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:

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

For portability, most Arvados extensions should go into the hints section of your CWL file. This makes it possible for your workflows to run other CWL runners that do not recognize Arvados hints. The difference between hints and requirements is that hints are optional features that can be ignored by other runners and still produce the same output, whereas requirements will fail the workflow if they cannot be fulfilled. For example, arv:IntermediateOutput should go in hints as it will have no effect on non-Arvados platforms, however if your workflow explicitly accesses the Arvados API and will fail without it, you should put arv:APIRequirement in requirements.

hints:
  arv:RunInSingleContainer: {}
  arv:RuntimeConstraints:
    keep_cache: 123456
    outputDirType: keep_output_dir
  arv:PartitionRequirement:
    partition: dev_partition
  arv:APIRequirement: {}
  cwltool:LoadListingRequirement:
    loadListing: shallow_listing
  arv:IntermediateOutput:
    outputTTL: 3600
  arv:ReuseRequirement:
    enableReuse: false
  cwltool:Secrets:
    secrets: [input1, input2]
  cwltool:TimeLimit:
    timelimit: 14400
  arv:WorkflowRunnerResources:
    ramMin: 2048
    coresMin: 2
    keep_cache: 512
  arv:ClusterTarget:
    cluster_id: clsr1
    project_uuid: clsr1-j7d0g-qxc4jcji7n4lafx

arv:RunInSingleContainer

Apply this to a workflow step that runs a subworkflow. Indicates that all the steps of the subworkflow should run together in a single container and not be scheduled separately. If you have a sequence of short-running steps (less than 1-2 minutes each) this enables you to avoid scheduling and data transfer overhead by running all the steps together at once. To use this feature, cwltool must be installed in the container image.

arv:RuntimeConstraints

Set Arvados-specific runtime hints.

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.|

arv:PartitionRequirement

Select preferred compute partitions on which to run jobs.

Field Type Description
partition string or array of strings

arv:APIRequirement

For CWL v1.1 scripts, if a step requires network access but not specifically access to the Arvados API server, prefer the standard feature NetworkAccess . In the future, these may be differentiated by whether ARVADOS_API_HOST and ARVADOS_API_TOKEN is injected into the container or not.

Indicates that process wants to access to the Arvados API. Will be granted network access and have ARVADOS_API_HOST and ARVADOS_API_TOKEN set in the environment. Tools which rely on the Arvados API being present should put arv:APIRequirement in the requirements section of the tool (rather than hints) to indicate that that it is not portable to non-Arvados CWL runners.

Use arv:APIRequirement in hints to enable general (non-Arvados-specific) network access for a tool.

arv:IntermediateOutput

Specify desired handling of intermediate output collections.

Field Type Description
outputTTL int If the value is greater than zero, consider intermediate output collections to be temporary and should be automatically trashed. Temporary collections will be trashed outputTTL seconds after creation. A value of zero means intermediate output should be retained indefinitely (this is the default behavior).
Note: arvados-cwl-runner currently does not take workflow dependencies into account when setting the TTL on an intermediate output collection. If the TTL is too short, it is possible for a collection to be trashed before downstream steps that consume it are started. The recommended minimum value for TTL is the expected duration of the entire the workflow.

cwltool:Secrets

Indicate that one or more input parameters are “secret”. Must be applied at the top level Workflow. Secret parameters are not stored in keep, are hidden from logs and API responses, and are wiped from the database after the workflow completes.

Field Type Description
secrets array Input parameters which are considered “secret”. Must be strings.

arv:WorkflowRunnerResources

Specify resource requirements for the workflow runner process (arvados-cwl-runner) that manages a workflow run. Must be applied to the top level workflow. Will also be set implicitly when using --submit-runner-ram on the command line along with --create-workflow or --update-workflow. Use this to adjust the runner’s allocation if the workflow runner is getting “out of memory” exceptions or being killed by the out-of-memory (OOM) killer.

Field Type Description
ramMin int RAM, in mebibytes, to reserve for the arvados-cwl-runner process. Default 1 GiB
coresMin int Number of cores to reserve to the arvados-cwl-runner process. Default 1 core.
keep_cache int Size of collection metadata cache for the workflow runner, in MiB. Default 256 MiB. Will be added on to the RAM request when determining node size to request.

arv:ClusterTarget

Specify which Arvados cluster should execute a container or subworkflow, and the parent project for the container request.

Field Type Description
cluster_id string The five-character alphanumeric cluster id (uuid prefix) where a container or subworkflow will execute. May be an expression.
project_uuid string The uuid of the project which will own container request and output of the container. May be an expression.

arv:dockerCollectionPDH

This is an optional extension field appearing on the standard DockerRequirement. It specifies the portable data hash of the Arvados collection containing the Docker image. If present, it takes precedence over dockerPull or dockerImageId.

requirements:
  DockerRequirement:
    dockerPull: "debian:9"
    arv:dockerCollectionPDH: "feaf1fc916103d7cdab6489e1f8c3a2b+174"

Deprecated extensions

The following extensions are deprecated because equivalent features are part of the CWL v1.1 standard.

cwltool:LoadListingRequirement

For CWL v1.1 scripts, this is deprecated in favor of loadListing or 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.

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.

arv:ReuseRequirement

For CWL v1.1 scripts, this is deprecated in favor of WorkReuse .

Enable/disable work reuse for current process. Default true (work reuse enabled).

Field Type Description
enableReuse boolean Enable/disable work reuse for current process. Default true (work reuse enabled).

cwltool:TimeLimit

For CWL v1.1 scripts, this is deprecated in favor of ToolTimeLimit

Set an upper limit on the execution time of a CommandLineTool or ExpressionTool. A tool execution which exceeds the time limit may be preemptively terminated and considered failed. May also be used by batch systems to make scheduling decisions.

Field Type Description
timelimit int Execution time limit in seconds. If set to zero, no limit is enforced.

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