tw 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]

Options

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

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).

Example

Command:

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

Example output:

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	Default
`-i`, `--id`	Dataset unique identifier	No	`null`
`-n`, `--name`	Dataset name	No	`null`
`-w`, `--workspace`	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to `TOWER_WORKSPACE_ID` environment variable)	Yes	`TOWER_WORKSPACE_ID`

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

Example

Command:

tw datasets delete -i 6tYMjGqCUJy6dEXNK9y8kh

Example output:

Dataset '6tYMjGqCUJy6dEXNK9y8kh' deleted at 97652229034604 workspace

tw datasets download

Download a dataset.

tw datasets download [OPTIONS]

Options

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

View a stored dataset's contents.

Example

Command:

tw datasets download -n samplesheet1

Example output:

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 list

List datasets.

tw datasets list [OPTIONS]

Options

Option	Description	Required	Default
`-f`, `--filter`	Filter datasets by name substring	No	`null`
`-w`, `--workspace`	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to `TOWER_WORKSPACE_ID` environment variable)	Yes	`TOWER_WORKSPACE_ID`

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

Example

Command:

tw datasets list -f data

Example output:

Datasets at 97652229034604 workspace:

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

tw datasets view

View dataset details.

tw datasets view [OPTIONS]

Options

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

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

Example

Command:

tw datasets view -n samplesheet1

Example output:

Dataset at 97652229034604 workspace:


-------------+-------------------------------
    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 [OPTIONS]

tw datasets update

Update a dataset.

tw datasets update [OPTIONS]

Options

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

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

Example

Command:

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

Example output:

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

tw datasets url

Get dataset URL.

tw datasets url [OPTIONS]

Options

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

Example

Command:

tw datasets url -i 3m4n5o6p7q8r9s0t1u2v3w -w 123456789012345

Example output:

  Dataset URL

-----------

  https://api.cloud.seqera.io/workspaces/123456789012345/datasets/3m4n5o6p7q8r9s0t1u2v3w/v/1/n/samplesheet.csv

tw datasets add​

Options​

Example​

tw datasets delete​

Options​

Example​

tw datasets download​

Options​

Example​

tw datasets list​

Options​

Example​

tw datasets view​

Options​

Example​

tw datasets view versions​

tw datasets update​

Options​

Example​

tw datasets url​

Options​

Example​

tw datasets add

Options

Example

tw datasets delete

Options

Example

tw datasets download

Options

Example

tw datasets list

Options

Example

tw datasets view

Options

Example

tw datasets view versions

tw datasets update

Options

Example

tw datasets url

Options

Example