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Version: 26.1

Datasets

API: Dataset upload failure​

When uploading datasets via the Seqera UI or CLI, some steps are automatically done on your behalf. To upload datasets via the Seqera API, additional steps are required:

  1. Explicitly define the MIME type of the file being uploaded.
  2. Make two calls to the API:
    1. Create a dataset object.
    2. Upload the samplesheet to the dataset object.

Example:

Step 1: Create the dataset object.

curl -X POST "https://api.cloud.seqera.io/workspaces/$WORKSPACE_ID/datasets/" -H "Content-Type: application/json" -H "Authorization: Bearer $TOWER_ACCESS_TOKEN" --data '{"name":"placeholder", "description":"A placeholder for the data we will submit in the next call"}'

Step 2: Upload the datasheet into the dataset object.

curl -X POST "https://api.cloud.seqera.io/workspaces/$WORKSPACE_ID/datasets/$DATASET_ID/upload"  -H "Accept: application/json"  -H "Authorization: Bearer $TOWER_ACCESS_TOKEN"  -H "Content-Type: multipart/form-data" -F "file=@samplesheet_full.csv; type=text/csv"
tip

You can also use the tower-cli to upload the dataset to a particular workspace:

tw datasets add --name "cli_uploaded_samplesheet" ./samplesheet_full.csv

Datasets converted to 'application/vnd.ms-excel' data type​

This is a known issue when using Firefox browser with Seqera versions older than 22.2.0. You can either upgrade to 22.2.0 or higher, or use Chrome.

Seqera displays this error for this issue:

"Given file is not a dataset file. Detected media type: 'application/vnd.ms-excel'. Allowed types: 'text/csv, text/tab-separated-values'"

TSV-formatted datasets not shown​

An issue was identified in Seqera version 22.2 which caused TSV datasets to be unavailable in the input data drop-down on the launch screen. This has been fixed in version 22.4.1.

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