Steps and Master Steps
Steps & Master Steps section of the LIMS Documentation explain how to create and configure steps and master steps in the LIMS.
Overview of Steps and Master Steps
In Clarity LIMS, steps and master steps are techniques or procedures that are performed on a sample. They are the building blocks of the lab work.
Think of master steps as starting points to create the individual steps that are run in the lab.
The master step <--> step relationship is one to many:
Each step is derived from a master step.
A master step may be used as the foundation for multiple steps.
All steps are derived from a master step and inherit any properties configured on the master step.
If you configure properties at the step level, those properties only apply to that particular step.
To understand how properties set on the master step propagate down to the step level, see Rules for Propagation of Master Step Properties.
To access the Lab Work tab and configure workflows, protocols, steps, and master steps, 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.
Rules for Propagation of Master Step Properties
In Clarity LIMS, all steps are derived from a master step and inherit any properties configured on the master step.
The rules for how properties set on the master step propagate down to the step level apply to all properties. Those configured on the Master Step Settings configuration form and those configured on the step milestones.
By default, master step properties are not set (values are null). Therefore, by default, the property settings do not propagate down to the derived steps. This means that you can set, or not set, the property freely at the step level.
If you set a property on the master step, that property is locked (a
Locked icon displays) at the step level, and cannot be modified.
In some situations, you can add to or reorder a locked property at the step level, but you can never remove the property. For example, on the Step Settings form:
You can add and reorder the column headers that display in the Sample table, even if some of those column headers are set on the master step.
You cannot remove column headers that are set on the master step.
Master Step Property Propagation Rules
When you add a master step property setting, the setting is also added to all steps derived from that master step.
When you update a master step property setting, the setting is also updated on all steps derived from that master step. This overrides any previous values that had been applied at the Protocol Step level.
When you remove a master step property setting, the setting is also removed from all steps derived from that master step. There are a few exceptions to this rule where appropriate defaults must be applied to keep the step in a valid, workable state.
The following table summarizes what happens at the step level when a property setting is removed from the master step.
Reagent kits
Master Step/Step Settings
Removed. No defaults set.
Instrument types
Master Step/Step Settings
Removed. No defaults set.
Automation trigger
Master Step/Step Settings
Reverts to default - Button
(manually triggered)
Sample grouping
Queue, Ice Bucket, Placement milestones
Reverts to default - Group by Containers
Well sort order
Queue, Ice Bucket, Record Details milestones
Reverts to default - Row
Sample fields display
Queue, Ice Bucket, Placement, Record Details milestones
No action - the last fields that were configured to display remain there.
Destination containers
Placement milestone
Reverts to default - uses the Container Type specified in the 'OutputContainerType' Process Type Attribute if set, and Tube otherwise.
(If Tube has been deleted from the system, then the first single-well Container Type in the system is used.)
Removing the last destination container also removes the ability to set placement on the Master Step (you only have the option to turn on the placement screen if there is at least one multi-well container).
Destination containers on a QC Step
Placement milestone
Reverts to default - No placement
Placement pattern
Placement milestone
Reverts to default - Row
Skip alternating rows, Skip alternating columns.
Placement milestone
Reverts to default - No
Label groups
Add Labels milestone
Reverts to default - First group configured in LIMS (first by creation date, not by name)
Step data heading
Record Details milestone
Reverts to default - Step Data
Default group of defaults
Record Details milestone
Removed. No defaults set.
Step fields display
Record Details milestone
Removed. No defaults set.
Step field order
Record Details milestone
Reverts to default - Vertical
File attachment method
Record Details milestone
Reverts to default - Manual
eSignature
Record Details milestone
Reverts to default - Off
Sample details heading
Record Details milestone
Reverts to default - Sample Table
Sample display default
Record Details milestone
Reverts to default - Collapse
Enable QC flags
Record Details milestone on QC Steps
Reverts to default - No
File Column Display
Record Details milestone on QC Steps
Reverts to default - Show
File Attachment Method
Record Details milestone on QC Steps
Reverts to default - Manual
For details on configuring step and master step property settings, see Add and Configure Master Steps and Steps.
To configure each milestone, milestone, see Step Milestones.
About Step Types and Outputs
In Clarity LIMS, steps are categorized by type, where each type is based on the requirements and goals of the step, and the outputs generated by the step. Some step types have unique interfaces and properties designed to perform specific tasks, such as adding reagent labels or pooling samples.
The step type is set on the Master Step Settings configuration form, and all steps inherit the step type of the master step on which they are based. (To understand the relationship between master steps and steps, see Steps and Master Steps.)
The step type is also displayed on the Step Settings configuration form, but as a read-only property.
Step Inputs and Outputs
All step types must have a submitted sample or derived sample input, and may generate either derived sample outputs, measurement outputs, or no outputs.
Keep in mind that only one output type is permitted. A step cannot generate both a derived sample and a measurement output. The type of step you choose determines which output generation options display. For example:
Selecting the Standard step type only displays settings for derived sample generation.
Selecting the Standard QC step type only displays settings for measurement generation.
Selecting the No Outputs step type only displays settings for no output generation.
Downstream Functionality
The type of step you choose also enables or disables certain functionality downstream. For example:
Selecting the Pooling step type displays the Pooling screen when the step is run, allowing the ability to create pools of samples. Choosing this step type allows you to configure the number of aliquots used to generate the pools.
Selecting the Add Labels step type displays the Add Labels screen when the step is run, allowing the ability to configure reagent label format options.
Rules and Constraints
When creating a master step, you must choose a step type.
When you have saved a master step configuration:
Step type cannot be changed.
The number of outputs generated can be adjusted, or switch from a fixed number to a variable number (Standard, Standard QC, Add Labels, Pooling, Analysis step types).
Step Types
The following step types are available in Clarity LIMS:
Standard
Standard steps can have a fixed or variable ratio of samples entering the step to derived samples being generated from the step. After saving, you can switch between fixed and variable.
Default step output: By default, this step type generates one derived sample for every sample tracked in the step.
Derived sample generation
Fixed – For every sample that enters the step, a fixed number of derived samples are generated.
Fixed value set to 1, configurable
The number of derived samples generated is fixed. The number cannot be changed when running the step.
Variable – For every sample that enters the step, a variable number of derived samples are generated at run time.
The number of derived samples generated can be set. This option displays on the Ice Bucket screen.
Downstream functionality: Choosing this step type disables the Pooling and Add Labels screens. Derived sample outputs require placement.
Example steps of this type: Library Normalization, Fragment DNA
Standard QC
Standard QC steps may be included in QC protocols, and may also be included as inline QC steps in other protocol types.
Standard QC steps generate sample measurements, which can have a Fixed or Variable ratio of samples entering the step to measurements being generated.
Default step output: By default, this step type generates one measurement for every sample tracked in the step.
Measurement generation
Fixed – For every sample that enters the step, a fixed number of derived samples are generated.
Fixed value set to 1, configurable
The number of derived samples generated is fixed. The number cannot be changed when running the step.
Variable – For every sample that enters the step, a variable number of measurements are generated at run time.
The number of derived samples generated can be set. This option displays on the Ice Bucket screen.
Downstream functionality: Choosing this step type disables the Pooling and Add Labels screens. You may configure a QC step to display or not display the Placement screen.
Example steps of this type: Bioanalyzer QC, NanoDrop QC, Qubit QC
No Outputs
The No Outputs step type does not generate any outputs. You can use this step type for sorting steps or for aggregate QC steps.
Default step output: This step type does not generate any outputs. (This is not configurable.)
QC aggregation is the final step in a QC protocol. This step aggregates the data from the previous Standard QC steps to determine the overall quality of the samples. At the end of the step, samples either pass QC and proceed to the next protocol, or fail QC and are rerun or removed from the workflow.
At least one aggregate QC step is required in QC protocols.
At a minimum, one Standard QC step must be run before QC aggregation can occur.
Measurement generation
None - For every sample that enters the step, 0 measurements are generated.
None (not configurable)
No measurements are generated and cannot be change this at run time.
Downstream functionality: Choosing this step type disables the Pooling, Placement, and Add Labels screens.
Example steps of this type: Aggregate QC (DNA), Aggregate QC (RNA), Aggregate QC (Library Validation)
Add Labels
This step type is used to apply a reagent label (or molecular barcode) to each sample entering the step. It may be run on multiple tubes and on multiple plates. Running an Add Labels step allows for a permanent reagent label to be added to each sample. The label data appears while running the step, in a new column in the Sample Data table on the Record Details screen.
Add Labels steps generate derived samples, which can have a Fixed or Variable ratio of samples entering the step to derived samples being generated.
Default step output: By default, this step type generates one labeled derived sample for every sample that enters the step.
Derived sample generation
Fixed– For every sample that enters the step, a fixed number of labeled derived samples is generated.
Fixed value set to 1, configurable
The number of derived samples generated is fixed. The number cannot be changed when running the step.
Variable– For every sample that enters the step, a variable number of labeled derived samples is generated at run time.
The number of derived samples generated can be set. This option displays on the Ice Bucket screen.
Downstream functionality: Choosing this step type disables the Pooling screen and enables the Add Labels screen.
Example steps of this type: Add Multiple Reagents, Adenylate Ends and Ligate Adapters, PCR Amplification.
Pooling
This step type allows for multiple samples to be pooled into a single sample/container for sequencing efficiency. The number of pools is determined while running the step. Samples typically have a label, which is used to differentiate each sample at the demultiplexing stage.
Pooling steps generate pools that are created from a Fixed or Variable number of aliquots.
Default step output: By default, for every sample that enters the step, one aliquot is used to generate pools.
Aliquot generation
Fixed – For every sample that enters the step, a fixed number of aliquots is used to generate pools.
Fixed value set to 1, not configurable
The number of aliquots used to generate pools is fixed, and displays on the Pooling screen and cannot change this value when running the step.
Variable – For every sample that enters the step, a variable number of aliquots is used to generate pools at run time.
The number of aliquots used to generate pools can be set. This option displays on the Ice Bucket screen.
Downstream functionality: Choosing this step type disables the Add Labels screen and enables the Pooling screen.
The number of pools is determined on the Pooling screen.
By default, users are prevented from pooling samples without labels or with identical labels. You can modify this on the Pooling Settings configuration screen.
Example steps of this type: Pool Samples
Analysis
Analysis steps allow data to be manipulated by scripts, for example, they may be used to trigger secondary analysis or import data post analysis.
Analysis steps behave similarly to Standard QC steps and generate sample measurements. They can have a Fixed or Variable ratio of samples entering the step to measurements being generated.
Default step output: By default, this step type generates one measurement for every sample that enters the step.
Measurement generation
Fixed– For every sample that enters the step, a fixed number of measurements are generated.
Fixed value set to 1, configurable
The number of measurements generated by the step is fixed. and cannot be changed this when running the step.
Variable– For every sample that enters the step, a variable number of measurements are generated at run time.
The number of measurements generated can be set. This option displays on the Ice Bucket screen.
Downstream functionality: Choosing this step type disables the Pooling, Placement, and Add Labels screens.
Example steps of this type: Sample History Report, Process Summary Report
Demultiplexing
This is essentially an Analysis step that deals specifically with labeled samples. It separates pools of samples based on the label assigned to those samples.
Demultiplexing steps have a Fixed ratio of samples entering the step to measurements being generated.
Default step output: By default, this step type generates one measurement for every sample that enters the step.
Measurement generation
Fixed– For every sample that enters the step, a fixed number of measurements are generated.
Fixed value set to 1, not configurable
The number of measurements generated by the step is fixed. This is not configurable and cannot be change it when running the step.
Downstream functionality: Because samples are placed automatically by a script configured on the step, choosing this step type disables the Placement screen. Choosing this step type also disables the Pooling and Add Labels screens.
Example steps of this type: BCL Conversion and Demultiplexing.
Add and 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, see User Roles and Configured Role-Based Permissions.
View Master Steps and Steps
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.
On the main menu, select Configuration.
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.
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.
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.
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.
Master Step and Step Configuration Settings
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
Step type
Master step
Output generation
Master step
Output naming convention
Master step
Automation
Automations are enabled on the master step
Automations 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
Label uniqueness
Master step
Step file placeholders
Master step
Add a Master Step
On the Lab Work configuration screen, in the upper-right corner of the Master Steps list, select Add.
Below the main navigation panel, the master step configuration form displays.
To begin, type a name for your new master step.
Configure the settings for this master step - see Configure a Master Step, below.
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, see Rules for Propagation of Master Step Properties.
Configure a Master Step
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 Type
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, see Steps and Master Steps.
The step type you choose determines which step milestones are available for configuration.
Output Generation
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, see About Step Types and Outputs.
Output Naming Convention
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
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, see Derived Sample Naming Convention Tokens.
To add a token:
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.
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.
Automation
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, see Add and Configure Automations.
To enable an automation on a master step:
In the Automation section, click the Automation configuration screen link. The Automation configuration screen opens, with the Step Automation tab active.
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.)
Select Save.
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):
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.
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.
Repeat steps 1 and 2 to configure triggers for each automation added.
Save the automation configuration.
Instrument Types
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.
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):
In the Instrument Types section, select Add.
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.
Save the master step/step.
Reagent Kits
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. See 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):
In the Reagent Kits section, select Add.
The reagent kits are added to the master step/step configuration.
If necessary, you can remove a reagent kit by clicking the X button.
Save the master step/step.
Control Types
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.
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:
In the Control Types section, select Add.
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.
Remove a control type by clicking the X button.
Save the step.
Step Milestones
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, see Step Milestones.
Add a Step
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:
On the Lab Work configuration screen, in the Protocols list, select the protocol in which to add the new step.
In the upper-right corner of the Steps list, select Add.
Below the main navigation panel, the step configuration form displays.
Type a name for the new step.
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.
Select Save (this button is not enabled until a master step is selected).
In the Protocols list, select the protocol again.
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.
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.
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.
Configure a Step
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
Modify Master Steps and Steps
In the Master Steps list, select the master step you would like to modify.
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.
Delete Master Steps and Steps
In the Master Steps list, select the master step to delete.
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.
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