If you're comfortable with scripting and API usage, you can upload multiple cases at once using those methods. But if you're not a technical expert, don't worry. There is a user-friendly alternative available—importing a CSV file directly through the user interface.

Please follow the steps as described below.

1. Prepare a CSV file

CSV (Comma-Separated Values) is a simple file format used to store data in tabular form. A row represents a sample, and a column represents a data field.

Start by downloading a CSV template with an example line and mandatory and non-mandatory fields from the Add new case page set to Batch mode (see ). Fill the file with your data according to .

2. Upload a CSV file

1. Click on the + New case button on the .

2. Click on the Switch to batch button in the top right corner. You'll be directed to the Select file page of the Batch upload flow. Note: Here you can download a CSV template in the valid format.

3. Drag and drop a CSV file into the box or upload it from the file explorer. Wait for file upload and validation to finish.

3. Review file validation results

After validation is complete, you will be directed to the Batch validation page. It features validation results details for you to review:

• File name,

• Number of rows in the file,

• Number of cases to be created

• Number of errors found,

4. Create cases

1. Click on Create. A progress bar will appear on the right as the cases are created (Cases creation page).

2. If the cases have been created successfully, the Cases summary page will display the total number of cases that were created.

3. If there were any errors during the batch case creation process, the Cases summary page will display a table indicating the number of cases that were successfully created and the number of cases that failed.

You will have the option to download a CSV file containing two additional columns: Errors and Case ID. The Errors column will contain error messages for samples where case creation failed, while the Case ID column will contain the Case ID of a successfully created case for the lines where case creation was successful.

Prerequisites

• Download and install node js platform via https://nodejs.org/en/download Minimum version required: 16 Upgrade existing installation: nvm install --lts

Batch upload via CLI (Command Line Interface)

1. Download the batch case create script. Replace my-domain with your Emedgene domain. Illumina cloud: my-domain.emg.illumina.com Legacy Emedgene cloud: my-domain.emedgene.com

1. Download the CSV template file.

1. Edit the downloaded batchCases.csv file. See for more details.

2. Execute the batch cases creator as java script using the command below. Replace my-domain with your Emedgene domain and my-email with your user email. A prompt for your Emedgene password will appear, enter the password and press Enter.

1. In case of validation errors in the input CSV, an output CSV called batchCases_results.csv will be created in the same location with detailed error results.

2. -l will create a log file in the same location.

More information can be found by running

General CSV format requirements

The following are the general format requirements for a CSV file used to create multiple cases:

1. The file must have a .csv extension.

2. The file must contain a [Data] header.

3. The row after [Data] header must include the field names identifying the data in each column. The column names are case-sensitive.

4. The row after the column name header and each subsequent row represents a sample.

5. Each column represents a data field.

6. It is essential that there are no empty rows between the [Data] header and the last sample row.

7. Number of cases per file can’t be greater than 50.

CSV schema

1. Mandatory fields

Must be present in the sample table at all times.

1. Case Type;

2. Family Id;

3. Phenotypes OR Phenotypes Id.

2. Conditionally mandatory fields

If these fields are left empty, it will result in the creation of an empty sample.

1. BioSample Name;

2. Files Names;

3. Storage Provider Id;

This field is mandatory if Files Names is empty:

1. Sample Type.

This field is required if the "auto" option is used for Files Names (only relevant for BSSH):

1. Default Project.

3. Optional fields

The sample table may include these supported optional columns.

1. Boost Genes

2. Clinical Notes

3. Date Of Birth

4. Due Date

4. Custom fields

The sample table may contain custom columns to suit your specific needs and include any relevant information that is important for your workflow.

Each custom field must be assigned a unique name without spaces. Data from custom columns is saved per case under the Additional information section of .

Custom field examples:

Batch case .csv file validation rules

(highlighted in red), (highlighted in orange), and fields should be filled in according to the following rules.

Handling a proband sample with unknown sex

Required BSSH file path format:

For BSSH, it is necessary to use the actual names (numbers):

instead of aliases

Human-readable path for BSSH files in batch CSV

In version 37, we introduced an enhancement to the batch upload process that allows you to provide a human-readable path in their batch CSV for BSSH files.

Validations

When a batch CSV includes a human-readable path, the system performs the following validations for paths in BSSH storage:

1. Single File in the Path:

   • If the provided path contains exactly one file or dataset, the batch upload proceeds successfully.

2. Two Files in the Path:

Error Scenarios

• Multiple QCPassed Datasets: If two datasets in the same path are marked as QCPassed, the batch upload will fail with a descriptive error indicating the conflict.

• Excessive Files in the Path: If more than two files are found for the provided path, the batch upload will fail, instructing the user to provide a more specific or valid path.

Benefits

• Enables customers to use intuitive, human-readable paths in their workflows.

• Automatically handles dataset selection based on quality control status.