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#### Changed - increased runtime for a couple of small rules - decreased memory for headjobs to 500mb
#### Added - add AT_DROPOUT to all panel analyses QC deliverables
#### Changed - lower QSS filter threshold to 10 for WGS TO cases
#### Added - model validation for reference pydantic models `ReferencesCanFam` and `ReferencesHg` - `model_config = ConfigDict(extra="forbid")` to both models to warn the user with an error in case extra unknown arguments are provided - `test_init_CanFam` - `test_get_reference_output_paths_canfam`
#1651) #### Added - The `cytoband_coordinates_file` to `REFERENCE_FILES` dict for `GenomeVersion.HG19`. - Specify `"dir_name": "genome"`, file type, name and gzip for the `cytoband_coordinates_file`. - The `cytoband_coordinates_file` to the `ReferencesHg` model. - The `cytoband_coordinates_file` to the list returned by `CacheConfig.get_reference_output_paths`. - The `cytoband_coordinates_file` to the `AnalysisReferencesHg` model and the object returned by `get_analysis_references`. - The `cytoband_coordinates_file` to pytest.fixture `fixture_analysis_references_hg_data`. #### Changed - `test_get_reference_file_paths_by_compression` to include the additional file. - `test_get_reference_output_paths` to include the additional file. - `test_get_reference_file_paths_by_compression` to include the additional file.
#### Added - added cosmic argument to config case #### Removed - removed cosmic download from balsamic init
#### Changed - change SOR threshold in WGS TO from 3 to 4
#### Fixed - removes wgs gcbias gc_dropout from deliverables qc (only applicable to WGS) - removes wgs gcbias at_dropout from deliverables qc (only applicable to WGS)
#### Added - add new interactive CNV html report for targeted analyses - add cust-case-id to case config and CNV plots - add cancer-genelist with cancer genes from custs and oncokb - add bcftools split multialleles for DNAscope calls - add germline vcf to create VAF plot in CNVkit scatter #### Changed - changed DNAscope germline panel bedfile to padded bed - renamed old CNV pdf report for TGA to signify it is deprecated #### Removed - removed unused CNV report snakemake rule
#### Added - cnv report documentation
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #1666 +/- ##
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+ Coverage 99.33% 99.38% +0.05%
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Files 40 40
Lines 1958 1964 +6
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+ Hits 1945 1952 +7
+ Misses 13 12 -1
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#### Changed - Changed GC dropout QC threshold for myeloid panel from 1 to 3
#### Removed - removed cyvcf2 from docs requirements
#### Added - added a warning about purity and ploidy estimation from PureCN
3 tasks
#### Changed - increased GC dropout threshold to 3 from 2 for lymphoid panel
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Release branch for balsamic v19.0.0
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STATUS sheet: https://docs.google.com/spreadsheets/d/10dpLjxxU6xsDbNp6grUzhvPzo6Ubp9yxGDtvT7UDSrA/edit?gid=0#gid=0
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_v19.0.0branch, from the instructions given above:sudo <...>pip uninstall balsamicpip install --no-cache-dir -U git+https://github.com/Clinical-Genomics/BALSAMIC@release_v19.0.0balsamic init --cache-version 19.0.0 --account development -r -g hg19 --out-dir /home/proj/stage/cancer/balsamic_cache --qos highNOTE:
balsamic initfailed in the rules that fetch the containers and the clinvar preprocessing rule. Since there is no changes in containers, images have been copied over from the previous release. Clinvar files have not been updated and we have copied the ones from the previous release. In particular these two files have been copied:/home/proj/production/cancer/balsamic_cache/18.0.1/hg19/variants/clinvar_processed.vcf.gzand/home/proj/production/cancer/balsamic_cache/18.0.1/hg19/variants/clinvar_processed.vcf.gz.tbiExport most recent loqusDB databases by following: https://atlas.scilifelab.se/infrastructure/bioinformatic_pipelines/BALSAMIC/export_loqusdb_variants/--> Same databases as for v18.0.1 will be used.Confirm 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:
Release specific integration verifications:
[ADD]
Verification summary:
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/377
Pull-request for implementation-plan here: X