apply-galaxy-workflow-changeset

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

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.