Protocols

In Clarity LIMS, a protocol is a set of steps that must be performed in a specific sequence, as part of a lab's workflow. This section explain how to create and configure your lab protocols.

Configure Protocols

Clarity LIMS includes preconfigured protocols, each containing a series of steps through which a sample must pass. You can create custom protocols, adding steps that represent the steps that are run in your lab. You can then add the protocols to workflows so that lab users can work with them in Lab View.

Use the Lab Work configuration screen to view, add, and configure the protocols used in the lab. For an overview of this screen, see Lab Work Overview.

To access the Lab Work tab and configure protocols, the Configuration:update permission is required. By default, only the Administrator role has this permission. For details, see User Roles and Configured Role-Based Permissions.

View Protocols

1. On the main menu, select Configuration.

2. Select the Lab Work tab.

   The Workflows, Protocols, Steps, and Master Steps navigation panel displays.

3. In the Protocols list, select a protocol to highlight it:

   • The Workflows list updates, highlighting the workflows that contain the selected protocol.

   • The Steps list updates, highlighting the steps included in the selected protocol.

   • The Master Steps list updates, highlighting the master steps on which the highlighted steps are based.

4. Below the main navigation panel, review the protocol configuration form.

   This displays the name of the protocol and its settings.

Protocol Settings

The Protocol Settings area captures important information about the protocol—the date it was created, the date it was last modified, and other settings that determine how the protocol is used in the lab. The following table summarizes these settings.

Setting	Configuration options	What It Means in the Lab
QC Protocol?	QC protocols comprise a series of QC steps.	All steps share queue of samples. Samples do not move sequentially from step to step. Instead, they appear available/unavailable for a particular step based on configured filtering criteria.
	Non-QC protocols typically comprise a series of non-QC steps. However, you can include a QC step as part of a Non-QC protocol.	Each step has its own queue of samples. Samples move sequentially through the steps, until they have completed all steps in the protocol.
Protocol Type	Sample Prep Library Prep Sequencing Data Analysis Sample Analysis Other	See Non-QC protocol information in previous row.
Show in Lab View?	No	These protocols are hidden for both lab scientists and administrators in Lab View and are therefore not available for use in the lab. These protocols are only visible to administrative users in the configuration area.
	Yes	These protocols are displayed in Lab View and can be used by lab scientists to perform their work in the lab.
Capacity	The sample capacity of the protocol. This depends on the number of lab scientists in your facility, and the number of samples they can work with at any given time.	The Capacity setting controls the highlighting on the Overview and Projects dashboards, allowing you to see at a glance which protocols are approaching or exceeding sample capacity.

Add Protocols

When adding and configuring protocols, note the following details:

• When adding steps to a protocol, reordering steps, or removing steps from a protocol, changes are autosaved. You do not need to select Save after every modification.

• When Configure Next Steps, you must select Save to save your changes.

To add a protocol:

1. On the Lab Work configuration screen, in the upper-right corner of the Protocols list, select Add.

   Below the main navigation panel, the protocol configuration form displays.

2. To begin, type a name for the new protocol.

3. Select the settings for this protocol (For details, see Protocol Settings):

   • Select whether this is a QC or Non-QC protocol.

   • Select the Protocol Type:

     • If you are adding a QC protocol, this automatically is set to QC.

     • If you are adding a Non-QC protocol, select the type from the drop-down list.

     • In the Capacity field, enter the sample capacity of this protocol.

4. [Optional] To temporarily hide the protocol from Lab View, use the Show in Lab View? slider. Change the setting to No.

5. Select Save. The new protocol displays at the bottom of the Protocols list. You can move it to a different position in the list by dragging and dropping.

   To drag and drop on a mobile or touch-screen device, touch and hold the item you wish to drag. After a moment, the item appears to lift off the page and its color changes to white. You can then drag the item and drop it into its new position.

You can also copy a protocol and then modify the copy for use in other workflows. See Copy Protocols.

Add Steps to Protocols

This section provides an overview of the step creation process. For detailed information on steps and master steps, and step-by-step instructions for configuring them, see Add and Configure Master Steps and Steps.

To add a step to a protocol:

1. In the Protocols list, select the protocol.

2. In the upper-right corner of the Steps list, select Add.

   Below the main navigation panel, the step configuration form displays.

3. Type a name for the new step.

4. In the adjacent Master Step list, select the master step upon which to base the new step.

5. Select Save (this button is not enabled until you have selected a master step).

6. In the Protocols list, select the protocol again.

   • The step you added displays at the top of the Step list.

   • If this is a non-QC protocol, a 1 is in front of the step name, indicating that this is the first step in the protocol.(QC steps are not numbered as they are typically not sequential.)

   • In the Master Step list, the master step upon which the step is based is also highlighted.

7. Repeat steps 1–5 to add more steps to the protocol.

   • To delete a step, select it and select the Delete.

   • To reorder steps within the protocol, simply drag and drop them.

   To drag and drop on a mobile or touch-screen device, touch and hold the item you wish to drag. After a moment, the item appears to lift off the page and its color changes to white. You can then drag the item and drop it into its new position.

8. Select Save.

You can now configure the order in which the steps are run, and the method used to assign and run 'next steps.' See Configure Next Steps.

Configure Next Steps

When configuring non-QC protocols, the protocol configuration form includes a Next Steps table. This allows you to configure the sequence in which steps are run in the protocol. This table does not display for QC protocols, because the steps in a QC protocol are typically not sequential.

In the table:

• Each row represents a numbered step in the protocol.

• Each column represents a 'permitted next step' for each of the numbered steps.

• The cells at each row/column intersection indicate which steps are potential permitted next steps for the step represented in that row.

  • If there is an icon in the cell (an X or a checkmark), the step represented by that column may be selected or deselected as a permitted next step.

  • Previous and current steps cannot be selected as permitted next steps, and are shown as nonselectable cells.

• The bottom two rows determine whether the next steps are started and assigned manually or automatically. Manual is the default setting.

To configure next steps

1. In the Next Steps table, select a cell to select (or deselect) one or more permitted next steps.

2. In the Start Next Step and Assign Next Step rows, select a cell to switch between Manual and Automatic.

To assign a next step automatically, you also need to configure an automation and add it to the step. For details, see Add and Configure Automations.

Configure QC Filters

When configuring QC protocols, the protocol configuration form includes a QC Filters section. This section lets you configure QC logic to make sure that only certain samples are queued for each QC step. Typically, QC protocols contain multiple nonsequential steps that culminate in a QC aggregation step.

QC filters are composed of two drop-down lists.

The first list refers to the QC flag assigned at run time:

• Passed means that a pass QC flag was assigned to the sample at run time.

• Failed means that a fail QC flag was assigned to the sample at run time.

• Did not pass means that the sample did not run, or received a fail QC flag, at run time.

• Did not fail means that the sample did not run, or received a pass QC flag, at run time.

The second list refers to the master steps from which the steps are derived:

• All master steps used in the protocol are included in the list. Together, these form a statement (for example, Failed Bioanalyzer).

• Each statement may be followed by an'AND', which allows you to create an additive statement.

• Statements are separated by an'OR', which allows you to create mutually exclusive statements.

• Together, these AND/OR statements create the QC filter logic for a given step.

For example:

You may want the NanoDrop QC queue to show samples that have not passed NanoDrop QC (ie, they did not run, or received a fail QC flag), and that have passedBioanalyzer QC.

• If the procedures dictate that all samples must have passed Bioanalyzer QC and NanoDrop QC, use an 'AND' statement to ensure samples are not queued for a QC aggregation step unless they have passed both of these steps.

• If your lab procedures dictate that all samples must have passed Bioanalyzer QC or NanoDrop QC, use an 'OR' statement to ensure samples are not queued for QC aggregation unless they have passed one of these steps.

Modify Protocols

You may want to rename a protocol, or add or reorder steps. Some modifications are only permitted if the protocol is not included in an active or archived workflow.

NOTE: We recommend that you do not modify or delete the preconfigured protocols without first consulting the Clarity LIMS Support team.

To modify a protocol:

1. In the Protocols list, select the protocol.

2. Make your changes and select Save.

Note the following details:

• You can rename protocols in pending, active, and archived workflows.

• For non-QC protocols, you can modify the protocol type. For example, you can change a Sample Prep protocol to a Library Prep protocol.

• You can choose to hide or show the protocol in Lab View.

• You cannot change a QC protocol to a non-QC protocol, and vice versa.

• You cannot add, reorder, or delete steps if the protocol is included in an active or archived workflow.

Delete Protocols

To delete a protocol:

1. In the Protocols list, select the protocol.

2. On the protocol configuration form, select Delete.

Note the following details:

• You cannot delete a protocol if it is included in an active or archived workflow. In this case, the Delete button is not enabled.

• If you delete a protocol, the steps it contains, and the master steps on which those steps were based are not deleted.

Copy Protocols

After you have added and configured a protocol, you can copy it and then modify the copy for use in other workflows. This is useful if you have multiple protocols with similar base configuration, as it saves you having to recreate each one from scratch.

To access the Lab Work tab and configure protocols, the Configuration:update permission is required. By default, only the Administrator role has this permission. For details, see User Roles and Configured Role-Based Permissions.

When you copy a protocol, all of its steps are also copied—along with any step-level fields, automations, reagents, controls, and instruments configured on those steps.

You can also create copies of the master steps, or you can reuse the same master steps.

• Copying master steps does copy step-level fields.

• Reusing master steps does not copy step-level fields.

• If a copied master step has custom field default values that refer to other steps within the protocol, update those values to refer to the copied steps. See Update Custom Field Default on Copied Master Steps.

Copy a Protocol and its Step

1. On the main menu, select Configuration.

2. On the LIMS configuration screen, select the Lab Work tab.

3. In the main navigation panel, in the Protocols list, select the protocol to copy.

4. Below the navigation panel, select Copy.

5. The Copy Protocol Options dialog opens. This dialog provides two options:

   • Append name with—This option lets you specify text to be appended to the protocol name (default is _copy). This text also is appended to the copied step names, and to the master step names if you also choose to copy those. Note: Copied step-level field names do not have the text appended.

   • Copy Master Steps?—This option lets you choose to reuse the same master steps (this is the default behavior), or create copies of the master steps.

   • Selected an option and then select Continue to copy the protocol and steps.

6. The copied protocol displays in the Protocols list, and is selected along with its related steps and master steps.

   Below the navigation panel, the protocol configuration form displays. You can work with the protocol and its steps just as you would with any other protocol/steps in the system.

Update Custom Field Default on Copied Master Steps

If you have configured a custom field default on the master step you are copying, and the default value refers to the name of another step within the protocol, you must update that default value on the copied master step, so that it refers to the appropriate step in the copied protocol. The default values are not automatically updated to refer to the copied step names.

Similarly, if you have configured a script or logic that uses custom field defaults that refer to another step within the protocol, you must update those default values on the copied master step.

For example, in a QC protocol:

• The Aggregate QC step has various 'Copy Task' UDFs defined - eg, Copy Task 1 - Source Step and Copy Task 2 - Source Step.

• The values of these fields are determined by other QC steps within the protocol.

• The script that is configured on the QC Aggregate step references those QC step names, locates the specified custom field values from the steps, and uses them to determine QC results.

If the QC protocol is copied, the copy of the master step on which the Aggregate QC step is based must be updated so that the custom field default values refer to the appropriate steps within the protocol.