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.	✓
-d, --description	Optional dataset description.
--header	Treat first row as header
--overwrite	Overwrite the dataset if it already exists		false
-w, --workspace	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	✓	${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):

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	Default
-i, --id	Dataset unique identifier
-n, --name	Dataset name
-w, --workspace	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	✓	${TOWER_WORKSPACE_ID}

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	Default
--dataset-version	Dataset version to download
-i, --id	Dataset unique identifier
-n, --name	Dataset name
-w, --workspace	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	✓	${TOWER_WORKSPACE_ID}

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 list

List datasets.

tw datasets list [OPTIONS]

Options

Option	Description	Required	Default
-f, --filter	Filter datasets by name substring
-w, --workspace	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	✓	${TOWER_WORKSPACE_ID}

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

tw datasets list -f data

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
-n, --name	Dataset name
-w, --workspace	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	✓	${TOWER_WORKSPACE_ID}

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

tw datasets view -n samplesheet1

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.
-d, --description	Updated dataset description.
--header	Treat first row as header
-f, --file	Data file to upload
-i, --id	Dataset unique identifier
-n, --name	Dataset name
-w, --workspace	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	✓	${TOWER_WORKSPACE_ID}

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	Default
--dataset-version	Dataset version for URL
-i, --id	Dataset unique identifier
-n, --name	Dataset name
-w, --workspace	Workspace numeric identifier or reference in OrganizationName/WorkspaceName format (defaults to TOWER_WORKSPACE_ID environment variable)	✓	${TOWER_WORKSPACE_ID}

Example

tw datasets url -i 3m4n5o6p7q8r9s0t1u2v3w -w 123456789012345

# Output:
  Dataset URL

  -----------

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