ivadym commented 1 year ago

Balsamic Verification Report

Release Information

Version: 12.0.2
Release Type: Patch
Release Commit: c62ec13
Release Date: 2023-07-24

Person(s) involved in the development of new release

Developer/s: @khurrammaqbool @mathiasbio @ivadym
Verification operator/s: @mathiasbio, @ivadym
Verification reviewer/s: @pbiology

Summary

After adding TIDDIT tumor normal filtering, a bug was identified in ticket Ticket #248220. Consequently, there are issues processing the SV VCF with other tools.

These are the goals of this verification:

Validate the format of the header in the SV VCF (SV.somatic.<case-id>.svdb.clinical.filtered.pass.vcf.gz) to ensure its correctness (only relevant for WGS tumor normal analyses).
Verify the integrity of the different analysis types after updating the balsamic and varcall-cnvkit containers.

Changelog

Type	Pull Request	Performed tests
Fixed	#1203	Test: correctness of the SV VCF filtered file for WGS TN analysis
Changed	#1206	Test: pydantic version is <2.0 in `S_balsamic` environment
Changed	#1206	Test: rules using the `edit_vcf_info.py` script behave as expected
Changed	#1207	Test: rules using `varcall-cnvkit` container behave as expected

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.
[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 N/A N/A

Atlas Documentation N/A N/A
[x] Set up the stage environment with the necessary software and configurations:

Software Current Version Pull Request with the Required Updates

CG Version 40.1.2 N/A

Servers Version 16.1.3 N/A

Hermes Version 1.12.1 N/A

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

Software	Current Version	Pull Request with the Required Updates
CG	Version 40.1.2	N/A
Servers	Version 16.1.3	N/A
Hermes	Version 1.12.1	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` and `PCT_TARGET_BASES_1000X=0.861996`)	Pass
`equalbug`	UMI, tumor-normal	Fail (`GC_DROPOUT=1.087173` and `RELATEDNESS=-0.524`)	Pass

Test: correctness of the SV VCF filtered file for WGS TN analysis

Case ID	Description	Expected outcome	Status
`fleetjay`	Look at header lines in the final SV VCF for INFO AF_N_MAX, AF_T_MAX, and BND_ID	It should have the "Number=. " field between the "ID" and "Type" field.	Pass

Test: pydantic version is <2.0 in `S_balsamic` environment

Case ID	Description	Expected outcome	Status
N/A	Pydantic version has been locked	The version should be <2.0	Pass (v1.10.10)

Test: rules using the `edit_vcf_info.py` script behave as expected

Case ID	Description	Expected outcome	Status
`setamoeba`	Look for FOUND_IN in INFO field in `{var_type}.somatic.{case_name}.vardict.research.filtered.pass.vcf.gz` and compare file-sizes past and current version	The FOUND_IN field should be added properly to INFO field and size of VCF should be identical	Pass
`unitedbeagle`	Look for FOUND_IN in INFO field in`{var_type}.somatic.{case_name}.vardict.research.filtered.pass.vcf.gz`, and compare file-sizes past and current version	The FOUND_IN field should be added properly to INFO field and size of VCF should be identical	Pass

Test: rules using `varcall-cnvkit` container behave as expected

Case ID	Description	Expected Outcome	Status
`setamoeba`	Updated `CNVkit` dependencies, keeping the same `CNVkit` version.	`CNVkit` tumor-only output should remain unaffected. Output files identical to those in version `12.0.1`.	Pass
`unitedbeagle`	Updated `CNVkit` dependencies, keeping the same `CNVkit` version.	`CNVkit` tumor-normal output should remain unaffected. Output files identical to those in version `12.0.1`.	Pass
`uphippo`	Updated `CNVkit` dependencies, keeping the same `CNVkit` version.	`CNVkit` UMI tumor-only output should remain unaffected. Output files identical to those in version `12.0.1`.	Pass
`equalbug`	Updated `CNVkit` dependencies, keeping the same `CNVkit` version.	`CNVkit` UMI tumor-normal output should remain unaffected. Output files identical to those in version `12.0.1`.	Pass

Issues Identified

No issues identified.

Recommendations

Conclusion

The verification process for Balsamic v12.0.2 was conducted to ensure the integrity and correctness of the patch. The primary objective was to validate the format of the header in the SV VCF (SV.somatic.<case-id>.svdb.clinical.filtered.pass.vcf.gz) for WGS tumor-normal analyses and to verify the integrity of different analysis types after updating the balsamic and varcall-cnvkit containers.

Furthermore, no issues were identified during the verification process. As a result, the Balsamic Version 12.0.2 patch release is ready for deployment.

Approval

Verification review: Anders Lind, @pbiology
Date: 2023-07-26

Deployment

Responsible: VI, @ivadym
Date: 2023-07-27

pbiology commented 1 year ago

Looks great, approved!

ivadym commented 1 year ago

Deployed:

θ62° 16d [hiseq.clinical@hasta:~] [P_base] $ conda activate P_balsamic
θ67° 16d [hiseq.clinical@hasta:~] [P_balsamic] $ balsamic --version
balsamic, version 12.0.1
θ65° 16d [hiseq.clinical@hasta:~] [P_balsamic] 8s $ pip uninstall balsamic
Found existing installation: BALSAMIC 12.0.1
Uninstalling BALSAMIC-12.0.1:
  Would remove:
    /home/proj/production/bin/miniconda3/envs/P_balsamic/bin/balsamic
    /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages/BALSAMIC-12.0.1.dist-info/*
    /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages/BALSAMIC/*
    /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages/tests/*
Proceed (Y/n)? Y
  Successfully uninstalled BALSAMIC-12.0.1
θ61° 16d [hiseq.clinical@hasta:~] [P_balsamic] 9s $ balsamic --version
-bash: /home/proj/production/bin/miniconda3/envs/P_balsamic/bin/balsamic: No such file or directory
θ63° 16d [hiseq.clinical@hasta:~] [P_balsamic] 127 $ ll /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages/BALSAMIC/
ls: cannot access /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages/BALSAMIC/: No such file or directory
θ62° 16d [hiseq.clinical@hasta:~] [P_balsamic] 2 $ pip install --no-cache-dir -U git+https://github.com/Clinical-Genomics/BALSAMIC
Collecting git+https://github.com/Clinical-Genomics/BALSAMIC
  Cloning https://github.com/Clinical-Genomics/BALSAMIC to ./tmp/pip-req-build-0z1rn5_y
  Running command git clone --quiet https://github.com/Clinical-Genomics/BALSAMIC /home/hiseq.clinical/tmp/pip-req-build-0z1rn5_y
  Resolved https://github.com/Clinical-Genomics/BALSAMIC to commit c62ec134971c402858891bb805e3e30f39cd3aae
  Preparing metadata (setup.py) ... done
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Requirement already satisfied: pydantic<2.0,>=1.9.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (1.10.9)
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Requirement already satisfied: snakemake==6.5.3 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (6.5.3)
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Requirement already satisfied: PyPDF2>=1.26.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (3.0.1)
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Requirement already satisfied: cryptography==40.0.2 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (40.0.2)
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Requirement already satisfied: toml==0.10.2 in ./.local/lib/python3.7/site-packages (from BALSAMIC==12.0.2) (0.10.2)
Collecting cyvcf2==0.30.22 (from BALSAMIC==12.0.2)
  Downloading cyvcf2-0.30.22-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.1/7.1 MB 15.2 MB/s eta 0:00:00
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Requirement already satisfied: cffi>=1.12 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from cryptography==40.0.2->BALSAMIC==12.0.2) (1.15.1)
Requirement already satisfied: argcomplete>=1.9.4 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gsutil==5.23->BALSAMIC==12.0.2) (3.1.1)
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Requirement already satisfied: fasteners>=0.14.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gsutil==5.23->BALSAMIC==12.0.2) (0.18)
Requirement already satisfied: gcs-oauth2-boto-plugin>=3.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gsutil==5.23->BALSAMIC==12.0.2) (3.0)
Requirement already satisfied: google-apitools>=0.5.32 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gsutil==5.23->BALSAMIC==12.0.2) (0.5.32)
Requirement already satisfied: httplib2==0.20.4 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gsutil==5.23->BALSAMIC==12.0.2) (0.20.4)
Requirement already satisfied: google-reauth>=0.1.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gsutil==5.23->BALSAMIC==12.0.2) (0.1.1)
Requirement already satisfied: monotonic>=1.4 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gsutil==5.23->BALSAMIC==12.0.2) (1.6)
Requirement already satisfied: pyOpenSSL>=0.13 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gsutil==5.23->BALSAMIC==12.0.2) (23.2.0)
Requirement already satisfied: retry-decorator>=1.0.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gsutil==5.23->BALSAMIC==12.0.2) (1.1.1)
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Requirement already satisfied: cycler>=0.10 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from matplotlib==3.5.2->BALSAMIC==12.0.2) (0.11.0)
Requirement already satisfied: fonttools>=4.22.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from matplotlib==3.5.2->BALSAMIC==12.0.2) (4.38.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from matplotlib==3.5.2->BALSAMIC==12.0.2) (1.4.4)
Requirement already satisfied: packaging>=20.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from matplotlib==3.5.2->BALSAMIC==12.0.2) (23.1)
Requirement already satisfied: pillow>=6.2.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from matplotlib==3.5.2->BALSAMIC==12.0.2) (9.5.0)
Requirement already satisfied: pyparsing>=2.2.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from matplotlib==3.5.2->BALSAMIC==12.0.2) (3.1.0)
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Requirement already satisfied: wrapt in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from snakemake==6.5.3->BALSAMIC==12.0.2) (1.15.0)
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Requirement already satisfied: pyasn1-modules>=0.2.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from google-auth[aiohttp]>=2.5.0->gsutil==5.23->BALSAMIC==12.0.2) (0.3.0)
Requirement already satisfied: urllib3<2.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from google-auth[aiohttp]>=2.5.0->gsutil==5.23->BALSAMIC==12.0.2) (1.26.16)
Requirement already satisfied: aiohttp<4.0.0.dev0,>=3.6.2 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from google-auth[aiohttp]>=2.5.0->gsutil==5.23->BALSAMIC==12.0.2) (3.8.4)
Requirement already satisfied: pyu2f in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from google-reauth>=0.1.0->gsutil==5.23->BALSAMIC==12.0.2) (0.1.5)
Requirement already satisfied: zipp>=0.5 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from importlib-metadata->click==8.1.3->BALSAMIC==12.0.2) (3.15.0)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from requests->snakemake==6.5.3->BALSAMIC==12.0.2) (3.1.0)
Requirement already satisfied: idna<4,>=2.5 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from requests->snakemake==6.5.3->BALSAMIC==12.0.2) (3.4)
Requirement already satisfied: certifi>=2017.4.17 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from requests->snakemake==6.5.3->BALSAMIC==12.0.2) (2023.5.7)
Requirement already satisfied: gitdb<5,>=4.0.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gitpython->snakemake==6.5.3->BALSAMIC==12.0.2) (4.0.10)
Requirement already satisfied: attrs>=17.4.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from jsonschema->snakemake==6.5.3->BALSAMIC==12.0.2) (23.1.0)
Requirement already satisfied: importlib-resources>=1.4.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from jsonschema->snakemake==6.5.3->BALSAMIC==12.0.2) (5.12.0)
Requirement already satisfied: pkgutil-resolve-name>=1.3.10 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from jsonschema->snakemake==6.5.3->BALSAMIC==12.0.2) (1.3.10)
Requirement already satisfied: pyrsistent!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from jsonschema->snakemake==6.5.3->BALSAMIC==12.0.2) (0.19.3)
Requirement already satisfied: fastjsonschema in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from nbformat->snakemake==6.5.3->BALSAMIC==12.0.2) (2.17.1)
Requirement already satisfied: jupyter-core in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from nbformat->snakemake==6.5.3->BALSAMIC==12.0.2) (4.12.0)
Requirement already satisfied: traitlets>=5.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from nbformat->snakemake==6.5.3->BALSAMIC==12.0.2) (5.9.0)
Requirement already satisfied: multidict<7.0,>=4.5 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from aiohttp<4.0.0.dev0,>=3.6.2->google-auth[aiohttp]>=2.5.0->gsutil==5.23->BALSAMIC==12.0.2) (6.0.4)
Requirement already satisfied: async-timeout<5.0,>=4.0.0a3 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from aiohttp<4.0.0.dev0,>=3.6.2->google-auth[aiohttp]>=2.5.0->gsutil==5.23->BALSAMIC==12.0.2) (4.0.2)
Requirement already satisfied: yarl<2.0,>=1.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from aiohttp<4.0.0.dev0,>=3.6.2->google-auth[aiohttp]>=2.5.0->gsutil==5.23->BALSAMIC==12.0.2) (1.9.2)
Requirement already satisfied: frozenlist>=1.1.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from aiohttp<4.0.0.dev0,>=3.6.2->google-auth[aiohttp]>=2.5.0->gsutil==5.23->BALSAMIC==12.0.2) (1.3.3)
Requirement already satisfied: aiosignal>=1.1.2 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from aiohttp<4.0.0.dev0,>=3.6.2->google-auth[aiohttp]>=2.5.0->gsutil==5.23->BALSAMIC==12.0.2) (1.3.1)
Requirement already satisfied: asynctest==0.13.0 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from aiohttp<4.0.0.dev0,>=3.6.2->google-auth[aiohttp]>=2.5.0->gsutil==5.23->BALSAMIC==12.0.2) (0.13.0)
Requirement already satisfied: smmap<6,>=3.0.1 in /home/proj/production/bin/miniconda3/envs/P_balsamic/lib/python3.7/site-packages (from gitdb<5,>=4.0.1->gitpython->snakemake==6.5.3->BALSAMIC==12.0.2) (5.0.0)
Building wheels for collected packages: BALSAMIC
  Building wheel for BALSAMIC (setup.py) ... done
  Created wheel for BALSAMIC: filename=BALSAMIC-12.0.2-py3-none-any.whl size=92795234 sha256=513c5bee959610236600547fa612aa6dc74210f5c71a067156e77cc96d76ee08
  Stored in directory: /home/hiseq.clinical/tmp/pip-ephem-wheel-cache-kd62n9e5/wheels/67/53/85/a9b1f8619ee7ad1b4c3cdae9f0949db7479f041b1a560b9a80
Successfully built BALSAMIC
Installing collected packages: cyvcf2, BALSAMIC
  Attempting uninstall: cyvcf2
    Found existing installation: cyvcf2 0.9.0
    Uninstalling cyvcf2-0.9.0:
      Successfully uninstalled cyvcf2-0.9.0
Successfully installed BALSAMIC-12.0.2 cyvcf2-0.30.22
θ62° 16d [hiseq.clinical@hasta:~] [P_balsamic] 41s $ balsamic --version
balsamic, version 12.0.2

Clinical-Genomics / BALSAMIC

Verification Report [v12.0.2] #1204

Balsamic Verification Report

Release Information

Person(s) involved in the development of new release

Summary

Changelog

Pre-Verification Checklist

Verification Results

Workflow Integrity Verification Cases

Test: correctness of the SV VCF filtered file for WGS TN analysis

Test: pydantic version is <2.0 in `S_balsamic` environment

Test: rules using the `edit_vcf_info.py` script behave as expected

Test: rules using `varcall-cnvkit` container behave as expected

Issues Identified

Recommendations

Conclusion

Approval

Deployment

Clinical-Genomics / BALSAMIC

Verification Report [v12.0.2] #1204

Balsamic Verification Report

Release Information

Person(s) involved in the development of new release

Summary

Changelog

Pre-Verification Checklist

Verification Results

Workflow Integrity Verification Cases

Test: correctness of the SV VCF filtered file for WGS TN analysis

Test: pydantic version is <2.0 in S_balsamic environment

Test: rules using the edit_vcf_info.py script behave as expected

Test: rules using varcall-cnvkit container behave as expected

Issues Identified

Recommendations

Conclusion

Approval

Deployment

Test: pydantic version is <2.0 in `S_balsamic` environment

Test: rules using the `edit_vcf_info.py` script behave as expected

Test: rules using `varcall-cnvkit` container behave as expected