Franklin implements technical and procedural safeguards to uphold integrity, reliability and completeness of data processing. Automated alerts are configured to identify and surface deviations, incomplete validations, and critical system changes that may impact the accuracy or validity of the analysis. These controls are embedded within operational and development workflows to ensure early detection of potential issues and minimize manual oversight.
This article compiles all alerts, notifications, and built-in technical controls and safeguards that users should be aware of, providing clear visibility into the system's checkpoints.
Login
Login activity is monitored and alerts are generated for events such as failed login attempts, unexpected access times, or access from unrecognized locations. These alerts help ensure that only authorized personnel interact with the system
Search fields
Alerts triggered by the user's input in case of an unsupported or incorrect format (e.g., missing genomic coordinates) preventing downstream errors by enforcing consistent input structure at the point of entry.
For example:
Unsupported format
Wrong ref
Missing gene
User validation of transcript
When multiple transcript options are available for a given variant, users are required to actively select the clinically relevant transcript. This safeguard ensures that variant classification and downstream interpretation are based on the most appropriate transcript for the clinical context.
Sample sheet upload
Upload from a local file:
Users can upload a sample sheet in XLS, XLSX, or CSV format. If the upload fails (e.g., due to an internet outage), a notification will appear in the UI.
In such cases, users should:
Step 1: Verify their internet connection
Step 2: Confirm that the file format is valid (XLS, XLSX, or CSV)
If the issue persists after these checks, users should contact Franklin Support for further assistance.
Sample Sheet Validation:
Once the file is uploaded successfully, validation is performed on the sample sheet metadata—not the associated files. The validation outcomes are as follows:
No warnings or errors:
The sample sheet is acceptedAll cases are created
A success message is shown in the UI.
Warnings only:
The upload is completed and all cases are created.
An email is sent to the uploading user detailing each warning, including the line, column, and data item involved (e.g., line 55 – ethnicity ‘test 123’ doesn’t exist).
Users should review and correct the sample sheet accordingly.
If issues persist, contact Franklin Support.
Errors detected:
The upload completes but no cases are created.
All errors and warnings are shown in the UI
A detailed email is sent to the uploading user with the line, column, and data item causing the failure (e.g., line 55 – assay ‘TSO 501’ doesn’t exist).
Users must update the sample sheet based on the error reasons.
If resolution fails, contact Franklin Support.
Post-Validation Issues:
Once validation is completed, the system proceeds to create the samples and their linked cases. If an issue occurs during this stage:
A generic error message may appear without specific details.
Users should re-upload the sample sheet.
If the issue persists, they should contact Franklin Support.
Final Status:
Cases that are successfully created will appear in the system with the status: Pending Samples:
Sample to file linking:
The sample-to-file linking process acts as a safeguard by ensuring that only complete and correctly named data files are associated with each sample before any downstream analysis begins.
During the sample sheet upload, users must specify:
The S3 path where the sample files are stored.
The sample name for each entry.
Any files in the provided folder that are prefixed with the sample name are automatically linked to the corresponding sample.
If the exact set of required files is known when defining a workflow:
The expected file composition should be configured in the assay definition.
In such cases, linking will not proceed until all required files are detected in the specified S3 path.
Once the sample sheet is successfully uploaded:
The system begins checking for file availability immediately.
Subsequent checks are performed every 5 minutes, ensuring timely linking once all requirements are fulfilled.
Missing sample warning
This alert prevents users from proceeding with incomplete data and ensures corrective action is taken before analysis or reporting begins, supporting traceability and diagnostic integrity.
Confirmation prompts
Franklin includes confirmation prompts (“Are you sure” pop-ups) in scenarios where user actions may result in irreversible changes or data loss.
These prompts are triggered before critical operations such as deleting records, submitting finalized analyses, or navigating away from unsaved content. The purpose is to ensure that users explicitly acknowledge the consequences of their actions, particularly when changes cannot be undone or when unsaved edits will be discarded. This mechanism helps prevent accidental data modification, reinforces informed decision-making.
Environment mismatch alert on login
To prevent data access issues and ensure proper environment segregation, an alert is shown when users log into the community environment instead of their assigned organizational environment.
Session timeout
For organizations using SSO, users are notified when their session expires and prompted to sign in again through their identity provider. This ensures that only authenticated users maintain access
Quality control monitoring
Franklin quality control (QC) metrics are displayed in the Workbench screen as a separated tab. Those metrics include coverage metrics, sequencing quality, sex concordance, and relatedness checks.
QC thresholds are assay-specific and configurable, allowing users to define hard or soft warnings based on predefined criteria. Each assay is monitored appropriately and potential quality issues are flagged before interpretation begins.
Mandatory fields
Franklin enforces mandatory fields across key workflows to ensure completeness and standardization of critical data. These required fields must be filled before users can proceed.
Case processing
Notification displayed in the Case Workbench when a case is still processing. This alert indicates that the analysis is not yet complete and additional time is needed, helping users avoid acting on incomplete or partial results