The Harmoniser app validates and processes study metadata for inclusion in the Sequoia Portal.
It checks a study metadata CSV against the required harmoniser schema, cross-checks the submitted information against the Sequoia database, and then starts the harmonisation pipeline.
When processing is successful, the harmonised study is added to the studies database as unpublished and remains pending review before it becomes available in the portal.
Before you begin
Prepare a study metadata CSV that follows the required harmoniser schema.
The app validates the file before running the harmonisation workflow. Files that do not match the expected schema or contain conflicting metadata may not be processed successfully.
Name your job
Enter a clear Prefix to identify the harmonisation job. You may also add an optional Suffix to distinguish related submissions or versions.
[Screenshot 1: Highlight the Prefix and Suffix fields in the Job Identification section.]
For example:
- Prefix:
UKB_lipid_metadata - Suffix:
v1 - Prefix:
T2D_GWAS_submission - Suffix:
revised
Upload the study metadata CSV
Add your metadata file in the Study CSV section.
[Screenshot 2: Highlight the Study CSV section, including Upload New, Select Existing, and From Jobs Output.]
You can provide the CSV in three ways:
- Upload New — Upload a CSV file from your computer.
- Select Existing — Choose a CSV file already stored in the portal.
- From Jobs Output — Use a CSV file generated by a previous job.
The file must be in .csv format and no larger than 10 MB.
[Screenshot 3: Red box around the upload area, including the supported format and maximum file size.]
Select a project
Choose the destination project in the Project dropdown. This is required.
[Screenshot 4: Red box around the Project dropdown.]
The harmonisation job, validation records, and related outputs will be associated with this project.
Launch harmonisation
Review the job name, uploaded metadata file, and selected project. Then select Launch App.
[Screenshot 5: Red box and arrow pointing to “Launch App”.]
The portal will validate the metadata and, if validation is successful, start the harmonisation pipeline.
What happens after launch?
The workflow proceeds in the following order:
- The study metadata CSV is checked against the harmoniser schema.
- The submitted metadata is cross-checked against the Sequoia database.
- The harmonisation pipeline processes the study.
- The harmonised study is added to the studies database as unpublished.
- The study remains pending review before publication.
A completed harmonisation job does not automatically make the study visible to all portal users.
Tips
- Use the latest approved metadata template or schema before preparing your CSV.
- Confirm that study identifiers and metadata fields are complete and consistent before upload.
- Use a suffix such as
v1,v2, orrevisedwhen resubmitting an updated metadata file. - Check the project or job results area for validation messages if the pipeline does not start or complete as expected.