LogoLogo
  • Overview
  • publisher
    • Introduction
    • Getting Started
      • Logging in to Publisher
    • Data Sources
      • Connecting a Data Source
      • Managing a Data Source
      • Connectors
        • AWS S3 Permissions
        • Connecting to AWS S3 Storage
        • Google Cloud Storage (GCS) Permissions
        • Connecting to Google Cloud Storage
        • PostgreSQL Permissions
        • Connecting to PostgreSQL
        • PostgreSQL on Azure Permissions
        • Microsoft Azure Blob Storage Permissions
        • Connecting to Microsoft Azure Blob Storage
        • Connecting to HTTPS
        • Connecting to other sources via Trino
          • BigQuery
    • Collections
      • Creating a Collection
      • Sharing a Collection
      • Collection Filters
      • Editing Collection Metadata
      • Updating Collection Contents
    • Access Policies
      • Creating an Access Policy
      • Managing Access Policies
    • Questions
      • Adding Questions
      • Example Question
    • Settings
      • Viewing Current and Past Administrators
      • Adding an Administrator
      • Removing an Administrator
      • Setting Notification Preferences
  • Explorer
    • Introduction
    • Viewing a Collection
    • Browsing Collections
    • Asking Questions
    • Accessing a Private Collection
      • Requesting Access to a Private Collection
    • Filtering Data in Tables
      • Strings
      • Dates
      • Numbers
  • Workbench
    • Introduction
    • Getting Started
      • Logging into Workbench
      • Connecting an Engine
      • Finding or Importing a Workflow
      • Configuring Workflow Inputs
      • Running and Monitoring a Workflow
      • Locating Outputs
    • Engines
      • Adding and Updating an Engine
        • On AWS HealthOmics
        • On Microsoft Azure
        • On Google Cloud Platform
        • On Premises
      • Parameters
        • AWS HealthOmics
        • Google Cloud Platform
        • Microsoft Azure
        • On-Premises
        • Cromwell
        • Amazon Genomics CLI
    • Workflows
      • Finding Workflows
      • Adding a Workflow
      • Supported Languages
      • Repositories
        • Dockstore
    • Instruments
      • Getting Started with Instruments
      • Connecting a Storage Account
      • Using Sample Data in a Workflow
      • Running Workflows Using Samples
      • Family Based Analysis with Pedigree Information
      • Monitor the Workflow
      • CLI Reference
        • Instruments
        • Storage
        • Samples
        • OpenAPI Specification
    • Entities
    • Terminology
  • Passport
    • Introduction
    • Registering an Email Address for a Google Identity
  • Command Line Interface
    • Installation
    • Usage Examples
    • Working with JSON Data
    • Reference
      • workbench
        • runs submit
        • runs list
        • runs describe
        • runs cancel
        • runs delete
        • runs logs
        • runs tasks list
        • runs events list
        • engines list
        • engines describe
        • engines parameters list
        • engines parameters describe
        • engines health-checks list
        • workflows create
        • workflows list
        • workflows describe
        • workflows update
        • workflows delete
        • workflows versions create
        • workflows versions list
        • workflows versions describe
        • workflows versions files
        • workflows versions update
        • workflows versions delete
        • workflows versions defaults create
        • workflows versions defaults list
        • workflows versions defaults describe
        • workflows versions defaults update
        • workflows versions defaults delete
        • namespaces get-default
        • storage add
        • storage delete
        • storage describe
        • storage list
        • storage update
        • storage platforms add
        • storage platforms delete
        • storage platforms describe
        • storage platforms list
        • samples list
        • samples describe
        • samples files list
      • publisher
        • datasources list
  • Analysis
    • Python Library
    • Popular Environments
      • Cromwell
      • CWL Tool
      • Terra
      • Nextflow
      • DNAnexus
Powered by GitBook

© DNAstack. All rights reserved.

On this page
  • Overview
  • Understanding Workflow Inputs
  • Configuring Your Inputs

Was this helpful?

  1. Workbench
  2. Getting Started

Configuring Workflow Inputs

PreviousFinding or Importing a WorkflowNextRunning and Monitoring a Workflow

Last updated 4 months ago

Was this helpful?

Overview

Most WDL workflows require specific inputs to function correctly. Before running a workflow, you'll need to provide data files for processing and configure various parameters that control how the workflow operates. These parameters allow you to customize tool behavior and resource allocation for your specific needs.

Understanding Workflow Inputs

Workflow engines process inputs in JSON format, a structured text format designed for data exchange. While this is the required format for execution, Workbench provides two ways to configure your inputs:

  • Through a user-friendly web form interface

  • By editing the JSON file directly

Both methods achieve the same result - Workbench converts your inputs into a JSON file that's provided to the workflow engine along with the workflow script.

Configuring Your Inputs

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

When you reach the input configuration page, you'll see a table of all available input parameters. Here's how to configure them:

  1. Find the input you want to configure in the table

  2. Click the 'expand' symbol that appears when you hover over a row

  3. Use either the web form or JSON view to set your values

  4. Complete all required inputs (marked with red asterisks)

  5. Close the panel when finished with each input

If you miss any required inputs, Workbench will highlight them with a red 'danger' icon. You can quickly fix these by double-clicking the cell in the table or reopening the configuration panel.

Remember that your input configuration is not saved until you submit the workflow run. Navigating away from the page will lose your settings.

Finding or Importing a Workflow