Configuring Workflow Inputs


Most WDL workflows require that you specify certain inputs, such as data files to operate on and parameters that may be specific to a given run. Parameters are typically used to modulate the operation of the underlying bioinformatics tools, to turn certain options on or off, or to customize the allocation of computational resources.

Workflow engines that run WDL workflows require inputs to be provided in JSON format, which is a common structured text format.

Workbench provides you with two options for configuring workflow inputs: (1) fill out each required workflow input by entering their values into a web form, or (2) edit a JSON file directly. In either case, Workbench will turn the inputs you provide into a JSON file when you launch the run. The system will provide this inputs file to the workflow engine along with the workflow script.

Step-by-step instructions

This procedure assumes you have already selected a workflow to run as described in Finding or importing a workflow and have clicked on the workflow inputs configuration page.

  • Step 1: Click on the ‘expand’ symbol that appears in the leftmost column of the inputs table when you hover your cursor over a row. This will open the configuration form in a side panel.

  • Step 2: (optional) You can switch between the web form view and the JSON script view at any time by clicking the corresponding icons at the top of the panel.

  • Step 3: Fill out all required inputs (indicated by a red asterisk in the web form view) and any optional inputs you wish to provide.

  • Step 4: When you have filled out all required inputs (indicated by a red asterisk in the web form view), click the “Close” button at the bottom of the panel.

  • If a required input is missing, a red ‘danger’ icon will be displayed in the leftmost column as well as in the corresponding cells in the table of inputs after you close the panel. You can reopen the panel to correct the problem, or you can double-click a cell in the inputs table to edit its value directly.

CAUTION: Workbench will NOT save your inputs configuration if you navigate away from the page before submitting the workflow run.

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