{% codeblock as yaml %}
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:OutputStorageClass:
+ intermediateStorageClass: fast_storage
+ finalStorageClass: robust_storage
+
+ arv:ProcessProperties:
+ processProperties:
+ property1: value1
+ property2: $(inputs.value2)
+
+ arv:OutputCollectionProperties:
+ outputProperties:
+ property1: value1
+ property2: $(inputs.value2)
+
+ cwltool:CUDARequirement:
+ cudaVersionMin: "11.0"
+ cudaComputeCapability: "9.0"
+ cudaDeviceCountMin: 1
+ cudaDeviceCountMax: 1
+
+ arv:UsePreemptible:
+ usePreemptible: true
{% endcodeblock %}
h2(#RunInSingleContainer). arv:RunInSingleContainer
table(table table-bordered table-condensed).
|_. 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.|
+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 workflow.|
h2. 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.
+*Note: currently, workflows with secrets must be submitted on the command line using @arvados-cwl-runner@. Workflows with secrets submitted through Workbench will not properly obscure the secret inputs.*
+
table(table table-bordered table-condensed).
|_. Field |_. Type |_. Description |
|secrets|array<string>|Input parameters which are considered "secret". Must be strings.|
|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.|
+h2(#OutputStorageClass). arv:OutputStorageClass
+
+Specify the "storage class":{{site.baseurl}}/user/topics/storage-classes.html to use for intermediate and final outputs.
+
+table(table table-bordered table-condensed).
+|_. Field |_. Type |_. Description |
+|intermediateStorageClass|string or array of strings|The storage class for output of intermediate steps. For example, faster "hot" storage.|
+|finalStorageClass_uuid|string or array of strings|The storage class for the final output. |
+
+h2(#ProcessProperties). arv:ProcessProperties
+
+Specify extra "properties":{{site.baseurl}}/api/methods.html#subpropertyfilters that will be set on container requests created by the workflow. May be set on a Workflow or a CommandLineTool. Setting custom properties on a container request simplifies queries to find the workflow run later on.
+
+table(table table-bordered table-condensed).
+|_. Field |_. Type |_. Description |
+|processProperties|key-value map, or list of objects with the fields {propertyName, propertyValue}|The properties that will be set on the container request. May include expressions that reference @$(inputs)@ of the current workflow or tool.|
+
+h2(#OutputCollectionProperties). arv:OutputCollectionProperties
+
+Specify custom "properties":{{site.baseurl}}/api/methods.html#subpropertyfilters that will be set on the output collection of the workflow step.
+
+table(table table-bordered table-condensed).
+|_. Field |_. Type |_. Description |
+|outputProperties|key-value map, or list of objects with the fields {propertyName, propertyValue}|The properties that will be set on the output collection. May include expressions that reference @$(inputs)@ of the current workflow or tool.|
+
+h2(#CUDARequirement). cwltool:CUDARequirement
+
+Request support for Nvidia CUDA GPU acceleration in the container. Assumes that the CUDA runtime (SDK) is installed in the container, and the host will inject the CUDA driver libraries into the container (equal or later to the version requested).
+
+table(table table-bordered table-condensed).
+|_. Field |_. Type |_. Description |
+|cudaVersionMin|string|Required. The CUDA SDK version corresponding to the minimum driver version supported by the container (generally, the SDK version 'X.Y' the application was compiled against).|
+|cudaComputeCapability|string|Required. The minimum CUDA hardware capability (in 'X.Y' format) required by the application's PTX or C++ GPU code (will be JIT compiled for the available hardware).|
+|cudaDeviceCountMin|integer|Minimum number of GPU devices to allocate on a single node. Required.|
+|cudaDeviceCountMax|integer|Maximum number of GPU devices to allocate on a single node. Optional. If not specified, same as @cudaDeviceCountMin@.|
+
+h2(#UsePreemptible). arv:UsePreemptible
+
+Specify whether a workflow step should request preemptible (e.g. AWS Spot market) instances. Such instances are generally cheaper, but can be taken back by the cloud provider at any time (preempted) causing the step to fail. When this happens, Arvados will automatically re-try the step, up to the configuration value of @Containers.MaxRetryAttempts@ (default 3) times.
+
+table(table table-bordered table-condensed).
+|_. Field |_. Type |_. Description |
+|usePreemptible|boolean|Required, true to opt-in to using preemptible instances, false to opt-out.|
+
h2. 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@.
<pre>
requirements:
DockerRequirement:
- dockerPull: "debian:9"
+ dockerPull: "debian:10"
arv:dockerCollectionPDH: "feaf1fc916103d7cdab6489e1f8c3a2b+174"
</pre>
The following extensions are deprecated because equivalent features are part of the CWL v1.1 standard.
+{% codeblock as yaml %}
+hints:
+ cwltool:LoadListingRequirement:
+ loadListing: shallow_listing
+ arv:ReuseRequirement:
+ enableReuse: false
+ cwltool:TimeLimit:
+ timelimit: 14400
+{% endcodeblock %}
+
h2. cwltool:LoadListingRequirement
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
projects / arvados.git / blobdiff