Introduction to Dockstore

Welcome to the Dockstore Blog! This is our very first blog post and we are very excited to connect with current and potential Dockstore users through this medium. Let’s dig right in!

Dockstore.org is an open-source platform for sharing and using bioinformatics workflows and tools. Simply put, it is like an “app store” for bioinformatics tools and workflows. Researchers publish their workflows on Dockstore so that others in the community can easily find and reuse their analysis methods.

Dockstore Home Page: https://dockstore.org/

Tools and workflows on Dockstore use descriptor languages that follow community standards and are used to elaborate the steps and parameters in an analysis pipeline. For example, a variant calling pipeline may have multiple steps that each call a different library using BASH commands. Some workflows may leverage the use of a container, a technology to reproduce an exact compute environment with all software and dependencies, to make their tool portable and interoperable. Dockstore hosts all of the components required to make a tool or workflow reproducible. There is a link to the source repository (such as GitHub), a link to where the container file is hosted (such as DockerHub), a descriptor file, and parameter files.

We support several workflow languages, specifically, WDL, CWL, Galaxy, and Nextflow (Table 1). We have introductory materials to workflow languages in the Dockstore documentation, or you can learn more about them from their community pages.

[embed]Table 1. Workflow languages supported in Dockstore.org

Dockstore users can run workflows in different environments. Users can use our launch-with feature to launch workflows from Dockstore into their choice of cloud environment (Table 2).

Use Dockstore’s launch-with feature

Our Launch-with partners offer access to rich data resources hosted in the cloud. For example, NHLBI’s BioData Catalyst offers 3.42 petabytes of data for studying Heart, Lung, Blood, and Sleep diseases. Instead of downloading huge genomic files, you can easily launch your analysis from Dockstore into the cloud where the data lives without having to pay for data egress or hosting. You can learn more by visiting their individual web portals (Table 2).

[embed]Table 2. Dockstore’s current Launch-With Partners and the workflow languages and compute environments they support

If you prefer to run workflows on your local computer, you can explore Dockstore’s Command Line Interface (CLI) to develop, debug, and test your workflows.

Use Dockstore’s CLI

The Dockstore CLI does not currently support Galaxy workflows. Instead, you can launch Galaxy workflows into free-to-use Galaxy instances (see Table 2).

If you are new to developing workflows and using the Dockstore CLI, a good place to start is using the Hello World workflows on Dockstore. These workflows were part of the training materials developed in the Dockstore workshop from Bioinformatics Community Conference 2020. The workflow description contains links to the recording as well as the slides.

Why publish your workflow in Dockstore? Dockstore provides features that promote the FAIR guiding principles: Findable, Accessible, Interoperable, and Reusable. If you already have a tool or workflow, you can upload it directly to Dockstore or set up the Dockstore GitHub app to automatically sync your GitHub repository with a Dockstore entry. You can then snapshot a version of the workflow for posterity, export to Zenodo, export to ORCID, share your workflow with others, and more! More detailed information can be found in the Dockstore documentation and in upcoming blogs.

With this blog, we hope to expand our mission to empower researchers by increasing the reproducibility and transparency of their research methods. This blog will also serve as a learning resource to introduce new users to a variety of interesting topics. We will highlight relevant work from the research community and share exciting new feature updates. Stay tuned to find out more about Dockstore and the exciting research from Dockstore users.

[embed]What is Dockstore?

More Resources:

• Dockstore Documentation
• Launch With
• Getting Started with workflows