Case statuses in a case lifecycle

Case status overview

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 by 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.

Figure 1. Case lifecycle. Solid arrows indicate system-controlled status assignment; dashed arrows indicate user-controlled status assignment.

Table 1. Case status reference

Case status	Workflow stage	Control type	Origin
"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
"Re-Analysis"	The system is re-running the AI Shortlist algorithm.	System-controlled	Out-of-the-box

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Case status

Overview of case status behavior, history, and related workflows.

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Case progress indicator (v100.40.0+)

Understand progress indicator states for cases in processing or failure states.

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How to update a case status

Change the current case status from the case page or the Cases table.

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Case status management

Create custom statuses and reorder them for your organization.

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