-| --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.|
-
-h3. Specify workflow and output names
+|==--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).|
+|==--eval-timeout EVAL_TIMEOUT==|Time to wait for a Javascript expression to evaluate before giving an error, default 20s.|
+|==--print-dot==| Print workflow visualization in graphviz format and exit|
+|==--version==| Print version and exit|
+|==--validate==| Validate CWL document only.|
+|==--verbose==| Default logging|
+|==--quiet==| Only print warnings and errors.|
+|==--debug==| Print even more logging|
+|==--metrics==| Print timing metrics|
+|==--tool-help==| Print command line help for tool|
+|==--enable-reuse==| Enable container reuse (default)|
+|==--disable-reuse==| Disable container reuse|
+|==--project-uuid UUID==| Project that will own the workflow containers, 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 containers.|
+|==--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 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 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|
+|==--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 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 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(#names). Specify workflow and output names