set default binsize for mouse samples to 100

CHANGELOG.md

@@ -1,3 +1,7 @@
+## 0.2.8
+
+1. Set the default mouse binsize to 100 if the given binsize is not 100 or 500
+
 ## 0.2.7
 
 1. Rnafusion samplesheets will now contain multiple entries of the same sample when fastq files from multiple lanes are created by nf-cmgg/preprocessing

build.gradle

@@ -6,7 +6,7 @@ dependencies {
     implementation 'com.squareup.okhttp3:okhttp:5.3.2'
 }
 
-version = '0.2.7'
+version = '0.2.8'
 
 nextflowPlugin {
     nextflowVersion = '25.10.0'

src/main/groovy/nfcmgg/plugin/samplesheets/PreprocessingObserver.groovy

@@ -296,15 +296,24 @@ class PreprocessingObserver extends PipelineObserver {
         Map<String,Object> sampleData = inputData.find { entry -> entry.get('samplename', '') == sample } ?: [:]
         String sampleType = sampleData.get('sample_type', 'DNA')
         String tag = sampleData.get('tag', '')
+        String genome = sampleData.get('genome', null)
+        String organism = sampleData.get('organism', null)
+        Integer binsize = sampleData.get('binsize', null) as Integer
+        if (
+            (organism?.toLowerCase() == 'mus musculus' || genome?.toLowerCase() == 'mm10') &&
+            ![100, 500].contains(binsize)
+        ) {
+            binsize = 100
+        }
         return [
             'strandedness': 'unknown',
             'tag': tag,
-            'organism': sampleData.get('organism', null),
-            'genome': sampleData.get('genome', null),
+            'organism': organism,
+            'genome': genome,
             'sample_type': sampleType,
             'normdup': tag.toLowerCase() == 'copgt-m',
             'nipt': tag.toLowerCase() == 'cfdnaseq',
-            'binsize': sampleData.get('binsize', null),
+            'binsize': binsize,
             'vivar_project': sampleData.get('vivar_project', null),
             'family': sampleData.get('family_number', null),
             'library': sampleData.get('library', null),

tests/preprocessing_mock/sampleinfo.yaml

@@ -17,7 +17,7 @@
   tag: WES
   aligner: snap
   sample_type: DNA
-  binsize: 100
+  binsize: 50
   vivar_project: test_project
   family_number: mouse_family
   library: WES_prep