Parameter templates define the input parameters for a workflow. You can define input parameters to make your workflow more flexible and versatile. For example, you can define a parameter to be the Amazon S3 location of the reference genome files. Users can then run the workflow using various data sets.
We recommend using a parameter template for WDL and Nextflow workflows, and optionally for CWL workflows.
To define the input parameters, create a parameter template JSON file. In the file, each input parameter is a named object that must match the name of the workflow input. The input parameter object includes the following attributes:
description – This required attribute is a string that the console displays in the Start run page. This description is also retained as run metadata.
optional – This optional attribute indicates whether the input parameter is optional. If you don't specify the optional field, the input parameter is required.
The following example parameter template shows how to specify the input parameters.
{
"myRequiredParameter1": {
"description": "this parameter is required",
},
"myRequiredParameter2": {
"description": "this parameter is also required",
"optional": false
},
"myOptionalParameter": {
"description": "this parameter is optional",
"optional": true
}
} Parameter templates are optional for CWL workflows. HealthOmics inspects the “main” workflow definition to detect the input parameters to use. If you provide a parameter template for a CWL workflow, the template overrides the parameters detected in the workflow definition.
