Structured contract copied for validation or lookup.
- Purpose
- Validate Galaxy workflow test files before starting a Planemo or Galaxy-backed execution.
run-workflow-test
Execute a workflow's tests via Planemo; emit structured pass/fail and outputs.
Mold health
ok- Source layout
Directory Mold with only index.md frontmatter.
- Axis fields
generic fields are coherent.
- Eval plan
eval.md declares cases and check type.
- Typed refs
6 typed references; 0 resolver issues.
- On-demand triggers
All on-demand references describe triggers.
- Evidence checks
Hypothesis references include verification.
- axis
- generic
- name
- run-workflow-test
contract
Reference Loading
Typed Mold references describe what casting consumes and when the generated skill should load each artifact.
Command reference. Usually cast to a sidecar and loaded only when invoked.
- Purpose
- Run static schema and workflow-label checks before expensive workflow execution.
- Trigger
- Before invoking Planemo when a Galaxy workflow test file is present.
Tool-level install metadata. Aggregated into the cast bundle's Required Tools section.
- Purpose
- Runtime that executes the Galaxy or CWL workflow test; install before driving the harness.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Interpret assertion failures and choose the right fast inner-loop command before full reruns.
- Trigger
- When a workflow test file exists and the task is to run, iterate, or classify its test assertions.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Run workflow tests while preserving Planemo structured artifacts, Galaxy mode, invocation id, history id, and API follow-up context.
- Trigger
- When choosing between managed Galaxy, external Galaxy, full test runs, existing invocation checks, or direct workflow runs.
Background synthesis loaded by explicit progressive-disclosure metadata.
- Purpose
- Preserve invocation identifiers and state summaries needed to inspect workflow-level runtime failures after Planemo returns.
- Trigger
- When Planemo reports a failed, cancelled, missing-output, or ambiguous workflow invocation result.
Cast artifacts
- Claude skillrun-workflow-test— Execute a workflow's tests via Planemo; emit structured pass/fail and outputs.
Artifact handoffs
/ pipeline contractProduces
-
Structured pass/fail plus captured evidence — Planemo result, invocation/history/workflow ids, artifact paths, Galaxy mode, and (on failure) the observed modality and next reference surface — for debug-galaxy-workflow-output.
run-workflow-test
Execute an assembled workflow’s test file via planemo and emit a structured pass/fail with the artifacts a debug pass needs. One invocation runs the test once, captures the evidence, and — on failure — classifies the failure modality and names the next reference surface to inspect. It does not repair anything; that is debug-galaxy-workflow-output‘s job.
Sequence
- Validate before running. When a test file is present, run validate-tests for the static schema and workflow-label checks first. A run is expensive; do not spend one on a test file that fails static validation.
- Pick the Galaxy mode. Run against a Planemo-managed Galaxy or an existing/external Galaxy. Record which mode was used, how tools, workflows, and test data were staged, and the URLs or API credentials a follow-up inspection would need. The choice and its consequences are guided by planemo-workflow-test-architecture.
- Run and capture. Drive
planemo testwith structured output enabled. Preserve the invocation id, history id, workflow id, the Planemo structured result, and any test-output artifact paths — these are the inputs the debug Mold consumes. - Classify on failure. When the run exits non-zero or reports failed assertions, failed jobs, a failed invocation, missing outputs, or upload/staging problems, identify the observed failure modality and the single next reference surface to open: Planemo result, Galaxy job API, Galaxy invocation API, history contents, or the test assertion report. Use planemo-asserts-idioms to read assertion failures and galaxy-workflow-invocation-failure-reference to preserve invocation identifiers and state.
- Hand off. Emit the structured summary — green, or red with modality + captured artifacts + the named next surface — for debug-galaxy-workflow-output.
Keep this Mold’s output a faithful record of what happened, not a diagnosis. Mislabeling a staging failure as an assertion failure here sends the debug pass to the wrong reference surface.
Incoming References (9)
- CWL → GALAXYphase of pipeline— Path from a CWL Workflow to a Galaxy gxformat2 workflow. Lighter upstream extraction.
- INTERVIEW → GALAXYphase of pipeline— Interview-driven path to a Galaxy gxformat2 workflow through the shared freeform-summary handoff.
- NEXTFLOW → CWLphase of pipeline— Direct path from a Nextflow pipeline to a CWL Workflow + CommandLineTool set.
- NEXTFLOW → GALAXYphase of pipeline— Direct path from a Nextflow pipeline to a Galaxy gxformat2 workflow.
- PAPER → CWLphase of pipeline— Direct path from a paper to a CWL Workflow + CommandLineTool set.
- PAPER → GALAXYphase of pipeline— Direct path from a paper to a Galaxy gxformat2 workflow. No CWL intermediate.
- Galaxy workflow invocation failure referencerelated mold— Reference for Galaxy workflow invocation states, messages, failure reasons, and invocation API surfaces.
- Planemo workflow-test architecturerelated mold— Reference for Planemo workflow test/run architecture, Galaxy modes, API polling, and noisy failure boundaries.
- Galaxy workflow test formatrelated note— JSON Schema for the planemo workflow test format (`<workflow>-tests.yml`), vendored from `@galaxy-tool-util/schema`.