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In Clarity LIMS, a workflow is a set of protocols arranged in a sequence that corresponds to the way in which work is performed in the lab. This page explain how to create and configure your workflow.
After protocols are created and configured, add them to workflows that represent how samples move through your lab.
In Clarity LIMS, use the Lab Work configuration screen to view, add, and configure the workflows used in the lab. For an overview of this screen, see Lab Work.
To access the Lab Work tab and configure workflows, 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 workflows configured in the LIMS, along with the protocols and steps they contain. You can quickly see which workflows are active, which are archived, and which do not yet have protocols assigned to them.
To view workflow details:
On the main menu, select Configuration.
Select the Lab Work tab.
In the Workflows list, select a workflow to highlight it.
The Protocols list updates to show all protocols included in the workflow. These are highlighted and displayed sequentially at the top of the list. A dashed line separates these workflow protocols from the comprehensive list of all protocols in the system.
The Steps list updates, highlighting the steps included in the highlighted protocols.
The Master Steps list updates, highlighting the master steps on which the highlighted steps are based.
Note: You can also select a protocol, step, or master step to view the related workflows.
Below the main navigation panel, review the workflow configuration form. This displays the name of the workflow and its status.
The status of a workflow may be Pending, Active, or Archived. The following table provides an overview of each status setting and describes the implications of each.
The following section shows how to add a workflow to the LIMS and add protocols to it. When configuring workflows, keep the following in mind:
You are not required to add protocols immediately. If you prefer, you can create empty Pending workflows and assign protocols to them later.
You can only activate a Pending workflow if it contains at least one protocol.
When adding protocols to a workflow, reordering protocols within a workflow, or removing protocols from a workflow, your changes are autosaved. You do not have to select Save after every modification.
You cannot add empty protocols to a workflow. The protocol must include steps.
On the Lab Work configuration screen, in the upper-right corner of the Workflow list, select Add.
Below the main navigation panel, the workflow configuration form displays.
To begin, type a name for your new workflow.
Select Save.
The workflow is saved in a Pending state, and displays in the Workflow list of the main navigation panel.
In the Workflow list, select the workflow.
In the Protocol list, locate the first protocol to include and select Add.
The protocol is added to the workflow and displays at the top of the Protocol list. The 1 indicates that this is the first protocol in the workflow.
Repeat step 2 until you have added all required protocols to the workflow.
To remove a protocol from the workflow, select its Remove button.
Drag and drop to reorder protocols within the workflow.
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.
To view or modify a protocol, select the protocol to display its configuration form below the main navigation pane.
You can now save the workflow as a Pending workflow.
- or -
Select Activate to use this workflow immediately.
NOTE: After you activate a workflow, you cannot modify or delete it.
On the Lab Work configuration screen, in the Workflow list, select the Pending workflow to modify or activate.
Make your changes and select Save to save the workflow as a Pending workflow.
-or-
Select Activate to change the workflow status to Active and begin using the workflow.
When modifying or activating workflows, keep the following in mind:
You cannot activate empty workflows.
You can only modify a workflow while it remains in the Pending state. That is:
You cannot add a protocol to an Active or Archived workflow.
You cannot remove a protocol from an Active or Archived workflow.
You cannot rename or reorder protocols in an Active or Archived workflow.
You cannot delete protocols included in Active or Archived workflows.
While you cannot delete workflows after they have been activated, you can archive them. This makes them temporarily unavailable for use in the lab. You can reactivate an Archived workflow at any time.
To archive a workflow:
On the Lab Work configuration screen, in the Workflow list, select the Active workflow to archive.
In the Workflow Settings area, select Archive. Select Save.
To reactivate an archived workflow:
On the Lab Work configuration screen, in the Workflow list, select the Archived workflow to reactivate.
In the Workflow Settings area, select Activate. Select Save.
On the Lab Work configuration screen, in the Workflow list, select the pending workflow to delete.
On the workflow configuration form, select Delete.
Confirm the workflow deletion:
To proceed with the deletion, select Delete.
To cancel the deletion, select Cancel.
You can only delete a workflow while the workflow remains in the Pending state. You cannot delete Active or Archived workflows.
| Status | What It Means in the Lab | Configuration Implications |
|---|---|---|
Active
These workflows are currently in use - or available for use - in the system.
Samples can be assigned to these workflows so that lab scientists can work on them in Lab View.
Active workflow cannot be modified or deleted.
Protocols in an Active workflow cannot be reordered.
Protocols in an Active workflow can be modified or deleted, and modify their steps.
Active workflow can be made unavailable for use by changing its status to Archived. Samples that are currently queued or in progress for the workflow can complete it, but new samples cannot be added.
When a workflow in Active state is saved, it can only transition to the Archived state.
Pending
These workflows have not yet been activated.
These workflows are not available for use in the lab.
These workflows do not display in Lab View.
Samples cannot be added to these workflows from the Projects and Samples screen.
Pending workflows can be modified, for example, by renaming them, or by adding, modifying, or removing, modifying protocols.
Pending workflows can be activated.
Archived
These workflows are currently not in use in the system.
These workflows do not display in Lab View.
Samples cannot be added to these workflows from the Projects and Samples screen.
Samples that are currently queued or in progress for an Archived workflow can complete it.
After a workflow is saved in Archived state, it can only transition to the Active state.
An Archived workflow cannot be modified or deleted.
In an Archived workflow, protocols cannot be reordered.
Use the Lab Work configuration screen to model the workflows, protocols, and master steps used in the lab on the Lab Work configuration screen.
To access the Lab Work configuration screen, the Configuration:update permission is required. Without this permission, the Lab Work tab is not visible.
By default, only the administrator role has the Configuration:update permission. For more on user roles and permissions, see User Roles and Configured Role-Based Permissions.
On the main menu, select Configuration.
Select the Lab Work tab.
The main navigation panel lists the workflows, protocols, steps, and master steps configured in Clarity LIMS. From here, complete the following actions as needed:
View the relationships between workflows, protocols, steps, and master steps.
View workflow, protocol, step, and master step configuration in the form beneath the navigation panel.
See the status of workflows (pending, active, or archived).
Add and modify workflows, protocols, steps, and master steps.
Select a workflow, protocol, step, or master step to view related configuration items in the other lists.
Selecting a protocol highlights the following items:
All workflows that include the selected protocol are highlighted.
All steps in the selected protocol are highlighted.
All master steps from which the steps are derived are highlighted.
Selecting a workflow highlights the following items:
All protocols in the workflow, which display sequentially at the top of the Protocols list.
All steps in those highlighted protocols.
All master steps from which the highlighted steps are derived.
Zoom out in the browser to maximize the number of items visible in the lists. Drag the lower edge of the panel to see more list items.
The best practice method for creating and configuring lab work components in Clarity LIMS is as follows.
Create and configure master steps.
Create and configure protocols.
Create and configure steps, adding them to the appropriate protocols, and using the master steps Create and configure workflows, adding required protocols.
Create and configure workflows, adding required protocols.
While these are the recommended steps, you can create protocols first, or create workflows and add the protocols later. However, before creating a step, you must select the protocol in which to add the step, and the master step on which to base its configuration.
When working with workflows, protocols, steps, and master steps, there are some restrictions you should be aware of. These restrictions are summarized below, and are also described in the articles that discuss the configuration details of each component.
The following section also lists the restrictions associated with custom fields and automations.
Custom fields are configured on the Custom Fields configuration screen. Refer to Custom Fields.
Step automations are configured on the Automations configuration screen. Refer to Automations.
In Clarity LIMS, a protocol is a set of steps that must be performed in a specific sequence, as part of a lab's workflow. This section explain how to create and configure your lab protocols.
Clarity LIMS includes preconfigured protocols, each containing a series of steps through which a sample must pass. You can create custom protocols, adding steps that represent the steps that are run in your lab. You can then add the protocols to workflows so that lab users can work with them in Lab View.
Use the Lab Work configuration screen to view, add, and configure the protocols used in the lab. For an overview of this screen, see #lab-work-overview
To access the Lab Work tab and configure protocols, the Configuration:update permission is required. By default, only the Administrator role has this permission. For details, see User Roles and Configured Role-Based Permissions.
On the main menu, select Configuration.
Select the Lab Work tab.
The Workflows, Protocols, Steps, and Master Steps navigation panel displays.
In the Protocols list, select a protocol to highlight it:
The Workflows list updates, highlighting the workflows that contain the selected protocol.
The Steps list updates, highlighting the steps included in the selected protocol.
The Master Steps list updates, highlighting the master steps on which the highlighted steps are based.
Below the main navigation panel, review the protocol configuration form.
This displays the name of the protocol and its settings.
The Protocol Settings area captures important information about the protocol—the date it was created, the date it was last modified, and other settings that determine how the protocol is used in the lab. The following table summarizes these settings.
When adding and configuring protocols, note the following details:
When adding steps to a protocol, reordering steps, or removing steps from a protocol, changes are autosaved. You do not need to select Save after every modification.
When #configure-next-steps, you must select Save to save your changes.
To add a protocol:
On the Lab Work configuration screen, in the upper-right corner of the Protocols list, select Add.
Below the main navigation panel, the protocol configuration form displays.
To begin, type a name for the new protocol.
Select the settings for this protocol (For details, see #protocol-settings):
Select whether this is a QC or Non-QC protocol.
Select the Protocol Type:
If you are adding a QC protocol, this automatically is set to QC.
If you are adding a Non-QC protocol, select the type from the drop-down list.
In the Capacity field, enter the sample capacity of this protocol.
[Optional] To temporarily hide the protocol from Lab View, use the Show in Lab View? slider. Change the setting to No.
Select Save. The new protocol displays at the bottom of the Protocols list. You can move it to a different position in the list by dragging and dropping.
To drag and drop on a mobile or touch-screen device, touch and hold the item you wish to drag. After a moment, the item appears to lift off the page and its color changes to white. You can then drag the item and drop it into its new position.
You can also copy a protocol and then modify the copy for use in other workflows. See #copy-protocols.
This section provides an overview of the step creation process. For detailed information on steps and master steps, and step-by-step instructions for configuring them, see#add-and-configure-master-steps-and-steps.
To add a step to a protocol:
In the Protocols list, select the protocol.
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 Step list, select the master step upon which to base the new step.
Select Save (this button is not enabled until you have selected a master step).
In the Protocols list, select the protocol again.
The step you added displays at the top of the Step list.
If this is a non-QC protocol, a 1 is in front of the step name, indicating that this is the first step in the protocol.(QC steps are not numbered as they are typically not sequential.)
In the Master Step list, the master step upon which the step is based is also highlighted.
Repeat steps 1–5 to add more steps to the protocol.
To delete a step, select it and select the Delete.
To reorder steps within the protocol, simply drag and drop them.
To drag and drop on a mobile or touch-screen device, touch and hold the item you wish to drag. After a moment, the item appears to lift off the page and its color changes to white. You can then drag the item and drop it into its new position.
Select Save.
You can now configure the order in which the steps are run, and the method used to assign and run 'next steps.' See #configure-next-steps.
When configuring non-QC protocols, the protocol configuration form includes a Next Steps table. This allows you to configure the sequence in which steps are run in the protocol. This table does not display for QC protocols, because the steps in a QC protocol are typically not sequential.
In the table:
Each row represents a numbered step in the protocol.
Each column represents a 'permitted next step' for each of the numbered steps.
The cells at each row/column intersection indicate which steps are potential permitted next steps for the step represented in that row.
If there is an icon in the cell (an X or a checkmark), the step represented by that column may be selected or deselected as a permitted next step.
Previous and current steps cannot be selected as permitted next steps, and are shown as nonselectable cells.
The bottom two rows determine whether the next steps are started and assigned manually or automatically. Manual is the default setting.
To configure next steps
In the Next Steps table, select a cell to select (or deselect) one or more permitted next steps.
In the Start Next Step and Assign Next Step rows, select a cell to switch between Manual and Automatic.
To assign a next step automatically, you also need to configure an automation and add it to the step. For details, see #add-and-configure-automations.
When configuring QC protocols, the protocol configuration form includes a QC Filters section. This section lets you configure QC logic to make sure that only certain samples are queued for each QC step. Typically, QC protocols contain multiple nonsequential steps that culminate in a QC aggregation step.
QC filters are composed of two drop-down lists.
The first list refers to the QC flag assigned at run time:
Passed means that a pass QC flag was assigned to the sample at run time.
Failed means that a fail QC flag was assigned to the sample at run time.
Did not pass means that the sample did not run, or received a fail QC flag, at run time.
Did not fail means that the sample did not run, or received a pass QC flag, at run time.
The second list refers to the master steps from which the steps are derived:
All master steps used in the protocol are included in the list. Together, these form a statement (for example, Failed Bioanalyzer).
Each statement may be followed by an'AND', which allows you to create an additive statement.
Statements are separated by an'OR', which allows you to create mutually exclusive statements.
Together, these AND/OR statements create the QC filter logic for a given step.
For example:
You may want the NanoDrop QC queue to show samples that have not passed NanoDrop QC (ie, they did not run, or received a fail QC flag), and that have passedBioanalyzer QC.
If the procedures dictate that all samples must have passed Bioanalyzer QC and NanoDrop QC, use an 'AND' statement to ensure samples are not queued for a QC aggregation step unless they have passed both of these steps.
If your lab procedures dictate that all samples must have passed Bioanalyzer QC or NanoDrop QC, use an 'OR' statement to ensure samples are not queued for QC aggregation unless they have passed one of these steps.
You may want to rename a protocol, or add or reorder steps. Some modifications are only permitted if the protocol is not included in an active or archived workflow.
NOTE: We recommend that you do not modify or delete the preconfigured protocols without first consulting the Clarity LIMS Support team.
To modify a protocol:
In the Protocols list, select the protocol.
Make your changes and select Save.
Note the following details:
You can rename protocols in pending, active, and archived workflows.
For non-QC protocols, you can modify the protocol type. For example, you can change a Sample Prep protocol to a Library Prep protocol.
You can choose to hide or show the protocol in Lab View.
You cannot change a QC protocol to a non-QC protocol, and vice versa.
You cannot add, reorder, or delete steps if the protocol is included in an active or archived workflow.
To delete a protocol:
In the Protocols list, select the protocol.
On the protocol configuration form, select Delete.
Note the following details:
You cannot delete a protocol if it is included in an active or archived workflow. In this case, the Delete button is not enabled.
If you delete a protocol, the steps it contains, and the master steps on which those steps were based are not deleted.
After you have added and configured a protocol, you can copy it and then modify the copy for use in other workflows. This is useful if you have multiple protocols with similar base configuration, as it saves you having to recreate each one from scratch.
To access the Lab Work tab and configure protocols, the Configuration:update permission is required. By default, only the Administrator role has this permission. For details, see User Roles and Configured Role-Based Permissions.
When you copy a protocol, all of its steps are also copied—along with any step-level fields, automations, reagents, controls, and instruments configured on those steps.
You can also create copies of the master steps, or you can reuse the same master steps.
Copying master steps does copy step-level fields.
Reusing master steps does not copy step-level fields.
If a copied master step has custom field default values that refer to other steps within the protocol, update those values to refer to the copied steps. See #update-custom-field-default-on-copied-master-steps.
On the main menu, select Configuration.
On the LIMS configuration screen, select the Lab Work tab.
In the main navigation panel, in the Protocols list, select the protocol to copy.
Below the navigation panel, select Copy.
The Copy Protocol Options dialog opens. This dialog provides two options:
Append name with—This option lets you specify text to be appended to the protocol name (default is _copy). This text also is appended to the copied step names, and to the master step names if you also choose to copy those. Note: Copied step-level field names do not have the text appended.
Copy Master Steps?—This option lets you choose to reuse the same master steps (this is the default behavior), or create copies of the master steps.
Selected an option and then select Continue to copy the protocol and steps.
The copied protocol displays in the Protocols list, and is selected along with its related steps and master steps.
Below the navigation panel, the protocol configuration form displays. You can work with the protocol and its steps just as you would with any other protocol/steps in the system.
If you have configured a custom field default on the master step you are copying, and the default value refers to the name of another step within the protocol, you must update that default value on the copied master step, so that it refers to the appropriate step in the copied protocol. The default values are not automatically updated to refer to the copied step names.
Similarly, if you have configured a script or logic that uses custom field defaults that refer to another step within the protocol, you must update those default values on the copied master step.
For example, in a QC protocol:
The Aggregate QC step has various 'Copy Task' UDFs defined - eg, Copy Task 1 - Source Step and Copy Task 2 - Source Step.
The values of these fields are determined by other QC steps within the protocol.
The script that is configured on the QC Aggregate step references those QC step names, locates the specified custom field values from the steps, and uses them to determine QC results.
If the QC protocol is copied, the copy of the master step on which the Aggregate QC step is based must be updated so that the custom field default values refer to the appropriate steps within the protocol.
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.
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.
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.
Consumables are the , , , and other equipment used in the lab. Configure these items in Clarity LIMS and associate them with specific master steps. When the steps are run in the LIMS, the consumables used are recorded.
This section describes how to add and configure the control samples used in your lab, and enable them for use on specific master steps.
Controls behave like special samples that can be enabled at specific points in your workflows. However, unlike samples, controls do not need to belong to a project and do not have to be assigned to a workflow.
Add the control samples used in the lab to Clarity LIMS, and enable them for use on steps. When running a step on which control samples are enabled, the lab scientist can add those control samples to the Ice Bucket.
All users logged into the LIMS can access the Controls configuration screen. However, their user permissions determine what they are allowed to do in this screen.
By default, only the Administrator role has the Configuration:update permission. For more on user roles and permissions, see and .
There is no limit to the number of controls you can create or the number of steps on which you can enable a control. When adding a new control, you are not required to enable it on a step. You can do this action at any time.
Control sample/step configuration is bidirectional. Enable a control sample on a step in the following situations:
When adding control samples on the Controls configuration screen (described in this section).
On the main menu, select Configuration.
On the configuration screen, select the Consumables tab, then select Controls.
On the Controls configuration screen, select New Control.
Type a name for the control sample. This name displays in queues of steps on which controls are enabled. This field is the only required field.
[Optional] Enter additional details for the control sample:
Supplier—Enter the commercial vendor name. If this control sample was made in the lab, enter in-house.
Cat. #—Enter the catalog number.
Website—Enter the website of the commercial vendor. If it is an in-house control, enter the URL of the internal web page that contains details of the in-house control. When viewing details for the control sample, lab scientists can select the link to open the web page in a new browser window.
In the Control Use section, note the following defaults:
The status of the new control is set to Active.
The new control is not flagged as a single step only control.
Select Save.
The new control displays in the Control Samples list.
Enabling controls on steps makes them available for use in the lab.
To enable a control sample on a step, complete the following steps:
On the Controls configuration screen in the Control Samples list, select the control to enable on steps.
In the Control Use area, select the protocol that includes the step on which you want to enable the control. Type the first few letters of the protocol to filter the list.
In the adjacent list, select the step on which you want to enable the control.
Enable the control on additional steps, if necessary.
Select Save.
The Control Samples list now indicates that the control has been enabled on a step. Hovering over the 'On 1 step' label displays a popup that shows the protocol and step involved.
The status of a control may be Active or Archived.
Active controls are controls that are in use or available for use in the lab workflows.
Archived controls are controls that are not currently available for use in the lab workflows.
Lab users do not see archived controls when initiating steps.
Configuration details for archived controls are saved, so it is easy to reactivate them.
In the Control Samples list, archived controls are listed in their own group. Select the arrow to expand the list and view control details.
Single step only controls do not progress in workflows. When completing a step, lab users do not need to select a Next Step for these controls.
Use this option to represent single-use, disposable samples such as QC standards, molecular weight ladders, and blanks.
In the Control Samples list, select the control to archive.
On the Status of Control slider, select Archived.
Select Save.
In the Control Samples list, expand the archived control group and select the control to be activated.
On the Status of Control slider, select Active.
Select Save.
When deleting controls, keep the following details in mind:
You can only delete control samples that have not been used in a step.
If a control sample has been recorded in a step, or is currently being used in a step, you cannot delete it. The Delete button is not enabled.
On the Controls configuration screen in the Control Samples list, select the control to delete.
In the Control Sample Details area on the right, select Delete.
This section describes how to add and configure the reagent kits and lots used in your lab, and enable them for use on specific master steps.
Add the reagent kits and lots used in the lab to Clarity LIMS and enable them for use on specific steps. When lab scientists run samples through a step, they can record the reagent lots used.
All users logged into Clarity LIMS can access the Reagents configuration screen. However, their user permissions determine what they are allowed to do in this screen.
By default, only the Administrator role has the Configuration:update permission. For more on user roles and permissions, see and .
Enabling kits on steps makes them available for use in the lab. When running those steps, the reagent lots used are recorded
When a new reagent kit is added, it is not a requirement to enable it on a step. It can be enabled at any time.
Reagent kit/step configuration is bidirectional. Enable a reagent kit on a step in the following situations:
When adding reagents on the Reagents configuration screen (described in this section).
NOTE: The Configuration:update permission is required to add new reagent kits to Clarity LIMS.
On the main menu, select Configuration.
On the configuration screen, select the Consumables tab, then select Reagents.
On the Reagents configuration screen, select New Reagent Kit.
Type a name for the reagent kit. This name displays in queues of steps on which use of the reagent kit is enabled.
Enter details for the reagent kit to help with future reordering:
Supplier: Enter the commercial vendor name.
Cat. #: Enter the catalog number.
Website. Enter the website of the commercial vendor. When viewing details for the reagent kit, select the link to open the web page in a new browser window.
In the Reagent Kit Use section, the status of the new kit is set to Active. This status means that it is available to be used in the lab (after it is enabled on steps).
Select Save to add the new reagent kit.
The new kit displays in the Reagent Kits list.
On the Reagents configuration screen, in the Reagent Kits list, select the kit to enable on steps.
In the Reagent Kit Use area on the right, compete the following actions:
Select a protocol from the drop-down list. Type the first few letters of the protocol to filter the list.
In the adjacent list, select the step on which to enable the reagent kit.
Enable the control on additional steps, if necessary.
Select Save. The Reagent Kits list now indicates that the kit has been enabled on the selected steps.
On the Reagents configuration screen in the Reagent Kits list, select the kit for which you would like to add a new lot.
Below the Kit Details in the Lots area, select New Lot.
In the Lot Details area, enter the lot name.
[Optional] Enter additional details about the lot, such as the lot number and expiry date.
Specify a storage location and add notes about the reagent lot. For example, use this field to note why a lot is being archived).
Clarity LIMS automatically populates the LIMS ID and Created and Modified dates.
Select Save.
The new lot displays in the Reagent Kits list.
By default, when a new lot is added, the status is Pending. The Status of Reagent Lot slider at the bottom of the Lot Details area controls the lot status.
The status of a reagent kit may be Active or Archived. The status of a reagent lot may be Pending, Active, or Archived.
Note the following details about reagent kit status:
Active reagent kits are in use, or are available for use, in the lab workflows. By default, when a new kit is added, the status is saved as Active.
Archived reagent kits are kits that are not currently in use, or available for use, in the lab workflows. Configuration details for archived kits are saved, so reactivation is easy.
Archived kits are listed at the bottom of the main Reagent Kits list in the Archived Reagent Kits group.
Note the following details about reagent lot status:
Active reagent lots are in use, or are available for use, in the lab. Select the active reagent lots as they record work for a step.
Pending reagent lots have been ordered but not yet received in the lab. They are not available for selection by lab users running steps in Clarity LIMS. By default, when a new lot is added, the status is saved as Pending.
Archived reagent lots have typically expired or been used up. They are not available for selection by lab users. Note the following information:
When the expiry date for a lot has passed, Clarity LIMS automatically archives the lot.
Archived lots that have passed their expiry date cannot be reactivated.
Archived lots display in an Archived Reagent Lots group within the Reagent Kit details list.
In the Reagent Kits list, select the kit to be archived or reactivated.
In the Reagent Kit Use area on the right, select Archived / Active.
Select Save.
In the Reagent Kits list, select the kit containing the lot to be activated or archive
At the bottom of the Lot Details area on the Status of Reagent Lot slider, select Active / Archived.
Select Save.
In the Reagent Kits list, select the reagent kit or lot to delete.
In the Kit Details/Lot Details area on the right, select Delete.
When deleting reagent kits and lots, keep the following in mind:
Only reagent kits and lots that have not been used in a step can be deleted.
If a kit or lot has been recorded in a step, or is being used in a step, it cannot be deleted. The Delete button is not enabled.
This section describes how to add and configure the instruments and equipment used in your lab, and associate these items with master steps.
Add the instruments and equipment used in your lab to Local Analysis Software, and associate these items with specific steps. When running steps in the LIMS, lab scientists can record the instruments and equipment used.
All users logged into the LIMS can access the Instruments configuration screen. However, what they are allowed to do in this screen is determined by their user permissions.
By default, only the Administrator role has the Configuration:update permission. For more on user roles and permissions, see and .
When adding instruments to Clarity LIMS, there are two main steps involved:
Add a new instrument type (Configuration:update permission required).
Select an instrument type and then add a new instrument of that type. You cannot add an instrument without first selecting an instrument type
When initially setting up the system, add all the instrument types used in the lab. For example, HiSeq 3000, 2100 Bioanalyzer, NanoDrop 2000. Any logged in user can then add specific instruments to each type.
On the main menu, select Configuration.
On the configuration screen, select the Consumables tab, then select Instruments.
On the Instruments configuration screen, select New Instrument Type.
In the Instrument Type Details area, complete the following required information:
Enter the name of the type of instrument or equipment you are adding.
In the Vendor drop-down list, select an existing vendor from the list, or select Create new and type the new vendor name into the field. After you create a vendor, it is added to the list and can then be selected when creating other instrument types.
In the drop-down list that displays, select one or more master steps on which to enable this instrument type.
To remove a step from this field, select the X to the left of the step name.
The instrument type is made available for use on all steps that are created from the selected master steps. When running those steps in the LIMS, the appropriate instrument can be selected from the Record Details screen. This configuration is bidirectional - when configuring a master step, you can select instrument types to associate with that master step.
Select Save.
The new instrument type displays in the Instrument Types area. The ' zero instruments ' label indicates that no instruments of this type have yet been added
On the Instruments configuration screen, in the Instrument Types area, select the appropriate instrument type.
Select New Instrument.
In the Instrument Details area, enter the details for this instrument.
Instrument Name: Enter the name of the instrument. (This is the only required field.)
Serial number: Enter the serial number of the instrument, or other instrument-specific information.
Expires: Select the expiry date (or calibration date) of the instrument or equipment.
Valid dates are the current date or any date in the future.
After an instrument has been saved, a label displays next to this field. The label shows the number of days, and then hours, remaining before the instrument expires, or warns that the instrument has expired.
Software Name: Enter the name of the instrument software.
Software Version: Enter the instrument software version number.
Select Save.
In the Instrument Types area, the new instrument is nested under its instrument type.
To create another instrument of the same type, select Add Another New Instrument.
When creating instruments, note the following:
A LIMS ID is automatically assigned to the instrument.
The instrument record Created date is automatically populated.
The instrument record Modified date is automatically populated; this field keeps track of any changes made to the instrument details.
The instrument Status toggles between Active and Archived. By default, when adding a new instrument, its status is Active.
These instruments are in use, or available for use, in your lab workflows; they can be selected by lab users as they record work for a protocol step.
Users may edit the details of Active instruments.
These instruments are not currently in use in lab workflows (for example, they may be expired or under repair), and are not available for selection by lab users working in the LIMS.
When the expiry date for an instrument has passed, the LIMS automatically archives the instrument.
The details of Archived instruments are read-only. They may be viewed, but not edited.
Archived instruments are listed together in a single Archived Instruments group (no subgrouping by type), at the bottom of the Instrument Types area. If an archived instrument is reactivated, it once again displays under its respective instrument type.
When editing instrument types and instruments, keep the following in mind:
Only users with the Configuration:update permission type can edit instrument types.
Changes made to an instrument type, or to any instruments of that type, are reflected on all future steps on which the instrument type is enabled.
Steps that have already been run are not affected by changes made to instrument types or instruments.
When deleting instrument types and instruments, keep the following details in mind:
To delete instrument types, the Configuration:update permission is required.
When deleting an instrument type, all instruments of that type are also deleted and are no longer available for selection on steps.
You cannot delete an instrument type if any instruments of that type are in use.
You cannot delete an instrument if that instrument has been used in a step.
In the Instrument Types area, expand the Archived Instruments section and select the instrument to reactivate.
If the instrument has not expired, select Activate.
If the instrument has expired, reset the expiry date to a date in the future, and then select Activate.
Select Save.
In the Instrument Types area, the reactivated instrument displays under its instrument type. The instrument may now be selected when running steps.
This section describes how to add and configure label groups (reagent categories) and labels (reagent types or molecular barcodes), and enable them for use on specific master steps.
Add a label group for each reagent category used in your lab, and then add labels to the groups. Each label represents a reagent type (or molecular barcode) within the group/category.
Select the label groups to be used in the step when configuring the properties of steps generated from an Add Labels master step type.
To access the Labels configuration screen, the Configuration:update permission is required. Users who do not have this permission do not see the Labels option displayed under the Consumables tab.
By default, only the Administrator role has the Configuration:update permission. For more on user roles and permissions, see and .
When adding label groups and labels to the LIMS, there are several main steps involved:
Add a new label group.
Then, to add labels to the group:
Download a template label list (Microsoft® Excel® file) from the Labels configuration screen.
Add reagent type details to the downloaded template.
Upload the completed label list.
On the main menu, select Configuration.
On the configuration screen, select the Consumables tab and then select Labels.
On the Labels configuration screen, select New Label Group.
In the Label Group Details area, enter the name of the label group you are adding.
Numeric names are not permitted.
Duplicate names are not permitted.
You may use the name of a previously deleted label group.
Select Save.
The new label group is listed in the Label Groups list. Because there are no labels in the group, no count displays.
The Upload Label List and Download Label List buttons display in the Label Group Details area.
On the Labels configuration screen, in the Label Groups list, select the label group to which you want to add labels.
In the Label Group Details area, select Download Label List to download the template.
Open the template in Excel. It has two example label entries containing the following information:
Group Name (column A): Prepopulated with the name of the label group you selected in the LIMS.
Label ID (column B): No information is provided in this column as it is populated by the LIMS.
Label Name (column C): Provides examples of label name (reagent type) formats.
Sequence (column D): Provides examples of sequence properties of theIndex special type of the reagent type. Dual-indexes may be used, separated by a hyphen.
To complete your label list, add new rows between the opening and </LABEL ENTRIES> closing tags and enter reagent label information into these rows:
Group Name: (Required on upload) Enter the name of the label group (reagent category) into which you are adding labels.
Label ID: Leave this column empty. It is populated by the LIMS when you upload your completed label list.
Label Name: (Required on upload) Enter the names of the reagent labels (reagent types) you would like to add to the LIMS, using one of the example formats.
Sequence: (Optional on upload) Enter the index sequence of the Index special type of the reagent type, for example, "ATCACG." You may enter dual-indexes, separated by a hyphen.
Save your label list file.
In the Label Groups list, the label count shows the number of labels in the group.
When editing/deleting label groups, keep the following in mind:
The only item you can change directly in the LIMS is the label group name.
Deleting a label group does not affect historical run data. This information is preserved in the LIMS.
When editing and deleting labels (reagent types), keep the following in mind:
Changes you make to a label are reflected on all future steps on which the label is applied.
Steps that have already been run are not affected by changes you make to labels. The labels are mapped to samples in the run and historical run data are preserved.
When uploading a label list, the following conditions result in an error:
One or more of the four headers (Group Name, Label ID, Label Name, Sequence) is missing or misspelled.
Attempting to rename a label to the same name as an existing label within any label group.
Attempting to rename a label to the same name as an existing label—even if you are also renaming the other label at the same time.
Adding a label with the same name as another label within any label group.
Attempting to edit a label without providing the Label ID.
Providing labels for the wrong group. That is, the Group Name column does not match the name of the label group into which you are uploading labels.
Providing a sequence for a reagent that does not have the 'Index' special type.
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.
| Setting | Configuration options | What It Means in the Lab |
|---|---|---|
| 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 |
|---|---|---|
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.
When configuring a step (see ).
When configuring a master step or step. For details, see .
The LIMS automatically archives the instrument when the expiry date is reached (see ).
By default, the instrument status is set to Active. See .
Return to the Labels configuration screen, select Upload Label List and upload your completed labels list. If there are errors in the list, the upload does not complete. Refer to .
To make changes to the labels within the group, you must upload a modified label list. See .
Upload the modified label list. See .
Upload the modified label list. See .
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
QC Protocol?
QC protocols comprise a series of QC steps.
All steps share queue of samples.
Samples do not move sequentially from step to step. Instead, they appear available/unavailable for a particular step based on configured filtering criteria.
Non-QC protocols typically comprise a series of non-QC steps. However, you can include a QC step as part of a Non-QC protocol.
Each step has its own queue of samples.
Samples move sequentially through the steps, until they have completed all steps in the protocol.
Protocol Type
Sample Prep
Library Prep
Sequencing
Data Analysis
Sample Analysis
Other
See Non-QC protocol information in previous row.
Show in Lab View?
No
These protocols are hidden for both lab scientists and administrators in Lab View and are therefore not available for use in the lab.
These protocols are only visible to administrative users in the configuration area.
Yes
These protocols are displayed in Lab View and can be used by lab scientists to perform their work in the lab.
Capacity
The sample capacity of the protocol. This depends on the number of lab scientists in your facility, and the number of samples they can work with at any given time.
The Capacity setting controls the highlighting on the Overview and Projects dashboards, allowing you to see at a glance which protocols are approaching or exceeding sample capacity.
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 describes how to add and configure the containers used in your lab, and enable them for use on specific master steps.
Clarity LIMS is a container-based system requiring that samples reside in a container at every step of a workflow. Add the types of containers used in your lab to Local Analysis Software and enable them for use on specific steps.
When running a step in the LIMS, the lab scientist scans in the container barcode and proceeds to the Ice Bucket screen. In the Ice Bucket, the output container types that can be used in the step are listed.
To access the Containers configuration screen, the Configuration:update permission is required. Users who do not have this permission do not see the Containers option displayed under the Consumables tab.
By default, only the Administrator role has the Configuration:update permission. For more on user roles and permissions, see User Roles and Configured Role-Based Permissions.
When adding a new container to the LIMS, you are adding a container type (ie, a tube, a 96 well plate, a flow cell). When the container barcode is scanned, an instance of that container type is added.
On the main menu, select Configuration.
On the configuration screen, select the Consumables tab, then select Containers.
On the Containers configuration screen, select New Container.
In the Container Details area, enter the name of the container type you are adding. This is the only required field. When you have entered a name, the Save button becomes available.
[Optional] Specify the details of the rows and columns in the container:
In the Number fields, enter the number of rows and columns in the container.
Use the Naming toggle to specify whether the rows and columns have Alphabetic or Numeric labels.
For numeric rows and columns, use the Start at field to specify the number at which the row/column labels start.
[Optional] If you enter 1 in both row and column Number fields, an additional Yes/No toggle setting displays, asking "Do you want to skip the placement screen?".
Yes—The LIMS does not display the placement screen when the step is run. It automatically places the samples into the container.
No—The placement screen displays samples that need to be manually placed into the single well.
[Optional] List any unavailable wells (ie, wells in which samples must not be placed). Specify these in a comma-separated format, for example, A:1, A:2, A:3, A:4.
Note the following:
If you switch between Numeric and Alphabetic rows/columns, the list of unavailable wells updates to reflect the change.
If you change the Start at number for numeric rows/columns, the list of unavailable wells updates to reflect the change.
If you specify an invalid unavailable well, or change the dimensions of the container such that one or more of the specified unavailable wells becomes invalid, the List unavailable wells field turns red.
The Save button is only available when all specified unavailable wells are valid.
Select Save.
To prevent lab users from placing samples in specific wells of a container, list the unavailable wells in a comma-separated list. Each well must be listed individually. You cannot enter a range.
Wells that are marked as unavailable are shown with a dashed line border in the sample placement screen. If a sample is placed into an unavailable well, a Destination is unavailable error message displays.
On the Containers configuration screen, in the Containers list, select a container type.
The Container Details area displays the details for the selected container type.
Edit the details as required.
Select Save.
When editing container type details, keep the following in mind.
To view and edit container types, the Configuration:update permission is required.
Changes made to a container type are reflected on all future steps on which that container type is enabled.
Steps that have already been run are not affected by changes made to container type details.
When a container type has been used, its row, column, and unavailable wells settings are not editable.
On the Containers configuration screen, in the Containers list, select a container.
The container details display on the right.
Select Delete.
Confirm the deletion.The container is no longer be available for selection on steps.
When deleting container types, keep the following in mind:
To delete container types, the Configuration:update permission is required.
Container types cannot be deleted if an instance of that container type is in use, or has been used, in a step.
This section describes two tasks that Clarity LIMS administrators are often required to perform:
Temporarily prevent a user from logging in by archiving the user.
Email a link to a user that allows them to reset their Clarity LIMS password.
While Clarity LIMS does not enforce password changes, for best practice and security, we recommend that user passwords are changed frequently.
On the main menu, select Configuration.
Select User Management.
Select the Users tab to see a list of all current active and archived users in the system, categorized by role.
Select the user to archive.
The details for the selected user display in the User Details area on the right. The Status slider displays the current status of the user.
Select Archived to temporarily archive the user.
Select Save.
By default, every new user created in Clarity LIMS is an active user and can sign in to Clarity LIMS with their username and password.
On the main menu, select Configuration.
Select User Management.
Select the Users tab to see a list of all current active and archived users in the system.
Select the user whose password is to be reset.
The details for the selected user display in the User Details area on the right.
Select Login and Password and select Reset password.
This sends the user a link that allows them to reset their password.
The Send login instructions option sends the user the following information:
The URL for the login screen.
Instructions on how to set their login password.
This email is sent automatically when a new user is created, but you may occasionally need to resend it.
Clarity LIMS users are assigned roles. These roles control permissions and the ability to:
Access certain Clarity LIMS features.
Perform certain actions.
Sign in to the Clarity LIMS interfaces.
In a typical LIMS lab environment, there are four primary user roles:
The following sections describe the default permissions of the four primary user roles. Some user role permissions are configurable (see Configured Role-Based Permissions).
By default, both the System Administrator and Facility Administrator user roles have access to:
All configuration areas of the Clarity LIMS web interface, allowing them to:
Add and configure workflows, protocols, and steps.
Add consumables—reagents, controls, instruments, reagent labels, containers.
Add and configure custom fields.
Add and configure automations.
Supervisory and lab management functions in the Clarity LIMS web interface, allowing them to:
Review escalations.
Remove samples from workflows.
Move samples into the next step in a workflow.
Access the Overview and Projects dashboards.
User management, allowing them to:
Create, modify, and delete user accounts.
Modify user roles and permissions.
Approve access requests from external collaborators.
The Researcher role is typically assigned to the laboratory scientist. By default, individuals who are assigned this user role are able to:
Log in to Clarity LIMS.
Access Lab View.
Manage and work with samples contained in all projects in the system.
Edit their own user profiles—ie, they can change their own passwords and other profile information.
Access three Consumables configuration areas: Reagents, Controls, and Instruments, and do the following.
View reagent kits and add new reagent lots to those kits (researchers cannot create reagent kits).
View controls.
View instrument types and add new instruments to those instrument types (researchers cannot create instrument types).
Reactivate expired (archived) instruments by resetting the expiration date.
The Collaborator role is assigned to external collaborators who interact with Clarity LIMS using the LabLink Interface.
The Collaborator role is supported in v5.3 and later. It is not supported in v5.0.x to v5.2.x.
An external person can request a user ID through LabLink. By default, when the request is approved by an administrator, the collaborator is able to:
Sign in to LabLink.
Create, view, and delete projects. (Collaborators are automatically given full permissions to projects they create.)
Submit samples to projects, and delete samples from projects.
By default, collaborators do not have access to the main Clarity LIMS web interface.
The User Management configuration screen allows for viewing and managing users, clients, and accounts.
Users are the individuals who have access to the Clarity LIMS interface. Because each step in Clarity LIMS is associated with a user, you can make use of user profiles to track the work moving through your lab. While users are associated with the steps they perform as part of a project, they are not directly associated with that project—unless they are assigned as the project client.
Clients are directly associated with projects in Clarity LIMS. When you create a project, you must associate it with a client. Clients differ from users in that they are not able to log in and access the Clarity LIMS web interface. They are typically external collaborators or customers who submit samples to the lab.
Accounts must be directly associated with projects, users, and clients that are created in Clarity LIMS.
NOTE: Viewing user/client/account details, and adding, modifying, and deleting users/clients/accounts are role-based permissions. For more information, see Configured Role-Based Permissions.
This section describes how to add and manage users and clients in Clarity LIMS.
When creating users, keep the following in mind:
The username must be unique among active users in the system. This is validated when you save the user details.
If the username is already associated with an existing user, an error message displays and you are not be able to save the new user profile.
All users must provide their email address and reset their password upon upgrading their software to v5.4 (or later).
From User Management, select the Users tab.
Select inside the Role field to display a drop-down list of roles:
Select the role to assign to this user.
To remove a role from this field, select the X to the left of the role name.
[Optional] Enter a title, phone number, and fax number for the user.
Select Save.
An invitation email is automatically sent to the user. This email includes the login screen URL and information on how to set the login password. You may resend the login instructions email at any time (see #modify-user-details).
The user displays in the Users list.
[Optional] By default, the status of a new user is set to Active, which means that they can log in to Clarity LIMS. To temporarily prevent a user from logging in, change this setting by selecting Archived. (See also Manage User Access)
From User Management, select the Users tab.
Select the user to modify.
In the User Details area, modify the details as required. If you change the username, a password reset email is sent automatically to the user.
Select Login and Password to access the following options:
Send login instructions—Choose this option to re-send the user the login screen URL and information on how to set their login password.
Reset password—Choose this option to send the user a link that allows them to reset their login password (see Manage User Access).
Select Save.
From User Management, select the Users tab.
Select the user to delete.
In the User Details area, select Delete.
When deleting users, keep the following in mind:
You cannot delete a user if that user has logged in to Clarity LIMS.
You cannot delete a user if that user is associated with a project (eg, the user is the project client).
Deleting a user removes them from Clarity LIMS. You may instead prefer to archive the user or temporarily remove their access to the system. For details, see Manage User Access.
When adding new clients, each client must be a unique entry in the LIMS.
From User Management, select the Clients tab.
Select New Client.
In the Client Details area, complete the following required information:
Enter the first name and last name of the client.
Select inside the Account field and select the client account from the drop-down list.
Enter the client email address.
[Optional] Enter client title, phone number, and fax number.
Select Save.
The user displays in the Clients list, under their account name.
A client cannot be deleted if that client is associated with a project.
From User Management, select the Clients tab.
Select the client to delete.
In the Client Details area, select Delete.
Accounts are the organizations with which a facility conducts business. In the Clarity LIMS Projects and Samples screen, select the existing account from the Account drop-down list to associate projects and samples with it.
To create a new account, type directly into the Account field.
For Clarity LIMS v6.2 and later, you can also create a new account through the Accounts section of the User Management tab that is under Configuration.
From Configuration, select the User Management tab.
Select the Accounts tab.
In the Account Details area, select New Account.
Type a name for the account and complete any other applicable fields (eg, Billing Address).
Select Save.
From Configuration, select the User Management tab.
Select the Accounts tab.
In the Accounts list, select the account that you want to modify.
In the Account Details area, update the fields that need to be modified.
Select Save.
From Configuration, select the User Management tab.
Select the Accounts tab.
In the Accounts list, select the account that you want to delete.
Select Delete.
You cannot delete an account that is associated with a user or project.
This section describes how to update some of the details associated with your profile, including your password, email address, and profile photo.
After signing into Clarity LIMS, you can update some of the details associated with your profile, including your password, email address, and profile photo.
If the user is an LDAP account, then you cannot update the profile in Clarity LIMS.
In Clarity LIMS, at the right of the menu bar, select your username and then select Profile.
The Profile page opens, displaying the details associated with your user profile.
On this page, you can:
Change your password.
Change your email address.
Upload an image to associate with your profile.
On the Sign In screen, click the Forgot your password link.
In the Reset Your Password screen, enter your username or email address and click Submit.
Standard
Standard QC
Aggregate QC
Add Labels
Pooling
Analysis
Demultiplexing
In Clarity LIMS, custom fields are used to record information about a step, sample, or other LIMS component.
There are two types of custom fields: global fields and master step fields.
The default configuration includes both global and master step fields. You can add additional fields to meet the needs of your lab, and display those fields to the user at run time (see Step Milestones).
Global fields—Apply to the whole LIMS system. You can use these fields to record measurements and information about measurements, submitted samples, derived samples, accounts, containers, projects, and clients.
Master step fields apply to the master step on which they are configured, and are inherited by all steps derived from that master step.
To access the Custom Fields configuration screen, the Configuration:update permission is required. Users who do not have this permission do not see the Custom Fields tab.
By default, only the Administrator role has the Configuration:update permission. For more on user roles and permissions, see User Roles and Configured Role-Based Permissions.
Configure custom fields to record information about a step, sample, or other Clarity LIMS component.
For example, you can:
Use global fields to capture sample measurements and track information about projects.
Use master step fields to record instrument settings and other details about a specific step.
Configure automation scripts that populate custom fields or perform calculations at run time.
Create groups of defaults—collections of prepopulated master step fields that eliminate the need for manual input of values at run time and make sure that the correct information is always recorded.
When adding custom fields, keep the following in mind:
You cannot save a custom field until you have entered a name and selected a field type.
You cannot create a custom field on a global field object or master step with the same name as an existing field on that object/master step. For example, if you have a created a global field called 'Description' on the Account object, you cannot create another global field called 'Description' on the Account object. However, you can create a 'Description' field on the Project object.
If the field name you specify is the same as a field that has been deleted, the new field is created and the conflicting field name is renamed. Deleted fields do not display in the LIMS interface, but are saved in the database.
On the main menu, select Configuration.
On the configuration screen, select the Custom Fields tab.
On the Custom Fields configuration screen, select the Global Fields or Master Step Fields tab.
In the header of the global field object or master step for which you want to add a new field, select Add.
In the Field Details area, complete the required fields:
a. Type a name for the field.
b. Select the appropriate field type. See sections below for details.
Set the required field options:
Required: If this field must be filled in, set this option to Yes. Otherwise, set to No.
Read only: If you do not want the user to edit the field value at run time, set to Yes. To allow editing of the field at run time, set to No
The Field Options and Additional Options reflect the field type selected:
Default (for nondrop-down field types only): If you would like to set a default value, enter the value here.
Dropdown Items (for drop-down field types only):
To set a default item, add this value first and set the Set as Default toggle switch to Yes. You can only set the first item as the default, and you cannot reorder items after you have added them.
Repeat to add more items to the list.
To remove a list item, select the X button.
If you do not specify any drop-down items, or if you specify only one item and set it as the default value, upon save, the field converts to its equivalent nondrop-down type and custom entries are enabled.
Select Add and enter the first list item.
Complete other options, as required. See sections below for details.
Select Save. The new custom field is added to the bottom of the fields list. It is now available to be displayed on master step and/or step milestone screens.
For any field selected, the Field Details area displays the following information:
The field name.
The global field object (Derived Sample shown here), or the master step, with which the field is associated.
The field type.
The field options, that is, whether the field is:
Required—If set to Yes, the field must be filled in.
Read only—If set to Yes, the field cannot be edited at run time.
The default value for the field, if set.
For drop-down field types:
The Default option is replaced with a Dropdown Items list.
The first list item may be set as the default value for the field.
Additional options may also display, as described below. These differ depending on the field type. For example, the Range From and To fields only display for Numeric field types.
The following table describes the field types available for custom fields, and the additional options that apply to each type.
Custom Field Types and Additional Options
The Toggle Switch field type renders as a toggle switch on the Record Details screen.
Configuration options:
Default value configured as Yes or No: When the screen displays, Yes or No is selected by default. User can select Yes or No.
Default value configured as None Set: When the screen displays, neither Yes nor No is selected. User selects a value.
Required: The field may be configured as a required field, even if the default value is None Set. When the user enters the screen, neither Yes nor No is selected, but a value must be selected.
The following table explains how to use the additional options associated with the Numeric, Numeric Dropdown, Text Dropdown, and Hyperlink Dropdown field types.
Field Types Additional Options Usage
This section describes how to edit and delete custom fields.
On the Custom Fields configuration screen, select the Global Fields or Master Step Fields tab.
Expand the global field object group or master step containing the field to edit.
Select the field.
Make your changes and select Save.
When editing custom fields, keep the following in mind:
You cannot modify the field type, unless you are changing a drop-down field type to its equivalent nondrop-down type or vice versa. For example, you can change a Numeric Dropdown field to a Numeric field, or a Text field to a Text Dropdown field.
If you convert a drop-down field type to its equivalent nondrop-down type, Clarity LIMS removes all nondefault list values and enables custom entries upon saving. If a default drop-down option was set, it becomes the default for the nondrop-down field.
On the Custom Fields configuration screen, select the Global Fields or Master Step Fields tab.
Expand the global field group or master step containing the field you would like to delete.
Select the field and select Delete. Confirm the deletion.
When deleting custom fields, keep the following in mind:
You cannot delete a master step field if it has been assigned a value, or is in use in a step—that is, if a step derived from the master step with which the field is associated has been started.
If you delete a custom field, it no longer displays in the LIMS interface. However, its information is saved in the database for historical purposes.
You cannot restore a deleted field for use in the LIMS, but you can create a field with the same name. The original deleted field is renamed in the database.
You cannot reorder master step fields on the Custom Fields configuration screen. This configuration is instead available on the Record Details milestone. For details, refer to the #configure-step-data section of the #configure-record-details-milestone topic.
However, you can reorder global fields by simply clicking and dragging them into position.
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.
The order is reflected in various places in the LIMS interface, for example:
Submitted sample global field ordering is reflected on the Sample Management screen, in the Sample Details section.
Project global field ordering is reflected on the Project Details screen (on the Custom Fields tab) and on the Sample Management screen (in the Project Details section).
Groups of defaults are collections of prepopulated master step fields. Using these eliminates the need for lab scientists to manually enter field values each time they run the step, and makes sure that the correct information is recorded every time a step is run.
When you have added groups of defaults to a master step:
They become available for selection when you create a step based on the master step.
When running a step in Clarity LIMS, if the step has one or more groups of defaults configured, these steps display in a drop-down list in the upper-right corner of the Record Details screen. Select the desired group of defaults and the LIMS populates the step fields with the corresponding values.
If you have configured a default group of defaults, those values automatically populate the step fields.
On the Custom Fields configuration screen, select the Master Step Fields tab.
Expand the master step on which to configure a group of defaults.
Below the configured master step fields, in the Group of Defaults section, select Add.
In the Group of Defaults area on the right, the fields associated with the master step display.
Name the group of defaults.
Populate each field with the value to set for the group of defaults.
Select Save.
[Optional] When configuring the Record Details milestone for a step, if the related master step has one or more groups of defaults configured, you can select a default group to display.
[Optional] Reorder groups of defaults by clicking and dragging them into position.
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.
The order is reflected in the drop-down list that displays at the top of the Record Details screen.
Manage the permissions of the System Administrator, Facility Administrator, Researcher, and Collaborator user roles to restrict or allow the following actions:
Sign in to Clarity LIMS.
Sign in to the API.
View and interact with certain features of the interface.
Perform certain actions in the interface.
View and restrict any actions in the interface. [Clarity LIMS v6.1 and above]
Role-based permissions are controlled through the permissions-tool.jar tool, at /opt/gls/clarity/tools/permissions/.
For assistance with running the command-line permissions tool, contact the Illumina Support team.
Functionality includes the following commands:
#listroles—List all roles in the system.
#describerole—List names and descriptions of all permissions in the system.
#createrole—Create a role.
#showsummary—List permissions assigned to each role in the system.
#listpermissions—List permissions assigned to a specific role.
#assignpermission—Assign a permission to a role.
#removepermission—Remove a permission from a role.
NOTE: The permissions-tool.jar tool function names and property names are case-sensitive. If you type the incorrect case, your command or property cannot be understood.
There can be a delay (up to 20 minutes) before changes to some API-related permissions take effect.
List all user roles in the system:
Show permissions for a specific role:
Create a role:
Show assigned permissions for all roles:
List names and descriptions of all permissions:
Assign a permission to a role (the example assigns permission to create controls):
[Clarity LIMS v6.1 and above] Assign a permission to a role (the example assigns read-only permission to a role):
Refer to #supported-permissions.
Remove a permission from a role (the example removes permission to create controls):
Refer to #supported-permissions.
The sections below list LIMS permissions and actions, and the user roles to which each permission/action is assigned by default.
By default, System Administrators and Facility Administrators have all permissions listed.
The default role with AdministerLabLink permission is Administrator. This permission is added to the existing System Administrator & Facility Administrator roles.
The Collaborator role is based on the existing Collaborator role in LabLink v1.0.
Note: The existing Researcher role does not have the new permission and behaves similarly to the LabLink Collaborator role.
Default roles with this permission: Administrator, Researcher
The Sample:update permission is automatically granted to roles that have the Sample:create permission at the time of migration to Clarity LIMS v5.x. If you have removed create permissions from any default role, the role does not acquire the update permission.
Default roles with these permissions: Administrator
Users with ClarityLogin permission can access the Consumables > Controls tab and view control sample details (read only).
Default roles with these permissions: Administrator
Users with ClarityLogin permission can access the Consumables > Reagents tab. They can also view, edit, and delete reagent lots, and add lots to existing kits. No additional ReagentKit permissions are required.
Default roles with these permissions: Administrator
APILogin permission is required for role management. All users with ClarityLogin permissions can view and edit their own user details (except for assigning/removing roles).
Default roles with this permission: Not applicable. You can assign this permission to any role.
At least one System Administrator must be available to reconfigure user roles. Therefore, we recommend that you do not assign the Read-Only permission to the default Administrator and API users.
Default roles with these permissions: Administrator
In the LIMS user interface, the term 'contact' has been replaced with 'client.' However, the API still uses the permission Contact.
All users with ClarityLogin permission can view and edit their own user details (except for assigning/removing roles).
Default roles with these permissions: Administrator
In the LIMS user interface, the term 'contact' has been replaced with 'client.' However, the API still uses the permission Contact.
Users with ClarityLogin permission can view and edit their own client and user details.
Clients can edit their own details (except for assigning/removing roles) without having update permission.
Default roles with these permissions: Administrator
In the LIMS user interface, the term 'process' has been replaced with 'master step.' However, the API still uses the permission Process.
Default roles with this permission: Administrator
Default roles with this permission: Administrator
Default roles with this permission: Administrator, Researcher, Collaborator
Default roles with this permission: Administrator, Researcher, Collaborator
Default roles with this permission: Administrator
Default roles with this permission: Administrator
Default roles with this permission: Administrator
Default roles with this permission: Administrator
Default roles with this permission: Administrator
Default roles with this permission: None
Modifications are limited to what is available on the Record Details screen for the step.
Details such as sample placement or routing cannot be modified.
Only steps completed after upgrading to LIMS v5.1 can be edited. Steps completed in v5.0 or earlier cannot be edited.
Steps that were executed using the Process API cannot be edited.
For details, see Modify Completed Step Details .
When Clarity LIMS is running scripts via the External Program Plugin mechanism, it is not uncommon for these scripts to rely upon a file that contains information germane to the script. A common example would be using the sample input file generator script that is part of the Lab Instrument Toolkit. This script merges runtime information within a Clarity step into a file whose format is directed by a 'template' file.
Under the old method, template files must be saved to a folder accessible to the automation worker node. Typically
If a script needs a template file, the file is specified by including its full path in the syntax that invokes the script.
As of Clarity LIMS v5.1, template files can (optionally) be attached directly to an automation via the GUI.
We recommend that you use a combination of both methods, as follows.
Use the embedded template while developing the template. During this process, having the template file easily available for editing is helpful. After the template is finalized, move it to the server and adjust the automation command line to use the server path/filename instead of the file token.
This method allows for easy, iterative testing and precise traceability for production work. This method also facilitates reliable migrations involving the config-slicer tool and coordinated movement of associated /customextensions/ files.
Config-slicer does not currently migrate automations that need template files without additional manual manipulation after the configuration migration. Regardless of method, you must manipulate the system manually to complete the migration of the template files.
This section describes how to add and configure the three types of automations in Clarity LIMS: step automations, project automations, and derived sample automations.
To access the Automation configuration screen, the Configuration:update permission is required. Users who do not have the Configuration:update permission do not see the Automation tab.
By default, only the Administrator role has the Configuration:update permission. For more on user roles and permissions, see and .
You can create three types of automations in Clarity LIMS: step automations, project automations, and derived sample automations.
Step automations are reusable. After you have created an automation, you can enable it on multiple master steps.
If you intend the automation to be triggered manually, the name you choose for the automation is used to name the button that initiates it from the LIMS interface.
Two step automations can have the same name as long as they are unique in some other way. For example:
channel name is unique, or
command line is unique, or
run-program-per-event values are unique (available in the API only)
Attached files and associated master steps are ignored in these comparisons.
Two project automations cannot have the same name, regardless of the uniqueness of channel name and command line.
You cannot enable multiple automations with the same name on a master step, even if the automations are configured differently.
On the main menu, select Configuration.
On the configuration screen, select the Automation tab.
On the Step Automation tab, select New Automation.
In the Automation Details area, complete the required fields:
Type a name for the new automation.
In the Channel Name field, enter the channel to be used for this automation (for more information, refer to Automation Channels in the Clarity LIMS API documentation section).
In the Command Line field, enter the command line to be run when the automation is triggered. Copy/paste tokens from the Tokens list, as required. For details, refer to Step Automation Tokens in the Clarity LIMS API documentation section.
[Optional] Enable automation on steps:
In the Automation Use section, select inside the Enable on these Master Steps field and select the master step on which to enable the automation. (Note that this configuration is bidirectional—when configuring a master step, you can select automations to associate with that master step.)
If necessary, you can:
Repeat this process to enable the automation on multiple steps.
Select the X button to remove a step from the field.
Select Save.
The new step automation is now available to be configured on the selected master steps.
The Automations configuration screen includes a Template Files section that allows for the upload of a template file to an automation. Reference the file in the automation command line and use it to generate a file that is attached to the step—typically a sample sheet file that can be used to start the instrument run.
A token for the template file is automatically added to the Tokens list. When included in the command line, the token is replaced with the absolute path of the template file at run time.
Downloadable sample sheet template files are available for several Illumina instrument integrations. For details on modifying the example template for the needs of your lab, refer to the Lab Instrument Tool Kit section of the Clarity LIMS Integrations and Tool Kits documentation.
In the Template Files section, select Upload File.
In the Upload File dialog, select Choose File, and then browse to and select the appropriate template file.
Select Upload. The file is attached to the automation and listed in the Template Files section. When upload is complete, a new dynamic token is added to the Tokens list.
In the Command Line field:
Include a script that generates the output file.
Provide the template file token as a script parameter. You can copy and paste the token directly from the Tokens list. At run time, the token is replaced with the absolute path of the file.
Select Save.
In the Step Automation list, an icon indicates that a file is attached.
If necessary, you can:
Repeat this process to attach additional files to the automation.
Select the X button to remove the file from the automation.
You can also attach template files to automations via the API, using the files endpoint. For details, refer to the Clarity LIMS API documentation.
On the Derived Sample Automation tab, select New Automation.
In the Automation Details area, complete the required fields:
Type a name for the new automation.
In the Channel Name field, enter the channel to be used for this automation (for more information, refer to Automation Channels in the Clarity LIMS API documentation section).
In the Command Line field, enter the command line to be run when the automation is triggered. Copy/paste tokens from the Tokens list, as required.
For details, refer to Derived Sample Automation Tokens in the Clarity LIMS API documentation section.
Select Save.
The new derived sample automation is added to the Derived Sample Automations list, and is now available to be run on derived samples from the Projects dashboard.
The following examples show how derived sample automations can be used in the lab.
On the Project Automation tab, select New Automation.
In the Automation Details area, complete the required fields:
Type a name for the new automation.
In the Channel Name field, enter the channel to be used for this automation (for more information, refer to Automation Channels in the Clarity LIMS API documentation section).
In the Command Line field, enter the command line to be run when the automation is triggered. Copy/paste tokens from the Tokens list, as required. For details, refer to Project Automation Tokens in the Clarity LIMS API documentation section.
Select Save.
The new project automation is added to the Project Automations list, and is now available to be run on submitted samples from the Projects & Samples screen.
On the Automation Configuration screen, select one of the following tabs:
Step Automation
Project Automation
Derived Sample Automation
In the list of automations on the left, select the automation to edit.
Make your changes and select Save.
When editing step automations, keep the following in mind:
Changes you make to a step automation are reflected on all future steps on which that automation is enabled.
Steps that have already been run are not affected by changes you make to a step automation.
On the Automation Configuration screen, select one of the following tabs:
Step Automation
Project Automation
Derived Sample Automation
In the list of automations on the left, select the automation to delete.
Select Delete.
Information about deleted automations is saved in the Clarity LIMS database for historical purposes. However, there is no way to restore a deleted automation for use in Clarity LIMS.
Use an automation with the copyUDFs script and to copy custom fields from a step input to a step output. This example uses the Library Normalization master step, and shows how to copy the Concentration field from the step input samples to the output samples.
On the Lab Work configuration screen, select the Automation tab, then select the Step Automation tab.
Add a new automation.
Name the automation and enter the channel name.
In the Command Line field, copy the following command, replacing the { } placeholders with your own information:
bash -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar script:copyUDFs -u {username} -p {password} -i {processURI:v3:http} -f Concentration"
In the Automation Use section, enable the automation on the desired master step (this example uses the Library Normalization master step).
Save the automation.
Return to the Lab Work configuration screen and select the Lab Work tab. In the Master Steps list, select the master step on which you enabled the automation.
In the Automation section, the new automation is listed. Configure as follows:
Trigger Location: Record Details
Trigger Style: Automatic upon entry
NOTE: Automation triggers can be configured at the master step or the step level. If configured on the master step, the trigger settings are locked on all steps derived from that master step.
You can add it as an expanded view field or as a column header (for details, refer to ).
Save your changes.
At run time:
When the Record Details screen is entered, the automation are automatically triggered.
The copyUDFs script runs and copies the Concentration field values from the step input samples to the output samples.
Automations (formerly referred to as EPP triggers or automation actions) allow lab scientists to invoke scripts as part of their workflow. These scripts must successfully complete for the lab scientist to proceed to the next step of the workflow.
EPP automation/support is compatible with API v2 r21 and above.
The API documentation includes the terms External Program Integration Plug-in (EPP) and EPP node.
As of BaseSpace Clarity LIMS v5.0, these terms are deprecated. The term EPP has been replaced with automation. EPP node is referred to as the Automation Worker or Automation Worker node. These components are used to trigger and run scripts, typically after lab activities are recorded in the LIMS.
Automations have various uses, including the following:
Workflow enforcement—Makes sure that samples only enter valid protocol steps.
Business logic enforcement—Validates that samples are approved by accounting before work is done on them. This automation can also make sure that selected samples are worked on together.
Automatic file generation—Automates the creation of driver files, sample sheets, or other files specific to your protocol and instrumentation.
Notification—Notifies external systems of lab progress. For example, you can notify Accounting of completed projects so that they can then bill for services rendered.
You can enable automations on master steps in two configuration areas of Clarity LIMS:
On the Automations tab, when adding or configuring an automation. For more information, see .
On the Lab Work tab, on the master step configuration form. For more information, see .
After it is enabled on a master step, the automation becomes available for use on all steps derived from that master step.
You can configure the automation trigger on the master step, or on the steps derived from that master step.
| Field Type | Field Description | Additional Options |
|---|---|---|
| Additional Options | Usage |
|---|---|
| Allows: | Result of denied permission |
|---|---|
| Allows: | Result of denied permission |
|---|---|
| Action: | Allows: | Result of denied permission |
|---|---|---|
| Action: | Allows: | Result of denied permission |
|---|---|---|
| Action: | Allows: | Result of denied permission |
|---|---|---|
| Action: | Allows: | Result of denied permission |
|---|---|---|
| Action: | Allows: | Result of denied permission |
|---|---|---|
| Action: | Allows: |
|---|---|
| Action: | Allows: | Result of denied permission |
|---|---|---|
| Action: | Allows: | Result of denied permission |
|---|---|---|
| Action: | Allows: | Result of denied permission |
|---|---|---|
| Action: | Allows: | Result of denied permission |
|---|---|---|
| Action: | Allows: | Result of denied permission |
|---|---|---|
| Allows: | Result of denied permission |
|---|---|
| Allows: | Result of denied permission |
|---|---|
| Allows: | Result of denied permission |
|---|---|
| Allows: | Result of denied permission |
|---|---|
| Allows: | Result - permission granted |
|---|---|
| Allows: | Result - permission granted |
|---|---|
| Allows: | Result of denied permission |
|---|---|
| Allows: | Result - permission granted |
|---|---|
Step automations—Actions that are triggered when running samples through a step. Configure them to be triggered automatically (at the start/end of the step, or when a particular screen is entered or exited), or manually (when selecting a button on the Record Details screen). The automations are enabled on the master step, but the trigger points are configured at the master step or step level. See
Project automations—Actions that users can run on submitted samples, directly from the Projects & Samples screen. For example, you might configure an automation that gives the ability to assign the samples to a workflow. See
Derived sample automations—Actions that users can run on derived samples, directly from the Projects dashboard. For example, you could configure an automation that gives the ability to queue selected samples for a new workflow. In this case, the automation would trigger a custom script created for this purpose. See
Text
Field in which to type a line of text.
Field length is only limited by the database field used to store it. PostgreSQL limit - 1 Gb, Oracle limit - 4000 characters.
Not applicable
Numeric
Field in which to type a number.
Range From, To
Decimal Places Displayed
Hyperlink
Field containing a link to a website URL. Select the link to open the URL in a web browser.
None
Text Dropdown
Field in which to select from a list of predefined text options.
Custom Entries
Dropdown Items
Numeric Dropdown
Field in which to select from a list of numbers.
Custom Entries
Dropdown Items
Range From, To
Decimal Places Displayed
Hyperlink Dropdown
Field in which to select from a list of website URLs. Select a link to open the URL in a web browser.
Custom Entries
Dropdown Items
Multiline Text
Field in which to type multiple lines of text.
Not applicable
Toggle Switch
A field to toggle between Yes and No values.
None Set (Default)
Yes
No
Date
A calendar tool to select a date.
Not applicable
Range From, To
Use to define the range within which numeric values must fall. At run time, the user is prevented from entering a number outside of the defined range.
Decimal Places Displayed
Use to specify the number of decimal places to display in a numeric field. This value is used for display purposes only. The field stores the value as input by the user or script.
Note: If the user edits the value of a Numeric field (or gives the field focus by selecting inside it), the value that displays— including the number of decimal places, is written to the database, overwriting the existing value. For this reason, we recommend that you increase the number of decimal places to display to ensure sufficient precision.
Dropdown Items
Use to create a list of options to select at run time.
Custom Entries
Use to control whether or not the user may enter a value at run time. If set to No, a value from the predefined drop-down list must be selected. If set to Yes, a value must be entered into the field.
-a
--apiUri
REST API base URI (ends with "/api/<version>/") Must be completed as: http://<servername>/api/v2/
-p
--password
LIMS password (required)
-u
--username
LIMS sign-in username (required)
Action
Permission Required
System Administrator and Facility Administrator
Collaborator
Sign in to LabLink
CollaborationsLogin action
Yes
Yes
Manage Project
Projects create, read, update.
Yes
Yes
Manage Sample
Samples create, read, update.
Yes
Yes
Manage User
Users create, read, update.
Yes
No
Manage Configuration
Configuration update
Yes
No
View the Configuration page
AdministerLabLink
Yes
No
View the User Management page
AdministerLabLink
Yes
No
Sign in to ClarityLIMS
Access Lab View and Projects and Samples screen
Access Consumables > Reagents configuration tab; view, edit, and delete reagent lots; add lots to existing kits.
Access Consumables > Controls configuration tab and view control details
Access Consumables > Instruments configuration tab; add, edit, delete, and activate instruments; view instrument types.
Sign In screen
Sorry, you do not have permission to sign in to Clarity LIMS.
Access LIMS Rest API
Sign In screen
403 Forbidden error via http://host/api/*
create
Create project
Modify project details
Modify project custom fields
Projects and Samples
New Project button hidden
View project details (read-only)
Note: No permission is needed to upload files to a project
Update
Modify project details
Projects and Samples
Save button disabled (if delete is permitted)
Button menu hidden (if delete is not permitted)
View project details (read-only)
Delete
Delete project containing no samples.
Delete project containing samples (also requires Sample:delete permission)
Projects and Samples
Delete button disabled (if update is permitted)
Button menu hidden (if update is not permitted)
create
Submit/add samples
Upload sample list
Download sample list example
Modify samples.
Projects and Samples
Submit Samples title hidden
Download Example Sample List link hidden
Upload Sample List button hidden
Add Samples button hidden
Modify Samples button renamed Download List
Modify Samples button hidden (sample list)
Sample Management
Sample + button hidden
Update
Modify samples.
Projects and Samples
Modify Samples button renamed Download List
Delete
Delete a submitted sample on Projects and Samples screen, provided no work has been performed on the sample.
Delete a submitted sample in API, provided no work has been performed on the sample.
Projects and Samples
Delete button hidden
403 Forbidden error via http://host/api/sample
create
Create control samples.
Controls
New Control button hidden
New Control button hidden
Update
Modify control samples.
Archive control samples (requires both update and delete permissions)
Controls
Save button disabled (if delete is permitted)
Button menu hidden (if delete is not permitted)
View control sample details (read-only)
Delete
Delete control samples.
Archive control samples (requires both update and delete permissions)
Controls
Delete button disabled (if update is permitted)
Button menu hidden (if delete is not permitted)
Archived toggle disabled
create
Create reagent kits
Reagents
New Reagent Kit button hidden
View reagent kit details (read-only)
Update
Modify reagent kits
Archive reagent kits (requires both update and delete permissions)
Reagents
Save button disabled (if delete is permitted)
Button menu hidden (if delete is not permitted)
View kit details (read-only - except for Status)
Delete
Delete reagent kits
Archive reagent kits (requires both update and delete permissions)
Reagents
Delete button disabled (if update is permitted)
Button menu hidden (if delete is not permitted)
Archived toggle disabled
read
View client (researcher/contact) details, including details such as username and roles in API
View users and clients (contacts) on Users and Clients screen
403 Forbidden error via http://host/api/roles
create
Create user roles.
403 Forbidden error via http://host/api/roles
Update
Modify existing user roles.
Add/remove user role permissions
403 Forbidden error via http://host/api/roles
Delete
Delete user roles.
403 Forbidden error via http://host/api/roles
read
View project and sample details on the Projects & Samples screen
View lab activities, in-progress steps, and steps that are ready to be worked on in Lab View
read
View users and clients on Users and Clients screen
View client details, including details such as username and roles in API
403 Forbidden error via http://host/api/researchers
create
Create users and clients on Users and Clients screen (User:update permission is required to assign permissions to the user)
Send login instructions and password reset emails on Users and Clients screen (either this action or User:update is required)
Create clients in API.
Create user credentials and assign roles in API.
Users and Clients
New User button hidden
View user details (read-only)
403 Forbidden error via http://host/api/researchers
Update
Update users and clients on Users and Clients screen
Send sign in instructions and password reset emails on Users and Clients screen (either this action or User:create is required)
Modify client details in API.
Assign role to user in API.
Remove role from user in API.
Save button disabled (if delete is permitted)
Button menu hidden (if delete is not permitted)
View user/client details (read-only)
403 Forbidden error via http://host/api/researchers
Delete
Delete users and clients on Users and Clients screen.
Delete a client and associated user in API.
Delete button disabled (if update is permitted)
Button menu hidden (if delete is not permitted)
403 Forbidden error via http://host/api/researchers
read
View clients on Users and Clients screen
View client details in API
403 Forbidden error via http://host/api/researchers
create
Create clients on Users and Clients screen.
Create clients in API.
Contact:update permission is required to assign permissions to clients.
New User button hidden
View user details (read-only)
403 Forbidden error via http://host/api/researchers
Update
Update client details on Users and Clients screen.
Update client details in API.
Assign role to/remove role from client.
403 Forbidden error via http://host/api/researchers
This permission does not affect the display of clients in Project and Samples and Sample Accessioning screens.
Delete
Delete clients in API
Delete clients on Users and Clients screen.
Clients with associated user details cannot be deleted
Delete button disabled (if update is permitted)
Button menu hidden (if delete is not permitted)
403 Forbidden error via http://host/api/researchers
read
View master steps
403 Forbidden error via http://host/api/roles
create
Create master steps.
403 Forbidden error via http://host/api/roles
Update
Modify master steps.
403 Forbidden error via http://host/api/roles
read
Access the Overview Dashboard
No Dashboards button
update
Manage all configuration in the LIMS interface (ClarityLogin permission is also required)
Manage configuration in API (APILogin permission is also required)
403 Forbidden error via any URI that begins with http://host/api/configuration.
Requeue a sample in sample search.
Requeue a sample in container search.
Sample and Container Search
Requeue button hidden.
Assign sample to workflow from Projects and Samples screen.
Sample Management
Sample cannot be dragged into workflow widgets.
Workflow selection widget hidden
Workflow lozenge Remove button hidden
Delete workflow button hidden.
Remove sample from queue.
Remove sample from workflow.
Sample Management
Remove from this queue option hidden (if Move to next step is permitted)
Options button hidden (if Move to next step is not permitted)
Move sample to next step in workflow
Sample Management
Move to the next step option hidden (if Remove from this queue is permitted)
Options button hidden (if Remove from this queue is not permitted)
Rework a sample from a previous step.
Sample Management
In Select the next step of the sample drop-down list, Rework from an earlier step option displays.
On Protocol Step Results screen, a button displays to allow the sample to be reworked from an earlier step.
Review escalated samples.
Sample Escalation
Enter Review Comment box enabled.
Sign an eSignature on step completion.
Record Details
Error message in e-Signature popup
Edit button when viewing a completed step.
Select button to edit completed step details on Record Details screen.
Assign Next Steps.
Edit button displays.
Record Details
After clicking Edit button, Record Details fields are editable, as applicable/permitted.
