Remove sex column and add proband to vivar ss

.groovylintrc.json

@@ -1,11 +1,11 @@
 {
-    "extends": "recommended",
-    "rules": {
-        "DuplicateListLiteral": {
-            "enabled": false
-        },
-        "DuplicateStringLiteral": {
-            "enabled": false
-        }
+  "extends": "recommended",
+  "rules": {
+    "DuplicateListLiteral": {
+      "enabled": false
+    },
+    "DuplicateStringLiteral": {
+      "enabled": false
     }
-}
+  }
+}

CHANGELOG.md

@@ -1,3 +1,7 @@
+## 0.2.2
+
+Removed the `sex` field and added the `proband` field to the vivar samplesheet
+
 ## 0.2.1
 
 Removed the filter step on `purpose` fields in the preprocssing samplesheets
@@ -8,4 +12,4 @@ This release adds full support for all diagnostic pipelines used until now
 
 ## 0.1.0
 
-The first release of the plugin
+The first release of the plugin

build.gradle

@@ -6,7 +6,7 @@ dependencies {
     implementation 'com.squareup.okhttp3:okhttp:5.3.2'
 }
 
-version = '0.2.1'
+version = '0.2.2'
 
 nextflowPlugin {
     nextflowVersion = '25.10.0'

pixi.toml

@@ -11,3 +11,4 @@ version = "0.1.0"
 nextflow = ">=26.4.0,<27"
 openjdk = "21.*"
 gradle = ">=9.3.1,<10"
+prek = ">=0.4.1,<0.5"

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

@@ -67,7 +67,7 @@ class PipelineObserver implements TraceObserverV2 {
     void onFlowCreate(Session session) {
         this.location = this.location ?: getSamplesheetOutdir(session)
         this.inputData = getInputSamplesheetList(session)
-        this.samples = inputData*.get(sampleKey).findAll { sample -> sample != null}.toSet() as Set<String>
+        this.samples = inputData*.get(sampleKey).findAll { sample -> sample != null }.toSet() as Set<String>
         this.session = session
         log.info("Samplesheets will be generated in '$location'")
     }
@@ -83,7 +83,7 @@ class PipelineObserver implements TraceObserverV2 {
     }
 
     /**
-     * Safely get the sample name for a given base path. 
+     * Safely get the sample name for a given base path.
      * This method will try to find the best matching sample name from the input samplesheet based on the base path.
      * If no match is found, it will use the sample name extracted from the base path.
      * If multiple matches are found, it will use the longest match and log a warning.

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

@@ -137,9 +137,9 @@ class PreprocessingObserver extends PipelineObserver {
                     'tag',
                     'binsize',
                     ['vivar_project', 'project'],
-                    'sex',
                     'normdup',
                     'nipt',
+                    ['family_number', 'proband'],
                     ['cram', 'reads'],
                     ['crai', 'reads_index']
                 ]),

src/test/groovy/nfcmgg/plugin/samplesheets/OutputEntryTest.groovy

@@ -67,4 +67,5 @@ class OutputEntryTest extends Specification {
         entry.values == [id: 'test', cram: 'test.cram']
         mainEntry.values == values
     }
+
 }