---
layout: default
navsection: userguide
-title: CWL version and API support
+title: CWL version support
...
{% comment %}
Copyright (C) The Arvados Authors. All rights reserved.
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-h2. Upgrading to CWL v1.1
+Arvados supports CWL v1.0, v1.1 and v1.2.
-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":https://www.commonwl.org/v1.1/CommandLineTool.html#CommandInputParameter or "LoadListingRequirement":https://www.commonwl.org/v1.1/CommandLineTool.html#LoadListingRequirement (the extension @cwltool:LoadListingRequirement@ is deprecated.)
-
-If a step requires network access, use "NetworkAccess":https://www.commonwl.org/v1.1/CommandLineTool.html#NetworkAccess instead of the Arvados-specific "arv:APIRequirement":cwl-extensions.html#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":https://www.commonwl.org/v1.1/CommandLineTool.html#ToolTimeLimit instead of the deprecated @cwltool:TimeLimit@ .
+h2(#v12). Upgrading your workflows to CWL v1.2
-To control if an individual step can be reused, use "WorkReuse":https://www.commonwl.org/v1.1/CommandLineTool.html#WorkReuse instead of the deprecated @arv:ReuseRequirement@.
+If you are starting from a CWL v1.0 document, see "Upgrading your workflows to CWL v1.1":#v11 below.
-h2(#migrate). Differences in running CWL on the legacy jobs API vs containers API
+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.
-Most users can ignore this section.
+h2(#v11). Upgrading your workflows to CWL v1.1
-When migrating your Arvados cluster from using the jobs API (--api=jobs) (sometimes referred to as "crunch v1") to the containers API (--api=containers) ("crunch v2") there are a few differences in behavior:
+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":https://www.commonwl.org/v1.1/CommandLineTool.html#CommandInputParameter or "LoadListingRequirement":https://www.commonwl.org/v1.1/CommandLineTool.html#LoadListingRequirement (the extension @cwltool:LoadListingRequirement@ is deprecated.)
-A tool may fail to find an input file that could be found when run under the jobs API. This is because tools are limited to accessing collections explicitly listed in the input, and further limited to those individual files or subdirectories that are listed. For example, given an explicit file input @/dir/subdir/file1.txt@, a tool will not be allowed to implicitly access a file in the parent directory @/dir/file2.txt@. Use @secondaryFiles@ or a @Directory@ for files that need to be grouped together.
+If a step requires network access, use "NetworkAccess":https://www.commonwl.org/v1.1/CommandLineTool.html#NetworkAccess instead of the Arvados-specific "arv:APIRequirement":cwl-extensions.html#APIRequirement .
-A tool may fail when attempting to rename or delete a file in the output directory. This may happen because files listed in @InitialWorkDirRequirement@ appear in the output directory as normal files (not symlinks) but cannot be moved, renamed or deleted unless marked as "writable" in CWL. These files will be added to the output collection but without any additional copies of the underlying data.
+To prevent misbehaving steps from running forever and wasting resources, you can fail the step if it exceeds a certain running time with "ToolTimeLimit":https://www.commonwl.org/v1.1/CommandLineTool.html#ToolTimeLimit instead of the deprecated @cwltool:TimeLimit@ .
-A tool may fail when attempting to access the network. This may happen because, unlike the jobs API, under the containers API network access is disabled by default. Tools which require network access should add @arv:APIRequirement: {}@ to the @requirements@ section.
+To control if an individual step can be reused, use "WorkReuse":https://www.commonwl.org/v1.1/CommandLineTool.html#WorkReuse instead of the deprecated @arv:ReuseRequirement@.
projects / arvados.git / blobdiff