| name | summarize-galaxy-workflow |
| description | Read an existing Galaxy gxformat2 (or .ga) workflow and emit a structured summary for interview and change-set steps. |
summarize-galaxy-workflow
Follow the procedure below and use the artifact/reference sections as the runtime contract.
When To Use
- Read an existing Galaxy gxformat2 (or .ga) workflow and emit a structured summary for interview and change-set steps.
Inputs
- No upstream artifact inputs declared. See the procedure for user-supplied runtime inputs.
Outputs
- Write artifact
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.
- Write artifact
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.
Required Tools
Load Upfront
references/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.
Load On Demand
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.
Validation
- Validate
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.
Procedure
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.
Inputs
- A local workflow path or an HTTP(S) URL. Accept both gxformat2 (
.gxwf.yml / .gxfmt2.yml) and legacy native .ga.
- Optional pin/version metadata supplied by the harness or user.
- Optional sibling tests file (
*-tests.yml); if none is supplied or discoverable, emit tests: [].
Procedure
- Normalize format. If the input is native
.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.
- Validate. Run gxwf validate on the gxformat2 workflow and record
command, status, and diagnostics under documents.validation. If invalid, still emit source provenance and diagnostics; do not invent graph structure past what parses.
- Extract the interface. Record
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.
- Extract steps. For each step record its class,
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.
- Build the graph. Emit workflow-input → step, step → step, and step → workflow-output edges. Add
via markers for shape-affecting features (map-over, batch, collection reduction).
- Record tests. When a sibling tests file or embedded tests exist, record each case's name, job path, and expected outputs as the regression baseline. Do not fabricate expected outputs from tool names.
- Schema-check. Validate the assembled object with
foundry validate-summary-galaxy-workflow summary-galaxy-workflow.json before returning it.
Caveats Baked Into The Procedure
- Labels are load-bearing. Preserve step and input labels exactly; the change-set anchors edits to them, and a relabel here would silently break that anchoring.
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.- Post-job actions are preserved, not interpreted. Record each output's gxformat2 actions verbatim under
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.
- Existing tests are the regression baseline. Capture them faithfully; the update pipeline judges the modified workflow against them.
- Conversion is lossy-aware. If
.ga → gxformat2 conversion drops or rewrites anything, surface it in warnings[] rather than presenting a clean summary.
Non-Goals
- Modification. Interviewing for changes, building a change-set, and applying edits belong to interview-to-galaxy-workflow-changeset and apply-galaxy-workflow-changeset.
- Tool discovery or wrapper authoring.
tool_id / tool_shed_repository are recorded as-found; resolving newly introduced tools is the per-step Galaxy loop's job.
- Runtime execution. This skill summarizes structure; run-workflow-test owns execution.
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.
