|==--output-name OUTPUT_NAME==|Name to use for collection that stores the final output.|
|==--output-tags OUTPUT_TAGS==|Tags for the final output collection separated by commas, e.g., =='--output-tags tag0,tag1,tag2'==.|
|==--ignore-docker-for-reuse==|Ignore Docker image version when deciding whether to reuse past containers.|
-|==--submit==| Submit workflow runner to Arvados to manage the workflow (default).|
-|==--local==| Run workflow on local host (still submits containers to Arvados).|
+|==--submit==| Submit workflow to run on Arvados.|
+|==--local==| Run workflow on local host (submits containers to Arvados).|
|==--create-template==| (Deprecated) synonym for --create-workflow.|
|==--create-workflow==| Register an Arvados workflow that can be run from Workbench|
-|==--update-workflow== UUID|Update an existing Arvados workflow or pipeline template with the given UUID.|
+|==--update-workflow== UUID|Update an existing Arvados workflow with the given UUID.|
|==--wait==| After submitting workflow runner, wait for completion.|
|==--no-wait==| Submit workflow runner and exit.|
|==--log-timestamps==| Prefix logging lines with timestamp|
|==--no-log-timestamps==| No timestamp on logging lines|
|==--compute-checksum==| Compute checksum of contents while collecting outputs|
-|==--submit-runner-ram== SUBMIT_RUNNER_RAM|RAM (in MiB) required for the workflow runner (default 1024)|
-|==--submit-runner-image== SUBMIT_RUNNER_IMAGE|Docker image for workflow runner|
+|==--submit-runner-ram== SUBMIT_RUNNER_RAM|RAM (in MiB) required for the workflow runner job (default 1024)|
+|==--submit-runner-image== SUBMIT_RUNNER_IMAGE|Docker image for workflow runner job|
|==--always-submit-runner==|When invoked with --submit --wait, always submit a runner to manage the workflow, even when only running a single CommandLineTool|
+|==--match-submitter-images==|Where Arvados has more than one Docker image of the same name, use image from the Docker instance on the submitting node.|
|==--submit-request-uuid== UUID|Update and commit to supplied container request instead of creating a new one.|
|==--submit-runner-cluster== CLUSTER_ID|Submit workflow runner to a remote cluster|
-|==--name NAME==|Name to use for workflow execution instance.|
+|==--collection-cache-size== COLLECTION_CACHE_SIZE|Collection cache size (in MiB, default 256).|
+|==--name== NAME|Name to use for workflow execution instance.|
|==--on-error== {stop,continue}|Desired workflow behavior when a step fails. One of 'stop' (do not submit any more steps) or 'continue' (may submit other steps that are not downstream from the error). Default is 'continue'.|
-|==--enable-dev==|Enable loading and running development versions of CWL spec.|
-|==--storage-classes== STORAGE_CLASSES|Specify comma separated list of storage classes to be used when saving the final workflow output to Keep.|
-|==--intermediate-storage-classes== STORAGE_CLASSES|Specify comma separated list of storage classes to be used when intermediate workflow output to Keep.|
+|==--enable-dev==|Enable loading and running development versions of the CWL standards.|
+|==--storage-classes== STORAGE_CLASSES|Specify comma separated list of storage classes to be used when saving final workflow output to Keep.|
+|==--intermediate-storage-classes== INTERMEDIATE_STORAGE_CLASSES|Specify comma separated list of storage classes to be used when saving intermediate workflow output to Keep.|
|==--intermediate-output-ttl== N|If N > 0, intermediate output collections will be trashed N seconds after creation. Default is 0 (don't trash).|
|==--priority== PRIORITY|Workflow priority (range 1..1000, higher has precedence over lower)|
-|==--thread-count== THREAD_COUNT|Number of threads to use for container submit and output collection.|
+|==--thread-count== THREAD_COUNT|Number of threads to use for job submit and output collection.|
|==--http-timeout== HTTP_TIMEOUT|API request timeout in seconds. Default is 300 seconds (5 minutes).|
+|==--defer-downloads==|When submitting a workflow, defer downloading HTTP URLs to workflow launch instead of downloading to Keep before submit.|
+|==--varying-url-params== VARYING_URL_PARAMS|A comma separated list of URL query parameters that should be ignored when storing HTTP URLs in Keep.|
+|==--prefer-cached-downloads==|If a HTTP URL is found in Keep, skip upstream URL freshness check (will not notice if the upstream has changed, but also not error if upstream is unavailable).|
+|==--enable-preemptible==|Use preemptible instances. Control individual steps with arv:UsePreemptible hint.|
+|==--disable-preemptible==|Don't use preemptible instances.|
+|==--copy-deps==| Copy dependencies into the destination project.|
+|==--no-copy-deps==| Leave dependencies where they are.|
+|==--skip-schemas==| Skip loading of schemas|
|==--trash-intermediate==|Immediately trash intermediate outputs on workflow success.|
|==--no-trash-intermediate==|Do not trash intermediate outputs (default).|
h3(#federation). Run workflow on a remote federated cluster
By default, the workflow runner will run on the local (home) cluster. Using @--submit-runner-cluster@ you can specify that the runner should be submitted to a remote federated cluster. When doing this, @--project-uuid@ should specify a project on that cluster. Steps making up the workflow will be submitted to the remote federated cluster by default, but the behavior of @arv:ClusterTarget@ is unchanged. Note: when using this option, any resources that need to be uploaded in order to run the workflow (such as files or Docker images) will be uploaded to the local (home) cluster, and streamed to the federated cluster on demand.
+
+h3(#preemptible). Using preemptible (spot) instances
+
+Preemptible instances typically offer lower cost computation with a tradeoff of lower service guarantees. If a compute node is preempted, Arvados will restart the computation on a new instance.
+
+If the sitewide configuration @Containers.AlwaysUsePreemptibleInstances@ is true, workflow steps will always select preemptible instances, regardless of user option.
+
+If @Containers.AlwaysUsePreemptibleInstances@ is false, you can request preemptible instances for a specific run with the @arvados-cwl-runner --enable-preemptible@ option.
+
+Within the workflow, you can control whether individual steps should be preemptible with the "arv:UsePreemptible":cwl-extensions.html#UsePreemptible hint.
+
+If a workflow requests preemptible instances with "arv:UsePreemptible":cwl-extensions.html#UsePreemptible , but you _do not_ want to use preemptible instances, you can override it for a specific run with the @arvados-cwl-runner --disable-preemptible@ option.
+
+h3(#gpu). Use CUDA GPU instances
+
+See "cwltool:CUDARequirement":cwl-extensions.html#CUDARequirement .
projects / arvados.git / blobdiff