14360: Merge branch 'master' into 14360-dispatch-cloud

[arvados.git] / doc / user / cwl / cwl-extensions.html.textile.liquid

diff --git a/doc/user/cwl/cwl-extensions.html.textile.liquid b/doc/user/cwl/cwl-extensions.html.textile.liquid
index 95422b6bd32206019a8703e8a94a6c57735b92dd..d62002237a7e7b1d43aa7c59f4ef1afa7bc38b84 100644 (file)
--- a/doc/user/cwl/cwl-extensions.html.textile.liquid
+++ b/doc/user/cwl/cwl-extensions.html.textile.liquid
@@ -26,7 +26,7 @@ hints:
   arv:RunInSingleContainer: {}
   arv:RuntimeConstraints:
     keep_cache: 123456
-    keep_output_dir: local_output_dir
+    outputDirType: keep_output_dir
   arv:PartitionRequirement:
     partition: dev_partition
   arv:APIRequirement: {}
@@ -36,6 +36,17 @@ hints:
     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
 </pre>
 
 The one exception to this is @arv:APIRequirement@, see note below.
@@ -101,3 +112,50 @@ Enable/disable work reuse for current process.  Default true (work reuse enabled
 table(table table-bordered table-condensed).
 |_. Field |_. Type |_. Description |
 |enableReuse|boolean|Enable/disable work reuse for current process.  Default true (work reuse enabled).|
+
+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.
+
+table(table table-bordered table-condensed).
+|_. Field |_. Type |_. Description |
+|secrets|array<string>|Input parameters which are considered "secret".  Must be strings.|
+
+
+h2. cwltool:TimeLimit
+
+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.
+
+table(table table-bordered table-condensed).
+|_. Field |_. Type |_. Description |
+|timelimit|int|Execution time limit in seconds. If set to zero, no limit is enforced.|
+
+h2. 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.
+
+table(table table-bordered table-condensed).
+|_. 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.|
+
+h2(#clustertarget). arv:ClusterTarget
+
+Specify which Arvados cluster should execute a container or subworkflow, and the parent project for the container request.
+
+table(table table-bordered table-condensed).
+|_. 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.|
+
+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:8"
+    arv:dockerCollectionPDH: "feaf1fc916103d7cdab6489e1f8c3a2b+174"
+</pre>