By default, the name of the outputs generated by a step in the LIMS follows the naming convention of the inputs to the step.
When configuring a master 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 runtime. For example, for the Standard step type, the default naming convention resolves to the value of the {InputItemName} token (shown below).
The Tokens list provides a list of tokens you can use. You can copy and paste these directly into the Naming Convention text box.
If using multiple tokens, add a space between each entry.
Below the Naming Convention field, you will see a preview of how the token(s) will resolve.
Note that some runtime-specific items, such as dates and times, will not preview exactly as they will resolve at runtime.
NOTE:
Output names are limited to 100 characters. If a name exceeds this limit, the LIMS automatically removes characters from the middle of the name.
To pad a resolved value, add a colon (:) and a whole number to indicate the desired number of digits. For example, if {OutputItemNumber} resolves to 23, {OutputItemNumber:4} will resolve to 0023.
You can use simple tokens that will resolve to system-specified results, such as container location and LIMS ID of an output. These tokens are replaced with the appropriate value of the specified item at runtime. Tokens are case sensitive.
{InputItemName}
The name of the input used to generate the output.
{InputItemNameNoSpaces}
The name of the input used to generate the output, but with spaces removed.
{InputWellLocation}
The location or name of the well where the input resides.
To get a sub-string of the location or name of the well, add a colon (:), and one or two whole numbers to indicate the start index (zero-based, i.e. starts with 0. Inclusive) and end index (Exclusive). {InputWellLocation:<startIndex>,<endIndex>}
Example
If {InputWellLocation} has the value of A:3, the following examples show the derived values with the new format:
Lane {InputWellLocation} -> Lane A:3
Lane {InputWellLocation:0,1} -> Lane A
Lane {InputWellLocation:1,3} -> Lane :3
Lane {InputWellLocation:1} -> Lane :3
{InputContainerIdentifier}
The container identifier in which the input resides.
{InputItemNumber}
The number of the input used to generate the output, such as 7 of 20. You can pad the resolved value to a certain number of digits, and the LIMS will prefix the number with zeros. See note above.
{InputItemTotal}
The total number of inputs used to generate the outputs. You can pad the resolved value to a certain number of digits, and the LIMS will prefix the number with zeros. See note above.
{OutputItemLIMSID}
The LIMS ID of the output.
{OutputItemNumber}
The current output's absolute position within the order of all outputs, such as 9 of 40. You can pad the resolved value to a certain number of digits, and the LIMS will prefix the number with zeros. See note above.
{OutputItemTotal}
The total number of outputs generated. You can pad the resolved value to a certain number of digits, and the LIMS will prefix the number with zeros. See note above.
{OutputItemSubsetNumber}
The current output's relative position within its relative set, such as 1 of 2. You can pad the resolved value to a certain number of digits, and the LIMS will prefix the number with zeros. See note above.
{OutputItemSubsetTotal}
The fixed count of relative outputs per input. You can pad the resolved value to a certain number of digits, and the LIMS will prefix the number with zeros. See note above.
{AppliedReagentLabels}
The type of reagent label applied to the input.
{SubmittedSampleName}
The name of the sample’s related submitted sample - the original parent sample that was submitted to the LIMS.
{ProjectName}
The name of the project that contains the inputs to the step.
{ProcessLIMSID}
The LIMS ID of the step that created the outputs.
{ProcessTechnicianFullName}
The name of the lab scientist who runs the step.
{ProcessTechnicianFirstName}
The first name of the lab scientist who runs the step.
{ProcessTechnicianLastName}
The last name of the lab scientist who runs the step.
{ProcessTechnicianInitials}
The initials of the lab scientist who runs the step.
{DATE:MMM d, yyyy}
The date the step was run, according to the computer's clock.
{LIST:a,b,c}
With this variable, you can specify a comma-delimited list of words that will be used when generating output names. Clarity LIMS will cycle through the words from left to right, applying one word to each output name. When the last word has been used and there are further outputs that require names, Clarity LIMS will restart at the beginning of the list.
Complex tokens provide further flexibility with the use of parameters.
You can combine any alpha-numeric text with simple and complex tokens for highly specialized and unique output names.
When using complex tokens, you must specify parameters that will be used when the token is resolved.
You can only use one LIST and one DATE token per output string, but you can use any combination of parameters within those tokens.
With the DATE token, if you would like to include a word between parameters, enclose the word in single quotes (‘x‘).
Times and dates resolve to the time and date the process was run, according to the computer's clock.
Tokens and parameters are case sensitive.
Token
Resolves to
Usage
Example
a
AM/PM marker
The system returns the marker in the same format, regardless of how many times the token is repeated.
If runtime is in the afternoon:
a resolves to PM
H
Hour in day
(24-hour clock)
The number of times you repeat the token determines the minimum number of digits returned, with the system padding the value with zeros if necessary.
If runtime is 11 PM:
H resolves to 23
HHH resolves to 023
h
Hour in AM/PM
(12-hour clock)
The number of times you repeat the token determines the minimum number of digits returned, with the system padding the value with zeros if necessary.
If runtime is 11 PM:
h resolves to 11
hhh resolves to 011
m
Minute in hour
The number of times you repeat the token determines the minimum number of digits returned, with the system padding the value with zeros if necessary.
If runtime is 11:10:
m resolves to 10
mmm resolves to 010
s
Second in minute
The number of times you repeat the token determines the minimum number of digits returned, with the system padding the value with zeros if necessary.
If runtime is 11:10:23:
s resolves to 23
sss resolves to 023
S
Millisecond
The number of times you repeat the token determines the minimum number of digits returned, with the system padding the value with zeros if necessary.
If runtime is 1:10:23:01:
S resolves to 1
SS resolves to 01
z
Time zone - general
One token results in the abbreviated time zone. Four tokens results in the entire name.
If runtime is in the Pacific time zone, during daylight savings:
z resolves to PDT
zzzz resolves to Pacific Daylight Time
Z
Time zone - RFC 822
The system returns the time zone in the same format, regardless of how many times the token is repeated.
If runtime is in the Pacific time zone, during daylight savings:
Z resolves to -0800
Steps & Master Steps section of the LIMS Documentation explain how to create and configure steps and master steps in the LIMS.
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.
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.
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.
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.
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.
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.
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.
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).
The following step types are available in Clarity LIMS:
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.
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 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.
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
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.
To use a No Outputs step type for QC aggregation, enable QC flags on the Record Details milestone. See #configure-record-details-milestone.
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)
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.
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.
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.
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 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.
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
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.
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.
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.
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.
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
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.
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, see 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, see #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
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.
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.
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. See #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):
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.
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.
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. For details, see #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:
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.
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.
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.
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
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.
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.
| Property | Configured on Form | What Happens at Step Level |
|---|---|---|
| Setting | Options for This Step Type | Default | Description |
|---|---|---|---|
| Setting | Options for This Step Type | Default | Description |
|---|---|---|---|
| Setting | Options for This Step Type | Default | Description |
|---|---|---|---|
| Setting | Options for This Step Type | Default | Description |
|---|---|---|---|
| Setting | Options for This Step Type | Default | Description |
|---|---|---|---|
| Setting | Options for This Step Type | Default | Description |
|---|---|---|---|
| Setting | Options for This Step Type | Default | Description |
|---|---|---|---|
| Setting | Configured on | Notes |
|---|---|---|
| Step type | Default Naming Convention Token | Naming Convention Preview |
|---|---|---|
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
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.
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.
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.
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.
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.
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.
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.
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
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)
This section explains the relationship between milestones, master steps, and steps; shows how to access milestone configuration settings; and provides an overview of each milestone.
Milestones are the various stages of a step that are presented to lab users as they run samples through steps in Clarity LIMS.
Some screens (such as the Queue, Ice Bucket, and Record Details screens) display on all steps, while others only display on certain step types.
For example, the Pooling milestone only displays on steps of the Pooling type and the Add Labels screen only displays on steps of the Add Labels type. On all other step types, those milestones are disabled on both the master step and step configuration forms.
The following table shows the milestones that are available for display for each step type. For more information on step types, see #about-step-types-and-outputs.
Milestones Displayed for Step Types
| Step Type | Queue | Ice Bucket | Step Setup* | Pooling | Placement | Add Labels | Record Details |
|---|---|---|---|---|---|---|---|
*While the Step Setup screen is available for display on all step types, it is optional and does not display by default. To enable the Step Setup screen, you must first add file placeholders on the master step. For details, see #configure-step-setup-milestone.
You can configure milestone settings on the master step and step configuration forms.
When switching between the step and master step configuration forms while viewing or editing a milestone, you are returned to the parent step/master step form. You need to select the milestone name again to open its settings form.
Similarly, if you wish to return to the step or master step settings form, select the parent master step or step tab.
To configure a milestone:
Select it to open its settings form.
When configuring milestones on master steps and steps, consider the following details:
If you configure a list of items at the master step level—for example, expanded view fields, instrument types, reagent kits—the order in which they are listed on the master step is overwritten by the order set at the step level. Set the order of any list at the step level. This includes the order of the Sample table column headers.
If you remove configured settings from a master step, those settings on the related steps revert to their default values. The exception is 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.
Settings configured at the step level 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
When running samples through a step, the first screen that displays is the Queue screen. This screen provides a sample table to select samples to be placed into the Ice Bucket, reserving them for use.
The following components of the Queue Sample table are configurable on the Queue Settings form:
The Sample table column headers
The Sample table expanded view fields
Default grouping and well sort order of Sample table
On the Queue Settings form, configure the column headers that display in the Sample table, and the order in which they display.
Note the following:
No default column headers are configured at the master step level.
When configuring column headers on a new step, several default column headers will display. You can remove these, but the table must have at least one field remaining (this may be set on either the master step or the step).
Expanded view fields are hidden by default in the Sample table. These fields contain additional details about the samples in the queue. At run time, choose to display these details by clicking the Show/Hide Details button.
On the Queue Settings form, in the Expanded View Fields section, you can select additional fields to add to the body of the Sample table.
Note the following:
No default expanded view fields are configured at the master step or the step level.
If expanded view fields are configured at the master step level, they display as locked at the step level and cannot be removed. You can modify the order in which the locked fields display.
Expanded view fields are available for display in multiple milestone screens. The configuration options set in each milestone are specific to that milestone. You may choose to configure the expanded view fields differently in other milestones.
On the Queue screen, samples are grouped by Container and sorted by well Row by default.
On the Queue Settings form, in the Defaults section, you can modify these settings if necessary.
Samples move from the Queue into the Ice Bucket, where they are reserved for use for 30 minutes. The Ice Bucket screen displays for all step types. It comprises a Sample table that displays information about the samples entering the step.
The following components of the Ice Bucket screen are configurable on the Ice BucketSettings form:
The Sample table column headers
The Sample table expanded view fields
Default grouping and well sort order of Sample table
On the Ice Bucket Settings form, configure the column headers that display in the Sample table, and the order in which they display.
Note the following:
No default column headers are configured at the master step level.
When configuring column headers on a new step, several default column headers will display. You can remove these, but the table must have at least one field remaining (this may be set on either the master step or the step).
Expanded view fields are hidden by default in the Sample table. These fields contain additional details about the samples in the Ice Bucket. At run time, choose to display these details by clicking the Show/Hide Details button.
On the Ice Bucket Settings form, in the Expanded View Fields section, you can select additional fields to add to the body of the Sample table.
Note the following:
No default expanded view fields are configured at the master step or the step level.
If expanded view fields are configured at the master step level, they display as locked at the step level and cannot be removed. However, you can modify the order in which the locked fields display.
Expanded view fields are available for display in multiple milestone screens. However, the configuration options set in each milestone are specific to that milestone; you may choose to configure the expanded view fields differently in other milestones.
By default in the Ice Bucket screen, samples are grouped by Container and sorted by well Row.
On the Ice BucketSettings form, in the Defaults section, you can modify these settings if necessary.
The Step Setup screen is an optional screen. By default, it does not display at run time.
This screen lets you provide the lab scientist running the step—and provide Clarity LIMS—with access to files before samples are placed. You can then configure step automations that parse these files and use the information to place samples into destination containers, based on the result file specifications.
If you enable the display of the Step Setup screen (you can enable it on any step type), it displays immediately after the Ice Bucket screen.
The Step Setup Settings screen allows you to do the following:
Add file placeholders that will be populated at run time. Configure these on the master step.
After you have added file placeholders, you can then enable the display of the Step Setup Settings screen at run time. You can configure this on the master step or the step. However, as with all master step settings, if you enable the screen on the master step, it displays on all steps derived from that master step.
Configure the attachment method for each file added—manual or automatic. You may configure this on the master step or the step.
To enable the Step Setup screen, you must first configure one or more file placeholders on the master step.
On the Lab Work tab, in the Master Steps list, select the master step on which you would like to configure the file placeholders.
Select the Step Setup milestone.
In the File Placeholders section, select Add.
Type a name for the file placeholder.
[Optional] You can copy and paste tokens from theTokens list into the name field. For details, see Derived Sample Naming Convention Tokens.
Enter instructional text.
To set the attachment method, select the Attachment toggle switch to set the file attachment method.
If you set the attachment method to Auto, configure a step automation to generate and attach the file. For details, see #add-and-configure-automations.
To remove a file placeholder, select the X button.
On the Lab Work tab, in the Master Steps or Steps list, select the master step or step on which you would like to configure Step Setup file placeholders.
Select the Step Setup milestone.
At the top of the Step Setup Settings screen, select the toggle switch to enable the Step Setup screen. The screen now displays at run time.
When the Step Setup screen is enabled, it becomes available for selection as an automation trigger location. If you configure an automation trigger location on the Step Setup screen, the Step Setup screen cannot be disabled.
When you create a step and choose the Pooling step type, the Pooling milestone is enabled. When running the step, the Pooling screen allows the lab scientist to create pools of samples.
The following components of the Pooling screen are configurable on the Pooling Settings form.
Enable and disable label uniqueness to control whether samples with the same labels, or no labels, may be pooled together. This must be configured on the master step.
Configure defaults for sample grouping and well sort order. You can configure these settings at the master step or step level.
Select the Label Uniqueness toggle switch to turn label uniqueness on and off.
When Label Uniqueness is On (default setting), samples with the same labels cannot be pooled together.
When Label Uniqueness is Off, samples with the same label or no labels may be pooled together.
Save your changes.
On the Pooling screen, by default samples are:
Grouped by Container
Sorted by well Row (A1, A2, A3, and so on)
Placed by Column (A1, B1, C1, and so on)
You can modify these settings if necessary.
The Placement screen is used for QC steps and for steps that generate derived samples. When the screen displays at run time, it allows manual placement of samples into the destination container.
Note the following:
In tube-only workflows, the Placement screen is disabled by default and samples are automatically placed. This is true for all step types, except Add Labels steps, in which a tube rack Placement screen displays to allow for manual placement of samples.
In the following step types, no sample placement occurs. The Placement screen is disabled and it does not display at run time. Analysis steps
Aggregate QC steps
Standard steps where derived sample generation is set to None.
The Placement Settings form allows for the following configuration.
Turn off the Placement screen and have samples placed automatically into corresponding wells of the destination container (source and destination containers must be the same).
Disable the Placement screen so that it does not display at run time and cannot be viewed. You can only do this on QC steps where no sample placement is required—ie, where samples remain in the same container throughout the step. The step cannot have destination containers configured.
Configure the destination containers that are permitted on the step.
Configure the sample placement defaults—grouping, well sort order, placement pattern, and whether to skip alternate rows/columns in the container.
When the Placement Screen toggle switch is enabled, the Placement screen displays at run time. The lab scientist manually places samples into the destination container.
To turn off the Placement screen:
Select the toggle switch to turn off the Placement Screen and enable autoplacement of samples.
At run time, bypass the Placement screen. If necessary, the user can return to the screen (by selecting its tab) to view placement details.
When the Placement Screen is disabled, the milestone label changes to Auto-Placement. However, if the source and destination containers are not of the same type, Clarity LIMS determines that autoplacement cannot occur and reenables manual placement so that samples can be placed.
Destination containers are the containers into which samples are placed at run time. These containers display to the user in a drop-down list on the Ice Bucket screen. The selected container is then used to set up the subsequent Placement screen.
On the Pooling screen, by default samples are:
Grouped by Container
Sorted by well Row (A1, A2, A3, and so on)
Placed by Column (A1, B1, C1, and so on)
Placed into all container wells - no rows or columns are skipped.
You can modify these settings if necessary.
When you create a step and choose the Add Labels step type, the Add Labels milestone is enabled. When running the step, the Add Labels screen allows the lab scientist to add a reagent label (also known as index or molecular barcode) to each sample.
Note the following:
To add a label group to a step, you must have first configured the label group on the Consumables > Labels configuration screen. For details, see #add-and-configure-labels-and-label-groups.
When you create an Add Labels step, the first label group configured in the system is added to the step automatically.
There must be at least one label group defined on either the master step or the step.
You cannot remove the last label group from the step/master step.
You cannot remove label groups added on the master step from the step.
Label groups are listed in alphanumeric order. The order is not modifiable.
The well sorting setting configured on the #configure-placement-milestone is also applied to the Add Labels screen.
Label groups are the only configurable components on the Add Labels Settings form.
The Record Details screen is where data are tracked on the step at run time. It includes information about the step, files generated by or uploaded to the step, e-Signature sign-off (if enabled), and information about the samples in the step.
The following components of the Record Details screen are configurable on the Record Details Settings form:
The step-level information (step data) tracked on the step. You can also change the heading of the step data section, and set a default value for the Group of Defaults configured on the master step.
Step file placeholders for files that is attached to the step at run time, and their attachment method.
The sample-level information tracked and displayed in the Sample table
Electronic signatures - this panel only displays if you have enabled the clarity.eSignature.enabled property.
The Step Data section of the Record Details screen allows you to track and display step-level data at run time, specifically the master step fields associated with the step.
On the Record Details Settings form, you can configure the following:
The heading that displays at the top of the section.
The default value for the Group of Defaults that displays in the upper-right corner of the screen.
The step data fields that display, and the order and layout in which they display. Note the following:
The default heading is 'Step Data Table'.
You are not required to set a default value for the Group of Defaults.
You are not required to add master step fields or multiline text fields.
When step fields and/or multiline text fields are added, they are arranged vertically by default.
As you configure the step data, the Preview area on the right updates to show you how the configuration displays at run time on the Record Details screen.
NOTE: Multiline text fields are much wider than step fields and always display below them on the Record Details screen. For this reason, they are configured separately.
*Groups of defaults and master step fields are defined on the Custom Fields > Master Step Fields configuration screen. For details, see #add-and-configure-custom-fields.
Configuring file placeholders allows you to attach sample measurement files to a step at run time. For example, you may want to attach an instrument input files or sample sheets, a QC measurement file, a log file, run report, or lab tracking form. Files may be manually uploaded or automatically generated and attached using a script. The default attachment method is manual attachment.
Note the following:
Configure step file placeholders on the master step. You cannot configure or modify these at the step level. A lock icon on the Step Settings form indicates this.
Create a placeholder for each file to be attached.
Configure the attachment method—Manual or Auto, at the master step or the step level. If the attachment method is set on the master step, it cannot be changed at the step level (lock icon displays on the Step Settings form).
The default attachment method is Auto.
In the Sample Table section, if the File Column Display is set to Hide, the Attachment toggle switch is set to Auto and is disabled. To manually attach files in the Sample table, the column must be visible.
The attachment method applies to the shared sample measurement files generated. If you need to set the attachment method for individual files generated for each sample, you can use the API to do this. For details, see API Reference.
At the bottom of the Record Details form, the Sample Table section lets you view and track data on your samples at run time.
On the Record Details Settings screen, you can configure the following components of the Record Details screen Sample table:
The table heading. (Default table heading is 'Sample Table'.)
The display of the QC flags field (when this field is enabled, mark samples with a QC pass or fail flag.
The default display of the Sample table listing. The default view is Collapsed - for faster loading time of the sample list.
The table columns that display in the Sample table, and the order in which they display.
The File Options Column and the File Attachment Method toggle switch only display on the Record Details Settings screen on steps that generate measurements. These settings allow you to choose if you want to display a column for sample files and choose how these files are attached to the step (manually or automatically).
Note the following:
You can enable QC flags on any step type that allows you to mark a sample with a pass or fail flag.
By default, QC flags are enabled on Standard QC steps. This setting is locked and cannot be changed.
By default, QC flags are disabled on Analysis steps. This setting is locked and cannot be changed.
Enable QC flags on a No Outputs step to use the step for QC aggregation.
Sample groupings are collapsed by default to optimize screen loading time, but can also be expanded by default.
If the step generates measurements, Sample File Options display. These allow you to choose if you want to view a column for Sample Files and choose how these files are attached (manually or automatically).
When configuring the Sample table:
No default column headers are configured at the master step level.
When configuring column headers on a new step, several default column headers display. You can remove these; however, the table must have at least one field remaining (this may be set on either the master step or the step).
The Sample table displays in multiple milestone screens. However, the configuration options set in each milestone are specific to that milestone; you may choose to configure other milestone Sample tables differently. The unique aspect of the Record Details Sample table is that the derived sample and submitted sample fields can be written to (according to their respective step type).
Clarity LIMS provides the ability to configure a step such that it requires sign-off by electronic signature (eSignature) before it can be completed.
Steps that have eSignature enabled display an eSignature enforcement button on the Record Details screen, and require valid eSignature credentials (username and password) to be entered.
Next Steps cannot be viewed until these credentials have been entered with eSignature signing permission.
Until the step has been completed, any changes made to the step will again require an eSignature sign off.
All eSignature events, successful or not, are recorded with the step and in the audit trail.
The eSignatures Review configuration panel displays on the Record Details Settings screen only if the clarity.eSignature.enabled property is enabled.
If the panel is enabled, you can configure electronic signatures (e-signatures) on a step or master step. This means that samples in the step cannot move forward (Next Steps button is disabled) until an e-signature has been entered with the appropriate role-based permission.
Milestone settings configured on the master step remain locked on all steps derived from the master step. In this scenario, the milestone displays on the step configuration form with a Locked icon, indicating that these settings are not configurable at the step level.
NOTE: As with all other step settings, if you enable e-signatures on a master step, the setting displays with a Locked icon and is enabled on all steps derived from that master step.
Standard
Standard QC
Aggregate QC
Add Labels
Pooling
Analysis
Demultiplexing
