# Documentation ## Omics AI - [Overview](https://docs.omics.ai/products/introduction.md) - [Introduction](https://docs.omics.ai/products/publisher/introduction.md) - [Getting Started](https://docs.omics.ai/products/publisher/getting-started.md) - [Logging in to Publisher](https://docs.omics.ai/products/publisher/getting-started/logging-in-to-publisher.md) - [Data Sources](https://docs.omics.ai/products/publisher/data-sources.md) - [Connecting a Data Source](https://docs.omics.ai/products/publisher/data-sources/connecting-a-data-source.md): How to connect to a new data source configuration - [Managing a Data Source](https://docs.omics.ai/products/publisher/data-sources/managing-a-data-source.md): How to edit and delete a data source and how to view logs of the data source. - [Connectors](https://docs.omics.ai/products/publisher/data-sources/connectors.md) - [AWS S3 Permissions](https://docs.omics.ai/products/publisher/data-sources/connectors/aws-s3-permissions.md) - [Connecting to AWS S3 Storage](https://docs.omics.ai/products/publisher/data-sources/connectors/connecting-to-aws-s3-storage.md): Amazon S3 is AWS’s object storage solution for the cloud. Object storage is optimized for storing massive amounts of unstructured data. - [Google Cloud Storage (GCS) Permissions](https://docs.omics.ai/products/publisher/data-sources/connectors/google-cloud-storage-gcs-permissions.md) - [Connecting to Google Cloud Storage](https://docs.omics.ai/products/publisher/data-sources/connectors/connecting-to-google-cloud-platform.md) - [PostgreSQL Permissions](https://docs.omics.ai/products/publisher/data-sources/connectors/postgresql-permissions.md) - [Connecting to PostgreSQL](https://docs.omics.ai/products/publisher/data-sources/connectors/connecting-to-postgresql.md): PostgreSQL is an advanced, enterprise class open source relational database that supports both SQL (relational) and JSON (non-relational) querying. - [PostgreSQL on Azure Permissions](https://docs.omics.ai/products/publisher/data-sources/connectors/postgresql-on-azure-permissions.md) - [Microsoft Azure Blob Storage Permissions](https://docs.omics.ai/products/publisher/data-sources/connectors/microsoft-azure-blob-storage-permissions.md) - [Connecting to Microsoft Azure Blob Storage](https://docs.omics.ai/products/publisher/data-sources/connectors/connecting-to-microsoft-azure-blob-storage.md): Azure Blob storage is Microsoft’s object storage solution for the cloud. Blob storage is optimized for storing massive amounts of unstructured data. Unstructured data is data that doesn’t adhere to - [Connecting to HTTPS](https://docs.omics.ai/products/publisher/data-sources/connectors/connecting-to-https.md): Hypertext Transfer Protocol Secure (HTTPS) is an extension of the Hypertext Transfer Protocol (HTTP). It uses encryption for secure communication over a computer network. - [Connecting to other sources via Trino](https://docs.omics.ai/products/publisher/data-sources/connectors/trino-connectors.md) - [BigQuery](https://docs.omics.ai/products/publisher/data-sources/connectors/trino-connectors/bigquery-permissions.md) - [Collections](https://docs.omics.ai/products/publisher/collections.md) - [Creating a Collection](https://docs.omics.ai/products/publisher/collections/creating-a-collection.md) - [Sharing a Collection](https://docs.omics.ai/products/publisher/collections/sharing-a-collection.md) - [Collection Filters](https://docs.omics.ai/products/publisher/collections/collection-filters.md) - [Editing Collection Metadata](https://docs.omics.ai/products/publisher/collections/editing-collection-metadata.md) - [Updating Collection Contents](https://docs.omics.ai/products/publisher/collections/updating-collection-contents.md) - [Access Policies](https://docs.omics.ai/products/publisher/access-policies.md) - [Creating an Access Policy](https://docs.omics.ai/products/publisher/access-policies/creating-an-access-policy.md) - [Managing Access Policies](https://docs.omics.ai/products/publisher/access-policies/managing-an-access-policy.md) - [Questions](https://docs.omics.ai/products/publisher/questions.md) - [Adding Questions](https://docs.omics.ai/products/publisher/questions/adding-questions.md) - [Example Question](https://docs.omics.ai/products/publisher/questions/example-question.md) - [Settings](https://docs.omics.ai/products/publisher/settings.md) - [Viewing Current and Past Administrators](https://docs.omics.ai/products/publisher/settings/viewing-current-and-past-admins.md) - [Adding an Administrator](https://docs.omics.ai/products/publisher/settings/adding-an-admin.md) - [Removing an Administrator](https://docs.omics.ai/products/publisher/settings/removing-an-admin.md) - [Setting Notification Preferences](https://docs.omics.ai/products/publisher/settings/changing-notification-preferences.md) - [Introduction](https://docs.omics.ai/products/explorer/introduction.md) - [Viewing a Collection](https://docs.omics.ai/products/explorer/viewing-a-collection.md): How to view collection tables and downloading table data. - [Browsing Collections](https://docs.omics.ai/products/explorer/browsing-collections.md) - [Asking Questions](https://docs.omics.ai/products/explorer/asking-questions.md) - [Accessing a Private Collection](https://docs.omics.ai/products/explorer/accessing-a-private-collection.md): How to access registered or controlled access Collections - [Requesting Access to a Private Collection](https://docs.omics.ai/products/explorer/accessing-a-private-collection/requesting-access-to-a-private-collection.md) - [Filtering Data in Tables](https://docs.omics.ai/products/explorer/filtering-data-in-tables.md): How to use filter operators of different data types to search and filter for specific table records. - [Strings](https://docs.omics.ai/products/explorer/filtering-data-in-tables/strings.md): How to use filter operators for facets containing values of string datatype. - [Dates](https://docs.omics.ai/products/explorer/filtering-data-in-tables/dates.md): How to use filter operators for facets containing values of date datatype. - [Numbers](https://docs.omics.ai/products/explorer/filtering-data-in-tables/numbers.md): How to use filter operators for facets containing values of number datatype. - [Introduction](https://docs.omics.ai/products/workbench/introduction.md) - [Getting Started](https://docs.omics.ai/products/workbench/getting-started.md) - [Logging into Workbench](https://docs.omics.ai/products/workbench/getting-started/log-into-workbench.md) - [Connecting an Engine](https://docs.omics.ai/products/workbench/getting-started/connect-an-engine.md) - [Finding or Importing a Workflow](https://docs.omics.ai/products/workbench/getting-started/finding-or-importing-a-workflow.md) - [Configuring Workflow Inputs](https://docs.omics.ai/products/workbench/getting-started/configuring-workflow-inputs.md) - [Running and Monitoring a Workflow](https://docs.omics.ai/products/workbench/getting-started/submitting-and-monitoring-a-workflow-run.md) - [Locating Outputs](https://docs.omics.ai/products/workbench/getting-started/locating-workflow-outputs.md) - [Engines](https://docs.omics.ai/products/workbench/engines.md) - [Adding and Updating an Engine](https://docs.omics.ai/products/workbench/engines/adding-and-updating-an-engine.md) - [On AWS HealthOmics](https://docs.omics.ai/products/workbench/engines/adding-and-updating-an-engine/aws-healthomics.md) - [On Microsoft Azure](https://docs.omics.ai/products/workbench/engines/adding-and-updating-an-engine/microsoft-azure.md) - [On Google Cloud Platform](https://docs.omics.ai/products/workbench/engines/adding-and-updating-an-engine/google-cloud-platform.md) - [On Premises](https://docs.omics.ai/products/workbench/engines/adding-and-updating-an-engine/on-premises.md) - [Parameters](https://docs.omics.ai/products/workbench/engines/parameters.md) - [AWS HealthOmics](https://docs.omics.ai/products/workbench/engines/parameters/aws-healthomics.md) - [Google Cloud Platform](https://docs.omics.ai/products/workbench/engines/parameters/google-cloud-platform.md) - [Microsoft Azure](https://docs.omics.ai/products/workbench/engines/parameters/microsoft-azure.md) - [On-Premises](https://docs.omics.ai/products/workbench/engines/parameters/on-premises.md) - [Cromwell](https://docs.omics.ai/products/workbench/engines/parameters/cromwell.md) - [Amazon Genomics CLI](https://docs.omics.ai/products/workbench/engines/parameters/amazon-genomics-cli.md) - [Workflows](https://docs.omics.ai/products/workbench/workflows.md) - [Finding Workflows](https://docs.omics.ai/products/workbench/workflows/discovering-workflows.md) - [Adding a Workflow](https://docs.omics.ai/products/workbench/workflows/adding-a-workflow.md) - [Support Files](https://docs.omics.ai/products/workbench/workflows/support-files.md): Bundle transformations, defaults, and dependencies alongside your workflow files - [Supported Languages](https://docs.omics.ai/products/workbench/workflows/supported-languages.md) - [Repositories](https://docs.omics.ai/products/workbench/workflows/repositories.md) - [Dockstore](https://docs.omics.ai/products/workbench/workflows/repositories/dockstore.md) - [Instruments](https://docs.omics.ai/products/workbench/instruments.md) - [Getting Started with Instruments](https://docs.omics.ai/products/workbench/instruments/getting-started-with-instruments.md) - [Connecting a Storage Account](https://docs.omics.ai/products/workbench/instruments/connecting-a-storage-account.md) - [Using Sample Data in a Workflow](https://docs.omics.ai/products/workbench/instruments/using-sample-data-in-a-workflow.md) - [Running Workflows Using Samples](https://docs.omics.ai/products/workbench/instruments/running-workflows-using-samples.md) - [Family Based Analysis with Pedigree Information](https://docs.omics.ai/products/workbench/instruments/adding-pedigrees.md) - [Monitor the Workflow](https://docs.omics.ai/products/workbench/instruments/monitor-the-workflow.md) - [Running Custom Workflows Using Samples](https://docs.omics.ai/products/workbench/instruments/running-custom-workflows-using-samples.md) - [Entities](https://docs.omics.ai/products/workbench/entities.md) - [Terminology](https://docs.omics.ai/products/workbench/terminology.md) - [Introduction](https://docs.omics.ai/products/passport/introduction.md) - [Registering an Email Address for a Google Identity](https://docs.omics.ai/products/passport/register-account-with-google.md) - [Installation](https://docs.omics.ai/products/command-line-interface/installation.md) - [Usage Examples](https://docs.omics.ai/products/command-line-interface/usage-examples.md) - [Working with JSON Data](https://docs.omics.ai/products/command-line-interface/working-with-json-data.md) - [Reference](https://docs.omics.ai/products/command-line-interface/reference.md) - [workbench](https://docs.omics.ai/products/command-line-interface/reference/workbench.md) - [runs submit](https://docs.omics.ai/products/command-line-interface/reference/workbench/runs-submit.md): Submit one or more Workflow Runs - [runs list](https://docs.omics.ai/products/command-line-interface/reference/workbench/runs-list.md): List all workflow runs - [runs describe](https://docs.omics.ai/products/command-line-interface/reference/workbench/runs-describe.md): Describe one or more runs - [runs cancel](https://docs.omics.ai/products/command-line-interface/reference/workbench/runs-cancel.md): Cancel one or more runs - [runs delete](https://docs.omics.ai/products/command-line-interface/reference/workbench/runs-delete.md): Delete one or more runs - [runs logs](https://docs.omics.ai/products/command-line-interface/reference/workbench/runs-logs.md): Retrieve log bytes for a run or a task - [runs tasks list](https://docs.omics.ai/products/command-line-interface/reference/workbench/runs-tasks-list.md): List the tasks for a run - [runs events list](https://docs.omics.ai/products/command-line-interface/reference/workbench/runs-events-list.md): Lists the events for a run - [engines list](https://docs.omics.ai/products/command-line-interface/reference/workbench/engines-list.md): List all engines - [engines describe](https://docs.omics.ai/products/command-line-interface/reference/workbench/engines-describe.md): Describe one or more engines - [engines parameters list](https://docs.omics.ai/products/command-line-interface/reference/workbench/engines-parameters-list.md): List all parameters for a specified engine - [engines parameters describe](https://docs.omics.ai/products/command-line-interface/reference/workbench/engines-parameters-describe.md): Describe one or more engine parameters - [engines health-checks list](https://docs.omics.ai/products/command-line-interface/reference/workbench/engines-health-checks-list.md): Lists engine health checks - [workflows create](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-create.md): Create a workflow in a namespace - [workflows list](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-list.md): List all workflows in a namespace - [workflows describe](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-describe.md): Describe one or more workflows - [workflows update](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-update.md): Update a workflow in a namespace - [workflows delete](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-delete.md): Delete a workflow in a namespace - [workflows versions create](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-versions-create.md): Create a version of a workflow in a namespace - [workflows versions list](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-versions-list.md): List all workflow versions for a given workflow - [workflows versions describe](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-versions-describe.md): Describe one or more workflow versions - [workflows versions files](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-versions-files.md): Prints or downloads workflow files - [workflows versions update](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-versions-update.md): Update a specific workflow version - [workflows versions delete](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-versions-delete.md): Delete a version of a workflow from a namespace - [workflows versions defaults create](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-versions-defaults-create.md): Interact with workflow versions defaults - [workflows versions defaults list](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-versions-defaults-list.md): List workflow defaults for a given workflow version - [workflows versions defaults describe](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-versions-defaults-describe.md): Describe workflow defaults for one or more default IDs - [workflows versions defaults update](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-versions-defaults-update.md): Update workflow defaults for a given default ID - [workflows versions defaults delete](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-versions-defaults-delete.md): Delete workflow defaults for a given default ID - [workflows versions dependencies create](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-versions-dependencies-create.md): Create a new workflow dependency - [workflows versions dependencies list](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-versions-dependencies-list.md): List workflow dependencies for a given workflow version - [workflows versions dependencies describe](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-versions-dependencies-describe.md): Describe specific workflow dependencies - [workflows versions dependencies update](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-versions-dependencies-update.md): Update an existing workflow dependency - [workflows versions dependencies delete](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-versions-dependencies-delete.md): Delete a workflow dependency - [workflows versions transformations create](https://docs.omics.ai/products/command-line-interface/reference/workbench/worfklows-versions-transformations-create.md): Interact with workflow transformations - [workflows versions transformations delete](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-versions-transformations-delete.md): Delete workflow transformation - [workflows versions transformations describe](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-versions-transformations-describe.md): Describe workflow transformation - [workflows versions transformations list](https://docs.omics.ai/products/command-line-interface/reference/workbench/workflows-versions-transformations-list.md): List workflow transformations - [namespaces get-active](https://docs.omics.ai/products/command-line-interface/reference/workbench/namespaces-get-active.md): Get the active namespace for the current user - [namespaces set-active](https://docs.omics.ai/products/command-line-interface/reference/workbench/namespaces-set-active.md): Set the active namespace for the current user - [namespaces get-default](https://docs.omics.ai/products/command-line-interface/reference/workbench/namespaces-get-default.md): Get the default namespace of a user (deprecated) - [namespaces list](https://docs.omics.ai/products/command-line-interface/reference/workbench/namespaces-list.md): List namespaces the authenticated user belongs to - [namespaces describe](https://docs.omics.ai/products/command-line-interface/reference/workbench/namespaces-describe.md): Describe one or more namespaces - [namespaces create](https://docs.omics.ai/products/command-line-interface/reference/workbench/namespaces-create.md): Create a new namespace - [namespaces update](https://docs.omics.ai/products/command-line-interface/reference/workbench/namespaces-update.md): Update an existing namespace - [namespaces members list](https://docs.omics.ai/products/command-line-interface/reference/workbench/namespaces-members-list.md): List members and their roles in a namespace - [namespaces members add](https://docs.omics.ai/products/command-line-interface/reference/workbench/namespaces-members-add.md): Add a member to a namespace - [namespaces members remove](https://docs.omics.ai/products/command-line-interface/reference/workbench/namespaces-members-remove.md): Remove a member from a namespace - [storage add](https://docs.omics.ai/products/command-line-interface/reference/workbench/storage-add.md): Add a new Storage Account - [storage delete](https://docs.omics.ai/products/command-line-interface/reference/workbench/storage-delete.md): Delete a Storage Account - [storage describe](https://docs.omics.ai/products/command-line-interface/reference/workbench/storage-describe.md): Describe one or more storage accounts - [storage list](https://docs.omics.ai/products/command-line-interface/reference/workbench/storage-list.md): List Storage Accounts - [storage update](https://docs.omics.ai/products/command-line-interface/reference/workbench/storage-update.md): Update a Storage Account - [storage platforms add](https://docs.omics.ai/products/command-line-interface/reference/workbench/platforms-add.md): Add a Platform - [storage platforms delete](https://docs.omics.ai/products/command-line-interface/reference/workbench/platforms-delete.md): Delete a Platform - [storage platforms describe](https://docs.omics.ai/products/command-line-interface/reference/workbench/platforms-describe.md): Describe one or more platforms - [storage platforms list](https://docs.omics.ai/products/command-line-interface/reference/workbench/platforms-list.md): List Platforms - [samples list](https://docs.omics.ai/products/command-line-interface/reference/workbench/samples-list.md): List Samples - [samples describe](https://docs.omics.ai/products/command-line-interface/reference/workbench/samples-describe.md): Describe one or more samples - [samples files list](https://docs.omics.ai/products/command-line-interface/reference/workbench/samples-files-list.md): List files for a sample - [publisher](https://docs.omics.ai/products/command-line-interface/reference/publisher.md) - [collections list](https://docs.omics.ai/products/command-line-interface/reference/publisher/collections-list.md): List all collections - [collections query](https://docs.omics.ai/products/command-line-interface/reference/publisher/collections-query.md): Query data from a collection - [collections create](https://docs.omics.ai/products/command-line-interface/reference/publisher/collections-create.md): Create a new collection - [collections describe](https://docs.omics.ai/products/command-line-interface/reference/publisher/collections-describe.md): View details of one or more collections - [collections status](https://docs.omics.ai/products/command-line-interface/reference/publisher/collections-status.md): Check the validation status of a collection - [collections items list](https://docs.omics.ai/products/command-line-interface/reference/publisher/collections-items-list.md): List items in a collection - [collections items add](https://docs.omics.ai/products/command-line-interface/reference/publisher/collections-items-add.md): Add files to a collection - [collections items remove](https://docs.omics.ai/products/command-line-interface/reference/publisher/collections-items-remove.md): Remove files from a collection - [collections tables list](https://docs.omics.ai/products/command-line-interface/reference/publisher/collections-tables-list.md): List all accessible tables in a collection - [collections tables get](https://docs.omics.ai/products/command-line-interface/reference/publisher/collections-tables-get.md): Get detailed information about a specific table - [datasources list](https://docs.omics.ai/products/command-line-interface/reference/publisher/datasources-list.md): List all data sources - [Analysis](https://docs.omics.ai/products/analysis.md) - [Python Library](https://docs.omics.ai/products/analysis/python-library.md) - [Popular Environments](https://docs.omics.ai/products/analysis/integrations.md) - [Cromwell](https://docs.omics.ai/products/analysis/integrations/cromwell.md) - [CWL Tool](https://docs.omics.ai/products/analysis/integrations/cwl-tool.md) - [Terra](https://docs.omics.ai/products/analysis/integrations/terra.md) - [Nextflow](https://docs.omics.ai/products/analysis/integrations/nextflow.md) - [DNAnexus](https://docs.omics.ai/products/analysis/integrations/dnanexus.md) --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on a page URL with the `ask` query parameter: ``` GET https://docs.omics.ai/products/introduction.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.