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validate-galaxy-workflow

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

reviewed target/galaxy

Mold health

ok
  • Source layout

    Every file beside index.md is one the mold kind declares.

  • Axis fields

    target-specific fields are coherent.

  • Eval plan

    Abstract oracle: the properties any cast of this Mold must satisfy.

    eval.md declares properties and check type.

    eval.md ↗
  • Scenarios

    Concrete cases bound to fixtures, run against the eval properties.

    scenarios.md declares cases bound to fixtures.

    scenarios.md ↗
  • Typed refs

    3 typed references; 0 resolver issues.

  • On-demand triggers

    All on-demand references describe triggers.

  • Evidence checks

    Hypothesis references include verification.

axis
target-specific
target
galaxy
name
validate-galaxy-workflow
contract

Reference Loading

Typed references describe what casting consumes, and when the generated skill should load each artifact.

CLI Command gxwf validate

Command reference. Usually cast to a sidecar and loaded only when invoked.

RuntimeOn DemandSidecarHypothesis
Purpose
Validate the assembled gxformat2 workflow before runtime testing.
Trigger
After all Galaxy steps and workflow tests have been assembled.
Verify
Run the cast skill on a complete IWC-derived workflow and confirm terminal validation findings are separated from runtime test failures.
Research galaxy-workflow-testability-design

Background synthesis loaded by explicit progressive-disclosure metadata.

RuntimeOn DemandVerbatimCorpus Observed
Purpose
Classify validation or pre-test findings that indicate missing labels, omitted workflow outputs, or untestable checkpoint structure.
Trigger
When terminal validation passes but workflow-level outputs, labels, or collection shapes look likely to break future workflow tests.

Cast artifacts

  • Claude skill validate-galaxy-workflow — Run terminal gxwf validation on an assembled Galaxy workflow and classify workflow-level failures.

How to install →

Artifact handoffs

/ pipeline contract

Produces

  • galaxy-workflow-validation-result json galaxy-workflow-validation-result.json

    Terminal gxwf validation handoff: the exact command run, a pass/fail/not-run status, the classified workflow-level diagnostics, and the residual runtime risks static validation cannot settle.

    consumed by

validate-galaxy-workflow

Validate the assembled Galaxy workflow before runtime testing. The Mold 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.

Emit the result

Write galaxy-workflow-validation-result.json on every run — clean or failing — so a downstream reviewer can cite what was actually checked rather than re-deriving it:

  • command — the exact gxwf validate invocation, including flags (prefer --json);
  • workflow_path — the file validated;
  • status — pass, fail, or not-run, with a not_run_reason whenever validation could not execute;
  • diagnostics[] — one entry per finding: severity, message, the step or field it addresses, and the authoring phase it routes back to;
  • residual_runtime_risks[] — for a clean run, the risks static validation cannot settle and the runtime artifact that would prove or disprove each.

A not-run status is never reported as a pass.

Incoming References (11)

  • advance-galaxy-draft-step related mold — Advance the gxformat2 draft by one step: pick the next drafty step, resolve a wrapper, implement the step, and validate.
  • mature-galaxy-workflow-for-iwc related mold — Apply the IWC publication checklist to an existing Galaxy workflow and emit a generalized, reviewable submission set.
  • review-galaxy-workflow related mold — Apply the pinned upstream IWC review policy to one Galaxy workflow or pull request and emit one evidenced advisory Markdown review.
  • CWL → GALAXY phase of pipeline — Translate a CWL Workflow into a Galaxy gxformat2 workflow, then assemble and run a Galaxy workflow test.
  • GALAXY WORKFLOW MATURATION phase of pipeline — Apply the pinned IWC publication checklist to an existing Galaxy workflow, then validate and retest the matured result.
  • GALAXY WORKFLOW REVIEW phase of pipeline — Post-construction review journey: summarize, validate, and test an existing Galaxy workflow, then apply pinned IWC policy.
  • INTERVIEW → GALAXY phase of pipeline — Interview-driven path to a Galaxy gxformat2 workflow through the shared freeform-summary handoff.
  • NEXTFLOW → GALAXY phase of pipeline — Direct path from a Nextflow pipeline to a Galaxy gxformat2 workflow.
  • PAPER → GALAXY phase of pipeline — Direct path from a paper to a Galaxy gxformat2 workflow. No CWL intermediate.
  • UPDATE-INTERVIEW → GALAXY phase of pipeline — Interview-driven, edit-in-place modification of an existing Galaxy gxformat2 workflow via a reviewable change-set, reusing the per-step draft loop.
  • Galaxy workflow invocation failure reference related mold — Reference for Galaxy workflow invocation states, messages, failure reasons, and invocation API surfaces.