Documentation

About the Dockstore

The Dockstore concept is simple, provide a place where users can share tools encapsulated in Docker and described with the Common Workflow Language (CWL) or Workflow Description Language (WDL), workflow languages used by members of and APIS created by the GA4GH Cloud Work Stream. This enables scientists, for example, to share analytical tools in a way that makes them machine readable and runnable in a variety of environments. While the Dockstore is focused on serving researchers in the biosciences the combination of Docker + CWL/WDL can be used by anyone to describe the tools and services in their Docker images in a standardized, machine-readable way.

Dockstore also attempts to work with new and alternative languages/standards such as Nextflow as popular challengers to CWL and WDL. We also work on the GA4GH Tool Registry standard as a way of sharing data with workflow platforms and partners. We are also working with the task execution, workflow execution, and data transfer standards developing at the GA4GH.

Built with Docker and Git

Docker repositories, like Docker Hub, Quay.io and GitLab, and source control repositories like GitHub, Bitbucket, and GitLab, provide much of the infrastructure we need. Docker repositories allow users to build, publish, and share both public and private Docker images. However, the services lack standardized ways of describing how to invoke tools contained within Docker containers. Workflow descriptor languages provide standardised ways to define the inputs, parameterizations, and outputs of tools in a controlled way. Together, these resources provide the necessary tools to share analytical tools in a highly portable way, a key concern for the scientific community.

Overview

Strategies

You can register your tools and workflows on Dockstore in three broad ways as depicted above.

A) Following our tutorials, you can save your descriptors on GitHub, build your Docker image automatically on Quay.io, and have Dockstore reach out and index your tools

B) Dockstore can retrieve your workflow descriptors from GitHub and other source control methods. You are responsible for ensuring that your descriptors point at valid Docker images.

For Dockstore 1.5.0+

C) You will be able to use our new hosted workflows service to store tools and workflows directly on dockstore.org to quickly get started, prototype your ideas, and share workflows with a limited audience.

In all three cases, you will have an opportunity to clean-up and configure your work before publishing to the rest of the world to see.

You can mix and match in a number of these approaches. For example, you can go beyond our simple tutorials and automated approach to manually register tools that point at locations like Docker Hub, Seven Bridges, and Amazon ECR. You can substitute WDL and Nextflow for the descriptor language for workflows. You might even be able to mix and match descriptor languages eventually!

Over time, we find “skinny” Docker images, those with single tools installed in them, are more helpful for extending and building new workflows with. That being said, “fat” Docker containers, which include multiple tools and even full workflows with frameworks like SeqWare or Galaxy, can have their place as well. Projects like the ICGC PanCancer Analysis of Whole Genomes (PCAWG) made use of “fat” Docker containers that had complex workflows that fully encapsulated alignment and variant calling. The self-contained nature of these Docker containers allowed for mobility between a wide variety of environments and greatly simplified the setup of these pipelines across a wide variety of HPC and cloud environments. Either approach works for the Dockstore so long as you can describe the tool or workflow inside the Docker container as a CWL/WDL-defined tool (which you can for most things).

Promoting Standards

We hope Dockstore provides a reference implementation for tool sharing in the sciences. The Dockstore is essentially a living and evolving proof of concept designed as a starting point for two activities that we hope will result in community standards within the GA4GH:

  • a best practices guide for describing tools in Docker containers with CWL/WDL/Nextflow
  • a minimal web service standard for registering, searching and describing CWL-annotated Docker containers that can be federated and indexed by multiple websites similar to Maven Central

We also implement certain utilities such as file provisioning plugins that support the GA4GH DOS (Data Object Service) standard or command-line launchers that present a common interface across CWL and WDL as almost a polyfill to demonstrate what we wish to use over time natively.

Building a Community

Several large projects in the Biosciences, specifically cancer sequencing projects such as PCAWG, PrecisionFDA, the Broad Institute, the University of California Santa Cruz, and Cancer IT at Sanger have registered between 10 and 60 workflows each in Dockstore as of August 2018. We hope this work will aid the community and promote the registration of a large number of high-quality workflows in the system.

Future Plans

We plan on expanding the Dockstore in several ways over the coming months. Please see our issues page for details and discussions.