# Command Line Interface

- [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


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