samples list

List Samples

samples list

Synopsis

omics workbench samples list
  [--max-results]
  [--page]
  [--page-size]
  [--storage-id]
  [--platform-type]
  [--instrument-id]
  [--workflow]
  [--workflow-version]
  [--state,[--state]]
  [--family-id,[--family-id]]
  [--sample,[--sample]]
  [--sex,[--sex]]
  [--perspective]
  [--search]
  [--created-since]
  [--created-until]
  [--analyzed]
  [--not-analyzed]

Description

List all samples that are indexed from platforms with comprehensive filtering and pagination options.

Examples

List all samples

omics workbench samples list

List max 10 samples from a specific platform type and storage account.

omics workbench samples list
  --max-results 10
  --platform-type pacbio
  --storage-id my-aws-account

List samples that have been analyzed (processed by workflows)

omics workbench samples list --analyzed

List samples from specific families with male sex

omics workbench samples list
  --family-id family-001
  --family-id family-002
  --sex MALE

List samples created within a specific time range that have been processed by a workflow

omics workbench samples list
  --workflow workflow-123
  --state COMPLETE
  --created-since 2023-01-01
  --created-until 2023-12-31

Search for samples by ID pattern

omics workbench samples list --search "HG00"

List samples from workflow perspective (shows all samples with analysis status for a workflow)

omics workbench samples list
  --perspective workflow
  --workflow workflow-123

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.

--storage-id=STORAGE_ID

Returns samples associated with the specified storage account ID.

--platform-type=PLATFORM_TYPE

Returns samples associated with the specified platform type (e.g., pacbio, custom).

--instrument-id=INSTRUMENT_ID

Returns samples associated with the specified instrument ID.

--workflow=WORKFLOW_ID

Returns samples that were processed by the specified workflow. If the workflow version is not specified, returns all workflow versions. When --perspective is set to workflow, this flag is required.

--workflow-version=WORKFLOW_VERSION_ID

Returns samples that were processed by the specified workflow version. If the workflow is not specified, returns all workflows.

--state=STATE

Returns samples with workflows in the specified states. This flag can be used multiple times to filter by multiple states.

Valid States: QUEUED, INITIALIZING, RUNNING, COMPLETE, EXECUTOR_ERROR, SYSTEM_ERROR, CANCELED, NOT_PROCESSED

--family-id=FAMILY_ID

Returns samples that are part of the specified families. This flag can be used multiple times.

--sample=SAMPLE_ID

Returns samples with the specified ID. This flag can be used multiple times to filter by multiple sample IDs.

--sex=SEX

Returns samples with the specified sex. This flag can be used multiple times.

Valid Values: MALE, FEMALE, UNKNOWN_SEX, OTHER_SEX

--perspective=PERSPECTIVE_TYPE

Returns samples from the specified perspective. If not specified, returns samples from the default perspective. If perspective is set to workflow, then the --workflow flag is required. When the perspective is set to workflow, all samples are returned with a flag indicating whether they were processed by the specified workflow or not.

Valid Values: DEFAULT, WORKFLOW

--search=TEXT

Searches samples by the specified search term. The search term is matched against sample ID in a case-insensitive way.

--created-since=DATE|DATETIME

Returns samples created after the specified date. The timestamp can be in ISO date format (YYYY-MM-DD) or datetime format (YYYY-MM-DDTHH:MM:SS.sssZ).

Examples: 2022-11-23, 2022-11-23T23:59:59.999Z

--created-until=DATE|DATETIME

Returns samples created before the specified date. The timestamp can be in ISO date format (YYYY-MM-DD) or datetime format (YYYY-MM-DDTHH:MM:SS.sssZ).

Examples: 2022-11-23, 2022-11-23T23:59:59.999Z

--analyzed

Returns samples that have been analyzed (have associated workflow runs). This is a convenience flag that filters for samples with states: QUEUED, INITIALIZING, RUNNING, COMPLETE.

--not-analyzed

Returns samples that have not been analyzed (no associated workflow runs). This is a convenience flag that filters for samples with state: NOT_PROCESSED.