> For the complete documentation index, see [llms.txt](https://docs.omics.ai/products/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.omics.ai/products/workbench/getting-started/submitting-and-monitoring-a-workflow-run.md).

# Running and Monitoring a Workflow

## 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

{% hint style="info" %}
This procedure assumes you have already [selected a workflow to run](/products/workbench/getting-started/finding-or-importing-a-workflow.md) and [configured its inputs](/products/workbench/getting-started/configuring-workflow-inputs.md), and that you are currently looking at the completed workflow inputs configuration page.
{% endhint %}

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 [Connecting to a Workflow Engine](/products/workbench/getting-started/connect-an-engine.md).
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

### Investigating a failed run

When a run fails, Workbench shows why:

* The run's **Overview** tab shows a **Run failed** banner with the failure reason reported for the run.
* On the **Logs** tab, a warning banner above the log viewer shows the failure reason for the selected task (or for the overall workflow).
* The log source toggle offers **stdout**, **stderr** and **backend log**; only the sources available for the selected task are shown. The cause of a failure isn't always in stderr, so check the **backend log** too. JSON log content is formatted for readability.

### Re-checking a run's status

If a run's status looks out of date, for example a run that shows as failed or aborted but may still be executing on the engine, click **Re-check status** in the run details header. It's available on any run that hasn't succeeded and needs the **Run Workflows** capability.

* For a failed or aborted run, Workbench asks the engine for the run's current status and updates it.
* For other runs, it reloads the run's status from Workbench.

Re-checking an **aborted** run asks for confirmation first: if the engine reports that the run is still executing, it resumes and keeps incurring compute costs.

{% hint style="info" %}
After a re-check, the button is unavailable for about 30 seconds.
{% endhint %}

To find your runs later, use the [Monitor](https://workbench.omics.ai/monitor) 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.

## 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 [Monitor](https://workbench.omics.ai/monitor) page using the "Actions" menu
* 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

A rerun keeps the original run's sample or samples. It appears in the sample's run history and in the **Sample** column of the Monitor page.

{% hint style="warning" %}
A rerun doesn't load its variants into the Variant Interpreter.
{% endhint %}

### **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**

**I**f 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

{% hint style="info" %}
Deleting runs only removes them from the monitoring table - all output files remain intact in your storage location.
{% endhint %}


---

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