Foundry
Agent Skill · cast

apply-galaxy-workflow-changeset

Apply a reviewed change-set to a concrete Galaxy workflow: untouched regions preserved, tool-introducing edits injected as drafty steps.

← 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:apply-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:

$apply-galaxy-workflow-changeset

Skill Bundle

/ packaged cast
attached files
4
upfront
3
on demand
1
cast rev
n/a
validated
0

Produces: 2 artifacts.

Consumes: 3 artifacts.

Artifact Contract

/ skill handoff

Produces

galaxy-workflow-draft

gxformat2 draft (see [[galaxy-workflow-draft-format]]) of the whole workflow: untouched steps carried at Resolved tier verbatim; tool-introducing/replacing edits injected as drafty steps with _plan_* fields for the per-step loop; direct edits applied inline.

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]]) of the whole workflow: untouched steps carried at Resolved tier verbatim; tool-introducing/replacing edits injected as drafty steps with _plan_* fields for the per-step loop; direct edits applied inline."
}

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

starting-galaxy-workflow

The normalized concrete gxformat2 workflow being modified, emitted by [[summarize-galaxy-workflow]] (passthrough when already gxformat2, the `.ga`→gxformat2 conversion otherwise). The substrate edits apply to — untouched regions must survive byte-for-byte.

Raw artifact contract 
{
  "id": "starting-galaxy-workflow",
  "description": "The normalized concrete gxformat2 workflow being modified, emitted by [[summarize-galaxy-workflow]] (passthrough when already gxformat2, the `.ga`→gxformat2 conversion otherwise). The substrate edits apply to — untouched regions must survive byte-for-byte.",
  "producers": [
    "summarize-galaxy-workflow"
  ]
}

galaxy-workflow-changeset

Reviewed, step-anchored change-set from [[interview-to-galaxy-workflow-changeset]]; the edit intents to realize.

Raw artifact contract 
{
  "id": "galaxy-workflow-changeset",
  "description": "Reviewed, step-anchored change-set from [[interview-to-galaxy-workflow-changeset]]; the edit intents to realize.",
  "producers": [
    "interview-to-galaxy-workflow-changeset"
  ]
}

open-requirements-ledger

Carried obligations ledger [[open-requirements-ledger]]: the run's open, resolved, and surrendered entries with their provenance. Absent on the first Mold of a run; start an empty one.

Raw artifact contract 
{
  "id": "open-requirements-ledger",
  "description": "Carried obligations ledger [[open-requirements-ledger]]: the run's open, resolved, and surrendered entries with their provenance. Absent on the first Mold of a run; start an empty one.",
  "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

galaxy-workflow-draft-format

packaged

Represent the whole workflow as a draft: carry untouched steps at Resolved tier, inject tool-introducing/replacing edits as drafty steps with _plan_state / _plan_context / _plan_in / _plan_out.

upfront runtime verbatim hypothesis deterministic 12.6 KB
bundle
references/notes/galaxy-workflow-draft-format.md
source
content/research/galaxy-workflow-draft-format/index.md
Preview md 
---
type: research
title: "Galaxy workflow draft format"
tags:
  - target/galaxy
status: draft
created: 2026-05-06
revised: 2026-05-10
revision: 2
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, 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 alone when the wrapper is named but its settings are not, and defers entir
...
research

open-requirements-ledger

packaged

Close the open entries the change-set discharges, and append a blocking entry for an edited region whose output the rewired inputs cannot supply, so an edit-introduced gap is recorded rather than discovered downstream.

upfront runtime verbatim hypothesis deterministic 15.5 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: 2026-08-29
revision: 3
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 — and **source work it decided not to carry**. 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 behave identically
...
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 [[draft-validate]] 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 to the per-step loop.

Trigger: After writing the modified draft workflow file.

on-demand runtime sidecar hypothesis deterministic 8.6 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": "--offline",
      "name": "offline",
      "description": "Do not fetch uncached tools; read only the lo
...

SKILL.md


# apply-galaxy-workflow-changeset

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

## When To Use

- Apply a reviewed change-set to a concrete Galaxy workflow: untouched regions preserved, tool-introducing edits injected as drafty steps.

## Inputs

- Read artifact `starting-galaxy-workflow`. Produced by `summarize-galaxy-workflow`. The normalized concrete gxformat2 workflow being modified, emitted by summarize-galaxy-workflow (passthrough when already gxformat2, the `.ga`→gxformat2 conversion otherwise). The substrate edits apply to — untouched regions must survive byte-for-byte.
- Read artifact `galaxy-workflow-changeset`. Produced by `interview-to-galaxy-workflow-changeset`. Reviewed, step-anchored change-set from interview-to-galaxy-workflow-changeset; the edit intents to realize.
- 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: the run's open, resolved, and surrendered entries with their provenance. Absent on the first Mold of a run; start an empty one.

## 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) of the whole workflow: untouched steps carried at Resolved tier verbatim; tool-introducing/replacing edits injected as drafty steps with _plan_* fields for the per-step loop; direct edits applied inline.
- 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

- **`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-workflow-draft-format.md`: Research note copied verbatim into the bundle. Represent the whole workflow as a draft: carry untouched steps at Resolved tier, inject tool-introducing/replacing edits as drafty steps with _plan_state / _plan_context / _plan_in / _plan_out.
- `references/notes/open-requirements-ledger.md`: Research note copied verbatim into the bundle. Close the open entries the change-set discharges, and append a blocking entry for an edited region whose output the rewired inputs cannot supply, so an edit-introduced gap is recorded rather than discovered downstream.
- `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 draft-validate 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 to the per-step loop. Use when: after writing the modified draft workflow file.

## Validation

- Validate `galaxy-workflow-draft.gxwf.yml` for artifact `galaxy-workflow-draft` against the galaxy-workflow-draft schema when a validator is available.

## Procedure

Apply a reviewed change-set to a concrete Galaxy workflow and emit a `galaxy-workflow-draft.gxwf.yml`. This skill plays the topology-settling role the `*-to-galaxy-template` skills play in the greenfield pipelines — but it starts from an already-concrete workflow, so its defining job is to change **only** what the change-set names and carry everything else through untouched.

**An edit is a drafty region.** The Foundry already drains drafty steps out of a partially-concrete workflow via advance-galaxy-draft-step. So this skill does not resolve tools or run an edit loop of its own. It represents the whole modified workflow as a draft (see galaxy-workflow-draft-format): untouched steps carried at Resolved tier verbatim, and any edit that introduces or replaces a tool injected as a **drafty step + `_plan_*`** for the per-step loop to realize.

### What to apply directly vs. defer

- **Direct edits (applied inline, no drafty step).** `remove-step`, `rewire`, `relabel` / `annotate`, `change-parameter`, `add-input` / `remove-input`, `add-output` / `expose-output`. These need no tool resolution: edit the concrete step/input/output in place and rewire consumers as the change-set dictates. A change-set of purely direct edits yields a draft with `draft: false` — an immediately concrete workflow, no loop iterations.
- **Deferred edits (injected as drafty steps).** `add-step` and `replace-tool` (when the replacement is a different tool or an unpinned version). Add the step at draft tier with `tool_id: TODO` (or Identity-pinned when the change-set pinned an id), and record the operation, source evidence, and constraints in `_plan_state` / `_plan_context` / `_plan_in` / `_plan_out` so advance-galaxy-draft-step can resolve a wrapper and concretize it.

### Preserve untouched regions

Every step, input, and output the change-set does not name must survive byte-for-byte: same `tool_id`, `tool_version`, `tool_state`, labels, and connections. Do not reorder, reformat, re-case, or "tidy" an unrelated region — a structural diff of the emitted workflow against the input must touch only the change-set's targets and their necessary consequences (e.g. rewiring a consumer of a replaced producer). Gratuitous churn is a defect, not a style choice.

### Computability and the ledger

An edit can create a gap the connection graph won't catch: a rewire whose source doesn't carry what the consumer needs, or a `replace-tool` whose new tool can't supply a downstream port. Before handing off, check each edited region is computable from what feeds it. Where you find a gap you can't wire, append a **blocking** entry to the open-requirements-ledger naming the edit, the uncomputable output, and the missing evidence — so the per-step loop or repair-galaxy-draft-topology acts on it rather than discovering it late. Never fabricate a connection to make the graph look complete.

### Hand off

Run draft-validate on the emitted draft (sentinel form, topology, `_plan_*` placement). On green, hand the draft to advance-galaxy-draft-step, which drains any injected drafty steps and extracts the concrete `galaxy-workflow.gxwf.yml`. If the change-set was all direct edits, the loop is a no-op and the workflow is already concrete.

## 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.