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Mid-Course Map

Page Maps

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  section["Orientation"]
  page["Mid-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 Modules 01 to 03 feel stable and you need a deliberate bridge into scaling, software boundaries, publish trust, and operating-context review. The goal is to keep the middle of the course shaped by workflow questions instead of by repository sprawl.

Use this map for these pressures

If the pressure is... Start with Keep nearby Capstone cross-check
where a structural workflow change belongs Module 04 Boundary Review Prompts Capstone File Guide
where workflow orchestration ends and helper software begins Module 05 Review Checklist Capstone Architecture Guide
what downstream users are actually allowed to trust Modules 06 to 07 Proof Matrix Capstone Review Worksheet
which differences across local, CI, and scheduler contexts are policy-only Module 08 Topic Boundaries Capstone Proof Guide

Module clusters

Modules 04 to 05: scaling and software seams

Use this cluster when the workflow already feels real, but the repository is starting to split across files, helper code, and validation surfaces.

  • Module 04 teaches scaling, interfaces, and reviewable repository structure.
  • Module 05 teaches the boundary between Snakemake logic and the software it drives.

Leave this cluster able to explain where a change belongs before you edit it.

Modules 06 to 07: publish trust and architecture

Use this cluster when the workflow is becoming a downstream-facing system.

  • Module 06 teaches versioned publish contracts and downstream trust.
  • Module 07 teaches workflow architecture and stable file APIs.

Leave this cluster able to separate internal run state from public outputs.

Module 08: operating contexts

Use this step when the main pressure is execution context rather than workflow meaning.

  • Module 08 teaches how local, CI, and scheduler policy differ without semantic drift.

Leave this step able to explain what changed across contexts and why the workflow promise did or did not change.

When to leave this route

Move to mastery-map.md once the question becomes stewardship, migration, or whether Snakemake should keep owning the concern at all.

Good next move after this map

Open exactly one of these before resuming: