dahak-taco documentation¶

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

(insert icholy/ttygif here.)

Getting Started¶

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

These sections will cover how to get up and running with taco.

Installation - how to install taco

Usage - basic usage of taco

Workflows - what are taco workflows, how do you run them, and what do they include?

Tests - how to run taco unit tests

Workflows¶

The actual taco workflow is defined using Snakemake rules, and these files should live in their own repository, separate from taco.

Each repository can define a single workflow, or multiple workflows.

Several example taco workflow repositories are available:

taco-simple - illustrates the implementation of several "hello world" style taco workflows.
taco-read-filtering - implements a read filtering taco workflow.
taco-taxonomic-classification - implements a taxonomic classification taco workflow.

Each repository provides documentation and a Quick Start guide.

Cloud Platforms¶

We include instructions for getting up and running with taco on various cloud platforms. This is a great application of the taco-simple workflow.

AWS Setup
HPC - TBA

Configuration and Parameter Sets¶

taco takes two input files: a workflow configuration file, which specifies the workflow targets, and a workflow parameters file, which specifies parameters to control the workflow.

Workflow configuration and parameter files are workflow-dependent and live in workflow repositories.

Individual configuration files or parameter sets are workflow-dependent, and are defined or included in the repository that defines that workflow.

For a simple example of how configuration and parameter files are used, see the taco-simple repository, which contains several "hello world" style taco workflows.

Advanced Topics¶

For instructions on building, modifying, and improving the documentation for taco, see Documentation.

If you are interested in creating a new workflow, see DevWorkflows.md. Also see the taco-simple repository, which illustrates simple "hello world" style workflows using taco best practices.

For more information about the development workflow, branches, tags, and the release process, see Development.