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Review Checklist

Page Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  section["Reference"]
  page["Review Checklist"]
  capstone["Capstone evidence"]

  family --> program --> section --> page
  page -.applies in.-> capstone
flowchart LR
  orient["Orient on the page map"] --> read["Read the main claim and examples"]
  read --> inspect["Inspect the related code, proof, or capstone surface"]
  inspect --> verify["Run or review the verification path"]
  verify --> apply["Apply the idea back to the module and capstone"]

Use this checklist when reviewing a Snakemake workflow, module exercise, or capstone change. The goal is to keep workflow trust tied to contracts and evidence.

Workflow truth

  • Which file contracts are authoritative for this question?
  • Does dynamic discovery leave durable evidence instead of runtime folklore?
  • Would a dry-run still help a reviewer understand the workflow shape honestly?

Policy and repository boundaries

  • Which differences belong to operating policy rather than workflow meaning?
  • Does a profile or repository-layer change risk semantic drift?
  • Is reusable code living in the right place instead of leaking workflow semantics into helpers?

Authority and layer ownership

  • Which surface is authoritative for this question: workflow contract, discovery evidence, policy, or publish boundary?
  • Which layer should own the next change: Snakefile, rules, modules, scripts, package code, or profiles?
  • Would another maintainer know where this behavior belongs without oral explanation?

Publish trust

  • Which outputs are safe for downstream trust and which remain internal run state?
  • Does the published contract stay smaller and clearer than the whole repository?
  • Which evidence bundle should another maintainer inspect before approving change?

Stewardship

  • Which command or saved bundle gives the narrowest honest answer for the current claim?
  • Which layer owns the next change: Snakefile, rules, modules, scripts, package code, or profiles?
  • Which ambiguity would you require the author to make explicit before accepting the workflow?