> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/case_status/out-of-the-box-case-statuses.md). # 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](/emedgene/emedgene-analyze-manual/settings/user_roles/iam-scopes-emedgene-roles.md) for assignment and reassignment[^1]. ### 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](/emedgene/emedgene-analyze-manual/settings/management/test-statuses.md) 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.

Case lifecycle diagram — **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	Assigned by
"Uploading"	Data upload in progress.	System-controlled	Out-of-the-box	System
"In progress"	Analysis currently running.	System-controlled	Out-of-the-box	System
"Delivered"	Analysis completed; case ready for review.	System-assigned, user-reassignable	Out-of-the-box	System
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	User
"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	User
"Pending sequencing"	Case created; awaiting sequencing data.	System-controlled. Exception: user-reassignable to "Trash bin"	Out-of-the-box	System
"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	System
"Re-Analysis"	The system is re-running the AI Shortlist algorithm.	System-controlled	Out-of-the-box	System

## Learn more


Case status	Overview of case status behavior, history, and related workflows.	Learn more
Case progress indicator (v100.40.0+)	Understand progress indicator states for cases in processing or failure states.	Learn more
How to update a case status	Change the current case status from the case page or the Cases table.	Learn more
Case status management	Create custom statuses and reorder them for your organization.	Learn more

[^1]: Replacement with another status --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/case_status/out-of-the-box-case-statuses.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.