> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/clarity-lims/api-and-database.md). # API and Database - [API Portal](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs.md) - [REST](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest.md) - [Filtering List Resources](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest/filtering-list-resources.md) - [HTTP Response Codes and Errors](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest/http-response-codes-and-errors.md) - [Requesting API Version Information](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest/requesting-api-version-information.md) - [REST General Concepts](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest/rest-general-concepts.md) - [REST Web Services](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest/rest-web-services.md) - [Traversing a Genealogy](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest/traversing-a-genealogy.md) - [Viewing Paginated List Resources](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest/viewing-paginated-list-resources.md) - [Working with Batch Resources](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest/working-with-batch-resources.md) - [Working with User-Defined Fields (UDF) and Types (UDT)](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest/working-with-user-defined-fields-udf-and-types-udt.md) - [XML UTF-8 Character Encoding](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/rest/xml-utf-8-character-encoding.md) - [Getting Started with API](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/getting-started-with-api.md) - [API-Based URIs (LIMS v4 and later)](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/getting-started-with-api/api-based-uris-lims-v4-and-later.md) - [Development Prerequisites](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/getting-started-with-api/development-prerequisites.md) - [Integrating Scripts](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/getting-started-with-api/integrating-scripts.md) - [Structure of REST Resources](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/getting-started-with-api/structure-of-rest-resources.md) - [The Life Cycle of a Sample: Stages Versus Steps](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/getting-started-with-api/the-life-cycle-of-a-sample-stages-versus-steps.md) - [Understanding API Terminology (LIMS v5 and later)](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/getting-started-with-api/understanding-api-terminology-lims-v5-and-later.md) - [Automation](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation.md) - [Automation Channels](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/automation-channels.md) - [Automation Execution Environment](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/automation-execution-environment.md) - [Automation Testing](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/automation-testing.md) - [Automation Tokens](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/automation-tokens.md) - [Derived Sample Automation Tokens](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/automation-tokens/derived-sample-automation-tokens.md) - [Project Automation Tokens](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/automation-tokens/project-automation-tokens.md) - [Step Automation Tokens](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/automation-tokens/step-automation-tokens.md) - [Automation Triggers and Command Line Calls](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/automation-triggers-and-command-line-calls.md) - [Error Handling](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/error-handling.md) - [Supported Command Line Interpreters](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/supported-command-line-interpreters.md) - [Troubleshooting Automation](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/automation/troubleshooting-automation.md) - [Tips and Tricks](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks.md) - [Accessing Step UDFs from a different Step](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/accessing-step-udfs-from-a-different-step.md) - [Automating BCL Conversion](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/automating-bcl-conversion.md) - [Copying UDF Values from Source to Destination](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/copying-udf-values-from-source-to-destination.md) - [Creating Notifications When Files are Added via LabLink](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/creating-notifications-when-files-are-added-via-lablink.md) - [Creating Samples and Projects via the API](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/creating-samples-and-projects-via-the-api.md) - [Determining the Workflow(s) to Which a Sample is Assigned](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/determining-the-workflow-s-to-which-a-sample-is-assigned.md) - [Displaying Files From an Earlier Step](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/displaying-files-from-an-earlier-step.md) - [Finding QC Flags in Aggregate QC (Library Validation) via REST API](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/finding-qc-flags-in-aggregate-qc-library-validation-via-rest-api.md) - [Integrating Clarity LIMS with Upstream Sample Accessioning Systems](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/integrating-clarity-lims-with-upstream-sample-accessioning-systems.md) - [Obfuscating Sensitive Data in Scripts](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/obfuscating-sensitive-data-in-scripts.md) - [Remote HTTP Filestore Setup](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/remote-http-filestore-setup.md) - [Setting the Value of a QC Flag on an Artifact](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/setting-the-value-of-a-qc-flag-on-an-artifact.md) - [Standardizing Sample Naming via the API](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/standardizing-sample-naming-via-the-api.md) - [Transitioning Output Artifacts into the Next Step](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/transitioning-output-artifacts-into-the-next-step.md) - [Updating Preset Value of a Step UDF through API](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/tips-and-tricks/updating-preset-value-of-a-step-udf-through-api.md) - [Cookbook](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook.md) - [Get Started with the Cookbook](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/get-started-with-the-cookbook.md) - [Obtain and Use the REST API Utility Classes](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/get-started-with-the-cookbook/obtain-and-use-the-rest-api-utility-classes.md) - [Tips and Troubleshooting](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/get-started-with-the-cookbook/tips-and-troubleshooting.md): This article provides hints and tips to help you get the most out of the Cookbook recipes included in this section. - [Work with Batch Resources](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-batch-resources.md) - [Introduction to Batch Resources](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-batch-resources/introduction-to-batch-resources.md) - [Retrieve Multiple Entities with a Single API Interaction](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-batch-resources/page-4.md) - [Select the Optimal Batch Size](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-batch-resources/page-3.md) - [Update UDF/Custom Field Information with Batch Operations](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-batch-resources/update-udf-custom-field-information-with-batch-operations.md) - [Work with Containers](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-containers.md) - [Add an Empty Container to the System](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-containers/add-an-empty-container-to-the-system.md) - [Filter Containers by Name](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-containers/filter-containers-by-name.md) - [Find the Contents of a Well Location in a Container](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-containers/find-the-contents-of-a-well-location-in-a-container.md) - [Work with Controls](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-controls.md) - [Automated Removal of Controls from a Workflow](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-controls/automated-removal-of-controls-from-a-workflow.md) - [Work with Derived Sample Automations](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-derived-sample-automations.md) - [Rearray Samples](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-derived-sample-automations/rearray-samples.md) - [Remove Samples from Workflows](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-derived-sample-automations/remove-samples-from-workflows.md) - [Requeue Samples](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-derived-sample-automations/requeue-samples.md) - [Work with EPP/Automation and Files](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-epp-automation-and-files.md) - [Automation Trigger Configuration](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-epp-automation-and-files/automation-trigger-configuration.md) - [Process Execution with EPP/Automation Support](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-epp-automation-and-files/process-execution-with-epp-automation-support.md) - [Work with Files](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/page.md) - [Attach a File to a File Placeholder with REST](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/page/attach-a-file-to-a-file-placeholder-with-rest.md) - [Attach a File with REST and Python](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/page/page-9.md) - [Attach Files Located Outside the Default File Storage Repository](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/page/attach-files-located-outside-the-default-file-storage-repository.md) - [Work with Multiplexing](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-multiplexing.md) - [Apply Reagent Labels by Adding Reagents to Samples](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-multiplexing/apply-reagent-labels-by-adding-reagents-to-samples.md) - [Apply Reagent Labels when Samples are Imported](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-multiplexing/apply-reagent-labels-when-samples-are-imported.md) - [Apply Reagent Labels with REST](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-multiplexing/apply-reagent-labels-with-rest.md) - [Demultiplexing](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-multiplexing/demultiplexing.md) - [Find the Index Sequence for a Reagent Label](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-multiplexing/find-the-index-sequence-for-a-reagent-label.md) - [Pool Samples with Reagent Labels](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-multiplexing/pool-samples-with-reagent-labels.md) - [Work with Process/Step Outputs](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-process-step-outputs.md) - [Find the Container Location of a Derived Sample](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-process-step-outputs/find-the-container-location-of-a-derived-sample.md) - [Rename Derived Samples Using the API](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-process-step-outputs/rename-derived-samples-using-the-api.md) - [Traverse a Pooled and Demultiplexed Sample History/Genealogy](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-process-step-outputs/traverse-a-pooled-and-demultiplexed-sample-history-genealogy.md) - [Update UDF/Custom Field Values for a Derived Sample Output](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-process-step-outputs/update-udf-custom-field-values-for-a-derived-sample-output.md) - [View the Inputs and Outputs of a Process/Step](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-process-step-outputs/view-the-inputs-and-outputs-of-a-process-step.md) - [Work with Processes/Steps](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-processes-steps.md) - [Filter Processes by Date and Type](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-processes-steps/filter-processes-by-date-and-type.md) - [Find Terminal Processes/Steps](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-processes-steps/find-terminal-processes-steps.md) - [Run a Process/Step](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-processes-steps/run-a-process-step.md) - [Update UDF/Custom Field Information for a Process/Step](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-processes-steps/update-udf-custom-field-information-for-a-process-step.md) - [Work with the Steps Pooling Endpoint](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-processes-steps/work-with-the-steps-pooling-endpoint.md) - [Work with Projects and Accounts](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-projects-and-accounts.md) - [Add a New Project to the System with UDF/Custom Field Value](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-projects-and-accounts/add-a-new-project-to-the-system-with-udf-custom-field-value.md) - [Find an Account Registered in the System](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-projects-and-accounts/find-an-account-registered-in-the-system.md) - [Get a Project Name](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-projects-and-accounts/get-a-project-name.md) - [Remove Information from a Project](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-projects-and-accounts/remove-information-from-a-project.md) - [Update Contact (User and Client) Information](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-projects-and-accounts/update-contact-user-and-client-information.md) - [Work with Submitted Samples](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-submitted-samples.md) - [Adding Samples to the System](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-submitted-samples/adding-samples-to-the-system.md) - [Assigning Samples to Workflows](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-submitted-samples/assigning-samples-to-workflows.md) - [Renaming Samples](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-submitted-samples/renaming-samples.md) - [Show the Relationship Between Samples and Analyte Artifacts (Derived Samples)](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-submitted-samples/show-the-relationship-between-samples-and-analyte-artifacts-derived-samples.md) - [Updating Sample Information](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/work-with-submitted-samples/updating-sample-information.md) - [Working with User Defined Fields/Custom Fields](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/working-with-user-defined-fields-custom-fields.md) - [About UDFs/Custom Fields and UDTs](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/working-with-user-defined-fields-custom-fields/about-udfs-custom-fields-and-udts.md) - [Performing Post-Step Calculations with Custom Fields/UDFs](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/cookbook/working-with-user-defined-fields-custom-fields/performing-post-step-calculations-with-custom-fields-udfs.md) - [Application Examples](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples.md) - [Python API Library (glsapiutil.py) Location](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-16.md) - [Scripts That Help Automate Steps](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15.md) - [Adding Downstream Samples to Additional Workflows](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/adding-downstream-samples-to-additional-workflows.md) - [Advancing/Completing a Protocol Step via the API](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/advancing-completing-a-protocol-step-via-the-api.md) - [Applying Indexing Patterns to Containers Automatically](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/applying-indexing-patterns-to-containers-automatically.md) - [Assignment of Sample Next Steps Based On a UDF](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/assignment-of-sample-next-steps-based-on-a-udf.md) - [Automatic Placement of Samples Based on Input Plate Map](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/automatic-placement-of-samples-based-on-input-plate-map.md) - [Automatic Placement of Samples Based on Input Plate Map (Multiple Plates)](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/automatic-placement-of-samples-based-on-input-plate-map-multiple-plates.md) - [Automatic Pooling Based on a Sample UDF/Custom Field](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/automatic-pooling-based-on-a-sample-udf-custom-field.md) - [Automatic Sample Placement into Existing Containers](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/automatic-sample-placement-into-existing-containers.md) - [Completing a Step Programmatically](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/completing-a-step-programmatically.md) - [Creating Multiple Containers/Types for Placement](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/creating-multiple-containers-types-for-placement.md) - [Email Notifications](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/email-notifications.md) - [Finishing the Current Step and Starting the Next](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/finishing-the-current-step-and-starting-the-next.md) - [Invoking bcl2fastq from BCL Conversion and Demultiplexing Step](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/invoking-bcl2fastq-from-bcl-conversion-and-demultiplexing-step.md) - [Parsing Metadata into UDFs (BCL Conversion and Demultiplexing)](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/parsing-metadata-into-udfs-bcl-conversion-and-demultiplexing.md) - [Publishing Files to LabLink](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/publishing-files-to-lablink.md) - [Route Artifacts Based Off a Template File](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/route-artifacts-based-off-a-template-file.md) - [Routing Output Artifacts to Specific Workflows/Stages](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/routing-output-artifacts-to-specific-workflows-stages.md) - [Setting a Default Next Action](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/setting-a-default-next-action.md) - [Setting Quality Control Flags](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/setting-quality-control-flags.md) - [Starting a Protocol Step via the API](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-15/starting-a-protocol-step-via-the-api.md) - [Scripts That Validate Step Contents](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/scripts-that-validate-step-contents.md) - [Checking for Index Clashes Based on Index Sequence](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/scripts-that-validate-step-contents/checking-for-index-clashes-based-on-index-sequence.md) - [Checking That Containers Are Named Appropriately](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/scripts-that-validate-step-contents/checking-that-containers-are-named-appropriately.md) - [Validating Illumina TruSeq Index Adapter Combinations](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/scripts-that-validate-step-contents/validating-illumina-truseq-index-adapter-combinations.md) - [Validating Process/Step Level UDFs](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/scripts-that-validate-step-contents/page-14.md) - [Scripts Triggered Outside of Workflows/Steps](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-13.md) - [Adding Users in Bulk](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-13/adding-users-in-bulk.md) - [Assigning Samples to New Workflows](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-13/assigning-samples-to-new-workflows.md) - [Generating an MS Excel Sample Submission Spreadsheet](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-13/generating-an-ms-excel-sample-submission-spreadsheet.md) - [Moving Reagent Kits & Lots to New Clarity LIMS Server](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-13/moving-reagent-kits-and-lots-to-new-clarity-lims-server.md) - [Programatically Importing the Sample Submission Excel File](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-13/programatically-importing-the-sample-submission-excel-file.md) - [Repurposing a Process to Upload Indexes](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-13/repurposing-a-process-to-upload-indexes.md) - [Miscellaneous Scripts](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12.md) - [Copying Output UDFs to Submitted Samples](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/copying-output-udfs-to-submitted-samples.md) - [Creating Custom Sample Sheets](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/creating-custom-sample-sheets.md) - [Downloading a File and PDF Image Extraction](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/downloading-a-file-and-pdf-image-extraction.md) - [Generating a Hierarchical Sample History](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/generating-a-hierarchical-sample-history.md) - [Generic CSV Parser Template (Python)](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/generic-csv-parser-template-python.md) - [Illumina LIMS Integration](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/illumina-lims-integration.md) - [Parsing Sequencing Meta-Data into Clarity LIMS](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/parsing-sequencing-meta-data-into-clarity-lims.md) - [Protocol-based Permissions](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/protocol-based-permissions.md) - [Renaming Samples to Add an Internal ID](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/renaming-samples-to-add-an-internal-id.md) - [Self-Incremental Counters](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/self-incremental-counters.md) - [Submit to a Compute Cluster via PBS](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/page-12/submit-to-a-compute-cluster-via-pbs.md) - [Resources and References](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/resources-and-references.md) - [API Training Videos](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/resources-and-references/api-training-videos.md) - [Container States](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/resources-and-references/container-states.md) - [Suggested Reading](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/resources-and-references/suggested-reading.md) - [Understanding LIMS ID Prefixes](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/resources-and-references/understanding-lims-id-prefixes.md) - [Unsupported Artifact Types](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/resources-and-references/unsupported-artifact-types.md) - [Unsupported Process Types](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/resources-and-references/unsupported-process-types.md) - [Useful Tools](https://help.connected.illumina.com/clarity-lims/api-and-database/api-docs/application-examples/resources-and-references/useful-tools.md) --- # Agent Instructions This documentation is published with GitBook. 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