Finding or Importing a Workflow

Workbench supports workflows written in the Workflow Description Language (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 OpenWDL organization. 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 (CLI).

Accessing and Selecting Workflows

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

Navigate to the "Workflows" page in the sidebar to view available workflows. The table displays both DNAstack's curated workflows from sources like Dockstore 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

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

Additional Resources

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

• WDL specification on Github - Core language documentation, available functions, and developer resources

• OpenWDL community documentation - Beginner guides and common usage patterns

• Learn-WDL online course - Complete educational materials with video walkthroughs

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.