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Course Map

Page Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  section["Orientation"]
  page["Course Map"]
  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 need the whole course visible on one screen before you choose a reading path.

Arc 1: file contracts and dynamic discovery

Modules 01 to 02 establish the workflow's semantic floor.

  • Module 01 teaches rules, targets, dry-runs, and explicit file contracts.
  • Module 02 teaches dynamic DAGs, checkpoints, and disciplined discovery artifacts.

Leave this arc able to explain what the workflow plans to build and how discovery stays reviewable.

Arc 2: operations and software boundaries

Modules 03 to 05 turn workflow truth into a maintainable repository.

  • Module 03 teaches profiles, retries, staging, and operational policy.
  • Module 04 teaches scaling, interfaces, and reviewable repository structure.
  • Module 05 teaches the boundary between Snakemake logic and the software it drives.

Leave this arc able to separate workflow meaning from execution policy and helper code.

Arc 3: publish trust and architecture

Modules 06 to 08 scale the repository into a downstream-facing system.

  • Module 06 teaches versioned publish contracts and downstream trust.
  • Module 07 teaches workflow architecture and file APIs.
  • Module 08 teaches operating contexts and execution-policy drift.

Leave this arc able to explain which surfaces are public, internal, or policy-only.

Arc 4: incidents and governance

Modules 09 to 10 finish with long-lived workflow judgment.

  • Module 09 teaches observability, performance, and incident response.
  • Module 10 teaches governance, migration, and tool-boundary decisions.

Leave this arc able to review a real workflow repository and justify what should change next.

Route markers

  • Read First-Contact Map when you need the smallest honest starting route.
  • Read Mid-Course Map when Modules 01 to 03 already feel stable and you need the bridge into scaling, software seams, publish trust, and operating contexts.
  • Read Mastery Map when the pressure is stewardship, migration, or long-lived workflow trust review.