`tw datasets`

Manage datasets

Run tw datasets -h to view the list of supported operations.

Datasets are CSV (comma-separated values) and TSV (tab-separated values) files stored in a workspace, used as inputs during pipeline execution. The most commonly used datasets for Nextflow pipelines are samplesheets, where each row consists of a sample, the location of files for that sample (such as FASTQ files), and other sample details.

`tw datasets add`

Add a dataset

tw datasets add [OPTIONS] <FILENAME>

Arguments

Argument	Description	Required
`FILENAME`	Data file to upload	Yes

Options

Option	Description	Required	Default
`-n`, `--name`	Dataset name. Must be unique per workspace. Names consist of alphanumeric, hyphen, and underscore characters.	Yes
`-d`, `--description`	Optional dataset description.	No
`--header`	Treat first row as header. Default: false.	No
`-w`, `--workspace`	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	Yes
`--overwrite`	Overwrite the dataset if it already exists	No	`false`

Run tw datasets add -h to view the required and optional fields for adding a dataset.

Add a preconfigured dataset file to a workspace (include the --header flag if the first row of your samplesheet file is a header):

tw datasets add --name=samplesheet1 --header samplesheet_test.csv

Dataset 'samplesheet1' added at user workspace with id '60gGrD4I2Gk0TUpEGOj5Td'

note

The maximum supported dataset file size is 10 MB.

`tw datasets delete`

Delete a dataset

tw datasets delete [OPTIONS]

Options

Option	Description	Required
`-i`, `--id`	Dataset unique identifier	Yes
`-n`, `--name`	Dataset name	Yes
`-w`, `--workspace`	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	Yes

To delete a workspace dataset, specify either the dataset name (-n flag) or ID (-i flag):

tw datasets delete -i 6tYMjGqCUJy6dEXNK9y8kh

Dataset '6tYMjGqCUJy6dEXNK9y8kh' deleted at 97652229034604 workspace

`tw datasets download`

Download a dataset

tw datasets download [OPTIONS]

Options

Option	Description	Required
`-i`, `--id`	Dataset unique identifier	Yes
`-n`, `--name`	Dataset name	Yes
`--dataset-version`	Dataset version to download	No
`-w`, `--workspace`	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	Yes

View a stored dataset's contents:

tw datasets download -n samplesheet1

sample,fastq_1,fastq_2,strandedness
WT_REP1,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357070_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357070_2.fastq.gz,auto
WT_REP1,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357071_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357071_2.fastq.gz,auto
WT_REP2,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357072_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357072_2.fastq.gz,reverse
RAP1_UNINDUCED_REP1,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357073_1.fastq.gz,,reverse
RAP1_UNINDUCED_REP2,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357074_1.fastq.gz,,reverse
RAP1_UNINDUCED_REP2,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357075_1.fastq.gz,,reverse
RAP1_IAA_30M_REP1,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357076_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357076_2.fastq.gz,reverse

`tw datasets hide`

Hide one or more datasets

tw datasets hide [OPTIONS]

Options

Option	Description	Required
`-i`, `--id`	Dataset unique identifier(s). May be combined with --name.	Yes
`-n`, `--name`	Dataset name(s). May be combined with --id.	Yes
`-w`, `--workspace`	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	Yes

`tw datasets labels`

Manage dataset labels

tw datasets labels [OPTIONS] [labels]

Arguments

Argument	Description	Required
`<labels>`	Comma-separated list of labels.	No

Options

Option	Description	Required	Default
`-i`, `--id`	Dataset unique identifier	Yes
`-n`, `--name`	Dataset name	Yes
`-w`, `--workspace`	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	No
`--no-create`	Assign labels without creating the ones which were not found.	No
`--operations`, `-o`	Type of operation (set, append, delete) [default: set].	No	`set`

`tw datasets list`

List datasets

tw datasets list [OPTIONS]

Options

Option	Description	Required	Default
`-w`, `--workspace`	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	Yes
`-f`, `--filter`	Optional filter criteria, allowing free text search on name or ID and keywords: `username`, `label`, `visibility`, `createdAfter`, `createdBefore`, `usedAfter`, `usedBefore`. Example keyword usage: -f label:custom-label.	No
`--show-hidden`	Include datasets marked as hidden in the results.	No	`false`
`-l`, `--labels`	Show labels.	No	`false`
`--page`	Page number for paginated results (default: 1)	No
`--offset`	Row offset for paginated results (default: 0)	No
`--max`	Maximum number of records to display (default: 100)	No

Run tw datasets list -h to view the optional fields for listing and filtering datasets.

Command:

tw datasets list -f data

Datasets at 97652229034604 workspace:

Example output:

ID                     | Name     | Created
  ------------------------+----------+-------------------------------
    6vBGj6aWWpBuLpGKjJDpZy | dataset2 | Tue, 27 Aug 2024 14:49:32 GMT

`tw datasets show`

Make one or more hidden datasets visible

tw datasets show [OPTIONS]

Options

Option	Description	Required
`-i`, `--id`	Dataset unique identifier(s). May be combined with --name.	Yes
`-n`, `--name`	Dataset name(s). May be combined with --id.	Yes
`-w`, `--workspace`	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	Yes

`tw datasets view`

View dataset details

tw datasets view [OPTIONS]

Options

Option	Description	Required
`-i`, `--id`	Dataset unique identifier	Yes
`-n`, `--name`	Dataset name	Yes
`-w`, `--workspace`	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	Yes

Run tw datasets view -h to view the required and optional fields for viewing a stored dataset's details.

Command:

tw datasets view -n samplesheet1

Dataset at 97652229034604 workspace:

Example output:

-------------+-------------------------------
    ID          | 60gGrD4I2Gk0TUpEGOj5Td
    Name        | samplesheet1
    Description |
    Media Type  | text/csv
    Created     | Mon, 19 Aug 2024 07:59:16 GMT
    Updated     | Mon, 19 Aug 2024 07:59:17 GMT

`tw datasets view versions`

Display dataset versions.

tw datasets view versions

`tw datasets update`

Update a dataset

tw datasets update [OPTIONS]

Options

Option	Description	Required
`-i`, `--id`	Dataset unique identifier	Yes
`-n`, `--name`	Dataset name	Yes
`--new-name`	Updated dataset name. Must be unique per workspace. Names consist of alphanumeric, hyphen, and underscore characters.	No
`-d`, `--description`	Updated dataset description.	No
`--header`	Treat first row as header	No
`-f`, `--file`	Data file to upload	No
`-w`, `--workspace`	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	Yes

Run tw datasets update -h to view the required and optional fields for updating a dataset.

tw datasets update -n dataset1 --new-name=dataset2 -f samplesheet_test.csv

Dataset 'dataset1' updated at 97652229034604 workspace with id '6vBGj6aWWpBuLpGKjJDpZy'

`tw datasets url`

Get dataset URL

tw datasets url [OPTIONS]

Options

Option	Description	Required
`-i`, `--id`	Dataset unique identifier	Yes
`-n`, `--name`	Dataset name	Yes
`--dataset-version`	Dataset version for URL	No
`-w`, `--workspace`	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	Yes

Run tw datasets url -h to view the required and optional fields for obtaining a dataset URL.

$ tw datasets url -n dataset2

Dataset URL

-----------

https://api.cloud.seqera.io/workspaces/97652229034xxx/datasets/6vBGj6aWWpBuLpGKjJDxxx/v/2/n/samplesheet_test.csv

Help

Company

`tw datasets`

`tw datasets add`

Arguments

Options

`tw datasets delete`

Options

`tw datasets download`

Options

`tw datasets hide`

Options

`tw datasets labels`

Arguments

Options

`tw datasets list`

Options

`tw datasets show`

Options

`tw datasets view`

Options

`tw datasets view versions`

`tw datasets update`

Options

`tw datasets url`

Options

Help

Company

tw datasets add​

Arguments​

Options​

tw datasets delete​

Options​

tw datasets download​

Options​

tw datasets hide​

Options​

tw datasets labels​

Arguments​

Options​

tw datasets list​

Options​

tw datasets show​

Options​

tw datasets view​

Options​

tw datasets view versions​

tw datasets update​

Options​

tw datasets url​

Options​

`tw datasets add`

Arguments

Options

`tw datasets delete`

Options

`tw datasets download`

Options

`tw datasets hide`

Options

`tw datasets labels`

Arguments

Options

`tw datasets list`

Options

`tw datasets show`

Options

`tw datasets view`

Options

`tw datasets view versions`

`tw datasets update`

Options

`tw datasets url`

Options