---
layout: default
navsection: userguide
title: Arvados CWL Extensions
...

Arvados provides several extensions to CWL for workflow optimization, site-specific configuration, and to enable access the Arvados API.

To use Arvados CWL extensions, add the following @$namespaces@ section at the top of your CWL file:

<pre>
$namespaces:
  arv: "http://arvados.org/cwl#"
  cwltool: "http://commonwl.org/cwltool#"
</pre>

Arvados extensions must go into the @hints@ section, for example:

<pre>
hints:
  arv:RunInSingleContainer: {}
  arv:RuntimeConstraints:
    keep_cache: 123456
    keep_output_dir: local_output_dir
  arv:PartitionRequirement:
    partition: dev_partition
  arv:APIRequirement: {}
  cwltool:LoadListingRequirement:
    loadListing: shallow_listing
</pre>

h2. arv:RunInSingleContainer

Indicates that a subworkflow should run in a single container and not be scheduled as separate steps.

h2. arv:RuntimeConstraints

Set Arvados-specific runtime hints.

table(table table-bordered table-condensed).
|_. Field |_. Type |_. Description |
|keep_cache|int|Size of file data buffer for Keep mount in MiB. Default is 256 MiB. Increase this to reduce cache thrashing in situations such as accessing multiple large (64+ MiB) files at the same time, or performing random access on a large file.|
|outputDirType|enum|Preferred backing store for output staging.  If not specified, the system may choose which one to use.  One of *local_output_dir* or *keep_output_dir*|

*local_output_dir*: Use regular file system local to the compute node. There must be sufficient local scratch space to store entire output; specify this with @outdirMin@ of @ResourceRequirement@.  Files are batch uploaded to Keep when the process completes.  Most compatible, but upload step can be time consuming for very large files.

*keep_output_dir*: Use writable Keep mount.  Files are streamed to Keep as they are written.  Does not consume local scratch space, but does consume RAM for output buffers (up to 192 MiB per file simultaneously open for writing.)  Best suited to processes which produce sequential output of large files (non-sequential writes may produced fragmented file manifests).  Supports regular files and directories, does not support special files such as symlinks, hard links, named pipes, named sockets, or device nodes.|

h2. arv:PartitionRequirement

Select preferred compute partitions on which to run jobs.

table(table table-bordered table-condensed).
|_. Field |_. Type |_. Description |
|partition|string or array of strings||

h2. arv:APIRequirement

Indicates that process wants to access to the Arvados API.  Will be granted limited network access and have @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ set in the environment.

h2. cwltool:LoadListingRequirement

In CWL v1.0 documents, the default behavior for Directory objects is to recursively expand the @listing@ for access by parameter references an expressions.  For directory trees containing many files, this can be expensive in both time and memory usage.  Use @cwltool:LoadListingRequirement@ to change the behavior for expansion of directory listings in the workflow runner.

table(table table-bordered table-condensed).
|_. Field |_. Type |_. Description |
|loadListing|string|One of @no_listing@, @shallow_listing@, or @deep_listing@|

*no_listing*: Do not expand directory listing at all.  The @listing@ field on the Directory object will be undefined.

*shallow_listing*: Only expand the first level of directory listing.  The @listing@ field on the toplevel Directory object will contain the directory contents, however @listing@ will not be defined on subdirectories.

*deep_listing*: Recursively expand all levels of directory listing.  The @listing@ field will be provided on the toplevel object and all subdirectories.