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fix mito handling in vivar samplesheet #20

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Merged
nvnieuwk merged 2 commits into from
Nov 5, 2026
Merged

fix mito handling in vivar samplesheet #20

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5a6f156
fix mito handling in vivar samplesheet
nvnieuwk Oct 28, 2026
cd8242e
Merge branch 'main' into fix/vivar-mt
nvnieuwk Nov 5, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

1. Made the `output` section of the worksheet optional. This is especially useful for pipelines that perform quality checking.
2. It's now possible to use all data fields in the `values` section of the worksheet. The name of the `input` object has also been changed to `data`
3. Fixed the vivar samplesheet to use `sample` in the `id` field and to filter out mitochondrial samples based on `sample` instead of `id`

## 0.4.1

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3 changes: 2 additions & 1 deletion src/main/resources/worksheets/nfcmgg_preprocessing.yml
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Expand Up @@ -142,9 +142,10 @@ samplesheets:
|| data.genome?.toLowerCase() == 'mm10'
)
&& data.sample_type?.toLowerCase() in ['dna', 'tissue']
&& !data.id?.startsWith('mtD')
&& !data.sample?.startsWith('mtD')
fields:
id:
source: sample
organism:
tag:
binsize:
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