4 title: Arvados CWL Extensions
7 Copyright (C) The Arvados Authors. All rights reserved.
9 SPDX-License-Identifier: CC-BY-SA-3.0
12 Arvados provides several extensions to CWL for workflow optimization, site-specific configuration, and to enable access the Arvados API.
14 To use Arvados CWL extensions, add the following @$namespaces@ section at the top of your CWL file:
16 {% codeblock as yaml %}
18 arv: "http://arvados.org/cwl#"
19 cwltool: "http://commonwl.org/cwltool#"
22 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@.
24 {% codeblock as yaml %}
26 arv:RunInSingleContainer: {}
27 arv:RuntimeConstraints:
29 outputDirType: keep_output_dir
30 arv:PartitionRequirement:
31 partition: dev_partition
32 arv:APIRequirement: {}
33 cwltool:LoadListingRequirement:
34 loadListing: shallow_listing
35 arv:IntermediateOutput:
40 secrets: [input1, input2]
43 arv:WorkflowRunnerResources:
49 project_uuid: clsr1-j7d0g-qxc4jcji7n4lafx
52 h2(#RunInSingleContainer). arv:RunInSingleContainer
54 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.
56 h2. arv:RuntimeConstraints
58 Set Arvados-specific runtime hints.
60 table(table table-bordered table-condensed).
61 |_. Field |_. Type |_. Description |
62 |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.|
63 |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*|
65 *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.
67 *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.|
69 h2. arv:PartitionRequirement
71 Select preferred compute partitions on which to run jobs.
73 table(table table-bordered table-condensed).
74 |_. Field |_. Type |_. Description |
75 |partition|string or array of strings||
77 h2(#APIRequirement). arv:APIRequirement
79 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":https://www.commonwl.org/v1.1/CommandLineTool.html#NetworkAccess . In the future, these may be differentiated by whether ARVADOS_API_HOST and ARVADOS_API_TOKEN is injected into the container or not.
81 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.
83 Use @arv:APIRequirement@ in @hints@ to enable general (non-Arvados-specific) network access for a tool.
85 h2. arv:IntermediateOutput
87 Specify desired handling of intermediate output collections.
89 table(table table-bordered table-condensed).
90 |_. Field |_. Type |_. Description |
91 |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).
92 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.|
96 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.
98 table(table table-bordered table-condensed).
99 |_. Field |_. Type |_. Description |
100 |secrets|array<string>|Input parameters which are considered "secret". Must be strings.|
102 h2. arv:WorkflowRunnerResources
104 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.
106 table(table table-bordered table-condensed).
107 |_. Field |_. Type |_. Description |
108 |ramMin|int|RAM, in mebibytes, to reserve for the arvados-cwl-runner process. Default 1 GiB|
109 |coresMin|int|Number of cores to reserve to the arvados-cwl-runner process. Default 1 core.|
110 |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.|
112 h2(#clustertarget). arv:ClusterTarget
114 Specify which Arvados cluster should execute a container or subworkflow, and the parent project for the container request.
116 table(table table-bordered table-condensed).
117 |_. Field |_. Type |_. Description |
118 |cluster_id|string|The five-character alphanumeric cluster id (uuid prefix) where a container or subworkflow will execute. May be an expression.|
119 |project_uuid|string|The uuid of the project which will own container request and output of the container. May be an expression.|
121 h2. arv:dockerCollectionPDH
123 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@.
128 dockerPull: "debian:9"
129 arv:dockerCollectionPDH: "feaf1fc916103d7cdab6489e1f8c3a2b+174"
132 h1. Deprecated extensions
134 The following extensions are deprecated because equivalent features are part of the CWL v1.1 standard.
136 h2. cwltool:LoadListingRequirement
138 For CWL v1.1 scripts, this is deprecated in favor of "loadListing":https://www.commonwl.org/v1.1/CommandLineTool.html#CommandInputParameter or "LoadListingRequirement":https://www.commonwl.org/v1.1/CommandLineTool.html#LoadListingRequirement
140 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.
142 table(table table-bordered table-condensed).
143 |_. Field |_. Type |_. Description |
144 |loadListing|string|One of @no_listing@, @shallow_listing@, or @deep_listing@|
146 *no_listing*: Do not expand directory listing at all. The @listing@ field on the Directory object will be undefined.
148 *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.
150 *deep_listing*: Recursively expand all levels of directory listing. The @listing@ field will be provided on the toplevel object and all subdirectories.
152 h2. arv:ReuseRequirement
154 For CWL v1.1 scripts, this is deprecated in favor of "WorkReuse":https://www.commonwl.org/v1.1/CommandLineTool.html#WorkReuse .
156 Enable/disable work reuse for current process. Default true (work reuse enabled).
158 table(table table-bordered table-condensed).
159 |_. Field |_. Type |_. Description |
160 |enableReuse|boolean|Enable/disable work reuse for current process. Default true (work reuse enabled).|
162 h2. cwltool:TimeLimit
164 For CWL v1.1 scripts, this is deprecated in favor of "ToolTimeLimit":https://www.commonwl.org/v1.1/CommandLineTool.html#ToolTimeLimit
166 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.
168 table(table table-bordered table-condensed).
169 |_. Field |_. Type |_. Description |
170 |timelimit|int|Execution time limit in seconds. If set to zero, no limit is enforced.|