To requeue and rework samples, specific role-based permissions are required. For details, see Configured Role-Based Permissions.
Occasionally, a sample must be rerun through a particular step. For example, there may have been a technical error in the lab. More sequencing may be needed at the end of a workflow if there are not enough samples.
To solve this problem, return samples to the queue and repeat the step.
There are several ways to requeue samples:
Search for the step with samples to requeue, view all samples that have completed this step, and choose the ones to requeue. See
Search for a specific sample to requeue. See
In the header, select Search.
Select Protocol Step from the drop-down list of search categories, type the step to search for, and press the Enter key.
Select Sample from the drop-down list of search categories, type the sample name to search for, and press the Enter key.
Expand the search results details to view all the steps performed on the sample and select Requeue to return the sample to the queue for the required step.
In addition to requeueing samples for the same step, you can also rework samples from a previous step. For example, an action is needed if there is an insufficient quantity of a particular sample to meet the required target concentration level.
In the Assign Next Steps screen, select the next step drop-down list, select Rework from an earlier step.
All the steps performed on the sample are listed, up to and including the current step. Select the required step and select OK.
If a sample has been flagged for manager review, the manager can select Rework from an earlier step directly from the Review Samples screen.
In the search results list, select the arrow to the right of the step name to show details for all the samples that have been run through the step.
Select Requeue to requeue samples as required.
The Rework from <step name> option is reflected in the next steps field.
The sample no longer advances in the workflow, but the sample is now found in the queue for the selected rework step.
As lab scientists work with samples in the lab, they may request a manager to review a sample at a certain step in the workflow. When a request for review occurs, an alert notification displays in Lab View, in the Recent Activities area.
In Lab View, in the Recent Activities area, select an alert to go directly to the step containing the sample to be reviewed.
Review the sample, add a comment, and select Finish Review.
NOTE: You can also view and resolve alerts from
When working on a step, you can create multiple aliquots of each sample, move one aliquot to the next step in the workflow, and store the others for later use.
Add samples to the Ice Bucket.
In the Ice Bucket, create the required number of sample aliquots.
To create the same number of aliquots for all samples, select the number of derivatives to create and select Apply All. (The number adjacent to each sample updates automatically.)
To create a different number of aliquots for each individual sample, adjust the number adjacent to each sample.
To store an aliquot for later use, select Store for later from the next step drop-down list.
In the Search drop-down list, select Sample, type the sample name, and press the Enter key.
In the search results, all the sample aliquots are listed.
Select a sample aliquot to expand the details.
A prompt appears to confirm this step.
To modify the information captured on the Record Details screen of a completed step, the CanEditCompletedSteps permission is required. This functionality allows for modifications to correct errors and/or bad data.
The CanEditCompletedSteps permission is not assigned to any user roles by default. A Clarity LIMS administrator must explicitly assign the permission to each user who requires it. See the and sections for details.
NOTE: Signature is not enforced again when editing completed steps. For recommended best practice, the role with CanEditCompletedSteps permission should be the same role that electronically signs off on steps. See for details.
Users who have been assigned the CanEditCompletedSteps permission see an Edit button on the Assign Next Steps screen of completed steps. Selecting this button takes them to the Record Details screen, where they may modify certain step details.
After it is confirmed, the search results update and the sample are shown as queued for the next step in the workflow.
In Lab View, the sample aliquot is now ready to be worked on.
The following table lists and describes the step details that can be modified:
Step details
Description
Reagent lots
The reagent lots that were originally used when executing the step can be removed, and new ones added, but at least one lot must be selected. Reagent lots of any status (Pending, Active, Archived) can be used. Archived and expired lots can be selected.
Instruments
A new instrument can be selected. At least one instrument must be used. Instruments of any status (Active, Archived, Expired) can be used. Archived instruments can be selected.
Step custom fields
Step custom fields can be modified with the same constraints as when the step was originally executed (e.g. readonly fields will still be readonly, required fields will still be required).
Sample table custom fields
Sample table custom fields can be modified with the same constraints as when the step was originally executed (e.g. read only fields will still be read only, required fields will still be required). The QC flag can be changed.
Files
Existing files can be removed and new files can be uploaded. Files that are script generated cannot be modified.
To ensure the integrity of data, the following rules and constraints are in place when editing a completed step:
Only steps that were completed in Clarity LIMS v5.1 and later are editable. If the system is upgraded to Clarity LIMS v5.1 or later, steps that were completed in a previous version cannot be edited.
Steps that were executed using the API cannot be edited.
If the configuration of a completed step changes after the step was run, it cannot be modified. This constraint includes any changes made to the protocol or workflow in which the step is included.
The automations enabled on the step.
The automation triggers configured on the step.
An automation cannot be rerun on a completed step. The details of the automation command line cannot be viewed.
Manager review/escalation comments on completed steps cannot be edited.
The eSignature is not enforced again when editing completed steps. The eSignature from the original step execution is retained. There is not a prompt for a new signature when editing the step.
On the Assign Next Steps screen of the completed step, select Edit (upper-right corner).
A prompt displays to confirm the desire to proceed and edit the step details.
Select Yes to confirm.
The Record Details screen displays.
Modify the step details as required.
Review your changes and select Save.
Lab View is the main screen in Clarity LIMS.
Lab View shows the protocols and steps used in the lab, and the number of samples queued for each step. Use this screen to do the following:
See recent lab activities.
See in-progress steps and steps that are ready to be worked on.
View and follow up on Alert Notifications.
When users run a step in the LIMS, they typically select a destination container type from a preconfigured list in the Ice Bucket screen, and then proceed to the Record Details screen - where they scan the barcode of a new container to add it to the LIMS.
However, users may sometimes want to place samples into an existing container - that is, a container whose barcode has already been entered into the LIMS. This is easily achieved in the Ice Bucket screen.
In Lab View, open the step containing the samples you want to place into an existing container.
Select the samples and add them to the Ice Bucket.
In the Ice Bucket screen, in the Container Options panel:
In the Destination Container drop-down list, select the desired container type.
In the Find Existing Container field, type the name or Clarity LIMS ID of the container in which to place the samples. While typing, Clarity LIMS presents a filtered list of containers with matching names or Clarity LIMS IDs. Select the appropriate container from the list.
Click Begin Work to proceed to the Record Details screen.
Occasionally, you must remove samples from a workflow queue in Clarity LIMS. Only administrator users can perform this operation.
In Clarity LIMS, open the step containing the samples to remove.
Select one or more samples, expand the Options drop-down list and select Remove.
The Options drop-down list is available to administrator users only.
If necessary, complete the following actions:
Search for the samples in Clarity LIMS.
Requeue them for a previous step.
Usually, samples move through the system according to the sequence of protocols and steps defined in a workflow.
However, sometimes samples are moved into the next step manually.
For example, suppose you must delete a step from a particular protocol. If there are samples queued for the step, they are not able to delete it. In this case, you can move the samples forward into the next step and proceed with the step deletion (see ).
In Clarity LIMS, open the step containing the samples to move.
Select one or more samples, expand the Options drop-down list and select Move.
The samples move into the subsequent step in the protocol.
In Clarity LIMS, the outcome of the next step selection for sample outputs depends on whether those outputs are derived samples, pools, or derivatives.
The following tables summarize the expected results when choosing next steps for these three output types.
Resolution Option
Input Result
Output Result
Next Step
Remains in workflow, but not queued for any steps
Queued for next step in the protocol
Mark Complete (last step in protocol; not last protocol in workflow)
Remains in workflow, but not queued for any steps
Queued for first step in next protocol
Mark Complete (last step in last protocol in workflow)
No longer in the workflow
No longer in the workflow
Repeat This Step
Requeued for same step
No longer in the workflow
Resolution Option
Input Result
Output Result
Next Step
Remains in workflow, but not queued for any steps
Queued for next step in the protocol
Mark Complete (last step in protocol; not last protocol in workflow)
Remains in workflow, but not queued for any steps
Queued for first step in next protocol
Mark Complete (last step in last protocol in workflow)
No longer in the workflow
No longer in the workflow
Repeat This Step
Requeued for same step
No longer in the workflow
Resolution Option
Input Result
Output Result
Next Step
Remains in workflow, but not queued for any steps
Queued for next step in the protocol
Mark Complete (last step in protocol; not last protocol in workflow)
Remains in workflow, but not queued for any steps
Queued for first step in next protocol
Mark Complete (last step in last protocol in workflow)
No longer in the workflow
No longer in the workflow
Repeat This Step
Remains in workflow but not in any of its queues
Replicates re-queued for replication step
Remove from Workflow
No longer in the workflow
No longer in the workflow
Request Review
In progress for same step
In progress for same step, but not in any queues
Rework from Earlier Step
Queued for specified earlier step
No longer in the workflow
Complete and Repeat (not last step in protocol)
Requeued for same step
Queued for next step in the protocol
Complete and Repeat (last step in protocol; not last protocol in workflow)
Requeued for same step
Queued for first step in next protocol
Complete and Repeat (last step in last protocol in workflow)
Requeued for same step
No longer in workflow
Remove from Workflow
No longer in the workflow
No longer in the workflow
Request Review
In progress for same step
In progress for same step, but not in any queues
Rework from Earlier Step (option not available for pooled output)
NA
NA
Complete and Repeat (not last step in protocol)
Requeued for same step
Queued for next step in the protocol
Complete and Repeat (last step in protocol; not last protocol in workflow)
Requeued for same step
Queued for first step in next protocol
Complete and Repeat (last step in last protocol in workflow)
Requeued for same step
No longer in workflow
Remove from Workflow
No longer in the workflow
No longer in the workflow
Request Review
In progress for same step
In progress for same step, but not in any queues
Rework from Earlier Step (this same step)
Requeued for same step
No longer in workflow
Rework from Earlier Step (another previous step)
Requeued for specified step
No longer in workflow
Complete and Repeat (not last step in protocol)
Requeued for same step
Queued for next step in the protocol
Complete and Repeat (last step in protocol; not last protocol in workflow)
Requeued for same step
Queued for first step in next protocol
Complete and Repeat (last step in last protocol in workflow)
Requeued for same step
No longer in workflow
Store for Later (only for replicates)
Remains in workflow<
Not in any queue