taco-simple¶

This repository implements several simple Snakemake workflows ("hello world" style) to illustrate how to define a dahak-taco workflow.

Setting Up Taco¶

Before you can run any of these workflows, you must first install taco. See dahak-taco documentation for installation instructions.

Once taco is installed, it will be available on the command line. The taco commands covered in this document should be run from the main workflow repository directory.

What's In This Repository¶

Required directories:

rules/ - contains rule and workflow definitions (REQUIRED)

Workflow files:

workflow-config/ - contains workflow configuration files
workflow-params/ - contains workflow parameter files
docker/ - contains custom Docker images for use in taco workflows
my-workflow-files/ - directory containing config/param/docker files that should be kept together

Documentation files:

docs/ - contains the documentation files (i.e., the document you're reading now)
mkdocs.yml - configuration file for mkdocs, the documentation generator used by this repo
mkdocs-material-dib/ - git submodule containing mkdocs theme

Workflows¶

List of workflows:

Workflow 1 - illustrates how to modify user parameters and use them to assemble input/output names.

Workflow 2 - illustrates how to modify user parameters and use wildcards to assemble input/output names.

Workflow 3 - (in progress) illustrates how to use custom Docker images as part of a taco workflow.

Workflow 4 - (in progress) illustrates how to use the --clean option to check parameters dictionary