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Walkthrough Guide

Guide Maps

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

  family --> program --> guide --> section --> page
  page -.checks against.-> proof
flowchart LR
  orient["Read the guide boundary"] --> inspect["Inspect the named files, targets, or artifacts"]
  inspect --> run["Run the confirm, demo, selftest, or proof command"]
  run --> compare["Compare output with the stated contract"]
  compare --> review["Return to the course claim with evidence"]

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 you have to reason about full execution.

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.

What The Bundle Is For

  • Domain Guide and Architecture Guide 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
  • index.md and File API explain which route or contract to inspect next

Best Review Order

  1. README.md
  2. Domain Guide and Architecture Guide
  3. route.txt
  4. Snakefile and list-rules.txt
  5. list-rules.txt and dryrun.txt
  6. File API and index.md
  7. commands.txt and review-questions.txt