Skip to content

Module Checkpoints

Page Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  section["Guides"]
  page["Module Checkpoints"]
  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 page when you are about to move on and want an honest readiness bar. Reading a module once is not the same thing as being ready for the next one. These checkpoints are meant to tell you whether the next module will build on stable understanding or on vague recognition.

How to use this page

For each module:

  1. answer the checkpoint question without looking at the text
  2. run the listed proof or inspection route
  3. stop if you still cannot explain the result in plain language

If you need to reread, reread the narrowest lesson that matches the gap instead of the whole module.

Readiness table

Module You are ready to move on when you can explain... Quick proof or inspection route Go back when...
Module 01 why one target exists in the workflow plan and another does not snakemake -n on the module example or Capstone Walkthrough Snakemake still feels like a command runner instead of a file-contract system
Module 02 how discovery becomes a durable artifact instead of an ambient side effect make PROGRAM=reproducible-research/deep-dive-snakemake capstone-walkthrough you can point to a checkpoint but not to the artifact that records what it discovered
Module 03 what belongs in a profile and what would change workflow meaning make PROGRAM=reproducible-research/deep-dive-snakemake capstone-profile-audit your explanation depends on one machine or one shell command
Module 04 where a scaling change belongs: rule file, module, file API, or validation surface Boundary Review Prompts plus make PROGRAM=reproducible-research/deep-dive-snakemake capstone-tour you are splitting files by discomfort rather than by ownership
Module 05 where workflow orchestration ends and helper software begins make PROGRAM=reproducible-research/deep-dive-snakemake proof you still treat scripts, packages, and environments as invisible implementation detail
Module 06 what is public in publish/v1/ and why it is smaller than the internal run state make PROGRAM=reproducible-research/deep-dive-snakemake capstone-verify-report you are still treating results/ as the downstream contract
Module 07 which file owns workflow entry, rule families, file APIs, and helper code boundaries Capstone File Guide you can name folders but not explain their responsibilities
Module 08 which differences across local, CI, and SLURM are policy and which would be semantic drift make PROGRAM=reproducible-research/deep-dive-snakemake capstone-profile-audit you are treating context drift as harmless because the workflow still runs
Module 09 which evidence surface you would inspect before editing a slow or flaky workflow Capstone Review Worksheet or make PROGRAM=reproducible-research/deep-dive-snakemake capstone-tour your first move is to change retries, threads, or grouping
Module 10 how to improve or migrate the repository without losing proof and public trust make PROGRAM=reproducible-research/deep-dive-snakemake capstone-confirm your migration plan is mostly taste, not preserved evidence

Common false positives

Do not call a module done just because:

  • the examples looked familiar
  • you can repeat the vocabulary
  • the strongest route passed once
  • you can follow the capstone without naming why the evidence matters

Those usually mean you have seen the surface, not learned the boundary.

Best companion pages