Skip to main content
Ctrl+K
Logo image
  • What is SeqsLab?
  • Run your first job

Tutorials

  • Deployment
    • Test drive SeqsLab
      • Data registration
      • Tool registration
      • Workflow execution
    • Deploy SeqsLab on Azure
      • Register an Azure resource provider
      • Grant tenant-wide admin consent to SeqsLab
      • Create a SeqsLab workspace
      • Request Azure backend quota
      • Manage SeqsLab users
      • Configure storage log access
  • CLI
    • Pull and run the SeqsLab CLI
  • Data Hub
    • Upload and register files using the SeqsLab CLI
  • Tools
    • Create an input JSON file
    • Validate workflow scripts
    • Register a TRS tool to the SeqsLab platform
      • Develop a tool
      • Configure the execution file
      • Register a tool
  • Jobs
    • Automated jobs
    • Interactive jobs
  • Run Sheet
    • Create a SeqsLab Run Sheet for sequencing experiments
    • Use the SeqsLab Run Sheet with the CLI

Tasks

  • Manage your jobs
  • Manage your labels

Case studies

  • GATK4 Germline SNPs Indels
  • GATK4 Joint Genotyping
  • Hi-C Data Processing

Explanations

  • SeqsLab Platform
    • SeqsLab on Azure
    • Security
      • Authentication
        • OAuth 2.0 and authentication flow
        • SeqsLab API tokens
      • Authorization
        • Role-based access control (RBAC)
        • Roles
        • Cybersecurity assurance
    • Compliance
  • SeqsLab Data Hub
  • SeqsLab Jobs
    • Workflow engine
    • Workflow description
      • WDL best practice guidelines
      • WDL workflow inputs
  • SeqsLab Genomics and Health Data Service
  • Operator pipelines
    • Operators
    • Operator types
  • API
    • Data repository service
      • SeqsLab DRS API
    • Tool registry service
      • SeqsLab TRS API
    • Workflow execution service
      • SeqsLab WES API

References

  • CLI commands
    • Authentication subcommands
    • Data Repository Service (DRS) subcommands
    • Work Execution Service (WES) subcommands
    • Role subcommands
    • Tool Registry Service (TRS) subcommands
    • User subcommands
    • Workspace subcommands
  • Operator pipelines
  • API references
    • DRS API reference
    • TRS API reference
    • WES API reference
  • .md

Tools

Tools#

Learn how to use Tools in SeqsLab:

  • Create an input JSON file

  • Validate workflow scripts

  • Register a TRS tool to the SeqsLab platform

    • Develop a tool

    • Configure the execution file

    • Register a tool

previous

Upload and register files using the SeqsLab CLI

next

Create an input JSON file

By ATGENOMIX, Inc.

© Copyright 2023.

All Atgenomix products and services are for research or investigational use only, and should not be used for diagnostic purposes.