runs list

List all workflow runs

Synopsis

omics workbench runs list 
  [--max-results=NUMBER]
  [--page=NUMBER]
  [--page-size=NUMBER]
  [--order=ORDER_STRING]
  [--submitted-since=DATE|DATETIME]
  [--submitted-until=DATE|DATETIME]
  [--engine=ENGINE_ID]
  [--search=TEXT]
  [--state=STATE,[--state=STATE]]
  [--tags=JSON_DATA]

Description

List all the runs matching the given filters, fetching each page of data sequentially and printing it to the console.

Examples

List all the runs without applying any filters.

omics workbench runs list

You can refine your search to list only runs that are in the RUNNING or QUEUED state.

omics workbench runs list --state RUNNING --state QUEUED

If you have a given time window you would like to list runs from, you can use the submitted-since and submitted-until flags to restrict the runs returned to those that were submitted within the defined window. For example, to return only runs that were submitted in the month of January 2023, I can use the following flags:

omics workbench runs list --submitted-since '2023-01-01' --submitted-until '2023-01-02'

The primary way metadata is added through runs is through the use of tags. You can filter the runs by the presence of one or more tags.

omics workbench runs list --tags sample_id=ax81900,sample_type=blood

Finally, you can combine multiple flags to create powerful filters. For example, If I wanted to return only failed runs submitted in the month of January 2023 that were of sample_type blood, submitted to the engine my-hpc then the command would look like the following:

omics workbench runs list \
  --submitted-since '2023-01-01' \
  --submitted-until '2023-01-02' \
  --state SYSTEM_ERROR \
  --engine my-hpc \
  --tags sample_id=ax81900,sample_type=blood

Flags:

--max-results=NUMBER

Limit the maximum number of results printed to the console.

--page=NUMBER

Used to set the offset page number. This allows for jumping into an arbitrary page of results.

--page-size=NUMBER

Used to set the number of results returned per page (default 100). Reducing the page size can help with poor internet connections.

--sort=SORT_STRING

Used to sort the runs ordered by a given string. The SORT_STRING consists of multiple properties you would like to order by, in the form column(:direction)?(;(column(:direction)?)*. The direction of the ordering is optional, and if it is omitted the default ordering is ascending.

Valid Directions: ASC, DESC Valid Columns: run_id, start_time, end_time, state, workflow_name, submitted_by, engine_id

Examples: run_id:ASC;start_time:DESC, state;workflow_name:DESC

--order=ORDER_STRING

Note: This flag is now deprecated - please use --sort instead. Return the runs ordered by the given property. The ORDER_STRING consists of the property you would like to order by, optionally followed by the direction of the ordering. If the direction is omitted it is assumed to be in descending order.

Valid Directions: ASC, DESC Valid Properties: run_id, start_time, end_time, state, workflow_name, submitted_by, engine_id

Examples: run_id ASC, start_time DESC

--state=STATE

Return the runs that are in a given state. This flag can be defined multiple times, with the result being runs that match any of the supplied states.

Valid States: QUEUED, UNKNOWN, INITIALIZING, RUNNING, PAUSED,CANCELING,COMPLETE, EXECUTOR_ERROR, SYSTEM_ERROR, CANCELED

--submitted-since=DATE|DATETIME

Return the runs that were submitted after the given date or time. The value can be in iso date format (YYYY-MM-DDTHH:MM:SSZ), or date format (YYYY-MM-DD).

Examples: 2023-01-01 or 2023-01-01T00:00:00Z

--submitted-until=DATE|DATETIME

Return the runs that were submitted before the given date or time. The value can be in iso date format (YYYY-MM-DDTHH:MM:SSZ), or date format (YYYY-MM-DD).

Examples: 2023-01-01 or 2023-01-01T00:00:00Z

--engine=ENGINE_ID

Return the runs that were executed using the given engine.

--search=TEXT

Perform a full-text search across various fields in a case-insensitive way, returning runs where the given search string was contained in the text of the field. Some properties which support full-text searching include the workflow URL, the state, the engine ID, the workflow name, the workflow type, the workflow language version, the workflow version name, the run ID, and more

--tags=TEXT

An optional flag to filter runs by one or more tags. Tags can be specified as a key-value pair, inlined JSON, or as a json file preceded by the "@" symbol. View JSON Data to see how tags can be defined.