Create and execute a Workflow

This guide covers the basics of creating and managing workflows, executing tasks, and customizing notifications.

Key terms and definitions

• Workflow: A structured sequence of tasks designed to complete a lab or operational process
• Task Schema: A template that defines the structure, fields, and execution type of task.
• Task Group: A collection of related tasks generated from a single task schema
• Task: An individual unit of work assigned to a user that represents a job to do in a process or workflow, defined by a schema
• Execution Type: Defines how a task is completed. Options include Direct (manual), Entry (via notebook), or Flowchart (node-based)
• Watchers: Users who are notified of task updates even if they are not assigned to the task
• Status Lifecycle: A defined sequence of statuses that a task progresses through (e.g., Pending → In Progress → Complete)
• Flowchart: A visual representation of task progression and dependencies within a workflow
• Metadata: Custom fields that describe attributes of a task group or task (e.g., project, due date)
• Activity Log: A chronological record of updates and user actions for traceability

Create Task groups

Use task groups in the Workflows application to represent your organization’s workflows, steps to complete processes, and the users completing them.

Task groups are collections of tasks that are created and tracked together. Each task group is based on a specific task schema and allows your team to organize, assign, and monitor related tasks as a unit. When creating task groups, you'll specify assignees (users responsible for completing specific tasks) and may also add watchers, who are informed of updates but do not complete the task themselves.

Tasks and task groups are determined on the Task schema. Before creating a task group, ensure you have at least one Task schema. While tasks can initially be created while creating your Task group, you may also add them afterwards by editing your task group. To create a Task group: 

1. Click the Workflows icon in the left-side menu
2. Click the local create icon at the top of the panel, then select the Task schema for your workflow:
3. In the pop-up modal that displays, select the project folder for the task group and (optional) watchers, and complete the Task table
   • Each row of the table is one task
   • For flowchart task groups, create more than one task by adding new rows to the Task table
4. Click Create

To control which users receive notifications about task group status changes, add or remove watchers in the Metadata tab.

Create Task groups from structured tables

You can create task groups from these structured tables:

• Inventory table
• Outputs table
• Plate Creation table
• Registration table
• Tasks table

To create a task group from a structured table:

1. Click the Create workflow tasks icon at the top of the table
2. Select the Task schema from the drop-down menu
3. Complete the Tasks table
   • For each task, enter the task parameters and assignees, if applicable
   • If the task group has at least one field that accepts the type of entity or inventory item contained in the structured table, Benchling automatically adds the item to the first applicable field
4. Click Create

Edit Task groups

After creating a task group, you may need to add or edit its metadata or associated tasks. Task group metadata is background information about its origin, like authors, project location, or watchers. Task information, like assignees and scheduled dates, is specific to individual tasks in a workflow.

Before editing a task group, ensure you have at least one task group created. To edit task group metadata:

1. Navigate to the desired task group
2. Click the Metadata tab
3. Hover over the field to edit and click the Edit icon
4. Make the necessary changes and click ✔ to save

You may also wish to modify tasks already within a Task Group. To do so:

1. After navigating to the task group, click the Task Group tab
2. Click Edit in the Tasks table menu
3. Double-click the cell you wish to edit
4. After entering your edits, click Submit to save

Add Tasks to an existing Task group

As you progress through a task group, you may need to include additional tasks in the initial task group. For example, if you realize that an additional sample needs to be processed, you can add a task to include that sample in the task group. To add tasks to an existing task group:

1. Click the Workflows icon in the Navigation bar, then select the Workflow to edit
2. Click Task Group at the top of the window
3. Click the Edit icon in the Task table menu
4. Click the Add Row icon to insert new tasks one at a time
5. Click Submit to save your changes

Tip: When adding more rows to your table, you can click and drag the horizontal stripes icon down until you have the correct number of rows. This works best when adding small numbers of rows.

Execute and complete Workflow Tasks

How you complete a task depends on its execution type. If its associated Task schema supports the:

• Entry execution type: you execute the task through a new or existing notebook entry
• Direct execution type: you manually the task’s its status in the task group
  • Tasks using this execution type are not executed into entries
• Flowchart execution type: you complete a chain of tasks defined in the flowchart’s Task schema 

When executing a task, select the task to execute and create or select an entry. After executing the task, you can complete its entry to send it for review. You can execute tasks individually in the Task Group view or in bulk in the expanded Workflows dashboard.

Note: During task execution, to use the shortcut for automatically linking tasks to outputs, ensure the Link output to task shortcut is configured on the Task schema before creating a workflow from the schema.

While in task execution, to use the Link output to task shortcut, click the link icon in the top-right corner of the Outputs table. What it links to depends on how many tasks it finds:

• If there is one task found per output, the task populates the cell automatically
• If multiple tasks are found per output, the output is duplicated into additional rows to ensure each output is linked to only one task
• If no task is found, @-mention the task in the cell

Entry execution

1. From the Workflows dashboard, hover over the task to execute and check the box to select it. If you are executing multiple tasks, ensure they have the same schema type
2. Click Execute in the top-right corner
3. In the pop-up window, select the entry type:
   • To select an existing entry, enter the entry title and select it from the drop-down menu. The entry must have been created from the execution template assigned to that task type
   • To create a new entry, enter the entry title, then select the initial day and project the entry is associated with
4. Click Execute
5. Navigate to the Entry created, and fill in the empty columns in the task row
6. Click Submit in the top-right corner of the Tasks table to send the task for review
7. @-mention the task in a row in the Outputs table to link the task to its output, if an Outputs table was configured
8. Click Submit in the top-right corner of the Outputs table to create outputs

Direct execution

1. From the Workflows dashboard, hover over the task to execute and check the box to select it. If you are executing multiple tasks, ensure they have the same schema type
2. Click Execute in the top-right corner
3. In the pop-up window, manually update the tasks in the outputs table within the task group, and then click Continue
4. Click Submit in the top-right corner of the Outputs table to create outputs

Flowchart Execution

After creating a Flowchart Task schema, users with appropriate permissions can create and execute flowchart tasks and task groups using the Flowchart visualization or Workflows dashboard. Accessing tasks in the dashboard enables you to assign different tasks to different users or teams and enables users to complete them asynchronously.

Before executing Flowchart workflow tasks, ensure you have Write permissions in the folder or project the flowchart task group is associated with. Start by visualizing a flowchart, and then proceed to execution.

Visualize a Flowchart

Flowchart task groups open automatically after creation. They are identical to regular Task groups, except the window is split with the Task group tab displayed on the left and the Flowchart visualization displayed on the right. This view displays each node, or step, in the Flowchart so you can quickly determine the status of the overall Workflow.

In the image below, data entered into the Tasks table is already mapped to the next node in the Flowchart, which is also the first user-configured Task schema in line. An empty circle icon on the second node of the Flowchart view indicates there is a pending Task in this Task group.

Execute the Flowchart

Before executing the Workflow, add any remaining data in the Flowchart’s task metadata. You can edit the Tasks table, like adding rows for more tasks, before executing the next task.

Samples from the flowchart’s Tasks table display as Pending in the succeeding tasks’ node.

To execute a flowchart workflow in the visualization: 

1. Click the second node of the Flowchart to open the first executable Task group in a separate tab of your workspace
2. Execute pending Tasks in the Task group and make any edits to the Tasks table, like adding assignees. This automatically sends the output data to the next node, based on the Task schema’s mapping
   • The task must have a Completed status; a failed Task’s progress through the Flowchart will be halted and no data is mapped downstream
3. Using this information, execute all Tasks within the Task groups. The Outputs node populates with mapped data after at least one task from the final task group is executed and completed
   • Clicking on the Outputs node returns you to the Flowchart’s task group’s page, where you can view all completed tasks in the Flowchart and their associated outputs
   • The Flowchart visualization displays all task statuses within each node

Task status lifecycles

Each task schema is associated with a status lifecycle that determines when a task can be marked as complete. This helps track progress and enforce process consistency.

Example lifecycle: Pending → In Progress → Complete

Each status transition can be configured to trigger system behaviors such as notifications or Flowchart transitions.

As you complete Tasks, you can manually update their statuses. How you update Tasks depends on their associated Task schemas. The sections below talk about how to update Task statuses based on their type. 

Direct execution

Executing a completion-based task does not create an associated Notebook entry. To update a direct execution task: 

1. In the Workflow, click Edit
2. In the Status column, click the ∨ icon and select the status
3. Click Submit

Entry execution

Executing an entry-based task updates the status from Pending to In Progress. You can manually update entry-based statuses in its workflow or entry. To update a task status:

1. In the Workflow, click Edit
2. In the Status column of the Tasks table, click the ∨ icon and select the status
3. Click Submit

An output is not required to manually set a task to Complete.

Entry review execution

Executing a review-based task updates the status from Pending to In Progress, while completing a review automatically updates the status to Completed. 

To send a task for review, click Submit in the top-right corner

Note: To review a task, you must have Write permissions on the project the entry is in and the project the task group is in.

Notifications

As Tasks move through status changes and assigned users, Workflows sends automatic email notifications to relevant roles. Learn about notification triggers and recipients, and see how to customize your notifications below.

Notification recipients include Assignees, Responsible Teams, and Watchers.

• Assignees are specific individuals a task has been assigned to
• Responsible Teams are specific Benchling teams that have been configured for notifications on the task group schema
• Watchers are users who are notified of task group activity, even if they aren’t the assignee. Use watchers to:
  • Keep managers or reviewers in the loop without assigning them tasks
  • Ensure relevant scientists are informed when downstream dependencies are completed
  • Provide visibility into workstreams across teams

Use the tables below to understand what events trigger notifications and which roles are notified. When you take an action, you will not receive a notification, even if you are in these roles. The previous assignee will not receive a notification if the assignee is changed.

Customize notification recipients

If you have Write permissions on a task group project, you can add watchers to ensure the right people are notified when important actions are taken. To edit task group watchers:

1. In the workflow, click the Metadata tab
2. Hover under the Watchers field and click the Edit icon
3. Enter a user and select their name from the list. To remove a user, click the X next to their name
4. Click ✔ to save

Note: The task group creator is automatically set as a watcher.

The responsible team is configured at the task schema level, and thus assigned when the task schema is created and cannot be updated.

For flowchart tasks, click Propagate watchers to notify watchers when all tasks in a workflow are completed.

Permissions determine who can create, edit, and execute Workflows and Tasks in Benchling. Access is typically tied to project roles and workspace settings. Permissions are summarized in the table below. 

Only Admins can configure task schemas. Editors can manage task groups and execute tasks. Viewers have read-only access to workflows.

Frequently asked questions

Q: What are the different execution types for tasks?

A: Tasks can have Direct, Entry, or Flowchart execution types, determining how they are completed.

Q: Can I edit a task after it's been created?

A: Yes, you can edit task details and metadata within the task group.

Q: How do I track the progress of a flowchart workflow?

A: Use the flowchart visualization to monitor task statuses and workflow progression.

Q: Who receives notifications about task updates?

A: Watchers and assigned users receive email notifications about relevant task changes.

Q: Can I add new tasks to an existing task group?

A: Yes, you can add tasks by editing the task group and inserting new rows in the Tasks table.

Q: Can I reassign a task to a different user after it’s been created?

A: Yes. You can reassign tasks by editing the assignee field in the Tasks table of the task group.

Q: Can I edit multiple tasks at once?

A: Bulk editing is supported through the Tasks table editor. Use the Edit option to adjust several rows before submitting.

Q: Can I make changes to a task schema after tasks have been created?

A: Schema changes will not retroactively affect existing tasks but will apply to new task groups going forward.