# samples list

## samples list

### Synopsis

```shell
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

```shell
omics workbench samples list
```

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

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

List samples that have been analyzed (processed by workflows)

```shell
omics workbench samples list --analyzed
```

List samples from specific families with male sex

```shell
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

```shell
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

```shell
omics workbench samples list --search "HG00"
```

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

```shell
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`.