Agent Skill · cast

workflow-brief-to-galaxy-interface

Map a reviewed Workflow Brief into a Galaxy workflow interface design brief, consulting retained source evidence when available.

← All cast skills · Source mold →

Install with Claude Code

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

Then invoke as:

/foundry-skills:workflow-brief-to-galaxy-interface

Install with Codex

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

Then select with /skills or invoke explicitly as:

$workflow-brief-to-galaxy-interface

Install with Antigravity

git clone https://github.com/galaxyproject/foundry
agy plugin install foundry/casts/claude

Then select with /skills or invoke explicitly as:

/workflow-brief-to-galaxy-interface

Skill Bundle

/ packaged cast

attached files: 7
upfront: 3
on demand: 4
cast rev: n/a
validated: 0

Produces: 2 artifacts.

Consumes: 4 artifacts.

Artifact Contract

/ skill handoff

Produces

workflow-brief-galaxy-interface

Reviewable Markdown brief: Galaxy workflow inputs, outputs, labels, collection shapes, checkpoint outputs, Workflow Brief provenance, supporting-evidence citations, confidence, and open questions.

markdownworkflow-brief-galaxy-interface.md

Raw artifact contract

{
  "id": "workflow-brief-galaxy-interface",
  "kind": "markdown",
  "default_filename": "workflow-brief-galaxy-interface.md",
  "description": "Reviewable Markdown brief: Galaxy workflow inputs, outputs, labels, collection shapes, checkpoint outputs, Workflow Brief provenance, supporting-evidence citations, confidence, and open questions."
}

open-requirements-ledger

Carried obligations ledger re-emitted by this step: entries it appended or closed updated, every other entry passed through with its provenance intact.

yamlopen-requirements.ledger.yml

Raw artifact contract

{
  "id": "open-requirements-ledger",
  "kind": "yaml",
  "default_filename": "open-requirements.ledger.yml",
  "description": "Carried obligations ledger re-emitted by this step: entries it appended or closed updated, every other entry passed through with its provenance intact."
}

Consumes

workflow-brief

Expert-reviewed implementation contract. Its objective, scope, requirements, acceptance criteria, and exclusions govern every interface decision.

Raw artifact contract

{
  "id": "workflow-brief",
  "description": "Expert-reviewed implementation contract. Its objective, scope, requirements, acceptance criteria, and exclusions govern every interface decision.",
  "inherited_schema": "[[workflow-brief-schema]]",
  "producers": [
    "freeform-summary-to-workflow-brief",
    "nextflow-summary-to-workflow-brief"
  ]
}

freeform-summary

Optional narrative source evidence; it may clarify the selected scope but cannot broaden or override the brief.

Raw artifact contract

{
  "id": "freeform-summary",
  "description": "Optional narrative source evidence; it may clarify the selected scope but cannot broaden or override the brief.",
  "optional": true,
  "producers": [
    "interview-to-freeform-summary",
    "summarize-paper"
  ]
}

summary-nextflow

Optional structured Nextflow source evidence; process, channel, parameter, and test facts are evidence rather than assumed Galaxy design.

Raw artifact contract

{
  "id": "summary-nextflow",
  "description": "Optional structured Nextflow source evidence; process, channel, parameter, and test facts are evidence rather than assumed Galaxy design.",
  "optional": true,
  "inherited_schema": "[[summary-nextflow]]",
  "producers": [
    "summarize-nextflow"
  ]
}

open-requirements-ledger

Carried workflow-run knowledge [[open-requirements-ledger]]. Absent on the first design Mold of a run; initialize an empty ledger.

Raw artifact contract

{
  "id": "open-requirements-ledger",
  "description": "Carried workflow-run knowledge [[open-requirements-ledger]]. Absent on the first design Mold of a run; initialize an empty ledger.",
  "optional": true,
  "producers": [
    "advance-galaxy-draft-step",
    "apply-galaxy-workflow-changeset",
    "compare-against-iwc-exemplar",
    "cwl-summary-to-galaxy-data-flow",
    "cwl-summary-to-galaxy-interface",
    "cwl-summary-to-galaxy-template",
    "freeform-summary-to-galaxy-data-flow",
    "freeform-summary-to-galaxy-interface",
    "freeform-summary-to-galaxy-template",
    "implement-galaxy-tool-step",
    "interview-to-galaxy-workflow-changeset",
    "mature-galaxy-workflow-for-iwc",
    "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",
    "workflow-brief-to-galaxy-data-flow",
    "workflow-brief-to-galaxy-interface",
    "workflow-brief-to-galaxy-template"
  ]
}

Attached Files

/ runtime references

Load upfront

research

open-requirements-ledger

packaged

Inherit open entries rather than re-deriving them, close the ones this brief's input, output, and label decisions settle, and append interface obligations the narrative never settles — an output the source names but never specifies, a parameter stated only qualitatively, a collection shape the prose doesn't determine.

upfront runtime verbatim hypothesis deterministic 18.5 KB

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

Preview md

---
type: research
title: "Open-requirements ledger"
tags:
  - target/galaxy
status: draft
created: 2026-06-16
revised: 2026-09-21
revision: 4
related_notes:
  - "[[galaxy-workflow-draft-format]]"
related_molds:
  - "[[advance-galaxy-draft-step]]"
  - "[[repair-galaxy-draft-topology]]"
  - "[[implement-galaxy-tool-step]]"
summary: "Carried workflow-run knowledge artifact for obligations, discoveries, decisions, brief-change recommendations, and convergence state."
---

# Open-requirements ledger

The `open-requirements-ledger` is the carried workflow-run knowledge artifact threaded through the source→Galaxy pipeline. It 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 — and **source work it decided not to carry**. It also records evidence discovered during implementation, decisions made within the approved scope, and recommended changes to an immutable Workflow Brief. Each Mold that surfaces an obligation **appends** it; each Mold whose decision closes one **marks it resolved**; the terminal path **surrenders** whatever remains open, explicitly, into the final artifact.

This ledger is about the workflow being built. It is distinct from the opt-in `foundry-feedback-ledger`, which records actionable defects or friction in the Foundry assets building it. It is also not the harness's phase-progress tracker: execution status belongs to harness state, checkpoints, and reports rather than requirement entries.

## 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 a
...

research

workflow-brief-design

packaged

Preserve the authority boundary between reviewed intent, optional source evidence, and downstream Galaxy design decisions.

upfront runtime verbatim hypothesis deterministic 7.3 KB

bundle: references/notes/workflow-brief-design.md
source: content/research/workflow-brief-design/index.md

Preview md

---
type: research
title: "Workflow Brief"
tags:
  - meta
status: draft
created: 2026-09-17
revised: 2026-09-20
revision: 5
summary: "Markdown Workflow Brief definition and section contract for scope, constraints, agent environment, and explicit blockers."
---

# Workflow Brief

A Workflow Brief is an expert-editable document describing what a workflow should achieve, what it should leave out, and the constraints under which an agent will build and run it. It is an input to design and implementation. The draft workflow captures the proposed steps, wiring, and tool state.

## Document shape

The brief is Markdown with a title and two sections: `## Workflow` and `## Agent Environment`. The workflow needs an objective; most details are optional. The agent environment must contain a description, which can explicitly record what still needs to be checked.

The `workflowBriefSchema` declaration uses the shared engine described in [[markdown-document-contract]] and lives in `packages/gxwf-foundry/src/workflow-brief.ts`. An illustrative document lives in `packages/gxwf-foundry/test/fixtures/workflow-brief/read-alignment.md`.

| Heading | Required | Content |
| --- | --- | --- |
| `## Workflow` | Yes | Scientific intent and scope. |
| `### Objective` | Yes, under Workflow | Scientific goal and desired outcome. |
| `### Sources` | No | Papers, interviews, repositories, relevant source pins, and evidence availability. |
| `### Scope` | No | Optional `#### Included` and `#### Excluded` describe selected work and boundaries. |
| `### Inputs and outputs` | No | Scientific roles and source-supported formats or organization. |
| `### Requirements and preferences` | No | Expert or source requirements, their strength, rationale, and evidence. |
| `### Acceptance criteria` | No | High-lev
...

schema

workflow-brief-schema

packaged

Validate the required Workflow Brief before treating it as the implementation contract.

upfront runtime verbatim cast-validated deterministic 2.0 KB

bundle: references/schemas/workflow-brief-schema.schema.json
source: package://@galaxy-foundry/gxwf-foundry#workflowBriefSchema

Preview json

{
  "name": "Workflow Brief",
  "title": "required",
  "sections": [
    {
      "heading": "Workflow",
      "min": 1,
      "max": 1,
      "content": true,
      "sections": [
        {
          "heading": "Objective",
          "min": 1,
          "max": 1,
          "content": true
        },
        {
          "heading": "Sources",
          "max": 1,
          "content": true
        },
        {
          "heading": "Scope",
          "max": 1,
          "content": true,
          "sections": [
            {
              "heading": "Included",
              "max": 1,
              "content": true
            },
            {
              "heading": "Excluded",
              "max": 1,
              "content": true
            }
          ]
        },
        {
          "heading": "Inputs and outputs",
          "max": 1,
          "content": true
        },
        {
          "heading": "Requirements and preferences",
          "max": 1,
          "content": true
        },
        {
          "heading": "Acceptance criteria",
          "max": 1,
          "content": true
        },
        {
          "heading": "Open questions",
          "max": 1,
          "content": true
        },
        {
          "heading": "Decisions",
          "max": 1,
          "content": true
        },
        {
          "heading": "Related artifacts",
          "max": 1,
          "content": true
        },
        {
          "heading": "Blockers",
          "max": 1
        }
      ]
    },
    {
      "heading": "Agent Environment",
      "min": 1,
      "max": 1,
      "content": true,
      "sections": [
        {
          "heading": "Tooling",
          "max": 1,
          "content": true
        },
        {
          "heading": "Constraints",
          "max": 1,
          "content": true
        },
        {
          "heading": "Containerization",
          "max": 1,
          "content": true
        },
        {
          "heading": "Blockers",
          "max": 1
        }
      ]
    }
  ]
}

Load on demand

research

galaxy-collection-semantics

packaged

Choose Galaxy collection input shapes (File / list / paired / list:paired / record) from the source's per-sample, paired, grouped, or nested data descriptions.

Trigger: When the brief or supporting evidence describes paired reads, per-sample groups, nested or grouped inputs, or any input that should become a Galaxy dataset collection.

on-demand runtime verbatim corpus-observed deterministic 1.9 KB

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

Preview md

---
type: research
title: "Galaxy collection semantics"
tags:
  - target/galaxy
status: draft
created: 2026-04-30
revised: 2026-05-05
revision: 3
license: MIT
license_file: LICENSES/galaxy.LICENSE
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"
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`. One file travels with 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.
>
> The Foundry also vendors Galaxy's auto-generated MyST/LaTeX rendering of the same YAML, which
> is what the human view below renders from. It is a site asset: casting does not carry it, so
> do not look for it beside this note in a skill bundle. 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: h
...

research

galaxy-collection-semantics

packaged

Choose Galaxy collection input shapes (File / list / paired / list:paired / record) from the source's per-sample, paired, grouped, or nested data descriptions.

Trigger: When the brief or supporting evidence describes paired reads, per-sample groups, nested or grouped inputs, or any input that should become a Galaxy dataset collection.

on-demand runtime verbatim corpus-observed deterministic 43.8 KB

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

packaged

Pick the right sample_sheet variant and translate described per-sample column metadata into Galaxy column_definitions when the source describes sample-sheet-shaped inputs.

Trigger: When the brief or supporting evidence describes a sample sheet, a per-sample/per-record table, or any table mapping samples to files that should become a Galaxy collection or sample-sheet input.

on-demand runtime verbatim corpus-observed deterministic 8.4 KB

bundle: references/notes/galaxy-sample-sheet-collections.md
source: content/research/galaxy-sample-sheet-collections/index.md

Preview md

---
type: research
title: "Galaxy sample_sheet collection types"
tags:
  - target/galaxy
status: draft
created: 2026-05-05
revised: 2026-05-06
revision: 2
related_notes:
  - "[[galaxy-collection-semantics]]"
  - "[[galaxy-collection-tools]]"
  - "[[nextflow-workflow-io-semantics]]"
  - "[[nextflow-params-to-galaxy-inputs]]"
  - "[[nextflow-path-glob-to-galaxy-datatype]]"
  - "[[nextflow-to-galaxy-channel-shape-mapping]]"
  - "[[nextflow-to-galaxy-reference-data-mapping]]"
related_molds:
  - "[[nextflow-summary-to-galaxy-interface]]"
  - "[[nextflow-summary-to-galaxy-data-flow]]"
sources:
  - "Galaxy PR #19305 (Implement Sample Sheets), merged 2025-07-30"
  - "lib/galaxy/model/dataset_collections/types/sample_sheet.py"
  - "lib/galaxy/model/dataset_collections/types/sample_sheet_util.py"
  - "lib/galaxy/model/dataset_collections/type_description.py"
  - "lib/galaxy/schema/schema.py (SampleSheetColumnDefinition, SampleSheetRow)"
  - "lib/galaxy/tools/wrappers.py (DatasetCollectionWrapper.sample_sheet_row)"
  - "lib/galaxy/tools/sample_sheet_to_tabular.xml"
  - "lib/galaxy/webapps/galaxy/api/dataset_collections.py (sample_sheet_workbook endpoints)"
  - "lib/galaxy/model/migrations/alembic/versions_gxy/3af58c192752_implement_sample_sheets.py"
summary: "Galaxy's sample_sheet collection family: typed column metadata, four variants, mapping rules, validator allowlist."
---

# Galaxy sample_sheet collection types

Reference for the Galaxy backend shape that targets structured per-row metadata — the natural landing zone for Nextflow `samplesheetToList` parameters and for any source-side idiom that pairs typed metadata columns with dataset references.

## Shape

A `sample_sheet` is a list-shaped collection where each element carries a typed `columns` row, and the parent collectio
...

research

galaxy-workflow-testability-design

packaged

Choose stable workflow input/output labels and promoted checkpoint outputs that future tests can address.

Trigger: When deciding labels, public outputs, checkpoint outputs, or fixture-compatible collection inputs.

on-demand runtime verbatim corpus-observed deterministic 7.8 KB

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

Preview md

---
type: research
tags:
  - target/galaxy
status: draft
created: 2026-05-03
revised: 2026-09-23
revision: 3
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."
---

# Design a Galaxy workflow that can be tested

Choose the workflow's public inputs and outputs while designing the analysis, before writing its `-tests.yml`. A workflow test supplies `job:` values by input name and checks `outputs:` by output name. It can only check results the workflow exposes. A good interface gives the test a reproducible input, an addressable result, and at least one assertion that would catch a meaningful wrong result.

This note concerns workflow design. [[iwc-test-data-conventions]] covers the test file's input fixtures, [[planemo-asserts-idioms]] covers assertion syntax, and [[iwc-shortcuts-anti-patterns]] explains when a smoke check is enough. [[iwc-workflow-testability-survey]] holds the broader corpus evidence.

## Name the public interface before writing tests

Give each input and promoted output a stable, descriptive public name. In an exported gxformat2 workflow this is commonly the entry's `id`. The structural [[gxformat2-schema]] also permits `label`. Check the **effective name in the workflow being tested** instead of assuming a step label, generated dataset name, or array position will become the test key. In the pinned [Scanpy workflow](https://github.com/galaxy
...

SKILL.md


# workflow-brief-to-galaxy-interface

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

## When To Use

- Map a reviewed Workflow Brief into a Galaxy workflow interface design brief, consulting retained source evidence when available.

## Inputs

- Read artifact `workflow-brief`. Schema: workflow-brief-schema. Produced by `freeform-summary-to-workflow-brief`, `nextflow-summary-to-workflow-brief`. Expert-reviewed implementation contract. Its objective, scope, requirements, acceptance criteria, and exclusions govern every interface decision.
- Read artifact `freeform-summary`. Optional; absence is allowed and must be reported honestly. Produced by `interview-to-freeform-summary`, `summarize-paper`. Optional narrative source evidence; it may clarify the selected scope but cannot broaden or override the brief.
- Read artifact `summary-nextflow`. Optional; absence is allowed and must be reported honestly. Schema: summary-nextflow. Produced by `summarize-nextflow`. Optional structured Nextflow source evidence; process, channel, parameter, and test facts are evidence rather than assumed Galaxy design.
- Read artifact `open-requirements-ledger`. Optional; absence is allowed and must be reported honestly. Produced by `advance-galaxy-draft-step`, `apply-galaxy-workflow-changeset`, `compare-against-iwc-exemplar`, `cwl-summary-to-galaxy-data-flow`, `cwl-summary-to-galaxy-interface`, `cwl-summary-to-galaxy-template`, `freeform-summary-to-galaxy-data-flow`, `freeform-summary-to-galaxy-interface`, `freeform-summary-to-galaxy-template`, `implement-galaxy-tool-step`, `interview-to-galaxy-workflow-changeset`, `mature-galaxy-workflow-for-iwc`, `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`, `workflow-brief-to-galaxy-data-flow`, `workflow-brief-to-galaxy-interface`, `workflow-brief-to-galaxy-template`. Carried workflow-run knowledge open-requirements-ledger. Absent on the first design Mold of a run; initialize an empty ledger.

## Outputs

- Write artifact `workflow-brief-galaxy-interface` as `workflow-brief-galaxy-interface.md`. Format: `markdown`. Reviewable Markdown brief: Galaxy workflow inputs, outputs, labels, collection shapes, checkpoint outputs, Workflow Brief provenance, supporting-evidence citations, confidence, and open questions.
- Write artifact `open-requirements-ledger` as `open-requirements.ledger.yml`. Format: `yaml`. Carried obligations ledger re-emitted by this step: entries it appended or closed updated, every other entry passed through with its provenance intact.

## Required Tools

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

## Load Upfront

- `references/notes/open-requirements-ledger.md`: Research note copied verbatim into the bundle. Inherit open entries rather than re-deriving them, close the ones this brief's input, output, and label decisions settle, and append interface obligations the narrative never settles — an output the source names but never specifies, a parameter stated only qualitatively, a collection shape the prose doesn't determine.
- `references/notes/workflow-brief-design.md`: Research note copied verbatim into the bundle. Preserve the authority boundary between reviewed intent, optional source evidence, and downstream Galaxy design decisions.
- `references/schemas/workflow-brief-schema.schema.json`: Schema file copied verbatim into the bundle. Validate the required Workflow Brief before treating it as the implementation contract.

## Load On Demand

- `references/notes/galaxy-collection-semantics.md`: Research note copied verbatim into the bundle. Choose Galaxy collection input shapes (File / list / paired / list:paired / record) from the source's per-sample, paired, grouped, or nested data descriptions. Use when: the brief or supporting evidence describes paired reads, per-sample groups, nested or grouped inputs, or any input that should become a Galaxy dataset collection.
- `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-sample-sheet-collections.md`: Research note copied verbatim into the bundle. Pick the right sample_sheet variant and translate described per-sample column metadata into Galaxy column_definitions when the source describes sample-sheet-shaped inputs. Use when: the brief or supporting evidence describes a sample sheet, a per-sample/per-record table, or any table mapping samples to files that should become a Galaxy collection or sample-sheet input.
- `references/notes/galaxy-workflow-testability-design.md`: Research note copied verbatim into the bundle. Choose stable workflow input/output labels and promoted checkpoint outputs that future tests can address. Use when: deciding labels, public outputs, checkpoint outputs, or fixture-compatible collection inputs.

## Validation

- None declared.

## Procedure

Read the reviewed, unchanged Workflow Brief and emit a reviewable Markdown interface brief for a Galaxy workflow. Capture workflow inputs, workflow outputs, labels, Galaxy collection shapes, checkpoint outputs worth exposing for tests, provenance, confidence, and open questions.

The Workflow Brief is authoritative for objective, included and excluded scope, expert requirements, and acceptance criteria. Consult a retained `freeform-summary` or `summary-nextflow` only as supporting evidence for the selected work. Evidence may supply methods, formats, parameters, datasets, or uncertainty that the concise brief omits, but it cannot silently add analyses or override an expert decision. A hand-authored brief with no source summary is valid.

Translate what the reviewed contract and available evidence support into Galaxy interface decisions. Record evidence as discoveries, authorized mappings as decisions, missing actionable detail as obligations, and any needed change to expert intent as a proposed brief-change recommendation in the ledger. Never edit the brief or apply a proposed change here.

The output is not a gxformat2 skeleton and not a workflow schema. It is a design handoff consumed by workflow-brief-to-galaxy-data-flow, workflow-brief-to-galaxy-template, and later test-plan work.

## Feedback Mode

- Feedback mode is off unless the caller explicitly enables `--feedback` or supplies a feedback-ledger path.
- When enabled, read `_feedback.md` before doing the work and use its registered `foundry-feedback.ledger.yml` protocol.
- Preserve harness-owned run and phase state. Append only concrete observations about a canonical Foundry source asset or a related project that this run showed to be at fault; do not put ordinary workflow requirements in this ledger.
- Before reporting completion, make one explicit pass over the work you just did. Do not ask yourself whether anything was unclear — recall what happened: where you guessed at something the instructions should have settled, needed information this bundle does not carry, hit an instruction that contradicted another or contradicted the artifacts in front of you, used a packaged reference that did not cover your case, or did something the procedure never describes.
- Append an entry for each such event that clears the protocol's bar. If none do, append nothing and report `no feedback` explicitly. Silence and a clean pass are not the same thing, and nothing downstream can tell them apart unless you say which one it was.
- Pass the same ledger path to any subagent used for this work, and merge updates serially so one writer cannot overwrite another.

## 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.