Self-Review Prompts

Page Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  section["Reference"]
  page["Self-Review Prompts"]
  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 page when you want short prompts that turn Snakemake concepts into active workflow judgment instead of passive familiarity.

Workflow truth

• Which file contract is doing the real work here?
• What durable evidence records checkpoint discovery instead of leaving it implicit?
• Which command would you run first to explain why the workflow wants to rerun?

Policy and publish boundaries

• Which difference belongs to operating policy rather than workflow meaning?
• Which outputs are public for downstream trust, and which are only internal run state?
• What would another maintainer need to inspect before trusting a publish change?

Stewardship

• Which repository layer should absorb the next non-trivial change?
• What would count as semantic drift rather than ordinary policy drift?
• Which saved evidence bundle would you trust first if logs disappeared?

Layer prompts

• Should this behavior live in Snakefile, rules, modules, scripts, package code, or profiles?
• Would moving it make the workflow easier to review or only more indirect?
• Which layer would you inspect first before approving a boundary-heavy change?