Arvados™ Docs
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  1. Welcome
    1. Welcome to Arvados™!
    2. Arvados Community and Getting Help
  2. Walkthough
    1. Processing Whole Genome Sequences
  3. Run a workflow using Workbench
    1. Accessing Arvados Workbench
    2. Running a workflow using Workbench
  4. Working at the Command Line
    1. Getting started at the command line
    2. Getting an API token
    3. Checking your environment
  5. 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
  6. Working with data sets
    1. Uploading data
    2. Downloading data
    3. Access Keep as a GNU/Linux filesystem
    4. Access Keep from macOS Finder
    5. Access Keep from Windows File Explorer
    6. Trashing and untrashing data
    7. Using arv-copy
    8. Using collection versioning
    9. Using storage classes
  7. Data Analysis with Workflows
    1. Starting a Workflow at the Command Line
    2. arvados-cwl-runner options
    3. Developing workflows with CWL
    4. Working with Docker images
    5. Guidelines for Writing High-Performance Portable Workflows
    6. Arvados CWL Extensions
    7. Federated Multi-Cluster Workflows
    8. CWL version support
    9. Analyzing workflow performance
  8. Working with git repositories
    1. Adding a new Arvados git repository
    2. Working with an Arvados git repository
  9. Reference
    1. Linking alternate login accounts
    2. Arvados SDK Examples
  10. Arvados License
    1. Arvados Free Software Licenses
    2. GNU Affero General Public License
    3. Apache License
    4. Creative Commons

CWL version support

Arvados supports CWL v1.0, v1.1 and v1.2.

Upgrading your workflows to CWL v1.2

If you are starting from a CWL v1.0 document, see Upgrading your workflows to CWL v1.1 below.

If you are starting from a CWL v1.1 document, you should be able to trivially change cwlVersion: v1.1 to cwlVersion: v1.2 to be able to take advantage of the new features of v1.2, such as conditional workflow steps.

Upgrading your workflows 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: Federated Multi-Cluster Workflows Next: Analyzing workflow performance

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.