---

name: debugging-reporting description: "Diagnose Snakemake workflows with linting, graph outputs, summaries, logs, reports, notebooks, generated unit tests, benchmarks, runtime profiles, and CI smoke checks." disable-model-invocation: true metadata: disco-role: operating license: MIT

Debugging and Reporting

Use this sub-skill when a user needs Snakemake 9.23.1 diagnostics, quality signals, report generation, generated tests, notebooks, benchmarks, failed logs, runtime profiles, or CI smoke validation.

Route by task

• For lint failures, DAG topology questions, --summary, failed job logs, runtime profiles, or benchmark files, use references/debugging-reference.md.
• For HTML/ZIP reports, report captions/categories/labels/metadata/styles, generated unit tests, notebooks, and CI smoke checks, use references/reporting-testing-reference.md.
• For common failure triage, use references/troubleshooting.md.
• For a safe local diagnostics command plan, run python scripts/workflow_diagnostics.py --snakefile Snakefile --target all --outdir diagnostics from the workflow directory.

Boundaries

• Own linting, graph/summary/report/test/notebook/benchmark/log/profile diagnostics and artifact interpretation.
• Route command scaffolding and executor/run semantics to ../execution-cli/SKILL.md.
• Route Snakefile syntax and rule design fixes to ../workflow-authoring/SKILL.md.
• Route storage-backed report dependencies, remote logs, and deployment plugins to ../deployment-storage/SKILL.md.
• Route embedded Python API/plugin calls to ../python-api-plugins/SKILL.md.

Snakemake 9.23.1 facts

• --reason is not a valid flag; dry-run output already includes job reasons.
• Safe first-pass diagnostics usually start with --cores 1 --dry-run --printshellcmds and add graph/lint/report/test flags as needed.
• Reports read provenance/runtime metadata from .snakemake; generate full reports after a successful run when possible.