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Capstone Review Worksheet

Guide Fit

flowchart TD
  family["Reproducible Research"] --> program["Deep Dive Snakemake"]
  program --> pressure["A concrete learner or reviewer question"]
  pressure --> guide["Capstone Review Worksheet"]
  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 worksheet when reviewing the Snakemake capstone as a workflow repository, not only as a lesson artifact.

The point is to make review concrete enough that another maintainer could compare your judgment with the same evidence.

Repository Contract

Answer these first:

  1. What is the repository claiming to build and publish?
  2. Which surfaces are public contracts and which are internal execution detail?
  3. Which files define the publish boundary?

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Workflow Truth

Review these surfaces together:

  • capstone/Snakefile
  • capstone/workflow/rules/
  • the discovered-set artifact and related checkpoint evidence

Write down:

  1. which rules define meaningful file contracts
  2. where dynamic discovery becomes explicit and durable
  3. whether any behavior still feels hidden or nondeterministic

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Policy And Operating Context

Review these surfaces together:

  • capstone/profiles/
  • capstone/Makefile
  • the dry-run and workflow-tour bundles

Write down:

  1. which settings are operating policy rather than workflow meaning
  2. what would change between local, CI, and scheduler contexts
  3. whether any policy surface leaks into semantics

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Publish Boundary

Review these surfaces together:

Write down:

  1. which outputs are safe for downstream trust
  2. which artifacts remain internal repository state
  3. whether the promoted contract is smaller and clearer than the whole repository

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Final Review Questions

Finish with these:

  • what is the repository's strongest design choice
  • what is the most fragile boundary
  • what would you inspect first before approving a migration
  • what would you refuse to change without new evidence

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