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Proof Ladder

Guide Fit

flowchart TD
  family["Reproducible Research"] --> program["Deep Dive Snakemake"]
  program --> pressure["A concrete learner or reviewer question"]
  pressure --> guide["Proof Ladder"]
  guide --> next["Modules, capstone, and reference surfaces"]
flowchart TD
  question["Name the exact question you need answered"] --> skim["Skim only the sections that match that pressure"]
  skim --> crosscheck["Open the linked module, proof surface, or capstone route"]
  crosscheck --> next_move["Leave with one next decision, page, or command"]

Read the first diagram as a timing map: this guide is for a named pressure, not for wandering the whole course-book. Read the second diagram as the guide loop: arrive with a concrete question, use only the matching sections, then leave with one smaller and more honest next move.

This page fixes a recurring problem: the course has enough proof routes that learners can easily overreach. They run the strongest command first, get buried in evidence, and lose the idea they were trying to verify.

Use this page to keep proof proportional to the question.

The Ladder

Move down this ladder only when the smaller step no longer answers the question honestly.

Proof level Command Best use Cost
1 make PROGRAM=reproducible-research/deep-dive-snakemake capstone-walkthrough first contact with repository meaning low
2 make PROGRAM=reproducible-research/deep-dive-snakemake capstone-tour executed repository review with bounded scope low to medium
3 make PROGRAM=reproducible-research/deep-dive-snakemake test ordinary executable proof of the reference workflow medium
4 make PROGRAM=reproducible-research/deep-dive-snakemake capstone-verify-report durable saved publish-contract evidence medium
5 make PROGRAM=reproducible-research/deep-dive-snakemake capstone-profile-audit targeted execution-policy and context review medium
6 make PROGRAM=reproducible-research/deep-dive-snakemake proof sanctioned multi-bundle corroboration high
7 make PROGRAM=reproducible-research/deep-dive-snakemake capstone-confirm strongest stewardship and confirmation pass highest

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Which Questions Belong To Which Level

Question Start at
what is this repository trying to prove capstone-walkthrough
how is the repository organized in executable form capstone-tour
does the workflow still behave correctly test
do I need durable proof I can review later capstone-verify-report
what differs across local, CI, and cluster policy capstone-profile-audit
how do the larger proof surfaces fit together proof
is this repository ready for the strongest review pass capstone-confirm

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Anti-Patterns This Ladder Prevents

The ladder exists to prevent these clumsy review habits:

  • running capstone-confirm when capstone-walkthrough would answer the question
  • treating one large proof bundle as automatically better than a narrower one
  • confusing publish review with operating-context review
  • burying a first-contact learner in incident evidence before the workflow contract is legible

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Best Companion Pages

Use these with the ladder:

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