Organization Settings (33.0+)

The Organization Settings page (33.0+) is accessible via the dropdown menu under Settings. Note: The Organization Settings page is accessible only for users having a Manager role.

The Organization Settings page features:

Environment settings

1. Organization URL (ILMN clouds only)

Associating URLs with your workgroup on ILMN Cloud

On ILMN Cloud, customers can easily associate URLs with their current workgroup by selecting from a list of predefined URL patterns. These URLs play a crucial role in organizing and accessing workgroup-specific resources.

Key Points to Remember:

• URL Selection: You can choose from a set of predefined URL patterns.

• Multiple Associations: A single URL can be associated with one or several workgroups.

• Activation Time: After selecting the URL for your workgroup, please allow 1 to 15 minutes for the changes to take effect.

Need a Custom URL?

If you would like to create a new custom URL pattern within your domain, please reach out to our technical support team at techsupport@illumina.com for assistance.

2. Platform version

Select a platform version for your organization from the options available in your region. Please allow 1-15 minutes for changes to become active. Keep in mind that this selection will not alter your pipeline version, only the software version. To change a pipeline version please contact techsupport@illumina.com.

Important! If you switch to a version older than 33.0, the feature will be removed from your Organization Settings, and you will need to reach out to support for platform version changes.

3. Case identifier

By default, Emedgene displays the Case ID in the "EMGXXXXXXXXX" format*.* However, you have the choice to use the Proband ID instead. Please note that the Proband ID has a visible 13-character limitation, with the remaining characters visible upon hovering.

4. Default page (34.0+)

The default page upon entering a case can be customized. You can choose between:

1. Candidates - default option;

2. Analysis*;

3. Analysis*;

4. Lab.

5 . Analysis tools columns order (34.0+)

You can customize the default order of Variant table columns. Just rearrange the columns by dragging and dropping them to your preferred sequence.

Lab Workflow settings (34.0+)

1. Presets

Here you can review and manage organization filter Presets.

1.1. Create Preset

Upon clicking on Add new, you will be redirected to Analysis tools page where you can create a Preset from active filters.

1.2. Review logic behind the Preset

Click on an downward arrow icon left to the Preset's name.

1.3. Edit Preset

1. Click on the ✏️_Edit_ icon;

2. Make the necessary changes. Editing the Preset requires basic understanding of JSON data format;

3. Click Save. The software will perform schema validation on the edited Preset. Note: you can modify the Preset's content but not its name. Note: the Preset can't be edited if it's locked.

1.4. Lock/unlock Preset

Locking the Preset prevents any user from changing it.

1. Click on the 🔓_Lock_/Unlock icon;

2. Click on Lock/Unlock in the popup window.

1.5. Delete Preset

1. Click on the 🗑️_Delete_ icon;

2. Confirm your decision by clicking Delete in the popup window.

Note: Only unused Presets can be deleted.

2. Preset groups

Here you can review and manage filter Preset groups.

In versions prior to 34.0, creating Preset groups required technical support. With 34.0+, Preset groups can be easily created by combining different Presets. Alternatively, you can upload a JSON file that defines the Presets in a Preset group. The file name and schema will be validated upon upload.

The section has two tabs:

• V2 (new)

Here you can create (from Presets/from a JSON file, view, edit, hide/unhide and download your organization's Preset groups.

• V1 (legacy)

Here you can view and download legacy Preset groups.

Migrating V1 _Preset groups_** to the improved V2 methodology**

Legacy Preset groups can be migrated to the new methodology via two simple steps: downloading the Preset group JSON file in the V1 (legacy) tab, then uploading it on the V2 (new) tab.

2.1. Create Preset group from existing Presets:

1. Click on Add new;

2. From the dropdown, select New;

3. Enter a name for the Preset group. Note: The Preset group can't be renamed later!

4. Select Presets to include in the Preset group. Click Add after selecting each Preset;

5. Drag and drop Presets to change the order;

6. Click on Save.

2.1. Create Preset group from JSON file:

This is the second step in the migration of the V1 (legacy) Preset group, after you have downloaded the Preset group JSON file.

1. Click on Add new;

2. From the dropdown, select From file;

3. From the file browser, select a JSON file that defines a Preset group;

4. The system will thoroughly validate the file;

5. If validation is successful, a Preset group will be created. Any underlying Presets that are missing from your organization will be added as well.

2.3. Review contents of the Preset group (V2 and V1)

Click on an downward arrow icon left to the Preset group's name.

2.4. Edit Preset group

1. Click on the ✏️_Edit_ icon; 2a. Add Presets to the group as needed. Select Presets to include in the Preset group from the dropdown. Click Add after selecting each Preset; 2b. Remove Presets from the group as needed. Click on the 🗙_Remove_ icon on right to the right of the Preset name. 2c. Drag and drop Presets to change the order;

2. Click Save.

2.5. Hide/unhide Preset group

When you hide a Preset group, it will no longer appear in the Preset groups list offered at case creation (Select preset group step).

Click on the 👁️_Hide/Unhide_ icon.

Note: A default Preset group cannot be hidden.

2.6. Download Preset group file (V2 and V1)

This is the first step in the migration of the V1 (legacy) Preset group to V2 methodology. A Preset group file contains preset names and the filters used to define each Preset in JSON format.

Click on the ⬇️_Download_ icon.

2.7. Revert *Preset group (*V1)

If a V1 Preset group that has undergone migration is set to revert, the corresponding V2 Preset group will be deleted.

Click on the ↩️_Revert_ icon to undo the migration.

Note: If a migrated Preset group has been assigned as default, it cannot be reverted.

3. Default Preset group

You can set a Preset group as default. The case is assigned to the default Preset group if no Preset group is selected or the default value is selected in the Add New Case Preset group selection step.

1. Click on the dropdown arrow;

2. Select the Preset group;

3. Click Save.

Note: A default Preset group cannot be hidden and cannot be reverted.