Merge pull request #336 from Plant-Food-Research-Open/fix/318

[GH-318] --hic_map_combinations does not allow self-referential combinationsnations anymore

Author: GallVp

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v3.1.0dev - [10-Aug-2026]
+## v3.1.0dev - [11-Aug-2026]
 
 ### `Added`
 
@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Fixed`
 
 1. Fixed an issue where `--hic_map_combinations` parameter set to "" was not being interpreted as `null` and resulted in no HiC maps being generated [#321](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/321)
+2. Fixed an issue where `--hic_map_combinations` parameter was not being validated correctly and allowed self-referential combinations to be specified [#318](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/318)
 
 ### `Dependencies`
 

subworkflows/local/utils_nfcore_assemblyqc_pipeline/main.nf

@@ -333,7 +333,7 @@ def validateInputParameters() {
     }
 }
 
-def validateInputTags(assemblyTags, hicCombinations) {
+def validateInputTags(List<String> assemblyTags, String hicCombinations) {
 
     def tagCounts = [:]
     assemblyTags.each { tag ->
@@ -345,11 +345,29 @@ def validateInputTags(assemblyTags, hicCombinations) {
         error("Please check input assemblysheet -> Multiple assemblies have the same tags!: ${repeatedTags}")
     }
 
-    def hicTags = hicCombinations != null ? hicCombinations.tokenize(' ').collect { it.tokenize(':') }.flatten() : []
+    def hicTags = hicCombinations != null ? hicCombinations.tokenize(' ').collect { combination -> combination.tokenize(':') }.flatten() : []
 
-    hicTags.each {
-        if ( it !in assemblyTags ) {
-            error("Please check input hic_map_combinations -> $it was not found in the assemblysheet!")
+    hicTags.each { hicTag ->
+        if ( hicTag !in assemblyTags ) {
+            error("Please check input hic_map_combinations -> $hicTag was not found in the assemblysheet!")
+        }
+    }
+
+    if ( hicCombinations == null || hicCombinations == "" ) {
+        return true
+    }
+
+    // Make sure that all hic combinations are unique
+    def hicCombinationsUnique = hicCombinations.tokenize(' ').unique()
+    if ( hicCombinationsUnique.size() != hicCombinations.tokenize(' ').size() ) {
+        error("Please check input hic_map_combinations -> Some combinations are repeated!")
+    }
+
+    // Make sure that no hic combination is self-referential
+    hicCombinationsUnique.each { hicCombination ->
+        def hicCombinationTags = hicCombination.tokenize(':')
+        if ( hicCombinationTags.size() != hicCombinationTags.unique().size() ) {
+            error("Please check input hic_map_combinations -> ${hicCombination} combination is self-referential!")
         }
     }
 

tests/hic/hictags.nf.test

@@ -0,0 +1,70 @@
+nextflow_function {
+
+    name "checkHiCParam"
+    script "../../subworkflows/local/utils_nfcore_assemblyqc_pipeline/main.nf"
+    function "validateInputTags"
+
+    test("HY -- HY -- pass") {
+        when {
+            function {
+                """
+                input[0] = [ "HY" ]
+                input[1] = "HY"
+                """
+            }
+        }
+
+        then {
+            assert function.success
+            assert function.result
+        }
+    }
+
+    test("HY1 HY2 -- HY1 HY1:HY2 -- pass") {
+        when {
+            function {
+                """
+                input[0] = [ "HY1", "HY2" ]
+                input[1] = "HY1 HY1:HY2"
+                """
+            }
+        }
+
+        then {
+            assert function.success
+            assert function.result
+        }
+    }
+
+    test("HY -- HY HY -- fail") {
+        when {
+            function {
+                """
+                input[0] = [ "HY" ]
+                input[1] = "HY HY"
+                """
+            }
+        }
+
+        then {
+            assert ! function.success
+            assert 'Please check input hic_map_combinations -> Some combinations are repeated!' in function.stdout
+        }
+    }
+
+    test("HY -- HY:HY -- fail") {
+        when {
+            function {
+                """
+                input[0] = [ "HY" ]
+                input[1] = "HY:HY"
+                """
+            }
+        }
+
+        then {
+            assert ! function.success
+            assert 'Please check input hic_map_combinations -> HY:HY combination is self-referential!' in function.stdout
+        }
+    }
+}