Clarity LIMS v6.2 & Lablink v2.4
Illumina Connected Software

Step Milestones

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.

Milestones and Step Types

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 TypeQueueIce BucketStep Setup*PoolingPlacementAdd LabelsRecord Details

Standard

Standard QC

Aggregate QC

Add Labels

Pooling

Analysis

Demultiplexing

*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.

Configuring Milestones

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

Configure Queue Milestone

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

Configure Sample Table Column Headers

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).

Add a Column Header

  1. On the Queue Settings form, in the Sample Table section, select Add.

  2. At the right of the screen, a list of fields displays, grouped by Measurement, Derived Sample, Submitted Sample, Container, and Project.

    These are the groups of custom fields configured on the Custom Fields > Global Fields configuration screen.

  3. Select the arrows to expand the groupings and view the fields within each group.

  4. Select one or more fields, and then select the checkmark to add them to the Sample Table area. Select fields individually, Shift + select to select multiple adjacent fields, or Ctrl + select to select multiple nonadjacent fields.

  5. As you add column headers, you may notice that the display changes from a horizontal to a vertical layout. This is an indication that you have exceeded the recommended optimum width of the table. You may want to consider removing some fields.

  6. Save your changes

    NOTE: While there is no limit to the number of column headers that can be added to the Sample table, we recommend a maximum of six columns. As more columns are added, each becomes narrower and this can make the heading text difficult to read.

Remove a Column Header

  1. Select the X button that displays beneath (or next to, if fields are listed vertically) the column header you want to remove.

  2. Save your changes.

Reorder Column Headers

  1. Select a column header and then drag it into its new position.

  2. Save your changes.

    NOTE: 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 will appear to lift off the page and its color will change to white. You can then drag the item and drop it into its new position.

Configure Sample Table Expanded View Fields

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.

Add Expanded View Fields

  1. In the Expanded View Fields section, select Add.

  2. At the right of the screen, a list of fields displays. These are the groups of custom fields configured on the Custom Fields > Global Fields configuration screen. Any fields already included in the Expanded View Fields list do not display in the list.

  3. Select the arrows to expand the groupings and view the fields within each group.

  4. Select one or more fields, and then select the checkmark to add them to the Expanded View Fields list. Select fields individually, Shift + select to select multiple adjacent fields, or Ctrl + select to select multiple nonadjacent fields.

  5. Save your changes.

Remove Expanded View Fields

  1. Select the X that displays next to the field you want to remove.

  2. Save your changes.

Reorder Expanded View Fields

  1. Select a field and then drag it into its new position.

  2. Save your changes.

Configure Sample Table Defaults

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.

Set Default Sample Grouping

  1. In the Sample Grouping drop-down list, select your preferred default sample grouping option.

  2. You can choose to group by:

    • The project (in which samples belong).

    • The container (in which the samples are currently located).

    • The submitted sample (from which the samples originated).

    • The previous step (the samples have undertaken).

  3. Save your changes.

Set Well Sort Ordering

  1. Select the Well Sort Order toggle switch to set the default well sort ordering to Column (A1, B1, C1, and so on) or Row (A1, A2, A3, and so on).

  2. Save your changes.

NOTE: Well Sort Order setting is only applicable to Sample List Table View.

Configure Ice Bucket Milestone

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

Configure Sample Table Column Header

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).

Add a Column Header

  1. On the Ice Bucket Settings form, in the Sample Table section, select Add.

  2. At the right of the screen, a list of fields displays, grouped by Measurement, Derived Sample, Submitted Sample, Container, and Project.

    These are the groups of custom fields configured on the Custom Fields > Global Fields configuration screen.

  3. Select the arrows to expand the groupings and view the fields within each group.

  4. Select one or more fields, and then select the checkmark to add them to the Sample Table area. Select fields individually, Shift + select to select multiple adjacent fields, or Ctrl + select to select multiple nonadjacent fields.

  5. As you add column headers, you may notice that the display changes from a horizontal to a vertical layout. This is an indication that you have exceeded the recommended optimum width of the table. You may want to consider removing some fields.

  6. Save your changes

    NOTE: While there is no limit to the number of column headers that can be added to the Sample table, we recommend a maximum of six columns. As more columns are added, each becomes narrower and this can make the heading text difficult to read.

Remove a Column Header

  1. Select the X button that displays beneath (or next to, if fields are listed vertically) the column header you want to remove.

  2. Save your changes.

Reorder Column Headers

  1. Select a column header and then drag it into its new position.

  2. Save your changes.

    NOTE: 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 will appear to lift off the page and its color will change to white. You can then drag the item and drop it into its new position.

Configure Sample Table Expanded View Fields

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.

Add Expanded View Fields

  1. In the Expanded View Fields section, select Add.

  2. At the right of the screen, a list of fields displays. These are the groups of custom fields configured on the Custom Fields > Global Fields configuration screen. Any fields already included in the Expanded View Fields list do not display in the list.

  3. Select the arrows to expand the groupings and view the fields within each group.

  4. Select one or more fields and then select the checkmark button to add them to the Expanded View Fields list. You can select fields individually, Shift + select to select multiple adjacent fields, or Ctrl + select to select multiple nonadjacent fields.

  5. Save your changes.

Remove Expanded View Fields

  1. Select the X that displays next to the field you want to remove.

  2. Save your changes.

Reorder Expanded View Fields

  1. Select a field and then drag it into its new position.

  2. Save your changes.

Configure Sample Table Defaults

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.

Set Default Sample Grouping

  1. In the Sample Grouping drop-down list, select your preferred default sample grouping option.

  2. You can choose to group by:

    • The project (in which samples belong).

    • The container (in which the samples are currently located).

    • The submitted sample (from which the samples originated).

    • The previous step (the samples have undertaken).

  3. Save your changes.

Set Well Sort Ordering

  1. Select the Well Sort Order toggle switch to set the default well sort ordering to Column (A1, B1, C1, and so on) or Row (A1, A2, A3, and so on).

  2. Save your changes.

NOTE: Well Sort Order setting is only applicable to Sample List Table View.

Configure Step Setup Milestone

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.

Add a File Placeholder

  1. On the Lab Work tab, in the Master Steps list, select the master step on which you would like to configure the file placeholders.

  2. Select the Step Setup milestone.

  3. In the File Placeholders section, select Add.

  4. Type a name for the file placeholder.

  5. [Optional] You can copy and paste tokens from theTokens list into the name field. For details, see Derived Sample Naming Convention Tokens.

  6. Enter instructional text.

Set the Attachment Method

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.

Remove a File Placeholder

To remove a file placeholder, select the X button.

Enable the Step Setup Screen

  1. 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.

  2. Select the Step Setup milestone.

  3. 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.

Configure Pooling Milestone

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.

Configure Label Uniqueness

  1. 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.

  2. Save your changes.

Configure Pooling Screen Defaults

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.

Set Default Sample Grouping

  1. In the Sample Grouping drop-down list, select your preferred default sample grouping option.

  2. You can choose to group by:

    • The project (in which samples belong).

    • The container (in which the samples are currently located).

  3. Save your changes.

Set Well Sort Ordering

  1. Select the Well Sort Order toggle switch to set the default well sort ordering to Column (A1, B1, C1, and so on) or Row (A1, A2, A3, and so on).

  2. Save your changes.

NOTE: Well Sort Order setting is only applicable to Sample List Table View.

Configure Placement Milestone

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.

Configure Display of the Placement Screen

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.

Configure Destination Containers

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.

Before You Begin

When creating a step that supports placement, keep the following details in mind:

  • By default, any destination containers configured on the master step are added to the step.

  • If the master step does not have a destination container set, and the step is not a QC step, then the Tube container type is added by default. If no such container type exists, the first 'tube-like' (eg., single well) container, and that failing, the first container type available, is associated to the step.

  • Destination containers configured at the master step level display as locked at the step level - you cannot remove them from the step. However, you can modify the order in which the locked containers display in the drop-down list.

Also note the following:

  • Destination containers configured at the master step level display as locked and cannot be removed at the step level. However, you can modify the order in which the locked containers display in the drop-down list.

  • To add destination containers to a step, you must have first configured those containers on the Containers configuration screen. See Add and Configure Containers

  • You can add, reorder, and remove containers freely, but you must choose at least one container if your step type requires placement (either via autoplacement or via manual placement during run time).

  • If the container is a tube or other single well container that is treated like a tube, an Autoplace label displays on the container, to inform you that the Placement screen does not display at run time. This behavior is controlled by a toggle switch that displays on the Containers configuration screen when configuring single-well containers. (The exception to this is for Add Labels steps, which display a tube rack Placement screen for placing samples into tube-like containers.)

Add a Destination Container

  1. In the Destination Containers section, select Add.

  2. At the right of the screen, a list of container types displays. These are the containers configured on the Containers configuration screen.

  3. Select one or more containers and then select the checkmark button to add them to the Destination Containers list. You can select containers individually, Shift + select to select multiple adjacent fields, or Ctrl + select to select multiple nonadjacent fields.

  4. Save your changes.

    NOTE: To add destination containers to a step, you must have first configured those containers on the Containers configuration screen. For details, see Add and Configure Containers.

Remove a Destination Container

  1. Select the X button that displays next to the container you want to remove. (you cannot remove the last container from a step.)

  2. Save your changes.

Reorder a Destination Container

  1. Select a container and then drag it into its new position.

  2. Save your changes.

    NOTE: To drag and drop on a mobile or touch-screen device, touch and hold the item you wish to drag. After a moment, the item appears to lift off the page and its color changes to white. You can then drag the item and drop it into its new position.

Configure Placement Screen Defaults

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.

Set Default Sample Grouping

  1. In the Sample Grouping drop-down list, select your preferred default sample grouping option.

  2. You can choose to group by:

    • The project (in which samples belong).

    • The container (in which the samples are currently located).

  3. Save your changes.

Set Well Sort Ordering

  1. Select the Well Sort Order toggle switch to set the default well sort ordering to Column (A1, B1, C1, and so on) or Row (A1, A2, A3, and so on).

    The well sort ordering configured here is also applied to the Add Labels screen.

  2. Save your changes.

NOTE: Well Sort Order setting is only applicable to Sample List Table View.

Set the Placement Pattern

  1. Select the Placement Pattern toggle switch to set the default placement pattern to either Column, Row, or Same Shape.

  2. Save your changes.

Skip Alternating Rows or Columns

  1. Select the Skip Alternating Rows or Skip Alternating Columns toggle switch to skip alternate rows or columns in the destination container when samples are placed.

  2. Save your changes.

Configure Add Labels Milestone

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.

Add a Label Group

  1. On the Add Labels Settings form, in the Label Groups section, select Add.

  2. At the right of the screen, the Label Groups list displays.

    These are the label groups configured on the Consumables > Labels configuration screen (see Add and Configure Labels and Label Groups).

  3. Select one or more label groups and then select the checkmark to add them to the Label Groups area. Select groups individually, Shift + select to select multiple adjacent fields, or Ctrl + select to select multiple nonadjacent groups.

    The selected label groups are added to the list.

  4. Save your changes.

Delete a Label Group

  1. To remove a label group, select its X button.

Remember that 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 - the X button does not display.

Configure Record Details Milestone

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.

Configure Step Data

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.

Change the Step Data Heading

  1. In the Step Data Heading field, type your preferred heading.

  2. Save your changes.

Select a Default Group of Defaults

  1. Expand the Group of Defaults drop-down list and select the group of defaults you would like to use.

  2. Save your changes.

Select the Master Step Fields to Display

  1. In the Master Step Fields section, select Add.

  2. At the right of the screen, the step fields that are configured on the master step are listed.

  3. Select a field and then select the checkmark button to add it to the Display Step Fields list. Select fields individually, Shift + select to select multiple adjacent fields, or Ctrl + select to select multiple nonadjacent fields. After you have added a field, it is removed from the list on the right.

  4. If necessary, you can reorder fields by clicking and dragging them into position.

    On the right, the preview area updates to show you how the fields display at run time.

  5. Save your changes.

Select the Multiline Text Fields to Display

  1. In the Multiline Text Fields section, select Add.

  2. At the right of the screen, any multiline fields that are configured on the master step are listed.

  3. Select a field and then select the checkmark button to add it to the Multiline Text Fields list. Select fields individually, Shift + select to select multiple adjacent fields, or Ctrl + select to select multiple nonadjacent fields. After you have added a field, it is removed from the list on the right.

  4. If necessary, reorder fields by clicking and dragging them into position. On the right, the preview area updates to show you how the fields display at run time.

  5. Save your changes.

Set the Field Order

  1. Select the Field Order toggle switch to determine whether step fields are arranged horizontally or vertically, and the tab order of the fields. Multiline fields are not included in the field order and always display below the step field columns.

    The preview area updates to show you how the fields display at run time.

  2. Save your changes.

Configure Step File Placeholders

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.

Add a Step File Placeholder

  1. On the Lab Work tab, in the Master Steps list, select the master step on which you would like to configure file placeholders.

  2. Select the Record Details milestone.

  3. In the Step File Placeholders section, select Add.

  4. Type a name for the file placeholder. You can copy and paste tokens into the name, if necessary. For details, see Derived Sample Naming Convention Tokens.

Set the Attachment Method

  1. On the Master Step Settings form or Step Settings form, select the Attachment toggle switch to determine whether files are to be attached manually or automatically by a script.

  2. Save your changes.

Configure the Sample Table

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).

Change the Sample Table Heading

  1. In the Table Heading field, type your preferred heading.

  2. Save your changes.

Enable/Disable QC Flags

  1. Select the Enable QC Flags toggle switch to enable or disable the QC column in the Sample table.

    • When enabled, the QC column displays and must be written to - each sample must be assigned either a QC pass or QC fail flag.

    • When disabled, the QC column does not display.

  2. Save your changes.

Set the Default Display for the Sample Table Fields

  1. Select the Sample Display Default toggle switch to set the default sample display to Expand or Collapse.

  2. Save your changes.

Add Sample Table Columns

  1. In the Table Columns section, select Add.

  2. At the right of the screen, a list of fields displays, grouped by Measurement, Derived Sample, Submitted Sample, Container, and Project. These are the groups of custom fields configured on the Custom Fields > Global Fields configuration screen.

  3. Select the arrows to expand the groupings and view the fields within each group.

  4. Select one or more fields and then select the checkmark button to add them to the Table Columns area. Select fields individually, Shift + select to select multiple adjacent fields, or Ctrl + select to select multiple nonadjacent fields.

  5. As you add column headers, you may notice that the display changes from a horizontal to a vertical layout. This is an indication that you have exceeded the recommended optimum width of the table, and you may want to consider removing some fields.

  6. Save your changes

    NOTE: While there is no limit to the number of column headers that can be added to the Sample table, we recommend a maximum of six columns. As more columns are added, each becomes narrower and this can make the heading text difficult to read.

Remove a Column Header

  1. Select the X button that displays beneath (or next to, if fields are listed vertically) the column header you want to remove.

  2. Save your changes.

Reorder Column Headers

  1. Select a column header and then drag it into its new position.

  2. Save your changes.

    NOTE: 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 will appear to lift off the page and its color will change to white. You can then drag the item and drop it into its new position.

Configure eSignatures

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.

Who Can Sign

Permission to sign an eSignature is a role-based permission. For details, refer to Configured Role-Based Permissions.

By default, lab scientists cannot sign off on their own work.

Configuration Tool and Properties

eSignature enforcement is achieved by configuring the eSignature.Enabled and eSignature.RequiresDifferentReviewer properties, using the omxprops-ConfigTool.jar tool at:

/opt/gls/clarity/tools/propertytool

  • eSignature.Enabled

    • Description: Enables/disables eSignature for step execution

    • Default value: false

    • Result: By default, eSignature enforcement on step execution is not enabled.

  • eSignature.RequiresDifferentReviewer

    • Description: Determines whether the eSignature must be provided by someone other than the person executing the step.

    • Default value: true

    • Result: By default, if eSignature.Enabled is set to "true", the eSignature must be provided by someone other than the person executing the step.

To change the default settings for eSignature enforcement, contact the Clarity LIMS Support team for assistance.

Configuring Steps to Require an eSignature

When eSignature is globally enabled, you can enable/disable eSignature requirement for any step.

This setting is available on the Record Details milestone in master step/step configuration (accessible from the Lab Work configuration screen). For details, see Configure Record Details Milestone.

By default, eSignature is enabled for steps.

When eSignature is enabled for a step:

  • The Record Details screen shows the eSignature button and the Next Steps button is disabled.

  • Selecting eSignature opens a dialog that requires valid eSignature credentials to be entered. Before proceeding to the next step, another user with the permission to sign eSignatures must sign in to the system and sign the eSignature.

  • After valid eSignature credentials have been entered, the Next Steps button is enabled. Hovering over the eSignature button displays a tooltip showing who signed the step and when.

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