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Capstone Architecture Guide

Guide Fit

flowchart TD
  family["Reproducible Research"] --> program["Deep Dive Snakemake"]
  program --> pressure["A concrete learner or reviewer question"]
  pressure --> guide["Capstone Architecture Guide"]
  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.

Use this page when a module asks you to review the capstone as a repository architecture, not only as a runnable workflow.

  1. Read Capstone Guide.
  2. Compare it with Repository Layer Guide and Capstone File Guide.
  3. Inspect the matching capstone files in the order the architecture guide names them.
  4. Use Proof Matrix to pick the strongest command for the boundary you are reviewing.

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What The Architecture Should Prove

  • workflow meaning is still visible in Snakefile and workflow/rules/
  • helper code has not swallowed the visible rule graph
  • profiles and config stay operational rather than analytical
  • the publish boundary remains smaller and clearer than the full repository state

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Best Moments To Use It

  • after Module 04, when repository growth and interface boundaries become central
  • after Module 07, when the full repository architecture becomes part of the lesson
  • after Module 10, when reviewing the capstone as a long-lived workflow product

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