Adding New Taco Workflows

If you wish to extend or modify taco by adding a new workflow, you can do so, but it's important to plan it out first!

Each Snakemake workflow is composed of a set of loosely-interconnected rules sharing parameters and handling pieces of the whole workflow.

The workflow lives in a directory in rules that is named after the workflow. For example, to add a new workflow called foobar:

rules/
    foobar/
    taxonomic_classification/
    read_filtering/
    functional_annotation/
    ...

Each rule or group of rules lives in a .rule file. All rule files have access to the entire configuration dictionary, which stores all workflow parameters.

Suppose our new workflow foobar had three distinct steps: buz, fuz, and wuz. Then we would create a rule file for each, and the foobar/ rules directory structure would be:

rules/
    foobar/
        buz.rule
        fuz.rule
        wuz.rule
        foobar.settings

Additionally, we need to set parameters for the workflow.

Each workflow has access to the "master" Snakemake parameters dictionary.

In addition, each workflow defines its own parameters dictionary to store parameters specific to that workflow.

This parameters dictionary is stored under a key that is the name of the workflow.

For example, if each of our three workflow steps took parameters, here is how we would organize the workflow's default parameters dictionary:

JSON:

{
    ...

    'foobar' : {

        'buz' : {
            'buz_param_1' : 1,
            'buz_param_2' : 'alpha'
        },

        'fuz' : {
            'fuz_param_1' : 50,
            'fuz_param_2' : 51,
            'fuz_param_3' : False
        },

        'wuz' : {
            'wuz_param_1' : 9.99,
            'wuz_param_2' : 9.98,
            'wuz_param_3' : 9.97,
            'wuz_param_4' : 9.96
        }
    }
    ...
}

YAML:

foobar:
  buz:
    - buz_param_1: 1
    - buz_param_2: "alpha"
  fuz:
    - fuz_param_1: 50
    - fuz_param_2: 51
    - fuz_param_3: false

  wuz:
    - wuz_param_1: 9.99
    - wuz_param_2: 9.98
    - wuz_param_3: 9.97
    - wuz_param_4: 9.96

The foobar.settings file must set this in a way that will not overwrite defaults; hence this business:

from snakemake.utils import update_config

if(not config['clean']):

    # Note: don't include http:// or https://
    config_default = { 
                        ... 
                     }

    update_config(config_default, config)
    config = config_default