Welcome to Dockstore Documentation!

Note

Our code lives on GitHub at dockstore/dockstore and dockstore/dockstore-ui2.

Dockstore is an open platform used by the GA4GH for sharing reproducible and interoperable tools, workflows, and services. For tools and workflows, we support Common Workflow Language (CWL), Workflow Description Language (WDL), Nextflow (NFL), and Galaxy.

If this is your first time learning about Dockstore, we recommend starting with the Getting Started Guide. This will introduce you to the core concepts of Dockstore, leaving you with a good understanding of the platform. However, if you are simply looking to launch tools and workflows, we recommend going straight to the End User Topics or our quickstart guide.

• Go to Dockstore
• System Status

About

• About Dockstore
• Dockstore Blog
• Changelog
• FAQ
• News and Events (Archived)
• Roadmap
• Dockstore Dictionary
• Templates

Getting Started

• Intro to Dockstore Tools and Workflows

• Getting started tutorial – designed for people totally new to writing workflows and working with Docker

  1. Intro

  2. Docker

  3. Language-specific introductions

     • Common Workflow Language (CWL)

     • Workflow Description Language (WDL)

     • Nextflow (NFL)

     • Galaxy

  4. Creating a Dockstore Account

  5. Register a tool on Dockstore

  6. Register a workflow on Dockstore

  7. Archive an Entry on Dockstore

  8. Delete an Entry on Dockstore

  9. Hosted tools and workflows

• Notebooks

• Services (preview)

• Registering tools, workflows, notebooks, and services with the Dockstore GitHub App

Launching tools and workflows from Dockstore

Dockstore partners with several compute platforms, allowing you to export workflows into these platforms with the click of a button. We also provide a CLI to run tools and workflows locally. Click on the links below for more information.

Cloud Partners

In addition to the above cloud partners, you can also launch workflows with BioData Catalyst or the Dockstore CLI.

Launching notebooks from Dockstore

Dockstore supports launching notebooks into several environments with the click of a button. Click on the links below for more information.

Notebook Environments

End user topics

• Introduction
• Faceted Search
• Starring Tools and Workflows
• Language Support
• ORCIDs in Dockstore
• Digital Object Identifiers

Videos (tutorials & presentations)

• Videos

Best practices guidelines

• Language-specific: CWL | Nextflow | WDL

• Best practices on Dockstore

• Best practices for secure and FAIR workflows

• Notebook portability

Dockstore CLI

• Installing the Dockstore CLI
• Dockstore CLI Overview
• Dockstore CLI FAQ
• Using a Cromwell config with the Dockstore CLI
• Set Up File Provisioning Plugins
• Developing File Provisioning Plugins
• Advanced CLI Features
• Dockstore Yaml Command Line Validator Tool

Advanced developer topics

Topics for advanced users who have already completed our getting started guide.

Note that not all features are available in all workflow languages. It can be worthwhile looking at Language Support to see what features are available to you.

• Dockstore Tools Overhaul

• Detailed comparison of tools and workflows

• Legacy features

• Docker registries

• Public and private tools

• Checker workflows, and how to run them using TRS

• Sharing workflows

• Aliases

• Docker alternatives

• Maximizing reproducibility

  • Creating snapshots and requesting DOIs

  • Checksum for files and Docker Images

• GA4GH Write API (intended as a proof-of-concept and for developers with a large number of tools)

• Using batch services (AWS, Azure, Google, and Consonance)

• Verified workflows and tools

• Workflow metrics

• Organizations and collections

Extras

• BCC 2020 Docker Training
• BCC 2020 WDL Training
• Posters and Talks
• User Created
• Dockstore Logo Usage Guidelines

In Affiliation with

                 

Workflow Languages

                 

Works With