Finding or Importing a Workflow
Overview
Workbench supports running workflows written in the Workflow Description Language (WDL, pronounced ‘widdle’). WDL is an open, community-driven workflow language stewarded by the OpenWDL organization.
DNAstack has authored a number of WDL workflows for processing Illumina, Oxford Nanopore, and PacBio sequencing data that are available through Workbench. In addition, Workbench supports importing workflows by uploading workflow files written in WDL through the user interface or the command-line interface (CLI) . For detailed instructions on how to import workflows in this way, see the relevant CLI doc.
To select a workflow that you want to run once it has been loaded into Workbench, navigate to the Workflows page in Workbench and use the search function.
Step-by-step instructions
This procedure assumes you have already connected Workbench to at least one workflow engine as described in Connecting to a workflow engine
Step 1: (optional) Import a workflow via the DNAstack Command Line Interface.
Step 2: Click "Workflows" in the navigation sidebar. This will bring up the Workflows page, where available workflows will be displayed in a table. The table includes workflows preloaded by DNAstack drawn from popular sources such as Dockstore, as well as any private workflows you may have imported previously.
Step 3: Use the search box to find a specific workflow. The search terms will be applied to workflow names, authors, and the latest version of the workflow.
Step 4: (optional) To view detailed information for a workflow of interest, either click on the workflow name or click on “Actions” in the rightmost column of the table, then click on the “View Workflow” option. This will bring up the workflow details page, which provides information about the workflow (“Overview” tab), a list of versions ( “Versions” tab), and associated files.
Step 5: To select the latest version of the workflow for execution, click the “Run Latest Version” button in the top right of the workflow details page. Alternatively, you can select a different version from the “Versions” tab.
that you can bypass the workflow details page by clicking on “Actions” in the table of workflows and selecting “Run Workflow”.
Whichever route you choose, selecting a workflow to run will take you to the workflow inputs configuration page.
Additional WDL resources and services
DNAstack offers custom workflow development services. If you’d like to know more, please contact the DNAstack team and we will reach out to discuss your needs.
Alternatively, there is a wealth of publicly available WDL workflows authored by various organizations and individuals in the research community. The largest repository of community-contributed WDL workflows is Dockstore, a free and open-source platform for sharing reusable and scalable analytical tools and workflows, developed by the Cancer Genome Collaboratory. Workflow files can be exported from Dockstore using the ‘Export as Zip’ option, then uploaded to Workbench using the CLI as noted above. Note that many of the workflows in Dockstore have already been preloaded into Workbench. These workflows will be marked as having “Dockstore” as their source.
If you plan to develop your own WDL workflows, you may be interested in the following resources:
WDL specification on Github Core language specification; includes a comprehensive description of available functions and a list of developer resources (language and IDE support, test tools, etc)
OpenWDL community documentation A community-contributed WDL documentation site that includes a beginner-level introduction to WDL and a cookbook-style collection of common patterns (use cases).
Learn-WDL online course A community-contributed set of educational materials. Includes full video walkthrough.
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