# 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](/emedgene/emedgene-analyze-manual/settings/user_roles/iam-scopes-emedgene-roles.md) for assignment and reassignment[^1].

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](/emedgene/emedgene-analyze-manual/settings/management/case-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.

**Table 1. Case status reference**

<table data-full-width="false"><thead><tr><th width="151">Case status</th><th width="277">Workflow stage</th><th width="181">Control type</th><th>Origin</th><th data-hidden>User-reassignable</th><th data-hidden>Assigned by</th></tr></thead><tbody><tr><td><strong>"Uploading"</strong></td><td>Data upload in progress.</td><td><mark style="background-color:orange;">System-controlled</mark></td><td>Out-of-the-box</td><td><img src="/files/e7xOsTnL5Z7FN9M3B4TK" alt="" data-size="original"></td><td>System</td></tr><tr><td><strong>"In progress"</strong></td><td>Analysis currently running.</td><td><mark style="background-color:orange;">System-controlled</mark></td><td>Out-of-the-box</td><td><img src="/files/e7xOsTnL5Z7FN9M3B4TK" alt="" data-size="original"></td><td>System</td></tr><tr><td><strong>"Delivered"</strong></td><td>Analysis completed; case ready for review.</td><td><mark style="background-color:blue;">System-assigned, user-reassignable</mark></td><td>Out-of-the-box</td><td><img src="/files/RFnaT7zG3AzBT96l6LVf" alt=""></td><td>System</td></tr><tr><td><strong>Custom status</strong></td><td>Indicates a custom case processing stage between "Delivered" and "Finalized".</td><td><mark style="background-color:purple;">User-controlled</mark></td><td>Custom</td><td></td><td></td></tr><tr><td><strong>"Finalized"</strong></td><td><p>The analysis and review of the case by the analyst group have been <a href="/pages/Qy9LKMN01NOJVyG1lfE9">completed</a>.</p><p><br>Typically assignment and reassignment of the "Finalized" status is configured to be restricted to organization managers and/or lab directors.</p></td><td><mark style="background-color:purple;">User-controlled</mark></td><td>Out-of-the-box</td><td><img src="/files/RFnaT7zG3AzBT96l6LVf" alt=""></td><td>User</td></tr><tr><td><p><strong>"Trash bin"</strong> (v38.0+) or</p><p><strong>"Move to trash"</strong> (≤v37.0)</p></td><td><p>Case marked for <a href="/pages/Utr2PQZAY42rAv5ZHczA">deletion</a>; access restricted.</p><p>Typically assignment and reassignment of the "Trash bin"/"Move to trash" status is configured to be restricted to organization managers and/or lab directors.</p></td><td><mark style="background-color:purple;">User-controlled</mark></td><td>Out-of-the-box</td><td><img src="/files/RFnaT7zG3AzBT96l6LVf" alt=""></td><td>User</td></tr><tr><td><strong>"Pending sequencing"</strong></td><td>Case created; awaiting sequencing data.</td><td><p><mark style="background-color:orange;">System-controlled</mark>.</p><p>Exception: user-reassignable to "Trash bin"</p></td><td>Out-of-the-box</td><td><img src="/files/e7xOsTnL5Z7FN9M3B4TK" alt="" data-size="original"></td><td>System</td></tr><tr><td><strong>"Issue reported"</strong></td><td><p>The case failed to run.</p><p>Please check the integrity of the uploaded files and ensure that the variant caller used is on Emedgene list of accepted <a href="/pages/x8fBUnhEuzwHv84twgiP">variant callers</a>.</p></td><td><p><mark style="background-color:orange;">System-controlled.</mark></p><p>Exception: user-reassignable to "Trash bin"</p></td><td>Out-of-the-box</td><td><img src="/files/e7xOsTnL5Z7FN9M3B4TK" alt="" data-size="original"></td><td>System</td></tr><tr><td><strong>"Reanalysis"</strong></td><td>The system is re-running the AI Shortlist algorithm.</td><td><mark style="background-color:orange;">System-controlled</mark></td><td>Out-of-the-box</td><td><img src="/files/e7xOsTnL5Z7FN9M3B4TK" alt="" data-size="original"></td><td>System</td></tr></tbody></table>

[^1]: Replacement with another status


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