This section explains the relationship between milestones, master steps, and steps; shows how to access milestone configuration settings; and provides an overview of each milestone.
Milestones are the various stages of a step that are presented to lab users as they run samples through steps in Clarity LIMS.
Some screens (such as the Queue, Ice Bucket, and Record Details screens) display on all steps, while others only display on certain step types.
For example, the Pooling milestone only displays on steps of the Pooling type and the Add Labels screen only displays on steps of the Add Labels type. On all other step types, those milestones are disabled on both the master step and step configuration forms.
The following table shows the milestones that are available for display for each step type. For more information on step types, see #about-step-types-and-outputs.
Milestones Displayed for Step Types
| Step Type | Queue | Ice Bucket | Step Setup* | Pooling | Placement | Add Labels | Record Details |
|---|---|---|---|---|---|---|---|
*While the Step Setup screen is available for display on all step types, it is optional and does not display by default. To enable the Step Setup screen, you must first add file placeholders on the master step. For details, see #configure-step-setup-milestone.
You can configure milestone settings on the master step and step configuration forms.
When switching between the step and master step configuration forms while viewing or editing a milestone, you are returned to the parent step/master step form. You need to select the milestone name again to open its settings form.
Similarly, if you wish to return to the step or master step settings form, select the parent master step or step tab.
To configure a milestone:
Select it to open its settings form.
When configuring milestones on master steps and steps, consider the following details:
If you configure a list of items at the master step level—for example, expanded view fields, instrument types, reagent kits—the order in which they are listed on the master step is overwritten by the order set at the step level. Set the order of any list at the step level. This includes the order of the Sample table column headers.
If you remove configured settings from a master step, those settings on the related steps revert to their default values. The exception is if this would leave the step in an unworkable state. For example, you cannot remove the last container from a step. Exceptions to this 'revert to default' rule are noted where applicable.
Settings configured at the step level only apply to that particular step.
To understand how properties set on the master step propagate down to the step level, see #rules-for-propagation-of-master-step-properties.
When running samples through a step, the first screen that displays is the Queue screen. This screen provides a sample table to select samples to be placed into the Ice Bucket, reserving them for use.
The following components of the Queue Sample table are configurable on the Queue Settings form:
The Sample table column headers
The Sample table expanded view fields
Default grouping and well sort order of Sample table
On the Queue Settings form, configure the column headers that display in the Sample table, and the order in which they display.
Note the following:
No default column headers are configured at the master step level.
When configuring column headers on a new step, several default column headers will display. You can remove these, but the table must have at least one field remaining (this may be set on either the master step or the step).
Expanded view fields are hidden by default in the Sample table. These fields contain additional details about the samples in the queue. At run time, choose to display these details by clicking the Show/Hide Details button.
On the Queue Settings form, in the Expanded View Fields section, you can select additional fields to add to the body of the Sample table.
Note the following:
No default expanded view fields are configured at the master step or the step level.
If expanded view fields are configured at the master step level, they display as locked at the step level and cannot be removed. You can modify the order in which the locked fields display.
Expanded view fields are available for display in multiple milestone screens. The configuration options set in each milestone are specific to that milestone. You may choose to configure the expanded view fields differently in other milestones.
On the Queue screen, samples are grouped by Container and sorted by well Row by default.
On the Queue Settings form, in the Defaults section, you can modify these settings if necessary.
Samples move from the Queue into the Ice Bucket, where they are reserved for use for 30 minutes. The Ice Bucket screen displays for all step types. It comprises a Sample table that displays information about the samples entering the step.
The following components of the Ice Bucket screen are configurable on the Ice BucketSettings form:
The Sample table column headers
The Sample table expanded view fields
Default grouping and well sort order of Sample table
On the Ice Bucket Settings form, configure the column headers that display in the Sample table, and the order in which they display.
Note the following:
No default column headers are configured at the master step level.
When configuring column headers on a new step, several default column headers will display. You can remove these, but the table must have at least one field remaining (this may be set on either the master step or the step).
Expanded view fields are hidden by default in the Sample table. These fields contain additional details about the samples in the Ice Bucket. At run time, choose to display these details by clicking the Show/Hide Details button.
On the Ice Bucket Settings form, in the Expanded View Fields section, you can select additional fields to add to the body of the Sample table.
Note the following:
No default expanded view fields are configured at the master step or the step level.
If expanded view fields are configured at the master step level, they display as locked at the step level and cannot be removed. However, you can modify the order in which the locked fields display.
Expanded view fields are available for display in multiple milestone screens. However, the configuration options set in each milestone are specific to that milestone; you may choose to configure the expanded view fields differently in other milestones.
By default in the Ice Bucket screen, samples are grouped by Container and sorted by well Row.
On the Ice BucketSettings form, in the Defaults section, you can modify these settings if necessary.
The Step Setup screen is an optional screen. By default, it does not display at run time.
This screen lets you provide the lab scientist running the step—and provide Clarity LIMS—with access to files before samples are placed. You can then configure step automations that parse these files and use the information to place samples into destination containers, based on the result file specifications.
If you enable the display of the Step Setup screen (you can enable it on any step type), it displays immediately after the Ice Bucket screen.
The Step Setup Settings screen allows you to do the following:
Add file placeholders that will be populated at run time. Configure these on the master step.
After you have added file placeholders, you can then enable the display of the Step Setup Settings screen at run time. You can configure this on the master step or the step. However, as with all master step settings, if you enable the screen on the master step, it displays on all steps derived from that master step.
Configure the attachment method for each file added—manual or automatic. You may configure this on the master step or the step.
To enable the Step Setup screen, you must first configure one or more file placeholders on the master step.
On the Lab Work tab, in the Master Steps list, select the master step on which you would like to configure the file placeholders.
Select the Step Setup milestone.
In the File Placeholders section, select Add.
Type a name for the file placeholder.
[Optional] You can copy and paste tokens from theTokens list into the name field. For details, see Derived Sample Naming Convention Tokens.
Enter instructional text.
To set the attachment method, select the Attachment toggle switch to set the file attachment method.
If you set the attachment method to Auto, configure a step automation to generate and attach the file. For details, see #add-and-configure-automations.
To remove a file placeholder, select the X button.
On the Lab Work tab, in the Master Steps or Steps list, select the master step or step on which you would like to configure Step Setup file placeholders.
Select the Step Setup milestone.
At the top of the Step Setup Settings screen, select the toggle switch to enable the Step Setup screen. The screen now displays at run time.
When the Step Setup screen is enabled, it becomes available for selection as an automation trigger location. If you configure an automation trigger location on the Step Setup screen, the Step Setup screen cannot be disabled.
When you create a step and choose the Pooling step type, the Pooling milestone is enabled. When running the step, the Pooling screen allows the lab scientist to create pools of samples.
The following components of the Pooling screen are configurable on the Pooling Settings form.
Enable and disable label uniqueness to control whether samples with the same labels, or no labels, may be pooled together. This must be configured on the master step.
Configure defaults for sample grouping and well sort order. You can configure these settings at the master step or step level.
Select the Label Uniqueness toggle switch to turn label uniqueness on and off.
When Label Uniqueness is On (default setting), samples with the same labels cannot be pooled together.
When Label Uniqueness is Off, samples with the same label or no labels may be pooled together.
Save your changes.
On the Pooling screen, by default samples are:
Grouped by Container
Sorted by well Row (A1, A2, A3, and so on)
Placed by Column (A1, B1, C1, and so on)
You can modify these settings if necessary.
The Placement screen is used for QC steps and for steps that generate derived samples. When the screen displays at run time, it allows manual placement of samples into the destination container.
Note the following:
In tube-only workflows, the Placement screen is disabled by default and samples are automatically placed. This is true for all step types, except Add Labels steps, in which a tube rack Placement screen displays to allow for manual placement of samples.
In the following step types, no sample placement occurs. The Placement screen is disabled and it does not display at run time. Analysis steps
Aggregate QC steps
Standard steps where derived sample generation is set to None.
The Placement Settings form allows for the following configuration.
Turn off the Placement screen and have samples placed automatically into corresponding wells of the destination container (source and destination containers must be the same).
Disable the Placement screen so that it does not display at run time and cannot be viewed. You can only do this on QC steps where no sample placement is required—ie, where samples remain in the same container throughout the step. The step cannot have destination containers configured.
Configure the destination containers that are permitted on the step.
Configure the sample placement defaults—grouping, well sort order, placement pattern, and whether to skip alternate rows/columns in the container.
When the Placement Screen toggle switch is enabled, the Placement screen displays at run time. The lab scientist manually places samples into the destination container.
To turn off the Placement screen:
Select the toggle switch to turn off the Placement Screen and enable autoplacement of samples.
At run time, bypass the Placement screen. If necessary, the user can return to the screen (by selecting its tab) to view placement details.
When the Placement Screen is disabled, the milestone label changes to Auto-Placement. However, if the source and destination containers are not of the same type, Clarity LIMS determines that autoplacement cannot occur and reenables manual placement so that samples can be placed.
Destination containers are the containers into which samples are placed at run time. These containers display to the user in a drop-down list on the Ice Bucket screen. The selected container is then used to set up the subsequent Placement screen.
On the Pooling screen, by default samples are:
Grouped by Container
Sorted by well Row (A1, A2, A3, and so on)
Placed by Column (A1, B1, C1, and so on)
Placed into all container wells - no rows or columns are skipped.
You can modify these settings if necessary.
When you create a step and choose the Add Labels step type, the Add Labels milestone is enabled. When running the step, the Add Labels screen allows the lab scientist to add a reagent label (also known as index or molecular barcode) to each sample.
Note the following:
To add a label group to a step, you must have first configured the label group on the Consumables > Labels configuration screen. For details, see #add-and-configure-labels-and-label-groups.
When you create an Add Labels step, the first label group configured in the system is added to the step automatically.
There must be at least one label group defined on either the master step or the step.
You cannot remove the last label group from the step/master step.
You cannot remove label groups added on the master step from the step.
Label groups are listed in alphanumeric order. The order is not modifiable.
The well sorting setting configured on the #configure-placement-milestone is also applied to the Add Labels screen.
Label groups are the only configurable components on the Add Labels Settings form.
The Record Details screen is where data are tracked on the step at run time. It includes information about the step, files generated by or uploaded to the step, e-Signature sign-off (if enabled), and information about the samples in the step.
The following components of the Record Details screen are configurable on the Record Details Settings form:
The step-level information (step data) tracked on the step. You can also change the heading of the step data section, and set a default value for the Group of Defaults configured on the master step.
Step file placeholders for files that is attached to the step at run time, and their attachment method.
The sample-level information tracked and displayed in the Sample table
Electronic signatures - this panel only displays if you have enabled the clarity.eSignature.enabled property.
The Step Data section of the Record Details screen allows you to track and display step-level data at run time, specifically the master step fields associated with the step.
On the Record Details Settings form, you can configure the following:
The heading that displays at the top of the section.
The default value for the Group of Defaults that displays in the upper-right corner of the screen.
The step data fields that display, and the order and layout in which they display. Note the following:
The default heading is 'Step Data Table'.
You are not required to set a default value for the Group of Defaults.
You are not required to add master step fields or multiline text fields.
When step fields and/or multiline text fields are added, they are arranged vertically by default.
As you configure the step data, the Preview area on the right updates to show you how the configuration displays at run time on the Record Details screen.
NOTE: Multiline text fields are much wider than step fields and always display below them on the Record Details screen. For this reason, they are configured separately.
*Groups of defaults and master step fields are defined on the Custom Fields > Master Step Fields configuration screen. For details, see #add-and-configure-custom-fields.
Configuring file placeholders allows you to attach sample measurement files to a step at run time. For example, you may want to attach an instrument input files or sample sheets, a QC measurement file, a log file, run report, or lab tracking form. Files may be manually uploaded or automatically generated and attached using a script. The default attachment method is manual attachment.
Note the following:
Configure step file placeholders on the master step. You cannot configure or modify these at the step level. A lock icon on the Step Settings form indicates this.
Create a placeholder for each file to be attached.
Configure the attachment method—Manual or Auto, at the master step or the step level. If the attachment method is set on the master step, it cannot be changed at the step level (lock icon displays on the Step Settings form).
The default attachment method is Auto.
In the Sample Table section, if the File Column Display is set to Hide, the Attachment toggle switch is set to Auto and is disabled. To manually attach files in the Sample table, the column must be visible.
The attachment method applies to the shared sample measurement files generated. If you need to set the attachment method for individual files generated for each sample, you can use the API to do this. For details, see API Reference.
At the bottom of the Record Details form, the Sample Table section lets you view and track data on your samples at run time.
On the Record Details Settings screen, you can configure the following components of the Record Details screen Sample table:
The table heading. (Default table heading is 'Sample Table'.)
The display of the QC flags field (when this field is enabled, mark samples with a QC pass or fail flag.
The default display of the Sample table listing. The default view is Collapsed - for faster loading time of the sample list.
The table columns that display in the Sample table, and the order in which they display.
The File Options Column and the File Attachment Method toggle switch only display on the Record Details Settings screen on steps that generate measurements. These settings allow you to choose if you want to display a column for sample files and choose how these files are attached to the step (manually or automatically).
Note the following:
You can enable QC flags on any step type that allows you to mark a sample with a pass or fail flag.
By default, QC flags are enabled on Standard QC steps. This setting is locked and cannot be changed.
By default, QC flags are disabled on Analysis steps. This setting is locked and cannot be changed.
Enable QC flags on a No Outputs step to use the step for QC aggregation.
Sample groupings are collapsed by default to optimize screen loading time, but can also be expanded by default.
If the step generates measurements, Sample File Options display. These allow you to choose if you want to view a column for Sample Files and choose how these files are attached (manually or automatically).
When configuring the Sample table:
No default column headers are configured at the master step level.
When configuring column headers on a new step, several default column headers display. You can remove these; however, the table must have at least one field remaining (this may be set on either the master step or the step).
The Sample table displays in multiple milestone screens. However, the configuration options set in each milestone are specific to that milestone; you may choose to configure other milestone Sample tables differently. The unique aspect of the Record Details Sample table is that the derived sample and submitted sample fields can be written to (according to their respective step type).
Clarity LIMS provides the ability to configure a step such that it requires sign-off by electronic signature (eSignature) before it can be completed.
Steps that have eSignature enabled display an eSignature enforcement button on the Record Details screen, and require valid eSignature credentials (username and password) to be entered.
Next Steps cannot be viewed until these credentials have been entered with eSignature signing permission.
Until the step has been completed, any changes made to the step will again require an eSignature sign off.
All eSignature events, successful or not, are recorded with the step and in the audit trail.
The eSignatures Review configuration panel displays on the Record Details Settings screen only if the clarity.eSignature.enabled property is enabled.
If the panel is enabled, you can configure electronic signatures (e-signatures) on a step or master step. This means that samples in the step cannot move forward (Next Steps button is disabled) until an e-signature has been entered with the appropriate role-based permission.
Milestone settings configured on the master step remain locked on all steps derived from the master step. In this scenario, the milestone displays on the step configuration form with a Locked icon, indicating that these settings are not configurable at the step level.
NOTE: As with all other step settings, if you enable e-signatures on a master step, the setting displays with a Locked icon and is enabled on all steps derived from that master step.
Standard
Standard QC
Aggregate QC
Add Labels
Pooling
Analysis
Demultiplexing
