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  • NHLBI BioData Catalyst® (BDC) Documentation
  • Community
    • Who We Are
    • BDC Glossary
    • Citation and Acknowledgement
    • Strategic Planning
    • Request for Comments
      • NHLBI BioData Catalyst Ecosystem Security Statement
      • NHLBI DICOM Medical Image De-Identification Baseline Protocol
    • BDC Video Content Guidance
    • Contributing User Resources to BDC
  • Written Documentation
    • Getting Started
    • Data Access
      • Data Interoperability
      • Understanding Access
      • Submitting a dbGaP Data Access Request
      • Checking Access
    • Explore Available Data
      • Dug Semantic Search
        • Search and Results
      • PIC-SURE User Guide
        • Getting Started
          • Requirements and Login
          • Available Data and Managing Data Access
            • TOPMed and TOPMed related datasets
            • BioLINCC Datasets
            • CONNECTS Dataset
        • Data Organization in PIC-SURE
        • PIC-SURE Features and General Layout
        • PIC-SURE Open Access vs. PIC-SURE Authorized Access
          • PIC-SURE Open Access
          • PIC-SURE Authorized Access
        • Data Analysis Using the PIC-SURE API
        • Additional Resources
        • PIC-SURE API Documentation
        • Appendix 1: BioData Catalyst Identifiers - dbGaP, TOPMed, and PIC-SURE
        • Appendix 2: Table of Harmonized Variables
      • Discovering Data Using Gen3
        • Dictionary
        • Exploration
        • Query
        • Workspace
        • Profile
        • PFB Files
        • Current Projects
    • Analyze Data
      • Transferring Files Between Seven Bridges and Terra
      • Seven Bridges
        • Knowledge Center
        • Getting Started Guide
        • Comprehensive Analysis Tips
        • Troubleshooting Tasks
        • GWAS with GENESIS workflows
        • Annotation Explorer
      • Terra
        • Account Setup
          • Billing
          • Managing Costs
        • Workspace Setup
          • Data Storage & Management
          • Collaboration
          • Security
        • Bring Data into a Workspace
          • Bring in Data from Gen3
          • From Terra’s Data Library
          • Use Your Own Data with Terra
        • Run Analyses
          • Batch Processing with Workflows
          • Interactive Analysis
          • Genome-Wide Association Studies
        • Troubleshooting & Support
      • Dockstore
        • Launch workflows with BioData Catalyst
        • Discover our catalog
        • Intro to Docker, WDL, CWL
        • Dockstore Forum
        • Contribute to the community
    • Community Tools & Integration
      • Bring Your Own Tool(s)
        • BYOT Glossary
        • Working with Docker
        • Creating, testing & scaling WDL workflows
        • Creating, testing & scaling CWL workflows
        • Version Control, Publishing & Validation of Workflows
        • Advanced Topics
      • Import a Dockstore App With Seven Bridges
    • Writing BDC into a Grant Proposal
    • Incurring Cloud Costs
    • Release Notes
      • 2025-04-15 BDC Release Notes
      • 2025-01-15 NHLBI BioData Catalyst Ecosystem Release Notes
      • 2024-10-21 NHLBI BioData Catalyst Ecosystem Release Notes
      • 2024-07-02 NHLBI BioData Catalyst Ecosystem Release Notes
      • 2024-04-01 NHLBI BioData Catalyst Ecosystem Release Notes
      • 2024-01-08 NHLBI BioData Catalyst Ecosystem Release Notes
      • 2023-10-04 NHLBI BioData Catalyst Ecosystem Release Notes
      • 2023-07-11 NHLBI BioData Catalyst Ecosystem Release Notes
      • 2023-04-04 BioData Catalyst Ecosystem Release Notes
      • 2023-01-09 BioData Catalyst Ecosystem Release Notes
      • 2022-10-03 BioData Catalyst Ecosystem Release Notes
      • 2022-07-11 BioData Catalyst Ecosystem Release Notes
      • 2022-04-04 BioData Catalyst Ecosystem Release Notes
      • 2022-01-24 BioData Catalyst Ecosystem Release Notes
      • 2021-10-04 BioData Catalyst Ecosystem Release Notes
      • 2021-07-09 BioData Catalyst Ecosystem Release Notes
      • 2021-04-02 BioData Catalyst Ecosystem Release Notes
      • 2021-01-15 BioData Catalyst Ecosystem Release Notes
      • 2020-10-23 BioData Catalyst Ecosystem Release Notes
      • 2020-08-24 BioData Catalyst Ecosystem Release Notes
      • 2020-04-02 BioData Catalyst Ecosystem Release Notes
    • Data Versioning Release Notes
    • NIH RECOVER Release Notes
  • Tutorials: Videos & Modules
    • Seven Bridges Tutorials
      • Genetic Association Testing using GENESIS Workflows
      • Estimating and Managing Your Cloud Costs
    • Terra Tutorials
      • Getting Started with Gen3 Data on Terra Tutorial
      • Genome Wide Association Study with 1000 Genomes Data Tutorial
      • Genome Wide Association Study with TOPMed Data Tutorial
      • TOPMed Aligner, or, How to Import Data From Gen3 into Terra and Run a Workflow on It
  • Data Management
    • Data Management Strategy
    • Instructions for Data Submission to BDC
      • De-identification Readme
      • Data Dictionary Requirement
    • dbGaP Study Configuration Process for Submission of Data to BDC
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  • Introduction to Docker
  • Introduction to Workflow Languages
  • Best Practices for Secure and FAIR Workflows

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  1. Written Documentation
  2. Analyze Data
  3. Dockstore

Intro to Docker, WDL, CWL

Technologies for reproducible analysis in the cloud

PreviousDiscover our catalogNextDockstore Forum

Last updated 4 years ago

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Introduction to Docker

Docker is a fantastic tool for creating light-weight containers to run your tools. It gives you a fast, VM-like environment for Linux where you can automatically install dependencies, make configurations, and setup your tool exactly the way you want, just as you would on a “normal” Linux host. You can then quickly and easily share these Docker images with the world using registries like Quay.io (indexed by Dockstore), Docker Hub, and GitLab.

Introduction to Workflow Languages

There are multiple workflow languages currently available to use with docker technology. In the BioData Catalyst ecosystem, SevenBridges uses CWL and Terra uses WDL. To learn more about how these language compare and differ, read Dockstore's documentation on and .

Once you have picked what language works best for you, prepare your pipeline for analysis in the cloud with these tutorials aimed at bioinformaticians:

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Best Practices for Secure and FAIR Workflows

Dockstore’s integration with BioData Catalyst allows researchers the ability to easily launch reproducible tools and workflows in secure workspace environments for use with sensitive data. This privilege to work with sensitive data requires assurances of safe software.

We believe we can enhance the security and reliability of tools and workflows through open, community-driven best practices that exemplify the FAIR (Findable, Accessible, Interoperable, Reusable) guiding principles. We have established a best practices framework for published in Dockstore. We ask that users try to implement these practices for all workflows they develop.

Learn how to create a Docker image
tools
workflows
Learn how to create a tool in Common Workflow Language (CWL
Learn how to create a tool in Workflow Descriptor Language (WDL
secure and FAIR workflows