Emedgene platform version >= 32
Download and install node js platform via https://nodejs.org/en/download
Minimum version required: 16
Upgrade existing installation: nvm install --lts
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
Download the CSV template file.
Edit the downloaded batchCases.csv file. See CSV format requirements for more details.
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.
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.
-l will create a log file in the same location.
More information can be found by running
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 in versions 32.0 or newer - importing a CSV file directly through the user interface.
Please follow the steps as described below.
Caution: Please note that refreshing or leaving the page, exiting the Add new case tab, or power failure of your computer before you've completed a batch case upload will result in loss of the case creation progress.
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 step 2). Fill the file with your data according to CSV format requirements.
Click on the + New case button on the Top navigation panel.
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.
Drag and drop a CSV file into the box or upload it from the file explorer. Wait for file upload and validation to finish.
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,
Status message:
if no errors were detected, a success message will be displayed;
If any errors were detected, an error message will be displayed. You will be given the option to download a file with error details to help you diagnose and correct any issues with the data. Once you've corrected the CSV file, reupload it.
Click on Create. A progress bar will appear on the right as the cases are created (Cases creation page).
If the cases have been created successfully, the Cases summary page will display the total number of cases that were created.
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.
The following are the general format requirements for a CSV file used to create multiple cases:
The file must have a .csv extension.
The file must contain a [Data] header.
The row after [Data] header must include the field names identifying the data in each column. The column names are case-sensitive.
The row after the column name header and each subsequent row represents a sample.
Each column represents a data field.
It is essential that there are no empty rows between the [Data] header and the last sample row.
Number of cases per file can’t be greater than 50.
On versions before 34.0, cells should not contain commas. Consider replacing the commas with semicolons.
Must be present in the sample table at all times.
Case Type;
Family Id;
Phenotypes OR Phenotypes Id.
If these fields are left empty, it will result in the creation of an empty sample.
BioSample Name;
Files Names;
Storage Provider Id;
This field is mandatory if Files Names is empty:
Sample Type.
This field is required if the "auto" option is used for Files Names (only relevant for BSSH):
Default Project.
The sample table may include these supported optional columns.
Boost Genes;
Clinical Notes;
Date Of Birth;
Due Date;
Execute now;
Gender;
Gene List Id;
Kit Id;
Label Id;
Opt In;
Relation;
Selected Preset;
Visualization Files.
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 Case Info.
Note: In cases with more than one sample, custom fields are only recognized and added to case information if their values appear within the same table row where the Relation field is equal to "proband".
Mandatory (highlighted in red), Conditionally mandatory (highlighted in orange), and Optional fields should be filled in according to the following rules.
For BSSH, it is necessary to use the actual names (numbers):
instead of aliases
| Field (column) name | Expected input | Field details | Example |
|---|---|---|---|
| Field (column) name | Expected input | Field details | Example |
|---|---|---|---|
Institution
Free text
Custom
GenoMed Solutions
Sample_Received_Date
Free text
Custom
24-02-2022
Sample_Type
Free text
Custom
Amniotic Fluid
BioSample Name
Free text
Conditionally mandatory. An empty sample will be created if the field is left blank.
NA24385
Boost Genes
1. "TRUE" 2. "FALSE"
Optional. Indicates whether the Boost genes mode will be used. "TRUE" means that variants in the targeted genes will receive upgraded scores during prioritization by the AI Shortlist algorithm. Default value is "FALSE". Only considered for proband.
TRUE
Case Type
1. "Whole Genome" 2. "Exome" 3. "Custom Panel" 4. Custom case type
Mandatory. Only considered for proband.
Whole Genome
Clinical Notes
Free text
Optional
A 14-year-old boy with a visual acuity of 20/200 in both eyes in whom hearing loss was first noted at 5 years of age on routine screening; audiometry revealed sensorineural hearing loss.
Date Of Birth
Date "YYYY-MM-DD"
Optional
2013-01-22
Default Project
Free text
Conditionally mandatory. Must be filled in if the "auto" option is used for Files Names (only relevant for BSSH).
GIAB
Due Date
Date "YYYY-MM-DD"
Optional
2023-05-03
Execute now
1. "TRUE" 2. "FALSE"
Optional. Default value is "TRUE". Use "FALSE" if you don’t want to run the case upon uploading the file.e Only considered for proband.
FALSE
Family Id
Free text
Mandatory
RM8392
Files Names
1. Semicolon-separated list of paths to .fastq, .fastq.gz, .vcf, .vcf.gz, .bam, .cram files without spaces 2. "existing" 3. "auto"
Conditionally mandatory. An empty sample will be created if the field is left blank. The "existing" option automatically locates FASTQ files based on the BioSample Name. Note: If data files for an existing case were sourced from the customer’s external bucket and later removed, attempting to create a case from those files will result in an error. With the "auto" option, BSSH users can automatically locate FASTQ files based on the BioSample Name and Default Project provided. When using BSSH without the "auto" option, ensure that your file path is formatted correctly.
/GIAB_cases/1/NA24385.dragen.hard-filtered.gvcf.gz;/QA_cases/Other/NA24385.dragen.cnv.vcf.gz;/QA_cases/Other/NA24385.dragen.repeats.vcf;
Sex / Gender*
1. "F" 2. "M" 3. "U"
Optional. Default value is "U".
*The field is labeled as Sex in versions 33.0 and later, and as Gender in older versions.
M
Gene List Id
integer
Optional. Must be the id of a previously defined Gene List. Only considered for proband.
12345
Kit Id
integer
Optional. Must be the id of a previously defined Kit. Only considered for proband.
23456
Label Id
integer
Optional. Must be the id of a previously defined Case Label. Only considered for proband.
34567
Opt In
1. "TRUE" 2. "FALSE"
Optional. Indicates whether the case subject consented to the extended sharing of data with your network(s). Default value is "TRUE".
FALSE
Phenotypes
Semicolon-separated list of HPO phenotype terms
"Unaffected" is used for non-affected family members.
Mandatory for proband sample if Phenotypes Id is empty. List must be under 100. It is possible to include non-HPO terms if Phenotypes Id is empty.
Abnormal pupillary function;Orthotopic os odontoideum;
Phenotypes Id
Semicolon-separated list of HPO phenotype IDs
Mandatory for proband sample if Phenotypes is empty.
List must be under 100.
HP:0007686;HP:0025375;
Relation
1. "proband" 2. "mother" 3. "father" 4. "sibling"
Optional. Default value is "proband". Values "proband", "father", "mother" can be only used once per Family ID. One sample with Relation "proband" is required per Family ID.
Mother
Sample Type
1. "FASTQ" 2. "VCF"
Conditionally mandatory. Required if Files Names is empty. Only considered for proband.
FASTQ
Selected Preset
1. Free text 2. "Default"
Optional. Must be the name of a previously defined Preset. If set to default, the default Preset will be applied. If left empty, no Preset will be applied.
High quality candidates
Storage Provider Id
Integer
Conditionally mandatory. Required if Files Names is not empty. Must be from the configured storage provider ID list.
208
Visualization Files
Semicolon-separated list of paths to sequence alignment data files of extension .bam, .cram; 🆕34.0+: also .tn.bw, .baf.bw, .roh.bed
Optional
/giab_project/NA24385.bam