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Read an existing Galaxy gxformat2 (or .ga) workflow and emit a structured summary for interview and change-set steps.
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Based on SOC occupation classification
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 | summarize-galaxy-workflow |
| description | Read an existing Galaxy gxformat2 (or .ga) workflow and emit a structured summary for interview and change-set steps. |
Follow the procedure below and use the artifact/reference sections as the runtime contract.
summary-galaxy-workflow as summary-galaxy-workflow.json. Format: json. Schema: summary-galaxy-workflow. Structured summary of an existing Galaxy workflow: source/format provenance, inputs, outputs, per-step tool_id/version/tool_state, edge graph, and any existing tests as a regression baseline.starting-galaxy-workflow as starting-galaxy-workflow.gxwf.yml. Format: yaml. The normalized concrete gxformat2 workflow this summary describes — passthrough when the input was already gxformat2, the .ga→gxformat2 conversion otherwise. The substrate apply-galaxy-workflow-changeset edits; distinct from the summary JSON, which is only context.foundry (foundry). npm install -g @galaxy-foundry/foundry.
Ephemeral run: npx --package @galaxy-foundry/foundry foundry.
Check: foundry --help.
Docs: https://github.com/galaxyproject/foundry/blob/main/packages/foundry/README.md
Bundled reference: references/cli/foundry.md.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/cli/validate.json: CLI command reference packaged as a sidecar. Validate the gxformat2 workflow before extraction and record diagnostics under documents.validation. Use when: before extracting structure from the workflow document.references/cli/foundry.md: CLI tool reference copied verbatim into the bundle. Schema-check summary-galaxy-workflow.json with foundry validate-summary-galaxy-workflow before returning it from the skill.references/schemas/summary-galaxy-workflow.schema.json: Schema file copied verbatim into the bundle. Validate the emitted Galaxy workflow summary JSON and provide downstream consumers the output contract.references/cli/convert.json: CLI command reference packaged as a sidecar. Convert a legacy .ga workflow to gxformat2 before summarizing, and record the conversion under documents.converted_path. Use when: the supplied workflow is native .ga rather than gxformat2.summary-galaxy-workflow.json before returning it: run foundry validate-summary-galaxy-workflow summary-galaxy-workflow.json from @galaxy-foundry/foundry. If the command is not on PATH, run npx --package @galaxy-foundry/foundry foundry validate-summary-galaxy-workflow summary-galaxy-workflow.json. This checks artifact summary-galaxy-workflow against the summary-galaxy-workflow schema.Read an existing Galaxy workflow and emit summary-galaxy-workflow.json. This skill is source-specific and target-agnostic: it records what the workflow is — inputs, outputs, steps, wiring, and existing tests — and leaves every modification decision to the downstream change-set and apply skills. It mirrors summarize-cwl on the Galaxy-as-source side.
gxformat2 is already a typed workflow graph, so do not infer structure — read it. The summary is an LLM-digestible index of the existing workflow that anchors the interview and the change-set; it is context, not the substrate edits apply to. The substrate the edits are applied against is the normalized gxformat2 workflow file, emitted here as starting-galaxy-workflow.gxwf.yml and consumed by apply-galaxy-workflow-changeset — not this JSON summary. Because this skill already normalizes .ga to gxformat2, it is the natural carrier for that substrate: a .ga input's converted form would otherwise have no declared home.
.gxwf.yml / .gxfmt2.yml) and legacy native .ga.*-tests.yml); if none is supplied or discoverable, emit tests: []..ga, convert it to gxformat2 with convert (--to format2) and record the output path in documents.converted_path. If it is already gxformat2, leave converted_path null. Set source.original_format accordingly. All downstream extraction reads the gxformat2 form. Emit this normalized gxformat2 as the starting-galaxy-workflow.gxwf.yml output — the substrate apply-galaxy-workflow-changeset edits, so a .ga input's converted form has a real carrier rather than living only inside the summary.command, status, and diagnostics under documents.validation. If invalid, still emit source provenance and diagnostics; do not invent graph structure past what parses.workflow_inputs (class data / collection / parameter, collection_type, optionality, defaults, format restrictions) and workflow_outputs (each promoted step/output source), preserving gxformat2 labels verbatim — those labels are the anchors the change-set will address.tool_id, tool_version, pinned tool_shed_repository, verbatim tool_state, named input connections with their upstream sources, declared outputs, and any when: guard. Keep tool_state verbatim so a later change-set can address an individual parameter. Record each declared output under out[] as {id, actions}, preserving the gxformat2 post-job actions on that output (hide, rename, add_tags, remove_tags, change_datatype, delete_intermediate, …) verbatim in actions — actions: null when the output has none. A hidden output that is not promoted to a workflow_outputs entry is only visible through its hide action here, so dropping it would blind an expose-output change-set to the very anchor it edits.via markers for shape-affecting features (map-over, batch, collection reduction).foundry validate-summary-galaxy-workflow summary-galaxy-workflow.json before returning it.tool_state is preserved, not interpreted. Record it verbatim. Deciding which parameter an interview wants changed is the change-set's job, not this skill's.out[].actions (hide, rename, add_tags, …); whether to expose a hidden output or drop a rename is the change-set's decision, not this skill's. Flattening out to bare names would erase that anchor..ga → gxformat2 conversion drops or rewrites anything, surface it in warnings[] rather than presenting a clean summary.tool_id / tool_shed_repository are recorded as-found; resolving newly introduced tools is the per-step Galaxy loop's job.