feat: Release v13.0.0 #1320
Merged
feat: Release v13.0.0 #1320
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…val of duplicate instances of BND variants
…er rule after svdb merge
…dless of normal presence
Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## master #1320 +/- ##
==========================================
+ Coverage 99.31% 99.44% +0.12%
==========================================
Files 29 39 +10
Lines 1756 1974 +218
==========================================
+ Hits 1744 1963 +219
+ Misses 12 11 -1
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. |
|
@Clinical-Genomics/cancer: System integration tests:Analysis:
Warning Additional QC metrics failing for the UMI worklfow:
Storage, delivery, and upload:
Identified and corrected issues:
|
18 tasks
Added: - Picard AddReadGroup command before VarDict - Samtools sort and index after merging reads with Sentieon Dedup Changed: for changes in existing functionality. - Increased memory and threads for VarDict
Removed: - Extra samtools and index command from WGS analysis
…IC into release_v13.0.0
Removed: - Removed bcftools command for setting soft-filter with maximum allele-frequency, which eventually leads to a hard removal of these variants.
mathiasbio
approved these changes
Jan 15, 2024
There was a problem hiding this comment.
Wow, took me a long time to read through all of these changes, and miraculously I found not a single typo or error anywhere. Amazing job @ivadym
(note for future generations: I'm kidding. The PRs have been reviewed already, and this can be merged when the validation report is approved)
3 tasks
|
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Changelog:
Added:
CADDSNV references feat: add cadd snv reference #1126CADDSNV annotation feat: add cadd snv annotation #1150stats,flagstat,idxstatto WGS workflow feat: core pipeline restructuring #1176--rerun-trigger mtimeoption to Snakemake command fix: Snakemake re-run behaviour #1217CADDcontainer feat: add cadd container #1222htslib(samtools, bcftools tabix) container feat: add htslib container #1234CADDscores for INDELs feat: add cadd annotations for indel #1238CADDreference to tests https://githuc.com/Clinical-Genomics/BALSAMIC/pull/1241cnvkitcontainer feat: add cnvkit container #1252PureCNcontainer feat: add purecn container #1255GATKcontainer feat: add gatk container #1266LOHto TGA workflow feat: add LOH analysis to TGA workflow #1278wkhtmltopdfto system requirements feat: TGA CNV report #1339Changed:
reference.jsonfile to use relative paths refactor: Update reference.json to use relative paths #1251PCT_PF_READS_IMPROPER_PAIRSQC threshold lowered to 5% perf: LowerPCT_PF_READS_IMPROPER_PAIRSQC threshold to 5% #1265<tumor/normal>.<LIMS_ID>.cramfix: cram file hk tags #1307Fixed:
gens_preprocessingrule missing python directive fix: gens_preprocessing rule missing python directive #1322Removed: