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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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  • Conversion tools
  • Running workflows outside of the BioData Catalyst ecosystem:

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  1. Written Documentation
  2. Community Tools & Integration
  3. Bring Your Own Tool(s)

Advanced Topics

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Last updated 4 years ago

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Conversion tools

If you want your workflow to be available to both WDL and CWL communities, you can use conversion tools to aid in the process. It is best practice to review if the conversion was correctly done.

Running workflows outside of the BioData Catalyst ecosystem:

If you are interested in using Docker on your High-Performance Compute cluster, you may find the tool helpful.

You can use the workflow runner for large parallelized CWL jobs in the AWS and/or Google clouds, locally, on Kubernetes, and/or high-performance computer clusters. is built for researchers and should run any CWL 1.0 workflow from Dockstore at scale. also has some experimental support for WDL.

cwl2wdl
Wdl2cwl
Singularity
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