "How to annotate a gxformat2 workflow with editor comments: one titled frame per analysis stage, populate contains_steps, color decorative."
---

# Galaxy workflow comments

Use this note when authoring or translating a Galaxy gxformat2 workflow and
deciding how to annotate it with editor comments — the top-level `comments:`
array the workflow editor renders as on-canvas frames and notes. Comments carry
no execution semantics; they document and visually organize the workflow. This
is presentation guidance, not a `content/patterns/` operation. Corpus evidence
behind every rule here lives in [[iwc-comments-survey]].

Comments are optional — roughly one in five IWC workflows use them. Add them when
the workflow has enough steps that a reader benefits from a stage map; skip them
on short linear workflows.

## 1. Box each analysis stage in a titled frame

The core move. Once topology is settled, partition the step set into `type:
frame` comments — one frame per logical stage of the analysis — and give each a
`title:` and a `contains_steps:` list of the step labels it groups:

```yaml
comments:
  - type: frame
    position: [687.5, 395.8]
    size: [498.9, 345.5]
    color: green
    title: Genome quality evaluation
    contains_steps:
      - run BUSCO
      - summarize BUSCO
```

`position` and `size` are editor-canvas geometry (floats); set them so the frame
encloses its steps, or copy them from 
...

research

galaxy-workflow-testability-design

packaged

Choose stable workflow input/output labels, testable checkpoint outputs, and fixture-compatible workflow interfaces while drafting the skeleton.

Trigger: When the template decides workflow inputs, workflow outputs, promoted checkpoints, or collection output identifiers that future tests will need to address.

on-demand runtime verbatim corpus-observed deterministic 11.4 KB

bundle: references/notes/galaxy-workflow-testability-design.md
source: content/research/galaxy-workflow-testability-design.md

Preview md

---
type: research
subtype: component
tags:
  - research/component
  - target/galaxy
status: draft
created: 2026-05-03
revised: 2026-05-06
revision: 2
ai_generated: true
related_notes:
  - "[[iwc-workflow-testability-survey]]"
  - "[[iwc-test-data-conventions]]"
  - "[[planemo-asserts-idioms]]"
  - "[[iwc-shortcuts-anti-patterns]]"
  - "[[planemo-workflow-test-architecture]]"
  - "[[implement-galaxy-workflow-test]]"
  - "[[gxformat2-schema]]"
  - "[[gxformat2-workflow-inputs]]"
  - "[[galaxy-datatypes-conf]]"
summary: "Design guidance for Galaxy workflow inputs, outputs, and checkpoints that make IWC-style workflow tests possible."
---

# Galaxy workflow testability design

Use this note when authoring or translating a Galaxy workflow **before** the `-tests.yml` file exists. It covers workflow structure choices that make later IWC-style tests meaningful: labels, promoted checkpoints, collection identifiers, and fixture-compatible inputs.

This is not a `content/patterns/` page. It is cross-cutting design guidance for Molds that need testable Galaxy workflows. Assertion syntax lives in [[planemo-asserts-idioms]]. Test YAML fixture shapes live in [[iwc-test-data-conventions]]. Accepted shortcut vs smell calls live in [[iwc-shortcuts-anti-patterns]]. Corpus evidence trail lives in [[iwc-workflow-testability-survey]].

## 1. Treat labels as API

Workflow input and output labels are not cosmetic. Planemo and IWC tests address workflow inputs and outputs by label, and the survey found exact label matches for every asserted output across 114 matched workflow/test pairs. A generated workflow should therefore pick stable, descriptive labels before test authoring starts.

Rules:

- Label every output that may need a test assertion.
- Treat input/output renames as breaking changes
...

research

nextflow-conditional-to-galaxy-subworkflow-when

packaged

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.

Trigger: 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.

on-demand runtime verbatim corpus-observed deterministic 13.7 KB

bundle: references/notes/nextflow-conditional-to-galaxy-subworkflow-when.md
source: content/research/nextflow-conditional-to-galaxy-subworkflow-when.md

Preview md

---
type: research
subtype: component
title: "Nextflow conditional to Galaxy subworkflow / when"
tags:
  - research/component
  - source/nextflow
  - target/galaxy
status: draft
created: 2026-05-08
revised: 2026-05-08
revision: 1
ai_generated: true
related_notes:
  - "[[nextflow-to-galaxy-reference-data-mapping]]"
  - "[[nextflow-to-galaxy-channel-shape-mapping]]"
  - "[[summary-nextflow]]"
  - "[[gxformat2-schema]]"
related_molds:
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[nextflow-summary-to-galaxy-template]]"
sources:
  - "https://github.com/galaxyproject/gxformat2"
  - "https://github.com/iwc-workflows"
summary: "Stub. Translate Nextflow conditionals into Galaxy `when:` (single-workflow v1). Subworkflow vs inline is an aesthetic call, not a rule."
---

# Nextflow conditional to Galaxy subworkflow / when

Stub. Surfaced from sarek emulation (2026-05-08). Companion to [[nextflow-to-galaxy-reference-data-mapping]] — same v1 posture (one Galaxy workflow per source pipeline; trench-coat shape is acceptable as a draft for human review), different gap (control flow rather than reference data).

## Posture

For v1 of the Nextflow-to-Galaxy translation Molds the output is a single Galaxy workflow per source pipeline, even when the source has substantial branching. IWC reviewers historically prefer sibling workflows for what looks like one pipeline with toggles, and we agree; but for the *translation step* a single artifact keeps the Mold pipeline deterministic, the harness simple, and the reviewer's mental model of "this draft maps 1:1 to the source" intact. Sibling-extraction is a polish pass a human or follow-up Mold runs *after* translation, not a decision the translation Mold makes.

The question this note addresses is: given that v1 is one Galaxy workflow, *h
...

research

nextflow-reference-data-classification

packaged

Cross-check source-side reference-data classifications before committing reference assets, optional inputs, and rebuild behavior into the gxformat2 skeleton.

Trigger: 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.

on-demand runtime verbatim corpus-observed deterministic 7.8 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

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.

Trigger: 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.

on-demand runtime verbatim corpus-observed deterministic 12.1 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
...

SKILL.md


# 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`, `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`, `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.