taco is an experimental command-line interface
for running dahak
workflows using Snakemake.
(insert icholy/ttygif here.)
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
Installation - how to install
Usage - basic usage of
Workflows - what are
how do you run them, and what do they include?
Tests - how to run
taco unit tests
The actual taco workflow is defined using Snakemake rules,
and these files should live in their own repository, separate
Each repository can define a single workflow, or multiple workflows.
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.
We include instructions for getting up and running with
taco on various cloud platforms.
This is a great application of the
- 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
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
For instructions on building, modifying, and improving
the documentation for
If you are interested in creating a new workflow,
see DevWorkflows.md. Also see
repository, which illustrates simple "hello world" style
taco best practices.
For more information about the development workflow, branches, tags, and the release process, see Development.