Reference Glossary

Page Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  section["Reference"]
  page["Reference Glossary"]
  capstone["Capstone evidence"]

  family --> program --> section --> page
  page -.applies in.-> capstone

flowchart LR
  orient["Orient on the page map"] --> read["Read the main claim and examples"]
  read --> inspect["Inspect the related code, proof, or capstone surface"]
  inspect --> verify["Run or review the verification path"]
  verify --> apply["Apply the idea back to the module and capstone"]

This glossary keeps Deep Dive Snakemake's recurring terms stable across modules, reference pages, and capstone review routes. Use it when the repository is clear enough to inspect, but the local meaning of a word still needs to be pinned down.

How to use this glossary

Open it when a term matters for a decision: where a change belongs, which surface is authoritative, or which proof route should answer the question. Do not read it as a list to memorize.

Terms in this directory

Term	Meaning in Deep Dive Snakemake
Anti-Pattern Atlas	A symptom-led catalog of recurring workflow mistakes, used when you recognize the smell before you remember the lesson that explains it.
Completion Rubric	The review standard for deciding whether someone can explain workflow behavior with evidence rather than slogans.
Module Dependency Map	The reading-order map that shows which modules support later ones and which ideas should come first.
Practice Map	The crosswalk from modules to capstone routes that corroborate the same concept.
Topic Boundaries	The page that distinguishes core course material from supporting context and out-of-scope extension work.