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
Updated obligations ledger: new unmet needs an edit surfaces appended; prior entries its edits close marked resolved.
yamlopen-requirements.ledger.yml
Raw artifact contract
{
"id": "open-requirements-ledger",
"kind": "yaml",
"default_filename": "open-requirements.ledger.yml",
"description": "Updated obligations ledger: new unmet needs an edit surfaces appended; prior entries its edits close marked resolved."
}
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]]: read open entries bearing on the edits; append any an edit cannot satisfy and mark resolved the ones it closes.
Raw artifact contract
{
"id": "open-requirements-ledger",
"description": "Carried obligations ledger [[open-requirements-ledger]]: read open entries bearing on the edits; append any an edit cannot satisfy and mark resolved the ones it closes.",
"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
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 12.5 KB
- bundle
references/notes/galaxy-workflow-draft-format.md- source
content/research/galaxy-workflow-draft-format.md
Preview md
---
type: research
subtype: design-spec
title: "Galaxy workflow draft format"
tags:
- research/design-spec
- target/galaxy
status: draft
created: 2026-05-06
revised: 2026-05-10
revision: 2
ai_generated: true
related_notes:
- "[[gxformat2-schema]]"
- "[[galaxy-data-flow-draft-contract]]"
- "[[discover-shed-tool]]"
- "[[galaxy-workflow-draft]]"
- "[[open-requirements-ledger]]"
related_molds:
- "[[nextflow-summary-to-galaxy-template]]"
- "[[cwl-summary-to-galaxy-template]]"
- "[[freeform-summary-to-galaxy-template]]"
- "[[compare-against-iwc-exemplar]]"
- "[[implement-galaxy-tool-step]]"
- "[[advance-galaxy-draft-step]]"
- "[[repair-galaxy-draft-topology]]"
summary: "gxformat2 draft superset: wrapper-tier TODOs (tool_id, tool_state, port names) plus _plan_state / _plan_context / _plan_in / _plan_out per tool step."
---
# Galaxy workflow draft format
The output artifact `galaxy-workflow-draft` produced by the `*-summary-to-galaxy-template` Molds is **gxformat2 with wrapper-tier relaxations and free-text planning fields**, sized to the gap between data-flow design and tool-resolved implementation.
Topology — workflow inputs and their collection shapes, workflow outputs, the step set, the producer→consumer edge graph, branches, and `when:` guards — is **settled by the template Mold itself**, drawing on the upstream interface and data-flow briefs (see [[galaxy-data-flow-draft-contract]]). The output is concrete gxformat2 with no topology TODOs. Wrapper-tier resolution — which Tool Shed wrapper, what parameters, the wrapper-determined port names that populate `in:` / `out:` / `outputSource` — is **evidence-gated per step** (see Resolution tiers below): a step resolves fully when the evidence pins wrapper and parameters together, pins identity alon
...
Carry the open-requirements ledger: append an edit's unmet need (e.g. a rewire with no reachable producer) rather than fabricating a connection, and mark resolved the ones its edits close.
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
...
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
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 8.1 KB
- bundle
references/cli/draft-validate.json- source
content/cli/gxwf/draft-validate.md
Preview json
{
"type": "cli-command",
"tool": "gxwf",
"command": "draft-validate",
"summary": "Validate a `class: GalaxyWorkflowDraft` workflow against draft-contract rules; with --concrete, also validate the extracted concrete subset.",
"source_path": "content/cli/gxwf/draft-validate.md",
"source_revision": 1,
"package": "@galaxy-tool-util/cli",
"description": "Validate a draft Galaxy workflow (class: GalaxyWorkflowDraft)",
"synopsis": "gxwf draft-validate [options] <file>",
"args": [
{
"raw": "file",
"name": "file",
"required": true,
"variadic": false,
"description": "Draft workflow file (.gxwf.yml)"
}
],
"options": [
{
"flags": "--format <fmt>",
"name": "format",
"description": "Force format: format2 (native is rejected for drafts)",
"takesArgument": true,
"argumentPlaceholder": "<fmt>",
"optionalArgument": false,
"negatable": false
},
{
"flags": "--json",
"name": "json",
"description": "Output structured JSON report",
"takesArgument": false,
"optionalArgument": false,
"negatable": false
},
{
"flags": "--report-html [file]",
"name": "reportHtml",
"description": "Write HTML report to file (or stdout if omitted)",
"takesArgument": true,
"argumentPlaceholder": "[file]",
"optionalArgument": true,
"negatable": false
},
{
"flags": "--report-markdown [file]",
"name": "reportMarkdown",
"description": "Write Markdown report to file (or stdout if omitted)",
"takesArgument": true,
"argumentPlaceholder": "[file]",
"optionalArgument": true,
"negatable": false
},
{
"flags": "--concrete",
"name": "concrete",
"description": "Additionally extract the concrete subset and run the regular `gxwf validate` checks on it",
"takesArgument": false,
"optionalArgument": false,
"negatable": false
},
{
"flags": "--cache-dir <dir>",
"name": "cacheDir",
"description": "Tool cache directory (for --concrete tool-state validation)",
"takesArgument": true,
"argumentPlaceholder": "<dir>",
"optionalArgument": false,
"negatable": false
},
{
"flags": "--no-tool-state",
"name": "toolState",
"description": "Skip tool-state validation in the --c
...
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: read open entries bearing on the edits; append any an edit cannot satisfy and mark resolved the ones it closes.
## 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`. Updated obligations ledger: new unmet needs an edit surfaces appended; prior entries its edits close marked resolved.
## Required Tools
- **`gxwf`** (gxwf). `npm install -g @galaxy-tool-util/cli@^1.8.1`.
Ephemeral run: `npx --yes --package @galaxy-tool-util/cli@1.8.1 gxwf`.
Check: `gxwf --help | grep -q draft-validate`.
Docs: https://github.com/jmchilton/galaxy-tool-util-ts/tree/main/packages/cli
## Load Upfront
- `references/notes/galaxy-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. Carry the open-requirements ledger: append an edit's unmet need (e.g. a rewire with no reachable producer) rather than fabricating a connection, and mark resolved the ones its edits close.
- `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. More generally, carry the ledger: read the entries bearing on the edits and mark resolved the ones the change-set closes.
### 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.
## 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.