From 5a6f156b4f31870db10b3e744a27c6500071681c Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 28 Oct 2026 16:52:31 +0100 Subject: [PATCH] fix mito handling in vivar samplesheet --- CHANGELOG.md | 1 + src/main/resources/worksheets/nfcmgg_preprocessing.yml | 3 ++- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index adfaec5..2dfc1d2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 diff --git a/src/main/resources/worksheets/nfcmgg_preprocessing.yml b/src/main/resources/worksheets/nfcmgg_preprocessing.yml index 704062c..0f86182 100644 --- a/src/main/resources/worksheets/nfcmgg_preprocessing.yml +++ b/src/main/resources/worksheets/nfcmgg_preprocessing.yml @@ -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: