Lab Work Overview

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.

To view and configure lab work components:

1. On the main menu, select Configuration.

2. Select the Lab Work tab.

   The main navigation panel lists the , , configured in Clarity LIMS. From here, complete the following actions as needed:

Best Practice for Lab Work Configuration

The best practice method for creating and configuring lab work components in Clarity LIMS is as follows.

1. Create and configure master steps.

2. Create and configure protocols.

3. Create and configure steps, adding them to the appropriate protocols, and using the master steps Create and configure workflows, adding required protocols.

Lab Work, Custom Fields and Automations Configuration Restrictions

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 .

• Step automations are configured on the Automations configuration screen. Refer to .

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.

To copy a custom field from step input to output

1. 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"

2. 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.

3. 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.

4. You can add it as an expanded view field or as a column header (for details, refer to ).

5. 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.

After signing into Clarity LIMS, you can update some of the details associated with your profile, including your password, email address, and profile photo.

Update User Profile

1. In Clarity LIMS, at the right of the menu bar, select your username and then select Profile.

2. The Profile page opens, displaying the details associated with your user profile.

3. On this page, you can:

Reset a forgotten password

1. On the Sign In screen, click the Forgot your password link.

2. In the Reset Your Password screen, enter your username or email address and click Submit.

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.

Old Methods (all versions)

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.

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.

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 ).

System Administrator and Facility Administrator

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.

Researcher

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.

Collaborator

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.

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.

Archive a User

1. On the main menu, select Configuration.

2. Select User Management.

3. Select the Users tab to see a list of all current active and archived users in the system, categorized by role.

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.

Reset a User Password

1. On the main menu, select Configuration.

2. Select User Management.

3. Select the Users tab to see a list of all current active and archived users in the system.

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.

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.

User Management Configuration Screen

• 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 .

Add and Manage Users and Clients

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).

Add a User

1. From User Management, select the Users tab.

2. Select inside the Role field to display a drop-down list of roles:

   • Select the role to assign to this user.

Modify User Details

1. From User Management, select the Users tab.

2. Select the user to modify.

3. 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.

Delete a User

1. From User Management, select the Users tab.

2. Select the user to delete.

3. 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 .

Add and Modify Clients

When adding new clients, each client must be a unique entry in the LIMS.

To add a client:

1. From User Management, select the Clients tab.

2. Select New Client.

3. In the Client Details area, complete the following required information:

Delete a Clients

A client cannot be deleted if that client is associated with a project.

1. From User Management, select the Clients tab.

2. Select the client to delete.

3. In the Client Details area, select Delete.

Add and Manage Accounts

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.

Add a New Account

1. From Configuration, select the User Management tab.

2. Select the Accounts tab.

3. In the Account Details area, select New Account.

Modify Account Details

1. From Configuration, select the User Management tab.

2. Select the Accounts tab.

3. In the Accounts list, select the account that you want to modify.

Delete an Account

1. From Configuration, select the User Management tab.

2. Select the Accounts tab.

3. In the Accounts list, select the account that you want to delete.

Controls Configuration Screen

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.

Containers Configuration Screen

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.

Labels Configuration Screen

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 .

Add and Configure Labels and Label Groups

When adding label groups and labels to the LIMS, there are several main steps involved:

1. Add a new label group.

2. Then, to add labels to the group:

   • Download a template label list (Microsoft® Excel® file) from the Labels configuration screen.

Add a New Label Groups

1. On the main menu, select Configuration.

2. On the configuration screen, select the Consumables tab and then select Labels.

3. On the Labels configuration screen, select New Label Group.

Add Label to Label Groups

1. On the Labels configuration screen, in the Label Groups list, select the label group to which you want to add labels.

2. In the Label Group Details area, select Download Label List to download the template.

3. Open the template in Excel. It has two example label entries containing the following information:

Edit and Delete Label Groups

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.

• To make changes to the labels within the group, you must upload a modified label list. See .

• Deleting a label group does not affect historical run data. This information is preserved in the LIMS.

Edit and Delete Label

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.

Label List Upload Error Conditions

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.

Configure Workflows

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.

View Workflows

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:

1. On the main menu, select Configuration.

2. Select the Lab Work tab.

3. In the Workflows list, select a workflow to highlight it.

Workflow 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.

Add Workflows

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.

Add a new workflow

1. On the Lab Work configuration screen, in the upper-right corner of the Workflow list, select Add.

2. Below the main navigation panel, the workflow configuration form displays.

3. To begin, type a name for your new workflow.

Add protocols to a workflow

1. In the Workflow list, select the workflow.

2. 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.

3. Repeat step 2 until you have added all required protocols to the workflow.

Modify and Activate Pending workflow

1. On the Lab Work configuration screen, in the Workflow list, select the Pending workflow to modify or activate.

2. 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.

Archive and Reactivate 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:

1. On the Lab Work configuration screen, in the Workflow list, select the Active workflow to archive.

2. In the Workflow Settings area, select Archive. Select Save.

To reactivate an archived workflow:

1. On the Lab Work configuration screen, in the Workflow list, select the Archived workflow to reactivate.

2. In the Workflow Settings area, select Activate. Select Save.

Delete Workflows

1. On the Lab Work configuration screen, in the Workflow list, select the pending workflow to delete.

2. On the workflow configuration form, select Delete.

3. Confirm the workflow deletion:

You can only delete a workflow while the workflow remains in the Pending state. You cannot delete Active or Archived workflows.

Reagents Configuration Screen

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

The Instruments Configuration Screen

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 .

Add and Configure Instruments

When adding instruments to Clarity LIMS, there are two main steps involved:

1. Add a new instrument type (Configuration:update permission required).

2. 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.

Add a New Instrument Type

1. On the main menu, select Configuration.

2. On the configuration screen, select the Consumables tab, then select Instruments.

3. On the Instruments configuration screen, select New Instrument Type.

Add a New Instrument

1. On the Instruments configuration screen, in the Instrument Types area, select the appropriate instrument type.

2. Select New Instrument.

3. In the Instrument Details area, enter the details for this instrument.

Instrument Status

The instrument Status toggles between Active and Archived. By default, when adding a new instrument, its status is Active.

Active instruments:

• 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.

Archived 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.

Edit in Instrument Types and Instruments

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.

Delete Instrument Types and 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.

Reactivate an Archived instrument

1. In the Instrument Types area, expand the Archived Instruments section and select the instrument to reactivate.

2. If the instrument has not expired, select Activate.

3. If the instrument has expired, reset the expiry date to a date in the future, and then select Activate.

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.

Simple Tokens

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

{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

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.

Configure 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

View Protocols

1. On the main menu, select Configuration.

2. Select the Lab Work tab.

   The Workflows, Protocols, Steps, and Master Steps navigation panel displays.

3. In the Protocols list, select a protocol to highlight it:

Protocol 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.

Add Protocols

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 , you must select Save to save your changes.

To add a protocol:

1. 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.

2. To begin, type a name for the new protocol.

3. Select the settings for this protocol (For details, see ):

Add Steps to 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.

To add a step to a protocol:

1. In the Protocols list, select the protocol.

2. In the upper-right corner of the Steps list, select Add.

   Below the main navigation panel, the step configuration form displays.

3. Type a name for the new step.

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.

To configure next steps

1. In the Next Steps table, select a cell to select (or deselect) one or more permitted next steps.

2. In the Start Next Step and Assign Next Step rows, select a cell to switch between Manual and Automatic.

Configure QC Filters

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.

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.

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.

Modify Protocols

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:

1. In the Protocols list, select the protocol.

2. 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.

Delete Protocols

To delete a protocol:

1. In the Protocols list, select the protocol.

2. 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.

Copy Protocols

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.

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 .

Copy a Protocol and its Step

1. On the main menu, select Configuration.

2. On the LIMS configuration screen, select the Lab Work tab.

3. In the main navigation panel, in the Protocols list, select the protocol to copy.

Update Custom Field Default on Copied Master Steps

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.

Automation Configuration Screen

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 User Roles and Configured Role-Based Permissions.

Add and Configure Automations

You can create three types of automations in Clarity LIMS: step automations, project automations, and derived sample automations.

• 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

Before you begin

• 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:

Add a Step Automation

1. On the main menu, select Configuration.

2. On the configuration screen, select the Automation tab.

3. On the Step Automation tab, select New Automation.

Attach Template Files to Step Automation

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.

To attach a template file:

1. In the Template Files section, select Upload File.

2. In the Upload File dialog, select Choose File, and then browse to and select the appropriate template file.

3. 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.

Add a Derived Sample Automation

1. On the Derived Sample Automation tab, select New Automation.

2. In the Automation Details area, complete the required fields:

   • Type a name for the new automation.

The following examples show how derived sample automations can be used in the lab.

Add a Project Automation

1. On the Project Automation tab, select New Automation.

2. In the Automation Details area, complete the required fields:

   • Type a name for the new automation.

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.

Edit an Automation

1. On the Automation Configuration screen, select one of the following tabs:

   • Step Automation

   • Project Automation

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.

Delete an Automation

1. On the Automation Configuration screen, select one of the following tabs:

   • Step Automation

   • Project Automation

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.

Custom Fields Configuration Screen

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 and .

Add and Configure Custom Fields

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.

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.

Add a Custom Field

1. On the main menu, select Configuration.

2. On the configuration screen, select the Custom Fields tab.

3. On the Custom Fields configuration screen, select the Global Fields or Master Step Fields tab.

Field Details

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.

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.

Field Types and Additional Options

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

Toggle Switch Field Types

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.

Additional Optional Usage

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

Edit and Delete Custom Fields

This section describes how to edit and delete custom fields.

Edit Custom Fields

1. On the Custom Fields configuration screen, select the Global Fields or Master Step Fields tab.

2. Expand the global field object group or master step containing the field to edit.

3. Select the field.

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.

Delete Custom Fields

1. On the Custom Fields configuration screen, select the Global Fields or Master Step Fields tab.

2. Expand the global field group or master step containing the field you would like to delete.

3. 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.

Reorder Global Fields

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 section of the 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).

Configure Groups of Defaults

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.

Add a Group of Defaults

1. On the Custom Fields configuration screen, select the Master Step Fields tab.

2. Expand the master step on which to configure a group of defaults.

3. Below the configured master step fields, in the Group of Defaults section, select Add.

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]