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Module Promise Map

Guide Fit

flowchart TD
  family["Reproducible Research"] --> program["Deep Dive Snakemake"]
  program --> pressure["A concrete learner or reviewer question"]
  pressure --> guide["Module Promise Map"]
  guide --> next["Modules, capstone, and reference surfaces"]
flowchart TD
  question["Name the exact question you need answered"] --> skim["Skim only the sections that match that pressure"]
  skim --> crosscheck["Open the linked module, proof surface, or capstone route"]
  crosscheck --> next_move["Leave with one next decision, page, or command"]

Read the first diagram as a timing map: this guide is for a named pressure, not for wandering the whole course-book. Read the second diagram as the guide loop: arrive with a concrete question, use only the matching sections, then leave with one smaller and more honest next move.

This page exists because strong module titles are not enough. A learner should be able to ask, for every module, “what is this module promising me, and how will I know it was delivered?”

Use this guide when a title sounds right but still feels too broad, too compressed, or too weakly tied to proof.

How To Read This Page

Each row names four things:

  • the module promise
  • the boundary of that promise
  • the learner outcome the module should leave behind
  • the first honest capstone corroboration route

If a module page drifts away from this contract, the drift should become visible here.

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Promise Table

Module Promise Boundary Learner outcome First corroboration
01 File-DAG Contract teach Snakemake as explicit file semantics, not command folklore rules, targets, dry-runs, publish boundary explain why planned work exists before execution capstone-walkthrough
02 Dynamic DAGs teach staged discovery without turning the plan into magic checkpoints, discovery artifacts, deterministic planning explain what a checkpoint may discover and what it must never hide test
03 Production Operations teach policy surfaces without semantic drift profiles, retries, staging, governance, verification gates distinguish workflow meaning from run-context policy capstone-tour
04 Scaling Boundaries teach larger repository design without interface blur modules, file APIs, CI gates, executor-proof semantics inspect a repository boundary without guessing where the contract lives capstone-tour
05 Software Boundaries teach the line between workflow logic and software stack wrappers, scripts, envs, helper-code ownership explain which logic belongs in rules versus helper code proof
06 Downstream Contracts teach stable outputs and publish trust versioned publish surfaces, reports, manifests, checksums review whether a downstream consumer could trust the workflow outputs capstone-verify-report
07 Workflow Architecture teach repository ownership and reusable boundaries rule families, helper code, file APIs, architectural split point to the owning boundary for a workflow change proof
08 Operating Contexts teach policy and environment variance honestly profiles, executors, staging, storage, operating drift explain what may change across contexts and what must not capstone-profile-audit
09 Incident Response teach diagnosis under workflow pressure logs, benchmarks, workflow-tour evidence, review order move from symptom to responsible boundary with less guesswork proof
10 Tool Boundaries teach stewardship, migration, and orchestration judgment governance, anti-patterns, handoff boundaries, review method decide whether Snakemake should still own the concern capstone-confirm

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Promise Failures This Page Guards Against

When module titles are strong but unchecked, courses usually fail in one of four ways:

  • the title promises judgment, but the module only delivers syntax
  • the title promises operations, but the proof routes stay abstract
  • the title promises architecture, but ownership remains blurry
  • the title promises publish trust or governance, but the capstone surface never corroborates it

This page makes those failures visible before they harden into course drift.

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Best Companion Pages

Use these pages with the promise map:

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