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
  • Submitting a Workflow
  • Monitoring Your Runs
  • Managing Workflow Runs
  • Resubmitting Workflows
  • Aborting Runs
  • Managing Run History
  • Monitoring and Navigation

Was this helpful?

  1. Workbench
  2. Getting Started

Running and Monitoring a Workflow

PreviousConfiguring Workflow InputsNextLocating Outputs

Last updated 4 months ago

Was this helpful?

Overview

When you submit a workflow, Workbench coordinates with your specified workflow engine to execute and track your analysis. The engine interprets your workflow, generating commands for individual tasks that are then dispatched to your cloud or on-premises backend. Throughout this process, the engine orchestrates computational resources, executes the work, and writes outputs to storage.

Submitting a Workflow

This procedure assumes you have already and , and that you are currently looking at the completed workflow inputs configuration page.

After configuring your workflow inputs, follow these steps to submit your run:

  1. Click "Submit Run" to open the Run Preview dialog, which summarizes key information including name, version, and parallel run count

  2. Select your workflow engine from the connected options. If none is listed, follow the instructions in .

  3. Optionally add tags to help organize your runs

    • Use the format key: value

    • Separate multiple tags with commas or press return

    • Tags can be used later for filtering and identification

  4. Click "Submit" to launch your workflow

Monitoring Your Runs

Workbench provides comprehensive monitoring of your workflows. During execution, you can:

  • View overall run status and progress

  • Track individual task completion

  • Access logs as they're generated

  • Review workflow details through Overview, Inputs, and Outputs tabs

Managing Workflow Runs

Workbench provides several tools for managing your workflow runs, whether they're in progress or completed.

Resubmitting Workflows

You can rerun workflows in two ways:

  • From the run monitoring details page via the "Rerun" button

When resubmitting, you'll go through the standard submission process where you can:

  • Keep your original configuration

  • Update your settings or parameters

  • Select a different workflow engine

  • Add new tags

Aborting Runs

For workflows in progress, you have several abort options:

  • Abort a single run through the "Actions" menu in the runs table

  • Abort multiple runs by:

    1. Selecting runs using the checkboxes in the table

    2. Clicking the three-dot menu at the top right

    3. Choosing "Abort Runs"

Managing Run History

To maintain your workflow history:

  • Delete individual runs:

    • Use the "Delete Run" option in the "Actions" menu

    • Click the trash can icon on the run's monitoring details page

  • Delete multiple runs:

    1. Select runs using the table checkboxes

    2. Open the three-dot menu

    3. Choose "Delete Runs"

Monitoring and Navigation

If you navigate away during execution, you can return to your run:

  • Click "Monitor" in the main menu to see all runs

  • Use filters to find specific runs:

    • Search by workflow name

    • Filter by creation date

    • Filter by completion status

    • Filter by custom tags

  • Click any run in the table to view its detailed monitoring page

Deleting runs only removes them from the monitoring table - all output files remain intact in your storage location.

To find your runs later, use the page, which displays both active and completed workflows. This page allows you to filter runs by workflow name, creation date, completion status, and tags. Click any run in the list to view its detailed monitoring page.

From the page using the "Actions" menu

selected a workflow to run
configured its inputs
Connecting to a Workflow Engine
Monitor
Monitor