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Clinical-Genomics / cg / 20094906667
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DEFAULT BRANCH: master
Ran 10 Dec 2025 10:12AM UTC
Jobs 1
Files 885
Run time 2min
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10 Dec 2025 10:09AM UTC coverage: 85.674% (+0.04%) from 85.636%
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Remove peddy and add somalier for Nallo (#4752) (minor)

## Description

Aim to fix issue #4698. 

### Added

- The values under `report_saved_raw_data > multiqc_somalier` (in file multiqc_data.json) are made available for the delivery report generation. The keys from that dictionary are all prefixed with `somalier_` to avoid clashes with other keys. 
- Test coverage for the delivery report generated by `Nallo`. 

### Changed

- The somalier `sex` is used instead of peddy `predicted_sex` for the metric "Kön" under the heading "kvalitetsmått" in the delivery report. 


---------

Co-authored-by: islean <isak.ohlsson.angnell@gmail.com>
Co-authored-by: Linnéa Löfdahl <linnea.lofdahl@scilifelab.se>

26 of 32 new or added lines in 5 files covered. (81.25%)

28347 of 33087 relevant lines covered (85.67%)

0.86 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
1
65.28
0.15% cg/meta/workflow/nf_analysis.py
5
87.04
-8.52% cg/models/nallo/nallo.py
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ID Job ID Ran Files Coverage
1 20094906667.1 10 Dec 2025 10:12AM UTC 885
85.67
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Source Files on build 20094906667
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  • Changed 4
  • Source Changed 0
  • Coverage Changed 4
Coverage ∆ File Lines Relevant Covered Missed Hits/Line
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