Datasets

When working with datasets, you might encounter the following issues.

Common issues

Dataset upload fails with the API

When you upload a dataset through the Seqera UI or CLI, Seqera performs some steps automatically. Uploading through the API requires two additional steps:

1. Explicitly define the MIME type of the file you upload.
2. Make two API calls: first create a dataset object, then upload the samplesheet to it.

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"}'

Upload the samplesheet to 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 upload a dataset to a workspace with the tw CLI:

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

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

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

This issue occurs in Firefox on Seqera versions earlier than 22.2.0.

To resolve, upgrade to 22.2.0 or later, or use Chrome.

TSV-formatted datasets not shown

In Seqera version 22.2, TSV datasets were unavailable in the input data drop-down on the launch form. This was fixed in version 22.4.1.