Verification Report [v15.0.1]

[ivadym]

Balsamic Verification Report

Release Information

• Version: v15.0.1
• Release Type: Patch
• Release Commit: ae2cf75
• Release Date: 2024-06-26

Person(s) involved in the development of new release

• Developer/s: VI
• Verification operator/s: VI
• Verification reviewer/s: MJ

Summary

The objective of this patch is to enable the application of a customised UMI filtering setting instead of the default minR=3,1,1.

These are the goals of this verification:

1. Confirm that the custom UMI filtering conditions are correctly applied to the analysis.
2. Ensure the integrity of the pipeline across various workflows and configurations.

Changelog

Type	Pull Request	Performed tests
Added	#1450	- Test UMI workflow with default settings - Test UMI workflow with custom settings

Pre-Verification Checklist

Before proceeding with the verification process, ensure that the following tasks have been completed:

• Install Balsamic in stage and production environments in hasta and build its cache.

• Confirm the availability of necessary resources, such as test cases.

• Review the changelog and ensure all changes and updates are documented:

  Document	Sections to Be Updated	Pull Request
  Balsamic Documentation	N/A	N/A
  Atlas Documentation	N/A	N/A

• Set up the stage environment with the necessary software and configurations:

  Software	Current Version	Pull Request with the Required Updates
  CG	Version 61.2.6	N/A
  Servers	Version 19.13.1	N/A
  Hermes	Version 4.4.4	N/A

Verification Results

Workflow Integrity Verification Cases

Case ID	Analysis type	Expected QC	Status
acetuna	QC, tumor-only	Pass	Pass
civilsole	WGS, tumor-only	Fail (PCT_60X=0.004532)	Pass
fleetjay	WGS, tumor-normal	Fail (PCT_60X=0.00836)	Pass
setamoeba	TGA, tumor-only	Pass	Pass
unitedbeagle	TGA, tumor-normal	Pass	Pass
uphippo	UMI, tumor-only	Fail (GC dropout=1.650392)	Pass
equalbug	UMI, tumor-normal	Fail (GC_DROPOUT=1.087173 and RELATEDNESS=-0.524)	Pass

• This section has been verified successfully

Storage, Delivery and Upload Integrity Verifications

Processes	Affected in current version	Affected workflows
New files to be stored	No	N/A
New files to be delivered	No	N/A
New files to be uploaded to Scout	No	N/A
Changes to Housekeeper IDs	No	N/A
Changes to Scout upload	No	N/A

Case ID	Analysis type	Storage status	Delivery status	Upload status
acetuna	QC, tumor-only	NA	NA	NA
civilsole	WGS, tumor-only	NA	NA	NA
fleetjay	WGS, tumor-normal	NA	NA	NA
setamoeba	TGA, tumor-only	Pass	NA	NA
unitedbeagle	TGA, tumor-normal	Pass	NA	NA
uphippo	UMI, tumor-only	Pass	NA	NA
equalbug	UMI, tumor-normal	Pass	NA	NA

• This section has been verified successfully, or been identified as irrelevant for the current verification

Version Specific Verification Cases

Case ID	Analysis type	Expected QC	Status
uphippo	UMI, tumor-norma	Pass	Pass

• This section has been verified successfully, or been identified as irrelevant for the current verification

Test UMI workflow with default settings

Case ID	Description	Expected outcome	Status
equalbug	Using the default minR value minR=3,1,1	Analysis finishing successfully	Pass

Test UMI workflow with custom settings

Case ID	Description	Expected outcome	Status
uphippo	Setting a custom umi-min-reads value minR=1,0,0	Analysis finishing successfully	Pass

Issues Identified

Failed test	Description	Severity	Status
Workflow integrity tests	Broken containers due to a major numpy release	High	Open. Being address in #1456 and #1457. Decision to use previous version containers.

Recommendations

Since all the tests and integrity tests are passing I recommend this be put in production! // MJ 2024-06-26

Conclusion

Proceeding with the deployment of version 15.0.1. using the containers from version 15.0.0..

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Approval

• Verification review: MJ
• Date: 2024-06-26

Deployment

• Responsible: VI
• Date: 2024-06-26

[mathiasbio]

Great job! 🌟 Looks like all is good as long as we use the old containers which I think is completely fine!

[ivadym]