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The Workflow Engine Contract: Declared Inputs, Outputs, and What the Engine Does in Return

The outcome demands a run that survives interruption and can be re-derived by someone else; hand-rolled orchestration gives neither. This is the layer that carries the array jobs, dependencies and container discipline of this curation across environments, and teaching it as a bargain rather than a magic wrapper is what lets a learner judge what an engine does and does not buy them.

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Defining Rules and File Dependencies in a Snakemake Workflow

A workflow management system replaces imperative driver scripts with a declarative set of *rules*, each stating its input files, output files, parameters, and the command that transforms inputs into …