feat: Release v16.0.0 #1491
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feat: Release v16.0.0 #1491
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feat: Remove GATK3
…ntainer feat: add msisensorpro container
The new version of multiqc supports picard mimicked reports from Sentieon tools: MultiQC/MultiQC#2110 This should solve this issue: #1290 where an ugly solution was implemented in the Dedup rule to make MultiQC accept dedup-stats from Sentieon dedup. It may also allow us to move away from Picard to generate our QC reports and instead use the Sentieon tools which should be faster and enable us to clear away some rules for a more streamlined and less messy workflow. #### Added - separate container for multiqc #### Changed - updated multiqc from 1.12 to 1.22.3 #### Removed - no longer necessary sed command in dedup rule - deprecated and unused TNhaplotyper rule
* add msisensorpro * changelog * change filenames * MSI to PDf * Refactor * update docs * fix qoutation mark
* update MSI table * changelog
#### Added - Sentieon install directory path and Sentieon license to case config arguments
* add MSI TN to storage * changelog * fix blank line * changelog
#### Added - QC threshold for lymphoma_MRD panel
#### Added
- UMI extraction and deduplication to TGA workflow
- Adapter trimming of fastqs to UMI workflow
- Cap base quality in bam for Manta input
#### Changed
- Refactored multi workflow rule-files to separate files to decrease complexity
- Refactored output files to in general comply with format {sample_type}.{sample_name}
- Replaced Picard QC tools with matching Sentieon QC tools
#### Removed
- UMI specific rules for UMI-extraction and alignment (using new TGA-rules instead)
- Fastq and UMI trimming command-line options
Merged this PR into this one: #1465
#### Added
- Added extension of target bed regions to a minimum size of 100 for CNV analysis
- PON for: Exome comprehensive 10.2
- PON for: GMSsolid 15.2
- PON for: GMCKsolid 4.2
#### Changed
- updated PON for GMCKSolid v4.1
- updated PON for GMSMyeloid v5.3
- updated PON for GMSlymphoid v7.3
Merged this PR into this one: #1448
#### Added
- Script to post-process CNVkit output to GENS-format
- DNAscope gnomad calling to TGA for GENS
#### Changed
- Parsing of GENS arguments changed to account for TGA
Merged this PR: #1475 into this one
#### Changed
- Refactored rules for bcftools filters
- Renamed final UMI bamfile to ensure hsmetrics are collected in multiqc json
- Changed ranked VCF from research to clincial
- Lowered min AF for TGA from 0.007 to 0.005
- Lowered maximal SOR for TNscope in TGA tumor only cases from 3 to 2.7
- Changed filter settings for research TNscope vcf, now either PASS or triallelic_site (fixing this issue: #1293)
#### Added
- TNscope for TGA workflows, merged with VarDict results
- New filter for VarDict for tumor in normal contamination
- Export TMP environment variables to rules that lack them
- Added genmod ranked VCFs to be delivered
- Added family-id to genmod in order to get ranked variants to Scout (solved this: #1045)
- Added DP and AF to INFO-field of TNscope vcfs for ranking model
- Raw TNscope calls and unfiltered research-annotated SNVs to delivery
#### Removed
- ML-model for TNscope is removed due to license issue with new version of Sentieon
- All code associated with TNhaplotyper
- Removed research.filtered.pass VCFs from delivery and storage list
* changelog * fix to version 1.2.0 * update to version 1.3.0 * split tasks * merge tasks * fix somalier container * fix nimble htslib bcftools version * fix depth * update nim to 1.6.20 * update nim to 2.2.0 * update somalier to 0.2.19 * fix nimble version to 1.6.6 * revert changes for somalier container * refactor * update software version information --------- Co-authored-by: Mathias Johansson <[email protected]>
* update somalier and dependecies * update docs * fix security hotspot * restrict redirects * update docs * changelog
#### Changed - Updated lychee-actions to 2.0.2 and increase maximal redirects to 10 - Fixing broken links in documentation
#### Changed - Renamed UMI bamfile in order for the sample id to be unique un multiqc_data.json and not overwritten by hsmetrics.
### Changed - Updated docs tools versions
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
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+ Coverage 99.44% 99.49% +0.05%
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Files 40 40
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+ Hits 1972 1981 +9
+ Misses 11 10 -1
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Arguments in long RUN instructions should be sorted Low
* fix vardict memory error * changelog * changelog --------- Co-authored-by: Mathias Johansson <[email protected]>
* increase vardict cores to 18
#### Fixed - TNscope tag to variant info-field for TGA workflow #### Removed - Removed VarDict germline filter, replaced by relative normal af / tumor af filter
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khurrammaqbool
approved these changes
Nov 19, 2024
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Description
Big update with a few primary features:
Added:
Changed:
SLEEP_BEFORE_STARTto 600s fix: Update scheduler script #1372vcf2cytosureversion to 0.9.1 and remove hardcoded versions chore: Update vcf2cytosure version #1456Removed:
gatk_contestrule feat: Remove GATK3 #1432Fixed:
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_v16.0.0branch, 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_v16.0.0balsamic init --out-dir <STAGE_PATH> --account <...> --cosmic-key ${COSMIC_KEY} --genome-version hg19 --cache-version 16.0.0 --run-mode local --snakemake-opt "--cores 40" -rbalsamic init --out-dir /home/proj/stage/cancer/balsamic_cache --account development --cosmic-key ${COSMIC_KEY} --genome-version hg38 --cache-version 16.0.0 --run-mode local --snakemake-opt "--cores 8" -rbalsamic init --out-dir /home/proj/stage/cancer/balsamic_cache --account development --cosmic-key ${COSMIC_KEY} --genome-version canfam3 --cache-version 16.0.0 --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: https://docs.google.com/spreadsheets/d/1g6uXPjCT0INrYS9n5mLblC_7TOgX3hz6j2mXoqp9apQ/edit?gid=0#gid=0
Hg38 integrity verifications:
Issues discovered for HG38:
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