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:

• WOMtool program

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"
}