feat: Release v17.0.0 #1543
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feat: Release v17.0.0 #1543
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#### Added - sex prediction tools and specified sex-verification for all workflows
#### Added - new argument `--soft-filter-normal` to disable hard filtration of matched normal filters #### Changed - refactored variant-filter constants and reworked bcftools filters - renamed high_normal_tumor_af_frac to in_normal
#### Removed - WGS-level GC bias metric from TGA workflow
#### Added - TNscope MNV merge script #### Changed - merge SNVs into MNVs in TNscope TGA - change raw delivery SNV file for TGA to before any post-processing
#### Changed - lowered threads for bcftools and CADD rules #### Fixed - changed name of benchmark files for annotation rules to avoid name conflicts
#### Changed - Replaced bcftools concat with custom python script for merging VCFs from VarDict and TNscope
#### Changed - VarDict java memory option and threads
#### Changed - pinned arraymancer version in somalier docker build recipe
#### Added - New ONC annotations from Clinvar #### Changed - Added GT field to IGH-DUX4 variant - Changed QC thresholds for WGS normal and WES
#### Added - max SOR 4 filter to WGS TN SNV quality filter
### Added - Adds an option to specify memory - Adds memory to tnscope tn wgs ### Changed - Set different resources for tnscope tga and wgs
### Changed - Disabled SV calling in TNscope
#### Added - max RPA 12 filter to TNscope TGA workflow - max SOR 3 filter to TNscope TGA TN workflow - filter to remove MERGED variants after MNV post-processing in TGA workflow #### Fixed - vcf sort step to TNscope VCF after MNV post-processing in TGA workflow - set correct exome DP filter by refactoring some retrieve filter functions
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #1543 +/- ##
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- Coverage 99.44% 99.40% -0.04%
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Files 40 40
Lines 1975 2019 +44
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+ Hits 1964 2007 +43
- Misses 11 12 +1
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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#### Removed - remove parallelization per chromosome for VarDict
…IC into release_v17.0.0
#### Changed - renamed CLNACC to CLNVID for Clinvar annotations
#### Fixed - excluded MEDIAN_COVERAGE from tumor coverage qc threshold
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Description
Big update with a few primary features:
Added:
Changed:
Removed:
Fixed:
Pre-Validation Checklist
Before proceeding with the validation process, ensure that the following tasks have been completed:
Install Balsamic in stage and production environments in hasta and build its cache.
BALSAMIC release_v17.0.0branch, from the instructions given above:sudo <...>tmux new -s <...>pip uninstall balsamicpip install --no-cache-dir -U git+https://github.com/Clinical-Genomics/BALSAMIC@release_v17.0.0balsamic init --out-dir /home/proj/stage/cancer/balsamic_cache --account development --cosmic-key ${COSMIC_KEY} --genome-version hg38 --cache-version 17.0.0 --run-mode local --snakemake-opt "--cores 8" -rConfirm the availability of necessary resources, such as test cases.
(Made script to verify this automatically: /home/proj/stage/cancer/validation/scripts/verify_presence_of_test_samples.sh)Review the changelog and ensure all changes and updates are documented:
Set up the stage environment with the necessary software and configurations:
Workflow integrity results
Workflow Integrity Verification Cases
More details here:
Issues:
* This is an new QC threshold for normals which should not fail for tumor samples: I opened up an issue to fix: #1549 and solved it here: #1555
Hg38 integrity verifications:
Issues discovered for HG38 previously in release 16.0.0 and which has not been solved here:
cg command:
cg workflow balsamic start --genome-version hg38 wgscasecollects loqusdb and other references specifically for hg19 and adds to the case.Despite starting the case manually the analysis fails on multiple places. Copying the failed case to a folder to investigate after release: /home/proj/development/cancer/failed_cases/hg38_release16.0.0_failed
Release specific integration verifications:
Storage, Delivery and Upload Integrity Verifications
Validation and implementation plan status
Pull-request for validation-report made here: https://github.com/Clinical-Genomics/validations/pull/241
Pull-request for implementation-plan here: LINK