القائمة
Read an existing Galaxy gxformat2 (or .ga) workflow and emit a structured summary for interview and change-set 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 | 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.