add tissue samples to vivar samplesheet

.groovylintrc.json

@@ -4,6 +4,9 @@
     "DuplicateListLiteral": {
       "enabled": false
     },
+    "DuplicateNumberLiteral": {
+      "enabled": false
+    },
     "DuplicateStringLiteral": {
       "enabled": false
     }

CHANGELOG.md

@@ -1,3 +1,7 @@
+## 0.2.3
+
+Added `tissue` samples to the vivar samplesheet
+
 ## 0.2.2
 
 Removed the `sex` field and added the `proband` field to the vivar samplesheet

build.gradle

@@ -6,7 +6,7 @@ dependencies {
     implementation 'com.squareup.okhttp3:okhttp:5.3.2'
 }
 
-version = '0.2.2'
+version = '0.2.3'
 
 nextflowPlugin {
     nextflowVersion = '25.10.0'

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

@@ -94,10 +94,13 @@ class PipelineObserver implements TraceObserverV2 {
      * @param basePath the base path for which to get the sample name
      * @return the sample name for the given base path
      */
-    protected String safeGetSample(String basePath) {
+    protected String safeGetSample(String inputBasePath) {
+        String basePath
         // Make sure SNP tracking data will be added to the correct sample
         if (basePath.startsWith('snp_')) {
-            basePath = basePath.replaceFirst('snp_', '')
+            basePath = inputBasePath.replaceFirst('snp_', '')
+        } else {
+            basePath = inputBasePath
         }
         List<String> possibleSamples = samples
             .findAll { sample -> basePath.startsWith(sample) }.toList() as List<String>

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

@@ -127,8 +127,9 @@ class PreprocessingObserver extends PipelineObserver {
         creator.dump(
             entries
                 .findAll { entry ->
+                    String type = entry.value.get('sample_type')?.toLowerCase()
                     // Only create samplesheet for DNA samples
-                    entry.value.get('sample_type')?.toLowerCase() == 'dna'
+                    type == 'dna' || type == 'tissue'
                 }
                 .values()
                 *.subKeys([