Agent Skill · cast

interview-to-galaxy-workflow-changeset

Interview a user against an existing Galaxy workflow summary and emit a reviewable, step-anchored change-set.

Install with Claude Code

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

Then invoke as:

/foundry-skills:interview-to-galaxy-workflow-changeset

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:

$interview-to-galaxy-workflow-changeset

Skill Bundle

/ packaged cast

attached files: 2
upfront: 2
on demand: 0
cast rev: n/a
validated: 0

Produces: 2 artifacts.

Consumes: 2 artifacts.

Artifact Contract

/ skill handoff

Produces

galaxy-workflow-changeset

Reviewable, ordered list of edit intents, each anchored to an existing step/input/output by label (or marked `new`), with edit kind, target, intent, and acceptance note. The human approval gate before any edits are applied.

markdowngalaxy-workflow-changeset.md

Raw artifact contract

{
  "id": "galaxy-workflow-changeset",
  "kind": "markdown",
  "default_filename": "galaxy-workflow-changeset.md",
  "description": "Reviewable, ordered list of edit intents, each anchored to an existing step/input/output by label (or marked `new`), with edit kind, target, intent, and acceptance note. The human approval gate before any edits are applied."
}

open-requirements-ledger

Updated obligations ledger: requested changes the workflow cannot support appended as open entries; prior entries this interview resolves 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: requested changes the workflow cannot support appended as open entries; prior entries this interview resolves marked resolved."
}

Consumes

summary-galaxy-workflow

Structured summary of the existing workflow from [[summarize-galaxy-workflow]]; the anchor set the change-set addresses (step labels, input labels, output names, tool_state keys).

Raw artifact contract

{
  "id": "summary-galaxy-workflow",
  "description": "Structured summary of the existing workflow from [[summarize-galaxy-workflow]]; the anchor set the change-set addresses (step labels, input labels, output names, tool_state keys).",
  "inherited_schema": "[[summary-galaxy-workflow]]",
  "producers": [
    "summarize-galaxy-workflow"
  ]
}

open-requirements-ledger

Carried obligations ledger [[open-requirements-ledger]]: read prior open entries; append requested changes the workflow cannot yet support.

Raw artifact contract

{
  "id": "open-requirements-ledger",
  "description": "Carried obligations ledger [[open-requirements-ledger]]: read prior open entries; append requested changes the workflow cannot yet support.",
  "producers": [
    "advance-galaxy-draft-step",
    "apply-galaxy-workflow-changeset",
    "compare-against-iwc-exemplar",
    "cwl-summary-to-galaxy-data-flow",
    "cwl-summary-to-galaxy-interface",
    "cwl-summary-to-galaxy-template",
    "freeform-summary-to-galaxy-data-flow",
    "freeform-summary-to-galaxy-interface",
    "freeform-summary-to-galaxy-template",
    "implement-galaxy-tool-step",
    "interview-to-galaxy-workflow-changeset",
    "nextflow-summary-to-galaxy-data-flow",
    "nextflow-summary-to-galaxy-interface",
    "nextflow-summary-to-galaxy-reference-data",
    "nextflow-summary-to-galaxy-template",
    "repair-galaxy-draft-topology"
  ]
}

Attached Files

/ runtime references

Load upfront

research

open-requirements-ledger

packaged

Carry the open-requirements ledger: append requested changes the current workflow cannot support rather than inventing or dropping them, and mark resolved the ones this step closes.

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-galaxy-workflow

packaged

Input contract: read the existing-workflow summary to anchor every change-set entry to a real step/input/output.

upfront runtime verbatim cast-validated deterministic 16.6 KB

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

Preview json

{
  "$schema": "http://json-schema.org/draft-07/schema#",
  "$id": "https://galaxyproject.org/foundry/schemas/summary-galaxy-workflow.schema.json",
  "$comment": "Canonical source: packages/foundry/src/schemas/summary-galaxy-workflow/summary-galaxy-workflow.schema.json in galaxyproject/foundry. Mold frontmatter cites this schema via [[summary-galaxy-workflow]] wiki-links; the cast pipeline imports the `summaryGalaxyWorkflowSchema` runtime export and serializes it into cast bundles.",
  "title": "Galaxy Workflow Summary",
  "description": "Structured summary emitted by the summarize-galaxy-workflow Mold. Galaxy gxformat2 is already a typed workflow language, so this schema records validated and normalized workflow structure (inputs, outputs, steps, edges, existing tests) rather than inferred pipeline semantics. When the user supplies a legacy .ga workflow it is converted to gxformat2 first and the conversion is recorded under documents.",
  "type": "object",
  "additionalProperties": false,
  "required": [
    "summary_version",
    "source",
    "documents",
    "workflow_inputs",
    "workflow_outputs",
    "steps",
    "graph",
    "tests",
    "warnings"
  ],
  "properties": {
    "summary_version": {
      "type": "string",
      "enum": [
        "1"
      ],
      "description": "Summary schema major version."
    },
    "source": {
      "$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": "#/$defs/WorkflowStep"
      }
    },
    "graph": {
      "$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",
        "format",
        "original_format",
        "release",
        "annotat
...

SKILL.md


# interview-to-galaxy-workflow-changeset

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

## When To Use

- Interview a user against an existing Galaxy workflow summary and emit a reviewable, step-anchored change-set.

## Inputs

- Read artifact `summary-galaxy-workflow`. Schema: summary-galaxy-workflow. Produced by `summarize-galaxy-workflow`. Structured summary of the existing workflow from summarize-galaxy-workflow; the anchor set the change-set addresses (step labels, input labels, output names, tool_state keys).
- Read artifact `open-requirements-ledger`. Produced by `advance-galaxy-draft-step`, `apply-galaxy-workflow-changeset`, `compare-against-iwc-exemplar`, `cwl-summary-to-galaxy-data-flow`, `cwl-summary-to-galaxy-interface`, `cwl-summary-to-galaxy-template`, `freeform-summary-to-galaxy-data-flow`, `freeform-summary-to-galaxy-interface`, `freeform-summary-to-galaxy-template`, `implement-galaxy-tool-step`, `interview-to-galaxy-workflow-changeset`, `nextflow-summary-to-galaxy-data-flow`, `nextflow-summary-to-galaxy-interface`, `nextflow-summary-to-galaxy-reference-data`, `nextflow-summary-to-galaxy-template`, `repair-galaxy-draft-topology`. Carried obligations ledger open-requirements-ledger: read prior open entries; append requested changes the workflow cannot yet support.

## Outputs

- Write artifact `galaxy-workflow-changeset` as `galaxy-workflow-changeset.md`. Format: `markdown`. Reviewable, ordered list of edit intents, each anchored to an existing step/input/output by label (or marked `new`), with edit kind, target, intent, and acceptance note. The human approval gate before any edits are applied.
- Write artifact `open-requirements-ledger` as `open-requirements.ledger.yml`. Format: `yaml`. Updated obligations ledger: requested changes the workflow cannot support appended as open entries; prior entries this interview resolves marked resolved.

## 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. Carry the open-requirements ledger: append requested changes the current workflow cannot support rather than inventing or dropping them, and mark resolved the ones this step closes.
- `references/schemas/summary-galaxy-workflow.schema.json`: Schema file copied verbatim into the bundle. Input contract: read the existing-workflow summary to anchor every change-set entry to a real step/input/output.

## Load On Demand

- None declared.

## Validation

- None declared.

## Procedure

Turn a modification interview into a **reviewable change-set** against an existing Galaxy workflow. This is the update pipeline's analogue of interview-to-freeform-summary: the harness owns the live interaction; the skill's job is the normalized handoff. But unlike the greenfield summary, the output is *anchored to concrete steps* of a workflow that already exists — it names what to change, not what to build.

The harness owns the interaction style (interactive session, saved transcript, or custom UI). Read the summary-galaxy-workflow first so every change is expressed against real labels rather than a mental model of the workflow.

### Output: the change-set

Emit Markdown: an ordered list of edit intents. Each entry carries:

- **kind** — one of: `add-step`, `replace-tool`, `remove-step`, `change-parameter`, `add-input`, `remove-input`, `add-output` / `expose-output`, `rewire`, `relabel` / `annotate`.
- **anchor** — the existing step label, input label, output name, or `tool_state` key the edit targets, quoted from the summary; or `new` for an added element.
- **intent** — what the user wants, in their words plus the concrete target value where they gave one (e.g. a parameter's new value).
- **acceptance** — how a reviewer or a test would confirm the edit landed (a new output is present, a parameter reads the new value, a step feeds its intended consumer).

Order edits so dependencies read top-to-bottom (add a step before rewiring its consumer). The change-set is a **reviewable artifact** — the natural human approval gate before apply-galaxy-workflow-changeset touches the workflow.

### Anchor discipline

Every entry must anchor to something the summary actually contains, or be explicitly marked `new`. Do not reference a step the workflow does not have, and do not silently rename an existing anchor. If the user asks for a change the workflow cannot support as described — an operation on a step that isn't there, a parameter a tool doesn't expose, a rewire that would break the graph — record it on the open-requirements-ledger as an open entry rather than inventing an anchor or quietly dropping the request.

### Don't over-specify

- **Don't resolve tools here.** An `add-step` or `replace-tool` names the *operation and any user-given tool/version*, not a resolved Tool Shed changeset — wrapper resolution is the per-step loop's job downstream. Record vague tool intent as intent plus, if needed, an open-requirements entry.
- **Don't apply the edit.** This skill decides *what* changes; apply-galaxy-workflow-changeset decides *how* the gxformat2 changes. Keep the two separate so the change-set stays reviewable.
- **Preserve scope.** Capture only what the interview supports. Do not fold in unrequested "while we're here" tidying — untouched regions must stay untouched, and a change-set that quietly widens scope propagates gratuitous churn downstream.

## 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.