dahak-taco documentation

dahak-taco is an experimental command-line interface for running dahak workflows using Snakemake.

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To get started with taco, and run your first workflow task, see the Getting Started section.

If you’re hungry for more dahak workflows, skip to the Workflow Walkthroughs section.

If you are already up and running with taco and are looking for information about the rules and their parameters, check out the Detailed Workflow API section.

If you are extending taco by adding new rules, workflows, or documentation, see the For Developers section.

Getting Started

taco is a command line utility that wraps Snakemake rules to run complex workflows.

These sections will cover what taco is and get you up and running with your first taco workflow.

Workflow Walkthroughs

taco is a lightweight wrapper around Snakemake tasks. Kind of like a corn tortilla.

The Snakemake rules and parameters are organized by workflow in the rules/ directory of this repository.

The walkthroughs below show examples of how to run each workflow.

For Developers

The sections below explain how taco works, so you know how to modify taco to suit your needs.

There are also sections for adding or modifying Snakemake rules, and for adding new workflows.

taco provides a set of workflows with default parameters that should work for many use cases.

However, to extend taco, or just understand what it is doing, take a look at the innards of taco: