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On this page
  • Understanding WDL Workflows
  • Accessing and Selecting Workflows
  • Importing Custom Workflows
  • Community Resources
  • Additional Resources

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  1. Workbench
  2. Getting Started

Finding or Importing a Workflow

PreviousConnecting an EngineNextConfiguring Workflow Inputs

Last updated 4 months ago

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supports workflows written in the (WDL). These workflows can come from DNAstack's curated collection, your own imports, or community resources. Before starting, ensure you have connected Workbench to at least one workflow engine.

Understanding WDL Workflows

WDL (pronounced 'widdle') is an open, community-driven workflow language stewarded by the . DNAstack provides pre-built WDL workflows for processing data from various sequencing platforms, including Illumina, Oxford Nanopore, and PacBio. You can also import custom workflows through the user interface or command-line interface ().

Accessing and Selecting Workflows

This procedure assumes you have already connected Workbench to at least one workflow engine as described in

Navigate to the "Workflows" page in the sidebar to view available workflows. The table displays both DNAstack's curated workflows from sources like and any private workflows you've imported. Use the search box to filter workflows by name, author, or version.

For detailed workflow information:

  1. Click the workflow name or select "View Workflow" from the Actions menu

  2. Review the Overview tab for general information

  3. Check the Versions tab for available versions

  4. Examine associated files and documentation

To run a workflow:

  • Click "Run Latest Version" from the workflow details page

  • Select a specific version from the Versions tab

  • Use the Actions menu to run directly from the workflows table

You can bypass the workflow details page by clicking “Actions” in the table of workflows and selecting “Run Workflow”.

After selecting a workflow, you'll be taken to the inputs configuration page to set up your run.

Importing Custom Workflows

You can add your own WDL workflows to Workbench in two ways:

  • Upload through the Workbench user interface

  • Import using the command-line interface (CLI)

For detailed CLI import instructions, refer to the CLI documentation.

Community Resources

Additional Resources

For those interested in WDL development, several resources are available:

DNAstack also offers custom workflow development services. Contact the DNAstack team to discuss your specific workflow needs.

Looking for a specific workflow feature? Use the search function to filter by workflow names, authors, and versions simultaneously.

Many public WDL workflows are available through , a free and open-source platform for sharing analytical tools and workflows. While many Dockstore workflows are pre-loaded in (marked with "Dockstore" as their source), you can export additional workflows from Dockstore using the 'Export as Zip' option and import them via the .

- Core language documentation, available functions, and developer resources

- Beginner guides and common usage patterns

- Complete educational materials with video walkthroughs

Workbench
Workflow Description Language
OpenWDL organization
CLI
Connecting
an Engine
Dockstore
Dockstore
Workbench
CLI
WDL specification on Github
OpenWDL community documentation
Learn-WDL online course