Create an input JSON file#


This tutorial will help you create the input JSON file.


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"