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Capstone Guide

Guide Fit

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

The Snakemake capstone is the course’s executable proof. It is the place where the course’s strongest claims become runnable:

  • explicit file contracts instead of hidden edges
  • dynamic discovery that leaves durable evidence
  • profiles as policy instead of tribal command lines
  • verification gates that make “it ran once” an unacceptable standard

How to use it while reading

  • After Module 01, inspect the rule contracts and the stable publish boundary.
  • After Module 02, inspect the checkpoint and the way discovery becomes explicit output.
  • After Module 03, inspect profiles, retries, and verification gates.
  • After Module 04, inspect module boundaries, file APIs, and CI-style proof surfaces.

Best entrypoints

Core commands

make PROGRAM=reproducible-research/deep-dive-snakemake capstone-walkthrough
make PROGRAM=reproducible-research/deep-dive-snakemake capstone-wf-dryrun
make PROGRAM=reproducible-research/deep-dive-snakemake capstone-tour
make PROGRAM=reproducible-research/deep-dive-snakemake capstone-verify-report
make PROGRAM=reproducible-research/deep-dive-snakemake capstone-confirm

Study questions

  • Which outputs are for internal workflow coordination and which are part of the public interface?
  • What exactly does the checkpoint discover, and what does it never hide?
  • Which proof artifacts would you inspect before trusting a run?
  • Where would you extend the workflow without weakening the publish contract?

Directory glossary

Use Glossary when you want the recurring language in this shelf kept stable while you move between repository routes, review surfaces, and proof commands.