clinical-genomics-lund / cll_genie Goto Github PK

The current workflow in cll_genie requires manual saving of comments before they can be reused in report creation. If a comment is not saved prior to report generation, it fails to appear under the 'User Comments' section on the results page. To address this issue, we propose an enhancement where comments entered into the textbox will be automatically saved to the 'User Comments' when a report is generated. This feature ensures that users' inputs are not lost and are properly displayed in the intended section. It's important to note that this automatic saving will only occur if the comment textbox is not empty at the time of report creation; empty textboxes will not result in empty comments being saved.

Remove clarity details, this app shall not talk to clarity and retrieve anything from clarity

Remove full and detailed type of analysis options. From now on vquest script will submit to IMGT server as a normal analysis mode and downloads a zip file which then be used for downstream processing

This GitHub issue addresses the need for synchronizing deletions between the cll_genie and local storage. Specifically, it proposes the automatic removal of analysis results from the local path whenever they are deleted in cll_genie. This feature aims to ensure data consistency and efficient storage management by preventing the accumulation of outdated or unnecessary files locally.

Create HTML report with placeholders for clarity to fill in patient data. From there clarity can create a pdf report and send it to RS LIMS

After reading excel file, convert the numeric columns to numeric

Change the sentences used to create report summary based on the hyper mutation status which rebeqa will provide.