Walkthrough Guide

Guide Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  guide["Capstone docs"]
  section["WALKTHROUGH_GUIDE"]
  page["Walkthrough Guide"]
  proof["Proof route"]

  family --> program --> guide --> section --> page
  page -.checks against.-> proof

flowchart LR
  command["make walkthrough"] --> bundle["Learner-first walkthrough bundle"]
  bundle --> rules["Rule list and dry-run"]
  rules --> contracts["Config, publish, and file-contract surfaces"]
  contracts --> review["Review questions and next commands"]

This guide explains the lightest honest entry into the capstone. The walkthrough bundle exists for first contact: it shows the visible rule surface, dry-run plan, policy files, contract-enforcement scripts, and the core study guides before the learner has to reason about full execution.

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When To Prefer The Walkthrough

Use make walkthrough when:

• you are entering the capstone for the first time
• you want to inspect the repository without executing the workflow yet
• you care about visible rule contracts more than runtime evidence

Use make tour later when you need executed proof artifacts.

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What The Bundle Is For

• README.md explains the repository contract
• DOMAIN_GUIDE.md, WORKFLOW_STAGE_GUIDE.md, and CHECKPOINT_GUIDE.md explain the smallest human-first story
• Snakefile, copied rule files, and list-rules.txt explain visible workflow meaning
• dryrun.txt explains the declared plan before execution
• copied profile and config files explain policy and validation inputs
• copied scripts explain how config and publish checks are enforced
• CHECKPOINT_GUIDE.md explains why dynamic discovery is visible rather than magical

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Best Review Order

1. README.md
2. DOMAIN_GUIDE.md and WORKFLOW_STAGE_GUIDE.md
3. route.txt
4. CHECKPOINT_GUIDE.md and Snakefile
5. list-rules.txt and dryrun.txt
6. ARCHITECTURE.md, EXACT_SOURCE_GUIDE.md, and FILE_API.md
7. commands.txt and review-questions.txt

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