Merge pull request nf-core#643 from genomic-medicine-sweden/upd_fix

Upd fix
genomic-medicine-sweden · Nov 1, 2024 · 2eae461 · 2eae461
2 parents 31249da + 86f0373
commit 2eae461
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Showing 2 changed files with 17 additions and 11 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - bcftools annotate declaration in annotate CADD subworkflow [#624](https://github.com/nf-core/raredisease/pull/624)
 - Rhocallviz subworkflow will only be invocated once per sample [#621](https://github.com/nf-core/raredisease/pull/621)
 - Allow for VEP version 112 to be used and set it to default [#617](https://github.com/nf-core/raredisease/pull/617)
+- Updated createCaseChannel function to include a check for maternal and paternal ids being set to a numeric 0 [#643](https://github.com/nf-core/raredisease/pull/643)
 
 ### Parameters
 

diff --git a/lib/CustomFunctions.groovy b/lib/CustomFunctions.groovy
@@ -2,34 +2,39 @@ import nextflow.Nextflow
 
 class CustomFunctions {
 
+    // Helper function to check if a value is neither 0, "0", nor ""
+    private static boolean isNonZeroNonEmpty(value) {
+        return (value instanceof String && value != "" && value != "0") ||
+                (value instanceof Number && value != 0)
+    }
 
     // Function to get a list of metadata (e.g. case id) for the case [ meta ]
     public static LinkedHashMap createCaseChannel(List rows) {
         def case_info    = [:]
-        def probands     = []
-        def upd_children = []
+        def probands     = [] as Set
+        def upd_children = [] as Set
         def father       = ""
         def mother       = ""
 
-        for (item in rows) {
-            if (item.phenotype == 2) {
-                probands.add(item.sample)
+        rows.each { item ->
+            if (item?.phenotype == 2) {
+                probands << item.sample
             }
-            if ( (item.paternal!="0") && (item.paternal!="") && (item.maternal!="0") && (item.maternal!="") ) {
-                upd_children.add(item.sample)
+            if (isNonZeroNonEmpty(item?.paternal) && isNonZeroNonEmpty(item?.maternal)) {
+                upd_children << item.sample
             }
-            if ( (item.paternal!="0") && (item.paternal!="") ) {
+            if (isNonZeroNonEmpty(item?.paternal)) {
                 father = item.paternal
             }
-            if ( (item.maternal!="0") && (item.maternal!="") ) {
+            if (isNonZeroNonEmpty(item?.maternal)) {
                 mother = item.maternal
             }
         }
 
         case_info.father       = father
         case_info.mother       = mother
-        case_info.probands     = probands.unique()
-        case_info.upd_children = upd_children.unique()
+        case_info.probands     = probands.toList()
+        case_info.upd_children = upd_children.toList()
         case_info.id           = rows[0].case_id
 
         return case_info