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fix: rename samplename in final vcf header #1310

Merged
merged 22 commits into from
Nov 4, 2023
Merged

fix: rename samplename in final vcf header #1310

merged 22 commits into from
Nov 4, 2023

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mathiasbio
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@mathiasbio mathiasbio commented Nov 1, 2023 •
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This PR:

This PR aims to change the name of the sample columns in the final VCFs to match the changes in the scout_load.yaml for sample-id, which will use LIMS-ID instead of TUMOR/NORMAL. (Clinical-Genomics/cg#2650)

Added:

  • New rule to create namemap to translate sample type names in vcf header to sampleID

Changed:

  • Renamed names of sample columns in final vcf (clinical.pass.vcf.gz) to sampleID

Removed:

PR specific tests

  • TGA T/N case finishes without error
  • And both clinical.pass vcfs have the changed sample-columns names
  • TGA UMI case finishes without error
  • And both clinical.pass vcfs have the changed sample-columns names
  • WGS T/N case finishes without error
  • And both clinical.pass vcfs have the changed sample-columns names
  • WGS T-only case finishes without errors
  • And both clinical.pass vcfs have the changed sample-columns names

Review and tests:

  • Tests pass
  • Code review
  • New code is executed and covered by tests, and test approve

@mathiasbio mathiasbio mentioned this pull request Nov 1, 2023
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@mathiasbio mathiasbio changed the base branch from master to develop November 1, 2023 10:17
@mathiasbio mathiasbio changed the title change: rename samplename in final vcf header fix: rename samplename in final vcf header Nov 1, 2023
@mathiasbio mathiasbio self-assigned this Nov 1, 2023
@mathiasbio mathiasbio added this to the Release 13 milestone Nov 1, 2023
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codecov bot commented Nov 1, 2023 •
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Codecov Report

Attention: 2 lines in your changes are missing coverage. Please review.

Files Coverage Δ
BALSAMIC/commands/base.py 100.00% <100.00%> (ø)
BALSAMIC/commands/config/base.py 100.00% <100.00%> (ø)
BALSAMIC/commands/config/case.py 100.00% <100.00%> (+3.44%) ⬆️
BALSAMIC/commands/config/pon.py 100.00% <100.00%> (+4.87%) ⬆️
BALSAMIC/commands/init/base.py 100.00% <100.00%> (ø)
BALSAMIC/commands/options.py 100.00% <100.00%> (ø)
BALSAMIC/commands/report/base.py 100.00% <100.00%> (ø)
BALSAMIC/commands/report/deliver.py 100.00% <100.00%> (ø)
BALSAMIC/commands/report/status.py 100.00% <100.00%> (ø)
BALSAMIC/commands/run/analysis.py 100.00% <100.00%> (ø)
... and 24 more

📢 Thoughts on this report? Let us know!.

@mathiasbio mathiasbio mentioned this pull request Nov 1, 2023
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16 tasks
@mathiasbio mathiasbio mentioned this pull request Nov 2, 2023
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@mathiasbio mathiasbio marked this pull request as ready for review November 2, 2023 15:43
@mathiasbio mathiasbio requested a review from a team as a code owner November 2, 2023 15:43
ivadym
ivadym reviewed Nov 2, 2023
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Looks good 👍 Left you some minor comments

BALSAMIC/snakemake_rules/annotation/final_vcf_reheader.rule Outdated Show resolved Hide resolved
BALSAMIC/snakemake_rules/annotation/varcaller_filter_tumor_normal.rule Outdated Show resolved Hide resolved
BALSAMIC/snakemake_rules/annotation/vcfheader_rename.rule Outdated Show resolved Hide resolved
BALSAMIC/snakemake_rules/variant_calling/somatic_sv_tumor_only.rule Show resolved Hide resolved
BALSAMIC/workflows/balsamic.smk Outdated Show resolved Hide resolved
ivadym
ivadym approved these changes Nov 2, 2023
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Look great after your last push! 🥇 🌟 🏎️ 💨 🌟 🥇

@sonarqubecloud SonarQubeCloud
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sonarqubecloud bot commented Nov 4, 2023

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@mathiasbio mathiasbio merged commit 66b049e into develop Nov 4, 2023
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@mathiasbio mathiasbio deleted the rename_sample_in_final_vcf branch November 4, 2023 09:13
@ivadym ivadym mentioned this pull request Nov 6, 2023
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@ivadym ivadym ivadym approved these changes

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BALSAMIC
Status: Archived
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Release 13
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@mathiasbio @ivadym