Glossary

Page Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  section["Dynamic Dags Discovery Integrity"]
  page["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"]

Use this glossary to keep the language of Module 02 stable while you move between the core lessons, worked example, exercises, and capstone evidence.

The goal is not extra jargon. The goal is to make sure dynamic behavior is described with clear nouns instead of mystical shortcuts.

Terms in this module

Term	Meaning in this module
checkpoint	A controlled point where Snakemake can reevaluate downstream jobs after a declared output has been produced.
discovered set	The concrete collection of samples, shards, or units that discovery found for one run.
discovery surface	The declared input boundary that decides what the workflow is allowed to discover.
dynamic DAG	A workflow graph whose downstream job set depends on data learned during the run.
fanout	The expansion from one validated unit list into many concrete per-unit targets.
manifest	A declared inventory of files that belong to a publish boundary, often with integrity information.
ownership domain	The family of paths a wildcard or rule is allowed to claim.
parse-time discovery	Discovery that happens while the Snakefile is being read, before job execution begins.
provenance	The run-identity evidence that explains which configuration and software state produced the outputs.
publish boundary	The versioned output surface a downstream consumer is allowed to trust.
registry	A durable file that records discovery in a structured way, such as discovered_samples.json.
scheduler cost	The overhead of launching, tracking, and coordinating jobs, apart from the useful work they perform.
software boundary	The declared environment or container surface that explains which tools a rule needs.
target list	The explicit set of files the workflow is trying to build for a given run.
wildcard constraint	A regex restriction that narrows which filename shapes a wildcard may claim.

The vocabulary standard for this module

When you explain a Module 02 situation, aim to say things like:

• "the discovered set is recorded in one owned registry"
• "that checkpoint is justified because the downstream target list is not known earlier"
• "this is a fanout-control problem, not just a syntax problem"
• "the publish boundary preserves the discovery fact for later review"
• "the workflow is slow because scheduler cost dominates useful work"

Those sentences are much more useful than saying only "Snakemake gets weird with dynamic workflows."