Deep Dive Snakemake¶

Deep Dive Snakemake is the workflow-engine program in the reproducible-research family. It is the right route when the core pressure is dynamic DAGs, publish contracts, executor policy, and production workflow governance.

Page Maps¶

graph LR
  family["Reproducible Research"]
  program["Deep Dive Snakemake"]
  course["Course home"]
  capstone["Capstone guide"]

  family --> program --> course
  course --> capstone

flowchart LR
  overview["Read this overview"] --> start["Open Start Here or Course Home"]
  start --> module["Study the workflow boundary or module page you need"]
  module --> capstone["Inspect the capstone workflow and proof guides"]
  capstone --> compare["Return here when comparing with Make or DVC"]

What This Program Covers¶

file contracts, wildcard discipline, and dynamic DAG control
profiles, executor semantics, and publish boundaries
workflow modularity, CI gates, and operational proof
recovery, scaling, and governance under production pressure

Local Catalog Route¶

Course home: Program guide
Learner entry: Start Here
Pressure routes: Pressure Routes
Promise review: Module Promise Map
Capstone guide: Capstone README

Local Commands¶

make PROGRAM=reproducible-research/deep-dive-snakemake docs-serve
make PROGRAM=reproducible-research/deep-dive-snakemake capstone-walkthrough
make PROGRAM=reproducible-research/deep-dive-snakemake capstone-tour
make PROGRAM=reproducible-research/deep-dive-snakemake test

Honesty Boundary¶

This program is not only a Snakemake command catalog. It assumes you want to know which workflow behaviors are contracts, which are operational policy, and which proof artifacts justify that claim.