Workflow 1¶

Goal¶

Workflow 1 illustrates the use of user parameters. Specifically, we modify the name parameter to make it uppercase, and use the extension parameter to set output file names.

Quick Start¶

To list available workflows:

$ taco ls

To get rules defined by a particular workflow:

$ taco ls workflow1

To run the workflow, use the included workflow configuration and parameter files:

$ taco workflow1 \
    --config-yaml=workflow-config/workflow1_config_simple.yaml \
    --params-yaml=workflow-params/workflow1_params_simple.yaml

or,

$ taco workflow1 \
    --config-yaml=my-workflow-files/config.yaml \
    --params-yaml=my-workflow-files/params.yaml

By default, this will generate output files in the data/ directory. To change the output directory, use the --prefix flag:

$ taco --prefix=my_data \
    workflow1 \
    --config-yaml=workflow-config/workflow1_config_simple.yaml \
    --params-yaml=workflow-params/workflow1_params_simple.yaml

If the directory does not exist, it will be created.

Workflow Rules¶

Output of taco ls workflow1:

hello_target

    Shell commands to say hello to <name>

goodbye_target

    Shell commands to say goodbye to <name>

The two rules above are just echoing text to a file.

master

    Shell commands to say hello and goodbye to <name>

This is a master rule that runs the two other rules by requiring their output files.

Workflow Configuration¶

The output files of the above rules are simple and hard-coded: hello.{ext} and goodbye.{ext}

In the workflow configuration file, specify a workflow target like hello.txt (note that this requires you set the extension to "txt", see next section).

YAML:

workflow_targets: "goodbye.txt"

or as a list:

workflow_targets: 
  - "hello.txt"
  - "goodbye.txt"

(Note that this rule, as structured, does not do wildcards - that's left for Workflow 3 - so we must specify the extension ".txt" in our workflow parameters file.

Workflow Parameters¶

The user defines two keys:

name - the name to print to the file
file_extension - the extension to use for the hello/goodbye files being created

Here is the default paramter dictionary defined in workflow1.settings:

    {
        "name" : "buzz lightyear",
        "file_extension" : "txt"
    }