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Triage failing Galaxy run outputs; classify the failure surface and capture evidence before recommending repairs.
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Based on SOC occupation classification
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.
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).
Path from a CWL Workflow to a Galaxy gxformat2 workflow — orchestrates the Foundry skills of the CWL → GALAXY pipeline in order, in a per-run working directory.
| name | debug-galaxy-workflow-output |
| description | Triage failing Galaxy run outputs; classify the failure surface and capture evidence before recommending repairs. |
Follow the procedure below and use the artifact/reference sections as the runtime contract.
workflow-test-result. Produced by run-workflow-test. Structured run handoff from run-workflow-test: Planemo result, invocation/job/artifact context, and the observed failure modality.workflow-debug-report as workflow-debug-report.md. Format: markdown. Failure-surface classification with captured job/invocation/collection/assertion evidence and a recommended next step or reference-gap follow-up.references/notes/galaxy-collection-semantics.md: Research note copied verbatim into the bundle. Diagnose collection shape, mapping, reduction, and element-identifier mismatches in failed Galaxy runs. Use when: a failing output is a collection, a mapped output, or an unexpectedly nested/flattened structure.references/notes/galaxy-collection-semantics.upstream.myst: Companion file copied verbatim into the bundle. Sibling of references/notes/galaxy-collection-semantics.md; read it where that note directs.references/notes/galaxy-collection-semantics.yml: Companion file copied verbatim into the bundle. Sibling of references/notes/galaxy-collection-semantics.md; read it where that note directs.references/notes/galaxy-tool-job-failure-reference.md: Research note copied verbatim into the bundle. Interpret Galaxy job-level failure evidence including stdio rules, exit code, job messages, and output dataset state. Use when: a failed workflow test includes errored jobs, tool stderr/stdout, non-zero exit codes, or red output datasets.references/notes/galaxy-workflow-invocation-failure-reference.md: Research note copied verbatim into the bundle. Interpret Galaxy invocation-level failure evidence including invocation state, structured messages, and step job summaries. Use when: a failed workflow test has invocation failure, missing workflow outputs, cancelled/paused steps, subworkflow failures, or collection population errors.references/notes/iwc-shortcuts-anti-patterns.md: Research note copied verbatim into the bundle. Decide whether a proposed debug fix aligns with accepted IWC testing shortcuts or masks a real failure. Use when: debugging suggests weakening assertions, widening deltas, switching to existence checks, or changing output labels.references/notes/nextflow-operators-to-galaxy-collection-recipes.md: Research note copied verbatim into the bundle. Trace collection output failures back to possibly lossy operator translations. Use when: debugging wrong nesting, missing elements, branch merges, bad joins, or gather/reduction mismatches.references/notes/planemo-asserts-idioms.md: Research note copied verbatim into the bundle. Classify whether a failure is an assertion-choice problem, tolerance problem, or real workflow-output regression. Use when: planemo reports output assertion failures or generated tests are too strict/too weak.references/notes/planemo-workflow-test-architecture.md: Research note copied verbatim into the bundle. Locate which Planemo artifact or Galaxy API surface preserves the failure evidence. Use when: planemo output is ambiguous, structured test JSON is available, or rerunning can be avoided by inspecting an existing invocation.Triage a failing Galaxy workflow test. Take the structured handoff from run-workflow-test, classify the failure surface before proposing any repair, and capture the reference evidence the surface requires. When the failure cannot be classified from existing references, recommend a focused follow-up rather than converting uncertainty into a guessed fix.
Classify before repairing. The same red output can be a tool/job failure, a workflow invocation failure, a collection-output mismatch, a missing workflow output, or an assertion mismatch — and each routes to a different reference surface and a different fix. Locate where the evidence lives first (planemo-workflow-test-architecture).
error/failed/stopped, record job id, tool id, exit code, job messages, the stdout/stderr distinction, and output dataset state per galaxy-tool-job-failure-reference; check whether the wrapper's failure semantics already explain it.