validate-galaxy-workflow

name	validate-galaxy-workflow
description	Run terminal gxwf validation on an assembled Galaxy workflow and classify workflow-level failures.

validate-galaxy-workflow

Follow the procedure below and use the artifact/reference sections as the runtime contract.

When To Use

• Run terminal gxwf validation on an assembled Galaxy workflow and classify workflow-level failures.

Inputs

• No upstream artifact inputs declared. See the procedure for user-supplied runtime inputs.

Outputs

• None declared.

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

• None declared.

Load On Demand

• references/cli/validate.json: CLI command reference packaged as a sidecar. Validate the assembled gxformat2 workflow before runtime testing. Use when: after all Galaxy steps and workflow tests have been assembled.
• references/notes/galaxy-workflow-invocation-failure-reference.md: Research note copied verbatim into the bundle. Keep static workflow validation findings distinct from Galaxy invocation/runtime failure surfaces. Use when: a workflow passes gxwf validation but still has likely runtime risks around invocation scheduling, outputs, conditionals, or collection population.
• references/notes/galaxy-workflow-testability-design.md: Research note copied verbatim into the bundle. Classify validation or pre-test findings that indicate missing labels, omitted workflow outputs, or untestable checkpoint structure. Use when: terminal validation passes but workflow-level outputs, labels, or collection shapes look likely to break future workflow tests.

Validation

• None declared.

Procedure

Validate the assembled Galaxy workflow before runtime testing. The skill owns the terminal validation pass: run gxwf validate, classify workflow-level diagnostics, and route failures back to the responsible authoring phase when possible.

This is separate from advance-galaxy-draft-step (which runs gxwf draft-validate --concrete inside the per-step loop) because terminal validation no longer has only one fresh step in scope and should reason over cross-step workflow structure.

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.