CLI Reference

Overview

The Workbench CLI provides a command-line interface for managing your storage connections, samples, and sequencing instruments. This reference documents the available commands and their usage.

Command Groups

The CLI organizes commands into three main functional areas.

Storage commands handle storage accounts and platform connections, including account management and platform configuration.

Samples commands allow you to work with biological samples, their files, and associated metadata.

Instruments commands help you manage and view your sequencing instruments.

Command Structure

All commands follow the base structure:

omics workbench <command-group> <command> [flags]

Terminology

Before using the CLI, it's helpful to understand these key terms:

• Storage: Operations for interacting with cloud storage from Workbench

• Storage Account: Created when a user saves credentials using the storage command

• Platform: A specific sequencing platform that has uploaded outputs to cloud storage

• Provider: The cloud provider (GCP, AWS, Azure)

• Instrument: An entity corresponding to a physical sequencing instrument

• Sample: A biological sample (unique within a namespace)

• File: A file belonging to a biological sample, including platform and instrument information