Verification Report [v14.0.1]

[khurrammaqbool]

Balsamic Verification Report

Release Information

• Version: v14.0.1
• Release Type: Patch
• Release Commit: b94831b
• Release Date: 2024-03-19

Person(s) involved in the development of new release

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

Summary

The purpose of this verification is to fix a bug appeared in PureCN rules crashing due to the purecn command failing to estimate purity and ploidy. This leads to the whole pipeline crash because of the bash strict mode in effect from snakemake. The solution, implemented in the current release, is to bypass the exit code and making the condition associated, in case of failing the command to estimate purity and ploidy, with the output generating default values of purity=0.02 and ploidy=2, with a comment "FAILED PURITY ESTIMATION" to the table.

In addition a small bug fix has been included wherein the wrong container name used in the CNVkit PON creation workflow has been corrected.

These are the goals of this verification:

1. Evaluate the solution performs as expected, the analysis completes without crashing and a default table is generated in case purity and ploidy estimation fails.

Changelog

Type	Pull Request	Performed tests
Fixed	https://github.com/Clinical-Genomics/BALSAMIC/pull/1406	Analysis completed generating the default table
Fixed	https://github.com/Clinical-Genomics/BALSAMIC/pull/1412	CNVkit PON creation rules no longer failing with missing container

Pre-Verification Checklist

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

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

  • BALSAMIC was installed on stage after making the BALSAMIC release_v14.0.1 branch, from the instructions given above:
    1. sudo <...>
    2. tmux new -s <...>
    3. Activate stage and conda environments.
    4. pip uninstall balsamic
    5. pip install --no-cache-dir -U git+https://github.com/Clinical-Genomics/BALSAMIC@release_v14.0.1
    6. COSMIC_KEY=<...>
    7. balsamic init --out-dir <STAGE_PATH> --account <...> --cosmic-key ${COSMIC_KEY} --genome-version hg19 --cache-version 14.0.1 --run-mode local --snakemake-opt "--cores 4" -r
    8. balsamic init --out-dir /home/proj/stage/cancer/balsamic_cache --account development --cosmic-key ${COSMIC_KEY} --genome-version hg38 --cache-version 14.0.1 --run-mode local --snakemake-opt "--cores 8" -r
    9. Merged https://github.com/Clinical-Genomics/BALSAMIC/pull/1412 to the release v14.0.1 branch
    10. Reinstalled BALSAMIC on stage and removed containers from the cache on stage
    11. balsamic init --out-dir /home/proj/stage/cancer/balsamic_cache --account development --cosmic-key ${COSMIC_KEY} --genome-version canfam3 --cache-version 14.0.1 --run-mode local --snakemake-opt "--cores 8" -r

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

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

  Document	Sections to Be Updated	Pull Request
  Balsamic Documentation	NA	NA
  Atlas Documentation	NA	NA

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

  Software	Current Version	Pull Request with the Required Updates
  CG	NA	NA
  Servers	NA	NA
  Hermes	NA	NA

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
bettertahr	TGA, tumor-only	(Fails to compute purity and ploity and uses default)	Pass
firstlobster	CNVkit PON test case (myeloid 5.3)	Workflow finishes without error and produces PON	Pass

• [x] 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	NA
New files to be delivered	No	NA
New files to be uploaded to Scout	No	NA
Changes to Housekeeper IDs	No	NA
Changes to Scout upload	No	NA

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	NA	NA	NA
unitedbeagle	TGA, tumor-normal	NA	NA	NA
uphippo	UMI, tumor-only	NA	NA	NA
equalbug	UMI, tumor-normal	NA	NA	NA

• [x] 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
bettertahr	TGA, tumor-only	(Fails to compute purity and ploity and uses default)	Pass
firstlobster	CNVkit PON test case (myeloid 5.3)	Workflow finishes without error and produces PON	Pass

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

Issues Identified

No Issues on related to the verification of BALSAMIC, but some challenges running the validation cases on stage. The documentation to install and run BALSAMIC on stage is not up-to-date.

Recommendations

• Prioritise the bug related to the validation cases being compressed, as it significantly affects the dynamics of the validation process.
• Update the documentation to install and run BALSAMIC on stage.
• Update validation report to add PON case created for the current verification.

Conclusion

BALSAMIC patch release v14.0.1 fixes two bugs. One related to the handling of the workflow in case the computation purity and ploidy fails and second a fix for container name in the PON workflow. The verification process has been conducted successfully. The patch release has been evaluated positively, for both bug fixes, with different QoS scenarios.

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Approval

• Verification review: VI
• Date: 2024-03-19

Deployment

• Responsible: KM
• Date: 2024-03-20

[ivadym]

Signed! @khurrammaqbool @mathiasbio

I've marked as NA the section you identified as irrelevant for more clarity and checked the CNV report PDF! Everything looks all right! ⭐

[ivadym]

I've just noticed that equalbug and uphippo have been started as balsamic analysis, not balsamic-umi. Similarly, acetuna should have been started as balsamic-qc. These workflows have not been verified.

[ivadym]

What's the status, @khurrammaqbool? Have we already rerun these cases? Are we deploying tomorrow? It would be good to bump the version today and copy the Balsamic cache from stage to production

[mathiasbio]

Have confirmed, equalbug, upphippo and acetuna has been re-run and finished yesterday with the correct workflow 👍 @ivadym

[ivadym]

Nice! Thanks @mathiasbio! I've updated the signature date so I think we're good to go 🛫