Claude skill · cast

cwl-summary-to-galaxy-template

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

Install

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

Then invoke as:

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

Skill Bundle

/ packaged cast

attached files: 9
upfront: 5
on demand: 4
cast rev: n/a
validated: 0

Produces: 1 artifact.

Consumes: 4 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

Raw artifact contract

{
  "id": "galaxy-workflow-draft",
  "kind": "yaml",
  "default_filename": "galaxy-workflow-draft.gxwf.yml",
  "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."
}

Consumes

summary-cwl

Structured CWL summary emitted by [[summarize-cwl]]; consulted while emitting placeholder steps.

Raw artifact contract

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

cwl-galaxy-interface

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

Raw artifact contract

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

cwl-galaxy-data-flow

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

Raw artifact contract

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

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.",
  "producers": [
    "compare-against-iwc-exemplar"
  ]
}

Attached Files

/ runtime references

Load upfront

research

component-cwl-workflow-anatomy

packaged

Preserve the lightweight CWL boundary and avoid re-inferring structure already present in the summary.

upfront runtime verbatim hypothesis deterministic 5.5 KB

bundle: references/notes/component-cwl-workflow-anatomy.md
source: content/research/component-cwl-workflow-anatomy.md

Preview md

---
type: research
subtype: component
title: "CWL workflow anatomy"
tags:
  - research/component
  - source/cwl
status: draft
created: 2026-05-10
revised: 2026-05-10
revision: 1
ai_generated: true
related_notes:
  - "[[summary-cwl]]"
  - "[[cwl-v1.2-schemas]]"
  - "[[galaxy-collection-semantics]]"
related_molds:
  - "[[summarize-cwl]]"
  - "[[cwl-summary-to-galaxy-interface]]"
  - "[[cwl-summary-to-galaxy-data-flow]]"
  - "[[cwl-summary-to-galaxy-template]]"
sources:
  - "https://www.commonwl.org/v1.2/Workflow.html"
  - "https://cwltool.readthedocs.io/en/stable/"
  - "https://github.com/common-workflow-language/cwl-utils#normalize-a-cwl-document"
  - "https://pypi.org/project/cwl-utils/"
  - "https://github.com/common-workflow-language/cwldep"
summary: "CWL structure relevant to summarize-cwl: normalized documents, steps, scatter, conditionals, requirements, and dependency handling."
---

# CWL Workflow Anatomy

CWL is a structured workflow language, not a pipeline framework that must be inferred from ecosystem conventions. The `summarize-cwl` Mold should therefore start from CWL's own validated object model and avoid recreating the heavy Nextflow extraction stack.

## Normalization Posture

Use `cwltool --validate` as the first gate. If validation fails, the summary should emit provenance plus validation diagnostics and stop before producing downstream-looking graph claims.

Use `cwl-normalizer` from `cwl-utils` as the default normalization surface. The cwl-utils README describes it as producing JSON CWL documents with dependencies packed together, upgrading to CWL v1.2 as needed, and optionally refactoring CWL expressions into separate steps. This is the right handoff for `summarize-cwl`: structured enough for extraction, still source-faithful, and not a Galaxy design
...

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 6.4 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]]"
related_molds:
  - "[[nextflow-summary-to-galaxy-data-flow]]"
  - "[[cwl-summary-to-galaxy-data-flow]]"
  - "[[paper-summary-to-galaxy-design]]"
  - "[[nextflow-summary-to-galaxy-template]]"
  - "[[cwl-summary-to-galaxy-template]]"
  - "[[paper-summary-to-galaxy-template]]"
  - "[[compare-against-iwc-exemplar]]"
sources:
  - "https://github.com/jmchilton/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.
- Abstract unresolved tool needs with input and output shapes.
- Confidence and rationale on inferred nodes, edges, transforms, and tool needs.

The Galaxy template
...

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 7.1 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]]"
related_molds:
  - "[[nextflow-summary-to-galaxy-template]]"
  - "[[cwl-summary-to-galaxy-template]]"
  - "[[paper-summary-to-galaxy-template]]"
  - "[[compare-against-iwc-exemplar]]"
  - "[[implement-galaxy-tool-step]]"
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. Everything deferred to the per-step implementation Mold is wrapper-tier: which Tool Shed wrapper, what parameters, and the wrapper-determined port names that populate `in:` / `out:` / `outputSource`.

## Relaxations vs. gxformat2

For tool steps, when the wrapper has not been picked:

- `tool_id` and `tool_version` MAY be the literal string `TODO`. Resolution belongs to [[discover-shed-tool]] and the per-step implementation Mold.
- `tool_shed_repos
...

research

gxformat2-schema

packaged

Use the gxformat2 structural vocabulary for workflow inputs, outputs, steps, and placeholder wiring.

upfront runtime verbatim corpus-observed deterministic 3.8 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]]"
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-datatypes-conf]] for valid values.
- `
...

schema

summary-cwl

packaged

Read CWL source graph, step ids, command surfaces, scatter, conditionals, requirements, and warnings while emitting placeholder steps.

upfront runtime verbatim cast-validated deterministic 19.2 KB

bundle: references/schemas/summary-cwl.schema.json
source: package://@galaxy-foundry/summary-cwl-schema#summaryCwlSchema

Preview json

{
  "$schema": "http://json-schema.org/draft-07/schema#",
  "$id": "https://galaxyproject.org/foundry/schemas/summary-cwl.schema.json",
  "$comment": "Canonical source: packages/summary-cwl-schema/src/summary-cwl.schema.json in jmchilton/foundry. Mold frontmatter cites this schema via [[summary-cwl]] wiki-links; the cast pipeline imports the `summaryCwlSchema` runtime export and serializes it into cast bundles.",
  "title": "CWL Workflow Summary",
  "description": "Structured per-source summary emitted by the summarize-cwl Mold. CWL is already a typed workflow language, so this schema records validated and normalized workflow/tool structure rather than inferred pipeline semantics.",
  "type": "object",
  "additionalProperties": false,
  "required": [
    "summary_version",
    "source",
    "documents",
    "workflow_inputs",
    "workflow_outputs",
    "steps",
    "tools",
    "graph",
    "tests",
    "warnings"
  ],
  "properties": {
    "summary_version": {
      "type": "string",
      "enum": [
        "1"
      ],
      "description": "Summary schema major version."
    },
    "source": {
      "$ref": "#/$defs/SourceRecord"
    },
    "documents": {
      "$ref": "#/$defs/DocumentSet"
    },
    "workflow_inputs": {
      "type": "array",
      "items": {
        "$ref": "#/$defs/WorkflowInput"
      }
    },
    "workflow_outputs": {
      "type": "array",
      "items": {
        "$ref": "#/$defs/WorkflowOutput"
      }
    },
    "steps": {
      "type": "array",
      "items": {
        "$ref": "#/$defs/WorkflowStep"
      }
    },
    "tools": {
      "type": "array",
      "items": {
        "$ref": "#/$defs/CommandLineTool"
      }
    },
    "graph": {
      "$ref": "#/$defs/WorkflowGraph"
    },
    "tests": {
      "type": "array",
      "items": {
        "$ref": "#/$defs/TestCase"
      }
    },
    "warnings": {
      "type": "array",
      "items": {
        "$ref": "#/$defs/Warning"
      }
    }
  },
  "$defs": {
    "SourceRecord": {
      "type": "object",
      "additionalProperties": false,
      "required": [
        "ecosystem",
        "workflow",
        "url",
        "version",
        "license",
        "slug",
        "cwl_version",
        "entrypoint"
      ],
      "properties": {
        "ecosystem": {
          "type": "string",
          "enum": [
            "cwl"
          ],
          "description": "Source ecosy
...

Load on demand

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 4.4 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]]"
  - "[[paper-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 backing; 
...

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 3.1 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]]"
  - "[[paper-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]] — k
...

research

galaxy-collection-semantics

packaged

Translate CWL arrays, records, scatter, and secondary-file shapes into Galaxy collection typing and map-over/reduction semantics.

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

on-demand runtime verbatim corpus-observed deterministic 1.8 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]]"
sources:
  - "https://github.com/galaxyproject/galaxy/blob/7765fae934fbfdee77e3be5f5b235e43735273ae/lib/galaxy/model/dataset_collections/types/collection_semantics.yml"
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/galaxyproject/galaxy/blob/7765fae934fbfdee77e3be5f5b235e43735273ae/doc/source/dev/collection_semantics.md
sha: 7765fae
```

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
...

SKILL.md


# cwl-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 CWL summary and prior Galaxy design briefs.

## Inputs

- Read artifact `summary-cwl`. Schema: summary-cwl. Produced by `summarize-cwl`. Structured CWL summary emitted by summarize-cwl; consulted while emitting placeholder steps.
- Read artifact `cwl-galaxy-interface`. Produced by `cwl-summary-to-galaxy-interface`. Galaxy interface brief from cwl-summary-to-galaxy-interface that pins workflow inputs, outputs, labels.
- Read artifact `cwl-galaxy-data-flow`. Produced by `cwl-summary-to-galaxy-data-flow`. Galaxy data-flow brief from cwl-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.

## Outputs

- Write artifact `galaxy-workflow-draft` as `galaxy-workflow-draft.gxwf.yml`. Format: `yaml`. 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.

## Load Upfront

- `references/notes/component-cwl-workflow-anatomy.md`: Research note copied verbatim into the bundle. Preserve the lightweight CWL boundary and avoid re-inferring structure already present in the summary.
- `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 placeholder wiring.
- `references/schemas/summary-cwl.schema.json`: Schema file copied verbatim into the bundle. Read CWL source graph, step ids, command surfaces, scatter, conditionals, requirements, and warnings while emitting placeholder steps.

## Load On Demand

- `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-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. Translate CWL arrays, records, scatter, and secondary-file shapes into Galaxy collection typing and map-over/reduction semantics. Use when: creating workflow inputs, outputs, and placeholder connections involving collections.
- `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.

## Validation

- None declared.

## Procedure

Read the original CWL source artifact, the CWL summary, the CWL-to-Galaxy interface brief, and the CWL-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.

CWL already carries structured workflow shape, so this skill should be lighter than nextflow-summary-to-galaxy-template. Treat the prior-step index as the working context: CWL source, CWL summary, 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`. What is deferred to per-step authoring is strictly wrapper-tier: `tool_id`, `tool_version`, `tool_shed_repository`, `tool_state`, and the wrapper-determined port names that surface in `in:` / `out:` / `outputSource`. Capture deferred intent 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.

Defer thoughtfully. When research surfaces a Foundry pattern page that names the exact recipe — a galaxy-collection-patterns reshape, a conditional-run-optional-step gate, a galaxy-tabular-patterns filter — fill the step in as completely as the pattern allows: concrete `tool_id`, parameters, port names from the pattern's worked example. Pattern pages encode resolved choices; emitting `TODO` over a covered recipe discards real evidence the per-step skill cannot recover. Defer only when the step is a domain-specific CWL `CommandLineTool` with no covering pattern, and pack `_plan_context` with the `baseCommand` / `arguments`, `DockerRequirement` URIs, `SoftwareRequirement` packages, and `EnvVarRequirement` / `ResourceRequirement` constraints the per-step skill needs to pick a wrapper.

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`.

Use CWL step ids as the first pass for placeholder labels, then revise labels only when the interface/data-flow briefs or IWC comparison notes give a clearer Galaxy convention. Preserve one placeholder per logical CWL step unless the data-flow brief explicitly asks to split an expression, nested workflow, or collection operation into Galaxy-native steps.

## 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.