Arvados™ Docs
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  1. Welcome
    1. Welcome to Arvados™!
    2. Arvados Community and Getting Help
  2. Run a workflow using Workbench
    1. Accessing Arvados Workbench
    2. Running a workflow using Workbench
    3. Create a Workflow with Composer
  3. Access an Arvados virtual machine
    1. Accessing an Arvados VM with Webshell
    2. Accessing an Arvados VM with SSH - Unix Environments
    3. Accessing an Arvados VM with SSH - Windows Environments
    4. Checking your environment
    5. Getting an API token
  4. Working with data sets
    1. Uploading data
    2. Downloading data
    3. Accessing Keep from GNU/Linux
    4. Accessing Keep from OS X
    5. Accessing Keep from Windows
    6. How Keep works
    7. Keep collection lifecycle
    8. Using arv-copy
    9. Using storage classes
    10. Using collection versioning
  5. Working with git repositories
    1. Adding a new Arvados git repository
    2. Working with an Arvados git repository
  6. Running workflows at the command line
    1. Running an Arvados workflow
    2. Using arvados-cwl-runner
  7. Develop an Arvados workflow
    1. Introduction to Crunch
    2. Writing a CWL workflow
    3. Writing Portable High-Performance Workflows
    4. Federated Multi-Cluster Workflows
    5. Arvados CWL Extensions
    6. CWL version and API support
    7. Customizing Crunch environment using Docker
  8. Reference
    1. Linking alternate login accounts
    2. Arvados SDK Examples
  9. Arvados License
    1. Arvados Free Software Licenses
    2. GNU Affero General Public License
    3. Apache License
    4. Creative Commons

CWL version and API support

Upgrading to CWL v1.1

CWL v1.1 introduces several features to the standard that were previously available as Arvados extensions. CWL v1.1 syntax is backwards compatible with v1.0, so you can just change cwlVersion: v1.0 to cwlVersion: v1.1 and update your script to using the standard features. On Arvados, there is only one behavior change between CWL v1.0 and v1.1 to be aware of: for performance reasons, Directory listings are no longer loaded by default. To control loading Directory listings, use loadListing or LoadListingRequirement (the extension cwltool:LoadListingRequirement is deprecated.)

If a step requires network access, use NetworkAccess instead of the Arvados-specific arv:APIRequirement .

To prevent misbehaving steps from running forever and wasting resources, you can fail the step if it exceeds a certain running time with ToolTimeLimit instead of the deprecated cwltool:TimeLimit .

To control if an individual step can be reused, use WorkReuse instead of the deprecated arv:ReuseRequirement.

Previous: Arvados CWL Extensions Next: Customizing Crunch environment using Docker

The content of this documentation is licensed under the Creative Commons Attribution-Share Alike 3.0 United States licence.
Code samples in this documentation are licensed under the Apache License, Version 2.0.