diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test b/modules/nf-core/bcftools/concat/tests/main.nf.test
index 442f4b4e892e..9c4e4baf0a15 100644
--- a/modules/nf-core/bcftools/concat/tests/main.nf.test
+++ b/modules/nf-core/bcftools/concat/tests/main.nf.test
@@ -19,12 +19,12 @@ nextflow_process {
                 input[0] = [
                     [ id:'test3' ], // meta map
                     [
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true)
                     ],
                     [
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true)
                     ]
                 ]
                 """
@@ -50,12 +50,12 @@ nextflow_process {
                 input[0] = [
                     [ id:'test3' ], // meta map
                     [
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true)
                     ],
                     [
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true)
                     ]
                 ]
                 """
@@ -87,12 +87,12 @@ nextflow_process {
                 input[0] = [
                     [ id:'test3' ], // meta map
                     [
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true)
                     ],
                     [
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true)
                     ]
                 ]
                 """
@@ -124,12 +124,12 @@ nextflow_process {
                 input[0] = [
                     [ id:'test3' ], // meta map
                     [
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true)
                     ],
                     [
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true)
                     ]
                 ]
                 """
@@ -162,8 +162,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test3' ], // meta map
                     [
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true)
                     ],
                     []
                 ]
@@ -191,12 +191,12 @@ nextflow_process {
                 input[0] = [
                     [ id:'test3' ], // meta map
                     [
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true)
                     ],
                     [
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true)
                     ]
                 ]
                 """
@@ -223,12 +223,12 @@ nextflow_process {
                 input[0] = [
                     [ id:'test3' ], // meta map
                     [
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true)
                     ],
                     [
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true)
                     ]
                 ]
                 """
@@ -256,12 +256,12 @@ nextflow_process {
                 input[0] = [
                     [ id:'test3' ], // meta map
                     [
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true)
                     ],
                     [
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true)
                     ]
                 ]
                 """
@@ -289,12 +289,12 @@ nextflow_process {
                 input[0] = [
                     [ id:'test3' ], // meta map
                     [
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true)
                     ],
                     [
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi', checkIfExists: true)
                     ]
                 ]
                 """
diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap
index b82169c9a35c..8d1a6363b832 100644
--- a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap
@@ -6,7 +6,7 @@
                     {
                         "id": "test3"
                     },
-                    "test3_vcf.vcf.gz:md5,85db49dd1629d60e1165f491df6348f6"
+                    "test3_vcf.vcf.gz:md5,0b4986bbb6bdc9e0ee12ba09e70092e9"
                 ]
             ],
             [
@@ -25,10 +25,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-15T11:26:25.259752"
+        "timestamp": "2025-11-26T16:53:25.503018154"
     },
     "homo_sapiens - [[vcf1, vcf2], []]": {
         "content": [
@@ -38,7 +38,7 @@
                         {
                             "id": "test3"
                         },
-                        "test3.vcf:md5,bba76244f79c4e307bd0c4c09095885f"
+                        "test3.vcf:md5,0b4986bbb6bdc9e0ee12ba09e70092e9"
                     ]
                 ],
                 "1": [
@@ -61,7 +61,7 @@
                         {
                             "id": "test3"
                         },
-                        "test3.vcf:md5,bba76244f79c4e307bd0c4c09095885f"
+                        "test3.vcf:md5,0b4986bbb6bdc9e0ee12ba09e70092e9"
                     ]
                 ],
                 "versions": [
@@ -70,10 +70,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-15T10:03:17.250013"
+        "timestamp": "2025-11-26T16:56:01.364652383"
     },
     "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - stub": {
         "content": [
@@ -182,7 +182,7 @@
                     {
                         "id": "test3"
                     },
-                    "test3_vcf.vcf.gz:md5,85db49dd1629d60e1165f491df6348f6"
+                    "test3_vcf.vcf.gz:md5,0b4986bbb6bdc9e0ee12ba09e70092e9"
                 ]
             ],
             [
@@ -201,10 +201,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-15T11:26:31.742638"
+        "timestamp": "2025-11-26T16:53:33.38516503"
     },
     "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]]": {
         "content": [
@@ -214,7 +214,7 @@
                         {
                             "id": "test3"
                         },
-                        "test3.vcf:md5,bba76244f79c4e307bd0c4c09095885f"
+                        "test3.vcf:md5,0b4986bbb6bdc9e0ee12ba09e70092e9"
                     ]
                 ],
                 "1": [
@@ -237,7 +237,7 @@
                         {
                             "id": "test3"
                         },
-                        "test3.vcf:md5,bba76244f79c4e307bd0c4c09095885f"
+                        "test3.vcf:md5,0b4986bbb6bdc9e0ee12ba09e70092e9"
                     ]
                 ],
                 "versions": [
@@ -246,10 +246,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-15T10:29:33.203302"
+        "timestamp": "2025-11-26T16:55:30.850726912"
     },
     "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index": {
         "content": [
@@ -258,7 +258,7 @@
                     {
                         "id": "test3"
                     },
-                    "test3_vcf.vcf.gz:md5,85db49dd1629d60e1165f491df6348f6"
+                    "test3_vcf.vcf.gz:md5,0b4986bbb6bdc9e0ee12ba09e70092e9"
                 ]
             ],
             [
@@ -277,10 +277,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-15T11:26:17.482474"
+        "timestamp": "2025-11-26T16:53:18.091429133"
     },
     "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub": {
         "content": [
diff --git a/modules/nf-core/bcftools/concat/tests/nextflow.config b/modules/nf-core/bcftools/concat/tests/nextflow.config
index c6a5142a2691..1d5fee9eb562 100644
--- a/modules/nf-core/bcftools/concat/tests/nextflow.config
+++ b/modules/nf-core/bcftools/concat/tests/nextflow.config
@@ -1,3 +1,3 @@
 process {
-    ext.args = "--no-version"
+    ext.args = "--no-version -a"
 }
diff --git a/modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config
index afa03d74e25c..2455b1457abc 100644
--- a/modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config
+++ b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config
@@ -1,4 +1,4 @@
 process {
     ext.prefix = { "${meta.id}_vcf" }
-    ext.args = "--output-type z --write-index=csi --no-version --allow-overlaps"
+    ext.args = "--output-type z --write-index=csi --no-version --allow-overlaps -a"
 }
diff --git a/modules/nf-core/bcftools/csq/tests/main.nf.test b/modules/nf-core/bcftools/csq/tests/main.nf.test
index 52229c9e6740..d5cfa92a5479 100644
--- a/modules/nf-core/bcftools/csq/tests/main.nf.test
+++ b/modules/nf-core/bcftools/csq/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true)
                 ]
                 input[1] = [
                     [ : ], // meta map
diff --git a/modules/nf-core/bcftools/csq/tests/main.nf.test.snap b/modules/nf-core/bcftools/csq/tests/main.nf.test.snap
index 02d2ac4bac81..b73c1da3b80d 100644
--- a/modules/nf-core/bcftools/csq/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/csq/tests/main.nf.test.snap
@@ -1,15 +1,15 @@
 {
     "homo_sapiens": {
         "content": [
-            "876b0b2fe3971805ff1d546775efe5f",
+            "a048c8564339aa411b019310f5a84326",
             [
                 "versions.yml:md5,05afacd9179e80fd0d23218033c3aca9"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-15T12:03:18.948435"
+        "timestamp": "2025-11-26T16:58:26.677826042"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/pluginfilltags/tests/main.nf.test b/modules/nf-core/bcftools/pluginfilltags/tests/main.nf.test
index d36fcd1eb533..084c647e668d 100644
--- a/modules/nf-core/bcftools/pluginfilltags/tests/main.nf.test
+++ b/modules/nf-core/bcftools/pluginfilltags/tests/main.nf.test
@@ -24,8 +24,8 @@ nextflow_process {
                 """
                 input[0] = Channel.of([
                     [id:'NA12878', region:"chr22:16570065-16609999"],
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz", checkIfExists: true),
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi", checkIfExists: true),
                 ])
                 input[1] = []
                 input[2] = []
@@ -119,8 +119,8 @@ nextflow_process {
                 """
                 input[0] = Channel.of([
                     [id:'NA12878', region:"chr22:16570065-16609999"],
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz", checkIfExists: true),
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi", checkIfExists: true),
                 ])
                 input[1] = []
                 input[2] = []
diff --git a/modules/nf-core/bcftools/pluginfilltags/tests/main.nf.test.snap b/modules/nf-core/bcftools/pluginfilltags/tests/main.nf.test.snap
index bf49b1e2e566..49187d93e79a 100644
--- a/modules/nf-core/bcftools/pluginfilltags/tests/main.nf.test.snap
+++ b/modules/nf-core/bcftools/pluginfilltags/tests/main.nf.test.snap
@@ -1,17 +1,17 @@
 {
     "homo_sapiens - vcf": {
         "content": [
-            "da09a942b1e3c0226208880743d3dd07",
+            "d986322f4617ed952c7fcf6ed61e7983",
             "NA12878.vcf.gz.csi",
             [
                 "versions.yml:md5,3eb4d1bb1b803aeb4d38e826dc83b8b2"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-15T12:08:35.564113"
+        "timestamp": "2025-11-26T17:05:08.490151651"
     },
     "homo_sapiens - vcf - samples": {
         "content": [
diff --git a/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test b/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test
index 9ce0ca70683d..09312c46186f 100644
--- a/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test
+++ b/modules/nf-core/cnvnator/cnvnator/tests/main.nf.test
@@ -17,8 +17,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [id:'test',single_end:false],// meta map
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/NA12878.chr22.bam', checkIfExists:true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/NA12878.chr22.bam.bai', checkIfExists:true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/NA12878.chr21_22.bam', checkIfExists:true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/NA12878.chr21_22.bam.bai', checkIfExists:true)
                     ]
                 input[1] = [[:],[]]
                 input[2] = [[:],[]]
diff --git a/modules/nf-core/cnvnator/convert2vcf/main.nf b/modules/nf-core/cnvnator/convert2vcf/main.nf
index ffbdf0f13fe5..6319498dd9e8 100644
--- a/modules/nf-core/cnvnator/convert2vcf/main.nf
+++ b/modules/nf-core/cnvnator/convert2vcf/main.nf
@@ -36,6 +36,8 @@ process CNVNATOR_CONVERT2VCF {
     def args   = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
+    echo ${args}
+
     touch ${prefix}.vcf
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test b/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test
index bd0895f311e0..0652c8a7c127 100644
--- a/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test
+++ b/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test
@@ -101,7 +101,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out.versions,
+                    path(process.out.vcf[0][1]).vcf.variantsMD5
+                ).match() }
             )
         }
     }
diff --git a/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test.snap b/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test.snap
index d7764d38a5f4..65eee5ac64d6 100644
--- a/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test.snap
+++ b/modules/nf-core/cnvnator/convert2vcf/tests/main.nf.test.snap
@@ -1,32 +1,10 @@
 {
     "test_cnvnator_convert2vcf": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.vcf:md5,d237cf67c66dbc8509d324e623a7d569"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,647a1ccc9e74133a2256ce82377310fc"
-                ],
-                "vcf": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.vcf:md5,d237cf67c66dbc8509d324e623a7d569"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,647a1ccc9e74133a2256ce82377310fc"
-                ]
-            }
+            [
+                "versions.yml:md5,647a1ccc9e74133a2256ce82377310fc"
+            ],
+            "b47837c71432a5ffc854c7936b5966d0"
         ],
         "meta": {
             "nf-test": "0.9.2",
diff --git a/modules/nf-core/somalier/ancestry/tests/main.nf.test b/modules/nf-core/somalier/ancestry/tests/main.nf.test
index a705b680eef7..d9866051e461 100644
--- a/modules/nf-core/somalier/ancestry/tests/main.nf.test
+++ b/modules/nf-core/somalier/ancestry/tests/main.nf.test
@@ -57,8 +57,8 @@ nextflow_process {
                     """
                     input[0] = [
                         [id:"NA12878"],
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true),
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true)
                     ]
                     input[1] = [
                         [id: "hg38"],
diff --git a/subworkflows/nf-core/vcf_extract_relate_somalier/tests/main.nf.test b/subworkflows/nf-core/vcf_extract_relate_somalier/tests/main.nf.test
index 90d8b3f8a759..119fd7efffbc 100644
--- a/subworkflows/nf-core/vcf_extract_relate_somalier/tests/main.nf.test
+++ b/subworkflows/nf-core/vcf_extract_relate_somalier/tests/main.nf.test
@@ -27,7 +27,7 @@ nextflow_workflow {
                 """
                 input[0] = Channel.of([
                     [id:"test"],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true),
                     [],
                     1
                 ])
@@ -53,8 +53,8 @@ nextflow_workflow {
                 """
                 input[0] = Channel.of([
                     [id:"test"],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true),
                     1
                 ])
                 input[1] = Channel.of([ [id: "Hg38"], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)])
@@ -88,7 +88,7 @@ nextflow_workflow {
 
                 input[0] = Channel.of([
                     [id:"test"],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true),
                     [],
                     1
                 ])
@@ -125,7 +125,7 @@ nextflow_workflow {
                 input[0] = Channel.of(
                     [
                         [id:"test", common:"test"],
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true),
                         [],
                         2
                     ],
@@ -168,7 +168,7 @@ nextflow_workflow {
                 input[0] = Channel.of(
                     [
                         [id:"test"],
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true),
                         [],
                         1
                     ],
@@ -204,11 +204,11 @@ nextflow_workflow {
                     input[0] = Channel.of([
                         [id:"test"],
                         [
-                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true),
                             file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true)
                         ],
                         [
-                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz.csi', checkIfExists: true),
                             file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz.tbi', checkIfExists: true)
                         ]
                     ])
@@ -255,7 +255,7 @@ nextflow_workflow {
                 input[0] = Channel.of(
                     [
                         [id:"test", common:"test"],
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true),
                         [],
                         []
                     ],
@@ -299,7 +299,7 @@ nextflow_workflow {
                 input[0] = Channel.of(
                     [
                         [id:"test", common:"test"],
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr21_22.vcf.gz', checkIfExists: true),
                         [],
                         []
                     ],