Case statuses in a case lifecycle
In Emedgene, case status indicates the current stage of a case—from data upload through analysis, review, and results finalization. Statuses are assigned either automatically by the system or by authorized users, depending on the workflow stage and user permissions.
Different statuses require different IAM scopes/Emedgene roles for assignment and reassignment.
Case statuses are grouped into three categories based on control type:
System-controlled: Assigned automatically by the system; cannot be reassigned by users.
User-controlled: Assigned and reassigned by authorized users.
System-assigned, user-reassignable: Assigned automatically by the system but can be reassigned by authorized users.
Case statuses by origin:
Out-of-the-box: Default options provided by the platform.
Custom: User-configured to align with specific workflows.
Case lifecycle
Each status represents a distinct stage in the case lifecycle. Figure 1 shows the possible transitions between statuses and the control type for each assignment, indicated by solid and dashed arrows. Table 1 provides an overview of case statuses.
Table 1. Case status reference
"Uploading"
Data upload in progress.
System-controlled
Out-of-the-box
"In progress"
Analysis currently running.
System-controlled
Out-of-the-box
"Delivered"
Analysis completed; case ready for review.
System-assigned, user-reassignable
Out-of-the-box
Custom status
Indicates a custom case processing stage between "Delivered" and "Finalized".
User-controlled
Custom
"Finalized"
The analysis and review of the case by the analyst group have been completed.
Typically assignment and reassignment of the "Finalized" status is configured to be restricted to organization managers and/or lab directors.
User-controlled
Out-of-the-box
"Trash bin" (v38.0+) or
"Move to trash" (≤v37.0)
Case marked for deletion; access restricted.
Typically assignment and reassignment of the "Trash bin"/"Move to trash" status is configured to be restricted to organization managers and/or lab directors.
User-controlled
Out-of-the-box
"Pending sequencing"
Case created; awaiting sequencing data.
System-controlled.
Exception: user-reassignable to "Trash bin"
Out-of-the-box
"Issue reported"
The case failed to run.
Please check the integrity of the uploaded files and ensure that the variant caller used is on Emedgene list of accepted variant callers.
System-controlled.
Exception: user-reassignable to "Trash bin"
Out-of-the-box
"Reanalysis"
The system is re-running the AI Shortlist algorithm.
System-controlled
Out-of-the-box
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