navsection: userguide
title: "Using arvados-cwl-runner"
...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
The following command line options are available for @arvados-cwl-runner@:
table(table table-bordered table-condensed).
|_. Option |_. Description |
-| --basedir BASEDIR| Base directory used to resolve relative references in the input, default to directory of input object file or current directory (if inputs piped/provided on command line).|
-| --version| Print version and exit|
-| --verbose| Default logging|
-| --quiet| Only print warnings and errors.|
-| --debug| Print even more logging|
-| --tool-help| Print command line help for tool|
-| --enable-reuse|Enable job reuse (default)|
-| --disable-reuse|Disable job reuse (always run new jobs).|
-| --project-uuid UUID| Project that will own the workflow jobs, if not provided, will go to home project.|
-| --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 jobs.|
-| --submit| Submit workflow to run on Arvados.|
-| --local| Control workflow from local host (submits jobs to Arvados).|
-| --create-template| (Deprecated) synonym for --create-workflow.|
-| --create-workflow| Create an Arvados workflow (if using the 'containers' API) or pipeline template (if using the 'jobs' API). See --api.|
-| --update-workflow UUID|Update an existing Arvados workflow or pipeline template with the given UUID.|
-| --wait| After submitting workflow runner job, wait for completion.|
-| --no-wait| Submit workflow runner job and exit.|
-| --api WORK_API| Select work submission API, one of 'jobs' or 'containers'. Default is 'jobs' if that API is available, otherwise 'containers'.|
-| --compute-checksum| Compute checksum of contents while collecting outputs|
-| --submit-runner-ram SUBMIT_RUNNER_RAM|RAM (in MiB) required for the workflow runner job (default 1024)|
-| --name NAME| Name to use for workflow execution instance.|
+|==--basedir== BASEDIR| Base directory used to resolve relative references in the input, default to directory of input object file or current directory (if inputs piped/provided on command line).|
+|==--version==| Print version and exit|
+|==--validate==| Validate CWL document only.|
+|==--verbose==| Default logging|
+|==--quiet==| Only print warnings and errors.|
+|==--debug==| Print even more logging|
+|==--tool-help==| Print command line help for tool|
+|==--enable-reuse==|Enable job reuse (default)|
+|==--disable-reuse==|Disable job reuse (always run new jobs).|
+|==--project-uuid UUID==| Project that will own the workflow jobs, if not provided, will go to home project.|
+|==--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 jobs.|
+|==--submit==| Submit workflow to run on Arvados.|
+|==--local==| Control workflow from local host (submits jobs to Arvados).|
+|==--create-template==| (Deprecated) synonym for ==--create-workflow.==|
+|==--create-workflow==| Create an Arvados workflow (if using the 'containers' API) or pipeline template (if using the 'jobs' API). See ==--api==.|
+|==--update-workflow== UUID|Update an existing Arvados workflow or pipeline template with the given UUID.|
+|==--wait==| After submitting workflow runner job, wait for completion.|
+|==--no-wait==| Submit workflow runner job and exit.|
+|==--api== WORK_API| Select work submission API, one of 'jobs' or 'containers'. Default is 'jobs' if that API is available, otherwise 'containers'.|
+|==--compute-checksum==| Compute checksum of contents while collecting outputs|
+|==--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, default arvados/jobs|
+|==--name== NAME| Name to use for workflow execution instance.|
+|==--on-error {stop,continue}|Desired workflow behavior when a step fails. One of 'stop' or 'continue'. Default is 'continue'.|
+|==--enable-dev==| Enable loading and running development versions of CWL spec.|
+|==--intermediate-output-ttl== N|If N > 0, intermediate output collections will be trashed N seconds after creation. Default is 0 (don't trash).|
+|==--trash-intermediate==| Immediately trash intermediate outputs on workflow success.|
+|==--no-trash-intermediate==|Do not trash intermediate outputs (default).|
+
h3. Specify workflow and output names
}
</code></pre>
</notextile>
+
+h3. Automatically delete intermediate outputs
+
+Use the @--intermediate-output-ttl@ and @--trash-intermediate@ options to specify how long intermediate outputs should be kept (in seconds) and whether to trash them immediately upon successful workflow completion.
+
+Temporary collections will be trashed @intermediate-output-ttl@ seconds after creation. A value of zero (default) means intermediate output should be retained indefinitely.
+
+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 for the entire the workflow.
+
+Using @--trash-intermediate@ without @--intermediate-output-ttl@ means that intermediate files will be trashed on successful completion, but will remain on workflow failure.
+
+Using @--intermediate-output-ttl@ without @--trash-intermediate@ means that intermediate files will be trashed only after the TTL expires (regardless of workflow success or failure).
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