القائمة
Triage failing Galaxy run outputs; classify the failure surface and capture evidence before recommending repairs.
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
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.