Configure Master Steps and Steps

Clarity LIMS includes preconfigured steps and master steps designed to support established lab processes. You can create additional steps and master steps to represent the procedures that are specific to your lab. There are two approaches:

• Create steps based on the preconfigured master steps. The steps you create inherit the properties of the configured master steps, and you can then set additional properties on the steps themselves.
• Create master steps, and then use them as the foundations on which to create your steps.

You can add the steps to protocols and workflows so that lab scientists can work with them in Lab View.

To access the Lab Work tab and configure steps and master steps, the Configuration:update permission is required. By default, only the Administrator role has this permission. For details, refer to User Roles and Configure Role-Based Permissions.

The Lab Work screen provides an at-a-glance view of all steps and master steps configured in the LIMS, along with the protocols and workflows in which they are included.

1. On the main menu, select Configuration.
2. On the LIMS configuration screen, select the Lab Work tab.

The Workflow, Protocol, Step, and Master Step navigation panel displays. This lists the workflows, protocols, steps, and master steps configured in the LIMS.

3. In the Master Steps list, select a master step to highlight it:
• The Steps list updates, highlighting the steps derived from the selected master step.

If multiple steps are derived from the same master step, the Master Steps list includes duplicate rows, each mapping to a different step, and each representing the same master step. All of these rows are highlighted.

• The Protocols list updates, highlighting all the protocols that contain the highlighted steps.
• The Workflows list updates, highlighting all workflows that include the highlighted protocols.
4. In the Steps list, select a step to highlight it: The Master Steps list updates, highlighting the master step on which the selected step is based.

If multiple steps are derived from the same master step, the Master Steps list includes duplicate rows, each mapping to a different step, and each representing the same master step. All of these rows are highlighted.

• The Protocols list updates, highlighting the protocol that contains the selected step.
• The Workflows list updates, highlighting all of the workflows that include the highlighted protocols.

Below the main navigation panel, the step and master step configuration forms display.

5. Select these tabs to switch between the forms and see which settings are configured on the step and which are configured on the underlying master step.

Table 1 shows which settings must be configured on the master step and which may be configured on the master step or on the step.

Settings configured on the master step are locked at the step level. On the step configuration form, these settings display with a Locked icon.

Table 1: Master Step and Step Settings

Setting

Configured on

Notes

Step type

Master step

 

Output generation

Master step

 

Output naming convention

Master step

 

Automation
• Automations are enabled on the master step
• Automation triggers may be set on master step or step.

 

Instrument types

Master step or step

 

Control types

Master step or step

 

Reagent kits

Master step or step

 

Step milestones

Master step or step

Some milestone settings must be configured on the master step.

Label groups

Master step or step

Refer to Add Labels Milestone.

Label uniqueness

Master step

Refer to Pooling Milestone.

Step file placeholders

Master step

Refer to Record Details Milestone.
1. On the Lab Work configuration screen, in the upper-right corner of the Master Steps list, select Add.
2. Below the main navigation panel, the master step configuration form displays.
3. To begin, type a name for your new master step.
4. Configure the settings for this master step - refer to Configure a Master Step, below.
5. Select Save to save your master step configuration.

When adding a master step, keep the following in mind:

• Each step is created from a master step. You can create multiple steps from the same master step.
• Any settings you configure on the master step are inherited by all steps derived from that master step.

To understand how properties set on the master step propagate down to the step level, refer to Rules for Propagation of Master Step Properties.

The following sections describe the settings available when configuring a master step. Note the following:

• Any settings saved as part of the master step configuration cannot be configured at step level. On the step configuration form, these settings display with a Locked icon.
• Some settings may be configured at the step level, as indicated in Table 1.
• The master step configuration form does not show the default setting values (this includes toggle switches).

Step types are configured on master steps.

Steps are categorized by step type, where each type is based on the requirements and goals of the step, and the output generated by the step (derived samples, measurements, or aliquots).

The step type is set on the master step, and all steps inherit the step type of the master step on which they are based. After you have chosen a step type and have saved it as part of a master step configuration, you cannot change it.

• If you are not sure which step type to choose, review About Step Types and Outputs.
• To understand the relationship between master steps and steps, refer to Overview of Steps and Master Steps.

The step type you choose determines which step milestones are available for configuration.

Configured on master step.

A step may generate a derived sample output, a measurement output, an aliquot output, or no output.

The type of step you choose determines which output generation options are available. Usually, you may choose to keep the default setting or modify the output generation configuration.

For details on the output generation options available for each step type, refer to About Step Types and Outputs.

Configured on master step.

By default, the name of the outputs generated by a step follows the naming pattern of the inputs to the step.

You can use tokens to configure the naming convention so that it resolves to other unique attributes of the output. These tokens function as placeholders that are replaced with actual values at run time. For example, for the Standard step type, the default naming convention resolves to the value of the {InputItemName} token.

The following table lists the default naming conventions for each of the step types.

Table 2: Default Naming Conventions for Step Types

Step type

Default Naming Convention Token

Naming Convention Preview

Standard

{InputItemName}

Input Sample

Standard QC

{InputItemName}

Input Sample

Aggregate QC

None - Aggregate QC steps do not produce outputs.

Not applicable

Add Labels

{InputItemName}-{AppliedReagentLabels}

Input Sample-N701-N501 (TAAGGCGA-TAGATCGC)

Pooling

{PoolName}

Pool #1

Analysis

{InputItemName}

Input Sample

Demultiplexing

{InputItemName} (FASTQ reads) {AppliedReagentLabels}

Input Sample (FASTQ reads) N701-N501 (TAAGGCGA-TAGATCGC)

The Tokens list provides a list of tokens you can use to configure the naming convention. For descriptions and examples, refer to Derived Sample Naming Convention Tokens.

To add a token:

1. Copy the token you want to use from the Tokens list and paste it into the Naming Convention field. If using multiple tokens, add a space between each entry.
2. Below the Naming Convention field, you can see a preview of how one or more tokens resolve. Some runtime-specific items, such as dates and times, do not preview exactly as they resolve at run time.

Automations are enabled on master step. Automation triggers may be set on master step or step.

A master step can be configured to update sample fields, assign QC flags, generate files, and submit files and command-line parameters to third-party programs, using automations and the Rapid Scripting API.

When you have configured an automation, you can enable it on one or more master steps and set its trigger location and style.

You can enable automations on master steps in two configuration areas of the LIMS:

• On the Automations tab, when adding/configuring an automation.
• On the master step configuration form.

After it is enabled on a master step, the automation becomes available for use on all steps derived from that master step.

You can set the trigger location and trigger style for an automation on the master step, or on the steps derived from that master step:

• On the master step—In this case, all steps derived from the master step inherit the automation and the trigger settings.
• On the steps derived from the master step—In this case, all steps inherit the automation from the master step, but you can configure different trigger settings for each step, if necessary.

To enable an automation on a master step, you must have first configured the automation on the Automation tab. For details, refer to Add and Configure Automations.

To enable an automation on a master step:

1. In the Automation section, click the Automation configuration screen link.

The Automation configuration screen opens, with the Step Automation tab active.

2. In the Automation Use section, select inside the Enable on the Master Steps field and select the master step on which to enable the automation. (If you make a mistake, select the X button to remove a master step from the field.)
3. Select Save.
4. Return to the master step configuration form. The automations are listed alphanumerically by name.

To set an automation trigger on a master step (or step):

1. In the Trigger Location drop-down list, select the stage of the step at which to enable the automation.
• The list displays all available stages of the step from which the automation can be triggered.
• Only valid options for the step are displayed, for example, the Pooling option only displays on Pooling steps, the Step Setup option only displays for steps on which the Step Setup screen is enabled.
• To ensure sequence of execution, only one automation can be associated with each trigger location.
2. In the Trigger Style drop-down list, select how to initiate the automation. For example, automatically on entry to or exit from the screen or manually when a button is selected on the screen.

The trigger location and style are saved with the automation configuration.

3. Repeat steps 1 and 2 to configure triggers for each automation added.
4. Save the automation configuration.

Configured on master step or step

You can specify the instrument/equipment types that may be used in a step. You can do this on the master step or at the step level. At run time, on the Record Details screen, the lab scientist selects from a list of instruments/equipment of that type.

To enable an instrument/equipment type on a master step or step, you must have first added the instrument type to the system. Refer to Add and Configure Instruments.

Note also that instrument type/master step configuration is bidirectional - when adding an instrument type, you can select master steps to associate with that instrument type.

To enable an instrument type on a master step (or step):

1. In the Instrument Types section, select Add.
2. At the right of the screen, a list of instrument/equipment types displays. Select one or more instrument/equipment types and select the checkmark button.

The instrument/equipment types are added to the master step/step configuration.

• If necessary, you can remove an instrument type by clicking the X button.
• Step configuration form only: You can reorder instrument types by dragging and dropping them. The order is reflected on the step Record Details screen, in the Instrument selection drop-down list.
3. Save the master step/step.

Configured on master step or step

You can specify the reagent kits that may be used in a step. You can do this on the master step or at the step level.

Configuring reagent kits on the step/master step enables reagent lot tracking on the Record Details screen at run time.

To enable a reagent kit on a master step or step, you must have first added the reagent kit to the system. Refer to Add and Configure Reagent Kits and Lots.

Note also that reagent kit/master step configuration is bidirectional—when adding a reagent kit, you can select master steps to associate with that kit.

To enable a reagent kit on a master step (or step):

1. In the Reagent Kits section, select Add.
2. At the right of the screen, a list of reagent kits displays. Select one or more kits and select the checkmark.

The reagent kits are added to the master step/step configuration.

If necessary, you can remove a reagent kit by clicking the X button.

3. Save the master step/step.

Configured on step

You can specify the control types that may be used in a step. This is done at the step level.

Selected controls are then available to add to the Ice Bucket when running the step.

To enable a control type on a step, you must have first added the control type to the system. Refer to Add and Configure Controls.

Note also that control type/step configuration is bidirectional—when adding a control type, you can select the steps to be associated with it.

To enable a control type on a step:

1. In the Control Types section, select Add.
2. At the right of the screen, a list of control types displays. Select one or more control types and select the checkmark.

The control types are added to the step configuration.

3. Remove a control type by clicking the X button.
4. Save the step.

Configured on master step or step

When running samples through steps in the LIMS, each screen displayed represents a specific stage, or 'milestone' of the step.

Some screens display on all steps, while others only display on certain step types.

For more on milestones, and instructions on configuring milestone settings, refer to Configure Step Milestones

When adding steps to the LIMS, first select a protocol to include the new step, and a master step on which to base it. The new step inherits all settings configured on the master step.

To add a new step:

1. On the Lab Work configuration screen, in the Protocols list, select the protocol in which to add the new step.
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 Steps list, select the master step upon which to base the new step.

If creating a step within a QC protocol, the Master Steps list only displays master steps that are Standard QC and Aggregate QC step types.

5. Select Save (this button is not enabled until a master step is selected).
6. In the Protocols list, select the protocol again.
7. The step added displays at the top of the Steps list.
• The '1' indicates that this is the first step in the protocol. (QC protocol steps are not numbered as they are typically not sequential.)
• In the Master Steps list, the master step upon which the step is based is also highlighted.
8. Repeat steps 1–5 to add more steps to the protocol.
• To delete a step, select it and select Delete.
• To reorder steps within the protocol, drag and drop them.
9. Select Save.

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 configure the order in which the protocol steps are run, and the method used to assign and run 'next steps.' Refer to Configure Protocols and refer to the Configuring next steps section.

On the step configuration form:

• Any settings that were configured on the master step are locked. On the step configuration form, these settings display with a Locked icon.
• You can configure settings that were not configured on the master step. These settings only apply to the step.
• Settings not configured on the master step typically use the default value at the step level, unless those settings are configured on the step.

If not locked on the master step, the following settings can be configured at the step level.

• Automation triggers
• Instrument types
• Reagent kits
• Control types
• Step Milestones
1. In the Master Steps list, select the master step you would like to modify.
2. Make your changes and select Save.

When modifying master steps and steps, keep the following in mind:

• You can change the master step on which a step is based, providing the new master step is of the same step type. The list of master steps is filtered to show valid options.
• If you remove configured settings from a master step, those settings on the derived steps revert to their default values, except if this would leave the step in an unworkable state. For example, you cannot remove the last container from a step. Exceptions to this revert to default rule are noted where applicable.
• If you rename a step, the Recent Activities list in Lab View continues to display the name of the step as it was when the step was run. This is because the step name in this case is derived from the activity record.
1. In the Master Steps list, select the master step to delete.
2. On the master step configuration form, select Delete.

When deleting master steps and steps, keep the following in mind:

• You cannot delete a step if it is included in an active or archived workflow.
• You cannot delete a master step if it is used to generate a step that is in an active or archived workflow.
• You cannot delete a master step if it has already been used to create one or more steps. First delete the step, and then delete the master step.