Create an input JSON file#
Objective#
This tutorial will help you create the input JSON file.
Prerequisites#
Before you begin, you will need the following:
1. Execute the WOMtool#
Execute the WOMtool program on your WDL main workflow script to generate the input JSON file in your computer terminal.
java -jar womtool.jar inputs MyMainWorkflow.wdl > MyMainWorkflowInputs.json
The command creates a myworkflow_inputs.json
file containing a list of all workflow inputs that you can customize from
run to run for the given WDL workflow. The file uses the following content structure:
{
"WorkflowName.TaskName.variableName": "Value_type",
"WorkflowName.SubworkflowName.TaskName.variableName": "Value_type"
}
2. Modify the input JSON file#
You will need to specify the actual values of the listed input variables for a particular workflow run.
Below is an example:
{
"MainWorkflow.Bwa.readR1": "File",
"MainWorkflow.Bwa.readR2": "File",
"MainWorkflow.Bwa.reference": "File",
"MainWorkflow.Bwa.sampleName": "String"
}
Specify the file paths and sample name directly in the JSON file or in a copy of the JSON file.
{
"MainWorkflow.Bwa.readR1": "/path/to/r1.fastq.gz",
"MainWorkflow.Bwa.readR2": "/path/to/r2.fastq.gz",
"MainWorkflow.Bwa.reference": "/path/to/ref.fa",
"MainWorkflow.Bwa.sampleName": "HG002"
}