القائمة
Apply a reviewed change-set to a concrete Galaxy workflow: untouched regions preserved, tool-introducing edits injected as drafty steps.
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
Carry an existing Galaxy workflow's tests forward as a regression baseline and augment them for a change-set's deltas, emitting a Galaxy test plan.
Triage failing Galaxy run outputs; classify the failure surface and capture evidence before recommending repairs.
Synthesize a Galaxy workflow test plan from a free-form summary and the Galaxy design briefs.
Assemble Galaxy workflow test fixtures and assertions.
Execute a workflow's tests via Planemo; emit structured pass/fail and outputs.
Convert one nf-core module dir into a Galaxy tool wrapper (tool.xml + macros.xml + _provenance.yml + remote-URL <test> blocks).
| 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. |
Follow the procedure below and use the artifact/reference sections as the runtime contract.
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.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.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.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.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.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/clireferences/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.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.galaxy-workflow-draft.gxwf.yml for artifact galaxy-workflow-draft against the galaxy-workflow-draft schema when a validator is available.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.
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.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.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.
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.
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.