Capstone Proof Guide¶

Guide Fit¶

flowchart TD
  family["Reproducible Research"] --> program["Deep Dive Snakemake"]
  program --> pressure["A concrete learner or reviewer question"]
  pressure --> guide["Capstone Proof Guide"]
  guide --> next["Modules, capstone, and reference surfaces"]

flowchart TD
  question["Do you need one bounded proof route?"] --> route["Choose the narrowest honest command"]
  route --> inspect["Inspect the matching evidence surface"]
  inspect --> next_move["Escalate only if the claim changes"]

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	`make PROGRAM=reproducible-research/deep-dive-snakemake capstone-profile-audit`	`proof`
steward-level confidence	`make PROGRAM=reproducible-research/deep-dive-snakemake proof`	`capstone-confirm`

Bounded proof pass¶

Read Capstone Guide.
Use Proof Matrix to choose the narrowest command.
Run that command from the capstone or course root.
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.