Deeper dive: WDLs, workflows, tasks

Allie Hajian
  • Updated

Learn how to dissect the parts of your WDL - inputs and outputs and tasks. Helpful when troubleshooting. 

Identifying workflow and task inputs and outputs

Inputs and outputs are defined in the WDL and can be at the "workflow" or the "task" level. Terra interprets the WDL and provides an input "form" to fill out. The outputs part of the form is optional. To access the inputs and outputs forms as well as more details on the inner workings of the WDL, click on the workflow card from within the Workflows page. 

To learn more about configuring workflow inputs and outputs, see How to configure workflow inputs

Understanding where the inputs and outputs are used by the WDL can help with troubleshooting, if your submission fails.  

This is an example of the configuration form you see after clicking on the workflow card (note that you need to be signed into Terra to see this workspace).

There are separate forms in tabs for the WDL script, inputs, and outputs:

How many workflows and how many tasks are in the CRAM to BAM WDL?

To look at the WDL script in the Exercise1_CRAM_to_BAM workflow of the Terra-Workflows-QuickStart workspace, click here and select the Script tab at the left. 

HINT: Click on the "Script" tab (at left in the workflow configuration form) to look at the WDL script and find this information.

  • Workflows-Deep_Dive_WDL_script_Screen_shot.png

    Answer: The WDL includes one workflow - CramToBamFlow (1) with two tasks - CramToBamTask (2) and ValidateSameFile (3).

    You can identify tasks by the "call" command. There are inputs listed for the workflow and separately for the tasks, followed by outputs for the workflow.

    In the Inputs tab, you can tell the difference between workflow inputs and task inputs by looking at the name in the first column. The first four inputs are the workflow inputs (i.e., correspond to the workflow, CramToBamFlow) according to the WDL.

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