Capstone Proof Guide

Page Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  section["Capstone"]
  page["Capstone Proof Guide"]
  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"]

Read the first diagram as a timing map: this guide is for one bounded proof route, not for whole-repository study. Read the second diagram as the rule: choose the narrowest honest command, inspect the matching evidence, then escalate only if the claim changes.

Use this page when a module makes a Snakemake design claim and you want the shortest honest route to the capstone evidence that supports it.

Enter this guide at the right time

Use this guide once the module idea is already legible in its local exercise.

Before that point, prefer Capstone Walkthrough so the repository stays smaller than the concept you are learning.

Start by proof need

If you need to prove...	Start here	Escalate only if needed
repository shape without execution	make PROGRAM=reproducible-research/deep-dive-snakemake capstone-walkthrough	capstone-tour
executed workflow behavior	make PROGRAM=reproducible-research/deep-dive-snakemake capstone-tour	proof
publish-boundary trust	make PROGRAM=reproducible-research/deep-dive-snakemake capstone-verify-report	capstone-confirm
execution-policy differences	Capstone Architecture Guide	proof
steward-level confidence	make PROGRAM=reproducible-research/deep-dive-snakemake proof	capstone-confirm

Bounded proof pass

1. Read Capstone Guide.
2. Use Proof Matrix to choose the narrowest command.
3. Run that command from the capstone or course root.
4. Record what the evidence proves before opening a stronger route.

Good stopping point

Stop when you can say:

• which command gave the narrowest honest answer
• which evidence surface actually settled the claim
• why a broader route would be unnecessary unless the claim changed

If you cannot say those three things, repeat the bounded route before escalating.