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Practice Map

Reference Position

flowchart TD
  family["Reproducible Research"] --> program["Deep Dive Snakemake"]
  program --> reference["Practice Map"]
  reference --> review["Design or review decision"]
  review --> capstone["Capstone proof surface"]
flowchart TD
  trigger["Hit a naming, boundary, or trade-off question"] --> lookup["Use this page as a glossary, map, rubric, or atlas"]
  lookup --> compare["Compare the current code or workflow against the boundary"]
  compare --> decision["Turn the comparison into a keep, change, or reject call"]

Read the first diagram as a lookup map: this page is part of the review shelf, not a first-read narrative. Read the second diagram as the reference rhythm: arrive with a concrete ambiguity, compare the current work against the boundary on the page, then turn that comparison into a decision.

This page collects the main practice surfaces for the whole course in one place.

Use it when you want to know what to build, what to run, and what the run is supposed to prove before you enter the capstone.

Module Practice Surfaces

Module Primary practice surface Main proof loop Best capstone follow-up
01 tiny file-contract workflow snakemake -n, then one concrete target inspect stable output patterns only after the local contract is predictable
02 dynamic-discovery lab with checkpoints snakemake -n, snakemake --summary compare discovered outputs with the capstone checkpoint story
03 profile-driven workflow lab snakemake --profile profiles/local -n, then --profile profiles/ci -n inspect verification and operating-policy targets
04 modular repository sketch snakemake --list-rules, snakemake -n compare local module boundaries with FILE_API.md
05 rule-and-script split lab snakemake -n, then one end-to-end run with recorded environment evidence inspect scripts, packages, and environment boundaries together
06 versioned publish lab snakemake --summary, then snakemake publish/v1/manifest.json inspect publish/v1/ and manifest structure deliberately
07 architecture review lab snakemake --list-rules, snakemake --summary read Snakefile, workflow/rules/, and FILE_API.md in sequence
08 multi-profile operating lab compare local, CI, and scheduler dry-runs inspect profiles/ and the Makefile policy targets together
09 incident review lab snakemake -n -p, snakemake --list-changes input code params compare logs, benchmarks, and verification surfaces
10 written workflow review review rubric plus evidence commands use the capstone as the specimen for governance and migration judgment

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Three Reusable Proof Loops

Contract loop

Use when you are checking whether the rule graph and outputs are explicit enough.

snakemake -n
snakemake --summary

Operating loop

Use when you are checking whether policy changes execution context without changing meaning.

snakemake --profile profiles/local -n
snakemake --profile profiles/ci -n

Incident loop

Use when you are investigating slow, noisy, or surprising behavior.

snakemake -n -p
snakemake --summary
snakemake --list-changes input code params

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Best Study Habit

For each module:

  1. build the smallest local example first
  2. write down what the proof command is supposed to demonstrate
  3. run the proof command and explain the result in words
  4. enter the capstone only after the local result is legible

That order keeps the course centered on comprehension instead of repository tourism.

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