Deep Dive Snakemake¶

Course Shape¶

flowchart TD
  family["Reproducible Research"] --> program["Deep Dive Snakemake"]
  program --> home["Deep Dive Snakemake"]
  home --> modules["Modules 00-10"]
  home --> guides["Guides"]
  home --> reference["Reference"]
  modules --> capstone["Capstone"]
  guides --> capstone
  reference --> capstone

flowchart TD
  promise["Read the course promise and learner fit"] --> route["Choose one stable entry lane"]
  route --> orientation["Anchor the workflow model in Module 00"]
  orientation --> modules["Read the modules in order"]
  modules --> proof["Use guides, reference, and capstone only when they answer the current question"]

Read the first diagram as the shape of the whole book. Read the second diagram as the intended learner route so the capstone and support shelves do not become accidental first lessons.

Deep Dive Snakemake teaches workflow design as a discipline of explicit file contracts, deterministic planning, safe dynamic behavior, and durable operational boundaries. The goal is not to collect workflow tricks. The goal is to build workflows another engineer can inspect, trust, and extend without folklore.

Use this course if¶

you want a workflow model instead of disconnected Snakemake snippets
you inherited a pipeline that runs but is hard to trust, review, or extend
you already use Snakemake and now need stronger publish, profile, and workflow-boundary judgment
you review whether a workflow can survive CI, shared filesystems, and long-lived change

Do not use this course as¶

a syntax refresher detached from workflow contracts
executor advice before workflow meaning is clear
a reason to use dynamic behavior without explicit discovery and publish boundaries

Choose one starting lane¶

If you are here because...	Start with	Stop when you can say...
Snakemake is still new	Start Here, Course Guide, Module 00	what a truthful file contract is and why the capstone is not your first lesson
you need to repair an existing workflow	Pressure Routes, Module 03, Module 04	whether the problem is workflow semantics, policy drift, interface sprawl, or incident pressure
you steward a long-lived workflow repository	Course Guide, Module 06, Module 07	which surfaces are public, which are policy, and which proof route is proportionate

Keep these support pages nearby¶

Need	Best page
shortest stable entry	Start Here
route shaped by urgency	Pressure Routes
stable support hub	Course Guide
module titles translated into promises	Module Promise Map
module exit bar	Module Checkpoints
workflow split decisions	Workflow Modularization
smallest honest proof route	Proof Ladder
capstone entry by module and question	Capstone Map

Module Table of Contents¶

Module	Title	Why it matters
Module 00	Orientation and Study Practice	establishes the learner route, proof surfaces, and capstone timing
Module 01	File Contracts and Workflow Graph Truth	teaches the workflow as a file-driven DAG instead of a script
Module 02	Dynamic DAGs, Discovery, and Integrity	makes checkpoints and changing sample sets reviewable
Module 03	Production Operations and Policy Boundaries	separates workflow semantics from operational policy
Module 04	Scaling Workflows and Interface Boundaries	scales the workflow without losing explicit interfaces
Module 05	Software Boundaries and Reproducible Rules	keeps helper code and rule meaning in the right layer
Module 06	Publishing and Downstream Contracts	makes the public artifact boundary versioned and trustworthy
Module 07	Workflow Architecture and File APIs	organizes the repository so ownership stays visible
Module 08	Operating Contexts and Execution Policy	compares local, CI, and cluster policy without semantic drift
Module 09	Performance, Observability, and Incident Response	reviews logs, benchmarks, and incidents with explicit evidence
Module 10	Governance, Migration, and Tool Boundaries	finishes with stewardship and tool-boundary judgment

How the capstone fits¶

The capstone is the executable proof surface for the course. It should corroborate a module idea that is already legible, not replace first exposure.

Use it in this order:

learn the concept in the local module exercise
choose the smallest honest route with Proof Ladder
enter the repository through Capstone Map or Command Guide
escalate to stronger review only when the current question actually needs it

Success signal¶

The course home has done its job when you know:

where to start without random browsing
which support page answers the next question
why the capstone is a proof surface rather than a first-contact playground
why later modules are consequences of earlier file-contract and publish-boundary choices

Failure modes this course is designed to prevent¶

treating a workflow as a script rather than a file-driven DAG
trusting a workflow because it ran once instead of because its contracts and proofs are visible
using the capstone as first contact and confusing repository size with conceptual clarity
treating publish, profile, and governance pages as substitutes for earlier workflow truth