diff --git a/modules/nf-core/glimpse/chunk/main.nf b/modules/nf-core/glimpse/chunk/main.nf
index 9ea9ef043c47..c8d92f472997 100644
--- a/modules/nf-core/glimpse/chunk/main.nf
+++ b/modules/nf-core/glimpse/chunk/main.nf
@@ -37,6 +37,7 @@ process GLIMPSE_CHUNK {
 
     stub:
     def prefix  = task.ext.prefix ?: "${meta.id}"
+
     """
     touch ${prefix}.txt
 
diff --git a/modules/nf-core/glimpse/chunk/tests/main.nf.test b/modules/nf-core/glimpse/chunk/tests/main.nf.test
index 4c278af1e60b..746feae002da 100644
--- a/modules/nf-core/glimpse/chunk/tests/main.nf.test
+++ b/modules/nf-core/glimpse/chunk/tests/main.nf.test
@@ -3,22 +3,25 @@ nextflow_process {
     name "Test Process GLIMPSE_CHUNK"
     script "../main.nf"
     process "GLIMPSE_CHUNK"
+    config "./nextflow.config"
+
     tag "glimpse"
     tag "glimpse/chunk"
     tag "modules_nfcore"
     tag "modules"
 
-    test("Should run without failures") {
-        config "modules/nf-core/glimpse/chunk/tests/nextflow.config"
-
+    test("homo_sapiens - vcf chr 22") {
         when {
+            params{
+                glimpse_args = "--window-size 2000000 --buffer-size 200000"
+            }
             process {
                 """
                 input[0] = [
                     [ id:'input' ], // meta map
-                    file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true),
-                    "chr21"
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz", checkIfExists:true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz.csi", checkIfExists:true),
+                    "chr22"
                 ]
                 """
             }
diff --git a/modules/nf-core/glimpse/chunk/tests/main.nf.test.snap b/modules/nf-core/glimpse/chunk/tests/main.nf.test.snap
index 0490a8e4de7f..bd580988fbec 100644
--- a/modules/nf-core/glimpse/chunk/tests/main.nf.test.snap
+++ b/modules/nf-core/glimpse/chunk/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Should run without failures": {
+    "homo_sapiens - vcf chr 22": {
         "content": [
             {
                 "0": [
@@ -7,7 +7,7 @@
                         {
                             "id": "input"
                         },
-                        "input.txt:md5,9e5562b3f94857b8189b59849ce65cfb"
+                        "input.txt:md5,38bc015bc7bb9f4fc0fdb08a698cfc78"
                     ]
                 ],
                 "1": [
@@ -18,7 +18,7 @@
                         {
                             "id": "input"
                         },
-                        "input.txt:md5,9e5562b3f94857b8189b59849ce65cfb"
+                        "input.txt:md5,38bc015bc7bb9f4fc0fdb08a698cfc78"
                     ]
                 ],
                 "versions": [
@@ -26,6 +26,10 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-16T15:55:52.457257547"
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-26T19:06:32.115560314"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/glimpse/chunk/tests/nextflow.config b/modules/nf-core/glimpse/chunk/tests/nextflow.config
index 8302ea19436e..8f4c838e95c4 100644
--- a/modules/nf-core/glimpse/chunk/tests/nextflow.config
+++ b/modules/nf-core/glimpse/chunk/tests/nextflow.config
@@ -1,9 +1,6 @@
 process {
     withName: GLIMPSE_CHUNK {
-        ext.args = [
-            "--window-size 2000000",
-            "--buffer-size 200000"
-        ].join(' ')
+        ext.args = { "${params.glimpse_args}" }
         ext.prefix = { "${meta.id}" }
     }
 }
diff --git a/modules/nf-core/glimpse/concordance/main.nf b/modules/nf-core/glimpse/concordance/main.nf
index 82e784745235..4a70a6afffed 100644
--- a/modules/nf-core/glimpse/concordance/main.nf
+++ b/modules/nf-core/glimpse/concordance/main.nf
@@ -20,7 +20,6 @@ process GLIMPSE_CONCORDANCE {
     tuple val(meta), path("*.rsquare.grp.txt.gz"), emit: rsquare_grp
     tuple val(meta), path("*.rsquare.spl.txt.gz"), emit: rsquare_spl
     path "versions.yml"                          , emit: versions
-
     when:
     task.ext.when == null || task.ext.when
 
@@ -42,13 +41,14 @@ process GLIMPSE_CONCORDANCE {
         $bins_cmd
 
     cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            glimpse: "\$(GLIMPSE_concordance --help | sed -nr '/Version/p' | grep -o -E '([0-9]+.){1,2}[0-9]')"
+    "${task.process}":
+        glimpse: "\$(GLIMPSE_concordance --help | sed -nr '/Version/p' | grep -o -E '([0-9]+.){1,2}[0-9]')"
     END_VERSIONS
     """
 
     stub:
     def prefix  = task.ext.prefix ?: "${meta.id}"
+
     """
     echo "" | gzip > ${prefix}.error.cal.txt.gz
     echo "" | gzip > ${prefix}.error.grp.txt.gz
diff --git a/modules/nf-core/glimpse/concordance/tests/main.nf.test b/modules/nf-core/glimpse/concordance/tests/main.nf.test
index ef6d36b8aff8..1a3bb2f80118 100644
--- a/modules/nf-core/glimpse/concordance/tests/main.nf.test
+++ b/modules/nf-core/glimpse/concordance/tests/main.nf.test
@@ -4,6 +4,8 @@ nextflow_process {
     script "../main.nf"
     process "GLIMPSE_CONCORDANCE"
 
+    config "./nextflow.config"
+
     tag "modules"
     tag "modules_nfcore"
     tag "glimpse"
@@ -12,64 +14,21 @@ nextflow_process {
     tag "bcftools/index"
 
     test("test_glimpse_concordance") {
-        setup {
-            run("GLIMPSE_PHASE") {
-                script "../../phase/main.nf"
-                process {
-                """
-                ch_sample     = Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt')
-                region        = Channel.fromList([
-                    ["chr21:16600000-16750000","chr21:16650000-16700000"]
-                ])
-                input_vcf     = Channel.of([
-                    [ id:'input'], // meta map
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true)
-                ])
-                ref_panel     = Channel.of([
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
-                ])
-                ch_map        = Channel.of([
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true),
-                ])
-
-                input[0]      = input_vcf
-                    | combine(ch_sample)
-                    | combine(region)
-                    | combine(ref_panel)
-                    | combine(ch_map)
-                """
-                }
-            }
-            run("BCFTOOLS_INDEX") {
-                script "../../../bcftools/index/main.nf"
-                process {
-                """
-                input[0] = GLIMPSE_PHASE.out.phased_variants
-                """
-                }
-            }
-        }
         when {
             process {
                 """
-                allele_freq = Channel.fromList([
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz",checkIfExists:true),
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz.csi",checkIfExists:true)
-                ]).collect()
-                truth = Channel.fromList([
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.bcf",checkIfExists:true),
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.bcf.csi",checkIfExists:true)
-                ]).collect()
-                estimate = GLIMPSE_PHASE.out.phased_variants
-                    | join (BCFTOOLS_INDEX.out.csi)
-                input[0] = estimate
-                    | combine (allele_freq)
-                    | combine (truth)
-                    | combine (["chr21"])
-                input[1] = []
-                input[2] = []
+                input[0] = channel.of([
+                    [ id: "NA12878" ],
+                    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),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr21.sites.vcf.gz",checkIfExists:true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr21.sites.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),
+                    "chr21"
+                ])
+                input[1] = 0.7
+                input[2] = 3
                 input[3] = []
                 """
             }
@@ -78,12 +37,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out.errors_cal,
-                    process.out.errors_spl,
-                    process.out.rsquare_spl,
-                    process.out.versions
-                ).match() }
+                { assert snapshot(process.out).match() }
             )
         }
 
diff --git a/modules/nf-core/glimpse/concordance/tests/main.nf.test.snap b/modules/nf-core/glimpse/concordance/tests/main.nf.test.snap
index 1fb0ee9c51de..81d2744ff198 100644
--- a/modules/nf-core/glimpse/concordance/tests/main.nf.test.snap
+++ b/modules/nf-core/glimpse/concordance/tests/main.nf.test.snap
@@ -1,38 +1,99 @@
 {
     "test_glimpse_concordance": {
         "content": [
-            [
-                [
-                    {
-                        "id": "input"
-                    },
-                    "input.error.cal.txt.gz:md5,15c6a120d9fd3ac8c0ff6a6aedc76571"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "NA12878"
+                        },
+                        "NA12878.error.cal.txt.gz:md5,b4af39e7acfebd69f2fe5fa496551a32"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "NA12878"
+                        },
+                        "NA12878.error.grp.txt.gz:md5,069e311f252ff6b6e748a68ce0bcb499"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "NA12878"
+                        },
+                        "NA12878.error.spl.txt.gz:md5,284843acf1662f2aeafc6fe5c47e629f"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "NA12878"
+                        },
+                        "NA12878.rsquare.grp.txt.gz:md5,06c70a1e2047710d6752b9d98e45cea0"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "NA12878"
+                        },
+                        "NA12878.rsquare.spl.txt.gz:md5,30a00f0b1de47fd63414d819b4304ded"
+                    ]
+                ],
+                "5": [
+                    "versions.yml:md5,b6c06f9736c60f9f548c3c082b522025"
+                ],
+                "errors_cal": [
+                    [
+                        {
+                            "id": "NA12878"
+                        },
+                        "NA12878.error.cal.txt.gz:md5,b4af39e7acfebd69f2fe5fa496551a32"
+                    ]
+                ],
+                "errors_grp": [
+                    [
+                        {
+                            "id": "NA12878"
+                        },
+                        "NA12878.error.grp.txt.gz:md5,069e311f252ff6b6e748a68ce0bcb499"
+                    ]
+                ],
+                "errors_spl": [
+                    [
+                        {
+                            "id": "NA12878"
+                        },
+                        "NA12878.error.spl.txt.gz:md5,284843acf1662f2aeafc6fe5c47e629f"
+                    ]
+                ],
+                "rsquare_grp": [
+                    [
+                        {
+                            "id": "NA12878"
+                        },
+                        "NA12878.rsquare.grp.txt.gz:md5,06c70a1e2047710d6752b9d98e45cea0"
+                    ]
+                ],
+                "rsquare_spl": [
+                    [
+                        {
+                            "id": "NA12878"
+                        },
+                        "NA12878.rsquare.spl.txt.gz:md5,30a00f0b1de47fd63414d819b4304ded"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b6c06f9736c60f9f548c3c082b522025"
                 ]
-            ],
-            [
-                [
-                    {
-                        "id": "input"
-                    },
-                    "input.error.spl.txt.gz:md5,35cb463e8db41e2180f21941ab0324e0"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "input"
-                    },
-                    "input.rsquare.spl.txt.gz:md5,55659f466775d828ee1ba723464bb460"
-                ]
-            ],
-            [
-                "versions.yml:md5,f79c864118d03a4afa93082c46c0d608"
-            ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-15T12:50:35.203335"
+        "timestamp": "2025-11-27T11:08:34.841155791"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/glimpse/concordance/tests/nextflow.config b/modules/nf-core/glimpse/concordance/tests/nextflow.config
new file mode 100644
index 000000000000..4ab697f9d031
--- /dev/null
+++ b/modules/nf-core/glimpse/concordance/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: GLIMPSE_CONCORDANCE {
+        ext.args = "--gt-validation --gt-target"
+    }
+}
diff --git a/modules/nf-core/glimpse/ligate/main.nf b/modules/nf-core/glimpse/ligate/main.nf
index fbef5738e8f3..a62b24d62c85 100644
--- a/modules/nf-core/glimpse/ligate/main.nf
+++ b/modules/nf-core/glimpse/ligate/main.nf
@@ -22,7 +22,7 @@ process GLIMPSE_LIGATE {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def suffix = task.ext.suffix ?: "vcf.gz"
     """
-    printf "%s\\n" $input_list | tr -d '[],' > all_files.txt
+    printf "%s\\n" $input_list | tr -d '[],' | sort -V > all_files.txt
 
     GLIMPSE_ligate \\
         $args \\
@@ -31,8 +31,8 @@ process GLIMPSE_LIGATE {
         --output ${prefix}.${suffix}
 
     cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            glimpse: "\$(GLIMPSE_ligate --help | sed -nr '/Version/p' | grep -o -E '([0-9]+.){1,2}[0-9]')"
+    "${task.process}":
+        glimpse: "\$(GLIMPSE_ligate --help | sed -nr '/Version/p' | grep -o -E '([0-9]+.){1,2}[0-9]')"
     END_VERSIONS
     """
 
diff --git a/modules/nf-core/glimpse/ligate/tests/main.nf.test b/modules/nf-core/glimpse/ligate/tests/main.nf.test
index 7289fc91acce..685deb3466eb 100644
--- a/modules/nf-core/glimpse/ligate/tests/main.nf.test
+++ b/modules/nf-core/glimpse/ligate/tests/main.nf.test
@@ -17,27 +17,30 @@ nextflow_process {
                 script "../../phase/main.nf"
                 process {
                 """
-                ch_sample     = Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt')
-                region        = Channel.fromList([
-                    ["chr21:16600000-16750000","chr21:16650000-16700000"],
-                    ["chr21:16650000-16800000","chr21:16700000-16750000"]
-                ])
-                input_vcf     = Channel.of([
+                ch_sample = channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt')
+                region    = channel.of(
+                    ["chr21:16570065-16597215","chr21:16570065-16592216"],
+                    ["chr21:16587172-16609999","chr21:16592229-16609999"]
+                )
+                input_vcf = channel.of([
                     [ id:'input'], // meta map
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.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)
                 ])
-                ref_panel     = Channel.of([
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
+                ref_panel = channel.of([
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr21.vcf.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr21.vcf.gz.csi", checkIfExists: true)
                 ])
-                ch_map        = Channel.of([
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true),
+                ch_map   = channel.of([
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr21.glimpse.map", checkIfExists: true)
                 ])
 
                 input[0]      = input_vcf
                     | combine(ch_sample)
                     | combine(region)
+                    | map { meta, vcf, index, sample, regionI, regionO ->
+                        [[id: meta.id, region : regionI], vcf, index, sample, regionI, regionO]
+                    }
                     | combine(ref_panel)
                     | combine(ch_map)
                 """
@@ -57,20 +60,28 @@ nextflow_process {
             process {
                 """
                 input[0] = GLIMPSE_PHASE.out.phased_variants
-                    | groupTuple()
-                    | join (BCFTOOLS_INDEX.out.csi.groupTuple())
+                    .join(BCFTOOLS_INDEX.out.csi)
+                    .map{ meta, vcf, index -> [meta.subMap("id"), vcf, index]}
+                    .groupTuple()
                 """
             }
         }
 
         then {
-            def lines = path(process.out.merged_variants.get(0).get(1)).linesGzip.last()
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions).match("versions") },
-                { assert snapshot(lines).match("ligate") }
+                { assert snapshot(
+                    process.out.merged_variants.collect {
+                        meta, vcf -> [
+                            meta,
+                            file(vcf).name,
+                            path(vcf).vcf.summary,
+                            path(vcf).vcf.variantsMD5
+                        ]
+                    },
+                    ["versions": process.out.versions]
+                ).match() }
             )
         }
-
     }
 }
diff --git a/modules/nf-core/glimpse/ligate/tests/main.nf.test.snap b/modules/nf-core/glimpse/ligate/tests/main.nf.test.snap
index 8eec13282905..7a1be2fc484d 100644
--- a/modules/nf-core/glimpse/ligate/tests/main.nf.test.snap
+++ b/modules/nf-core/glimpse/ligate/tests/main.nf.test.snap
@@ -1,16 +1,26 @@
 {
-    "versions": {
+    "test_glimpse_ligate": {
         "content": [
             [
-                "versions.yml:md5,0cc9dfe9c9c1087666c418aa3379cf85"
-            ]
+                [
+                    {
+                        "id": "input"
+                    },
+                    "input.vcf.gz",
+                    "VcfFile [chromosomes=[chr21], sampleCount=1, variantCount=836, phased=false, phasedAutodetect=false]",
+                    "bcb1deefc22f80c32d5ca5cedb56cd75"
+                ]
+            ],
+            {
+                "versions": [
+                    "versions.yml:md5,bd8cbcd55d6d05c480747657852fad35"
+                ]
+            }
         ],
-        "timestamp": "2023-10-17T11:56:25.087453677"
-    },
-    "ligate": {
-        "content": [
-            "chr21\t16799989\t21:16799989:T:C\tT\tC\t.\t.\tRAF=0.000468897;AF=0;INFO=1\tGT:DS:GP:HS\t0/0:0:1,0,0:0"
-        ],
-        "timestamp": "2023-10-17T11:56:25.116120487"
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-26T20:11:05.020643957"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/glimpse/phase/main.nf b/modules/nf-core/glimpse/phase/main.nf
index 53487557ada8..e5ba79718880 100644
--- a/modules/nf-core/glimpse/phase/main.nf
+++ b/modules/nf-core/glimpse/phase/main.nf
@@ -46,6 +46,7 @@ process GLIMPSE_PHASE {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}_${input_region.replace(":","_")}"
     def suffix = task.ext.suffix ?: "vcf.gz"
+
     """
     touch ${prefix}.${suffix}
 
diff --git a/modules/nf-core/glimpse/phase/tests/main.nf.test b/modules/nf-core/glimpse/phase/tests/main.nf.test
index 5c92cb1fc64f..583005c9184b 100644
--- a/modules/nf-core/glimpse/phase/tests/main.nf.test
+++ b/modules/nf-core/glimpse/phase/tests/main.nf.test
@@ -13,31 +13,29 @@ nextflow_process {
         when {
             process {
                 """
-                ch_sample = Channel.of([sample:'present'])
-                    | combine(Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt'))
-                    | concat(Channel.of([[sample: 'absent'], []]))
-                region        = Channel.fromList([
-                    ["chr21:16600000-16750000","chr21:16650000-16700000"],
-                    ["chr21:16650000-16800000","chr21:16700000-16750000"]
+                ch_sample = Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt')
+                region    = channel.fromList([
+                    ["chr21:16570065-16597215","chr21:16570065-16592216"],
+                    ["chr21:16587172-16609999","chr21:16592229-16609999"]
                 ])
-                input_vcf     = Channel.of([
+                input_vcf = channel.of([
                     [ id:'input'], // meta map
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.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)
                 ])
-                ref_panel     = Channel.of([
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
+                ref_panel = channel.of([
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr21.vcf.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr21.vcf.gz.csi", checkIfExists: true)
                 ])
-                ch_map        = Channel.of([
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true),
+                ch_map   = channel.of([
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr21.glimpse.map", checkIfExists: true)
                 ])
 
                 input[0]      = input_vcf
                     | combine(ch_sample)
                     | combine(region)
-                    | map { meta, vcf, index, metaS, sample, regionI, regionO ->
-                        [[id: meta.id + "_" + metaS.sample, region : regionI], vcf, index, sample, regionI, regionO]
+                    | map { meta, vcf, index, sample, regionI, regionO ->
+                        [[id: meta.id, region : regionI], vcf, index, sample, regionI, regionO]
                     }
                     | combine(ref_panel)
                     | combine(ch_map)
@@ -46,20 +44,17 @@ nextflow_process {
         }
 
         then {
-            String targetFileName = "input_present_chr21_16650000-16800000.vcf.gz"
-            File selectedFile = process.out.phased_variants.stream()
-                .filter(vector -> vector.size() > 1)
-                .map(vector -> new File(vector.get(1).toString()))
-                .filter(file -> file.getName().equals(targetFileName))
-                .findFirst()
-                .orElse(null)
-            String selectedFilename = selectedFile != null ? selectedFile.getPath() : null
-            def lines = path(selectedFilename).linesGzip.last()
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions).match("versions") },
-                { assert process.out.phased_variants.size() == 4},
-                { assert snapshot(lines).match("imputed") }
+                { assert snapshot(
+                    process.out.phased_variants.collect{ meta, vcf -> [
+                        meta,
+                        file(vcf).name,
+                        path(vcf).vcf.summary,
+                        path(vcf).vcf.variantsMD5
+                    ] },
+                    process.out.versions
+                ).match() }
             )
         }
 
diff --git a/modules/nf-core/glimpse/phase/tests/main.nf.test.snap b/modules/nf-core/glimpse/phase/tests/main.nf.test.snap
index d61cf86ece4d..1ba021845c94 100644
--- a/modules/nf-core/glimpse/phase/tests/main.nf.test.snap
+++ b/modules/nf-core/glimpse/phase/tests/main.nf.test.snap
@@ -1,19 +1,35 @@
 {
-    "versions": {
+    "test_glimpse_phase": {
         "content": [
             [
-                "versions.yml:md5,b24f49b2f5989a1f7da32c195334e96b",
-                "versions.yml:md5,b24f49b2f5989a1f7da32c195334e96b",
+                [
+                    {
+                        "id": "input",
+                        "region": "chr21:16570065-16597215"
+                    },
+                    "input_chr21_16570065-16597215.vcf.gz",
+                    "VcfFile [chromosomes=[chr21], sampleCount=1, variantCount=563, phased=false, phasedAutodetect=false]",
+                    "307c42e67924110b165f1fff0e5c14a"
+                ],
+                [
+                    {
+                        "id": "input",
+                        "region": "chr21:16587172-16609999"
+                    },
+                    "input_chr21_16587172-16609999.vcf.gz",
+                    "VcfFile [chromosomes=[chr21], sampleCount=1, variantCount=459, phased=false, phasedAutodetect=false]",
+                    "b138aad7ca677f696b7635802d3be82e"
+                ]
+            ],
+            [
                 "versions.yml:md5,b24f49b2f5989a1f7da32c195334e96b",
                 "versions.yml:md5,b24f49b2f5989a1f7da32c195334e96b"
             ]
         ],
-        "timestamp": "2023-10-17T15:27:55.512415434"
-    },
-    "imputed": {
-        "content": [
-            "chr21\t16799989\t21:16799989:T:C\tT\tC\t.\t.\tRAF=0.000468897;AF=0;INFO=1;BUF=1\tGT:DS:GP:HS\t0/0:0:1,0,0:0"
-        ],
-        "timestamp": "2023-10-17T15:27:55.99820664"
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-26T20:07:25.309393538"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/glimpse/sample/main.nf b/modules/nf-core/glimpse/sample/main.nf
index c05296812abc..0fcfb6b4f2f9 100644
--- a/modules/nf-core/glimpse/sample/main.nf
+++ b/modules/nf-core/glimpse/sample/main.nf
@@ -8,7 +8,7 @@ process GLIMPSE_SAMPLE {
         'biocontainers/glimpse-bio:1.1.1--hce55b13_1' }"
 
     input:
-    tuple val(meta), path(input)
+    tuple val(meta), path(input), path(index)
 
     output:
     tuple val(meta), path("*.{vcf,bcf,vcf.gz,bcf.gz}"), emit: haplo_sampled
@@ -38,6 +38,7 @@ process GLIMPSE_SAMPLE {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     def suffix = task.ext.suffix ?: "vcf.gz"
+
     """
     touch ${prefix}.${suffix}
 
diff --git a/modules/nf-core/glimpse/sample/meta.yml b/modules/nf-core/glimpse/sample/meta.yml
index ebb1b71cd559..2dd508a56348 100644
--- a/modules/nf-core/glimpse/sample/meta.yml
+++ b/modules/nf-core/glimpse/sample/meta.yml
@@ -22,9 +22,14 @@ input:
           e.g. [ id:'test', single_end:false ]
     - input:
         type: file
-        description: VCF/BCF file generated using GLIMPSE ligate
+        description: Imputed VCF/BCF file
         pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
         ontologies: []
+    - index:
+        type: file
+        description: Index file of the input VCF/BCF file.
+        pattern: "*.{vcf.gz.csi,bcf.gz.csi}"
+        ontologies: []
 output:
   haplo_sampled:
     - - meta:
diff --git a/modules/nf-core/glimpse/sample/tests/main.nf.test b/modules/nf-core/glimpse/sample/tests/main.nf.test
index 494c35296fea..cac8ac5159ce 100644
--- a/modules/nf-core/glimpse/sample/tests/main.nf.test
+++ b/modules/nf-core/glimpse/sample/tests/main.nf.test
@@ -4,59 +4,78 @@ nextflow_process {
     script "../main.nf"
     process "GLIMPSE_SAMPLE"
 
+    config "./nextflow.config"
+
     tag "modules"
     tag "modules_nfcore"
     tag "glimpse"
     tag "glimpse/sample"
     tag "glimpse/phase"
+    tag "bcftools"
+    tag "bcftools/index"
 
     test("test_glimpse_sample") {
-        config "./nextflow.config"
         setup {
             run("GLIMPSE_PHASE") {
                 script "../../phase/main.nf"
                 process {
                 """
-                ch_sample     = Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt')
-                region        = Channel.fromList([
-                    ["chr21:16600000-16750000","chr21:16650000-16700000"]
-                ])
-                input_vcf     = Channel.of([
+                ch_sample = Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt')
+                region    = channel.of(["chr21:16570000-16610000","chr21:16570000-16610000"])
+                input_vcf = channel.of([
                     [ id:'input'], // meta map
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.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)
                 ])
-                ref_panel     = Channel.of([
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
+                ref_panel = channel.of([
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr21.vcf.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr21.vcf.gz.csi", checkIfExists: true)
                 ])
-                ch_map        = Channel.of([
-                    file(params.modules_testdata_base_path + "delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true),
+                ch_map   = channel.of([
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr21.glimpse.map", checkIfExists: true)
                 ])
 
                 input[0]      = input_vcf
                     | combine(ch_sample)
                     | combine(region)
+                    | map { meta, vcf, index, sample, regionI, regionO ->
+                        [[id: meta.id, region : regionI], vcf, index, sample, regionI, regionO]
+                    }
                     | combine(ref_panel)
                     | combine(ch_map)
                 """
                 }
             }
+            run("BCFTOOLS_INDEX") {
+                script "../../../bcftools/index/main.nf"
+                process {
+                """
+                input[0] = GLIMPSE_PHASE.out.phased_variants
+                """
+                }
+            }
         }
         when {
             process {
                 """
                 input[0] = GLIMPSE_PHASE.out.phased_variants
+                    .join(BCFTOOLS_INDEX.out.csi)
                 """
             }
         }
 
         then {
-            def lines = path(process.out.haplo_sampled.get(0).get(1)).linesGzip.last()
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions).match("versions") },
-                { assert snapshot(lines).match("sampled") }
+                { assert snapshot(
+                    process.out.haplo_sampled.collect{ meta, vcf -> [
+                        meta,
+                        file(vcf).name,
+                        path(vcf).vcf.summary,
+                        path(vcf).vcf.variantsMD5
+                    ] },
+                    process.out.versions
+                ).match() }
             )
         }
 
diff --git a/modules/nf-core/glimpse/sample/tests/main.nf.test.snap b/modules/nf-core/glimpse/sample/tests/main.nf.test.snap
index 5892f99be2c7..b36088af4fcc 100644
--- a/modules/nf-core/glimpse/sample/tests/main.nf.test.snap
+++ b/modules/nf-core/glimpse/sample/tests/main.nf.test.snap
@@ -1,16 +1,25 @@
 {
-    "versions": {
+    "test_glimpse_sample": {
         "content": [
+            [
+                [
+                    {
+                        "id": "input",
+                        "region": "chr21:16570000-16610000"
+                    },
+                    "input.vcf.gz",
+                    "VcfFile [chromosomes=[chr21], sampleCount=1, variantCount=836, phased=true, phasedAutodetect=true]",
+                    "98729a14199e84f9da0a80591d76b280"
+                ]
+            ],
             [
                 "versions.yml:md5,6ae83ef08ccde17c6dc248b9133c0fb8"
             ]
         ],
-        "timestamp": "2023-10-17T16:00:45.692964159"
-    },
-    "sampled": {
-        "content": [
-            "chr21\t16749965\t21:16749965:T:A\tT\tA\t.\t.\tRAF=0.000312598;AF=0.001;INFO=0.001;BUF=1\tGT\t0|0"
-        ],
-        "timestamp": "2023-10-17T16:00:45.81432328"
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-11-26T20:15:47.765405625"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/glimpse2/chunk/tests/main.nf.test b/modules/nf-core/glimpse2/chunk/tests/main.nf.test
index 0b6545e1fb5c..14ca3190222f 100644
--- a/modules/nf-core/glimpse2/chunk/tests/main.nf.test
+++ b/modules/nf-core/glimpse2/chunk/tests/main.nf.test
@@ -43,7 +43,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz", checkIfExists:true),
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz.csi", checkIfExists:true),
                     "chr22:16570000-16610000",
-                    file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/phaseimpute/hum_data/reference_genome/GRCh38_chr22.glimpse.map", checkIfExists: true)
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr22.glimpse.map", checkIfExists: true)
                 ]
                 input[1]= "recursive"
                 """
diff --git a/modules/nf-core/glimpse2/chunk/tests/main.nf.test.snap b/modules/nf-core/glimpse2/chunk/tests/main.nf.test.snap
index 2a380092cb8a..d36e35b73040 100644
--- a/modules/nf-core/glimpse2/chunk/tests/main.nf.test.snap
+++ b/modules/nf-core/glimpse2/chunk/tests/main.nf.test.snap
@@ -77,7 +77,7 @@
                     {
                         "id": "test"
                     },
-                    "test.txt:md5,bf269cf00892ea2a9650817703805608"
+                    "test.txt:md5,3bfef0fe24564dd3f759ee390345970a"
                 ]
             ],
             [
@@ -85,9 +85,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-20T10:09:14.973419042"
+        "timestamp": "2025-11-26T20:44:36.241361838"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/glimpse2/concordance/main.nf b/modules/nf-core/glimpse2/concordance/main.nf
index a542993d69c1..945c3dd6a0e4 100644
--- a/modules/nf-core/glimpse2/concordance/main.nf
+++ b/modules/nf-core/glimpse2/concordance/main.nf
@@ -77,7 +77,7 @@ process GLIMPSE2_CONCORDANCE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        glimpse: "\$(GLIMPSE_concordance --help | sed -nr '/Version/p' | grep -o -E '([0-9]+.){1,2}[0-9]')"
+        glimpse2: "\$(GLIMPSE2_concordance --help | sed -nr '/Version/p' | grep -o -E '([0-9]+.){1,2}[0-9]' | head -1)"
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/glimpse2/concordance/tests/main.nf.test b/modules/nf-core/glimpse2/concordance/tests/main.nf.test
index d1c68bc208d0..f37c3da863f7 100644
--- a/modules/nf-core/glimpse2/concordance/tests/main.nf.test
+++ b/modules/nf-core/glimpse2/concordance/tests/main.nf.test
@@ -3,6 +3,9 @@ nextflow_process {
     name "Test Process GLIMPSE2_CONCORDANCE"
     script "../main.nf"
     process "GLIMPSE2_CONCORDANCE"
+
+    config "./nextflow.config"
+
     tag "glimpse2"
     tag "glimpse2/concordance"
     tag "glimpse2/phase"
@@ -11,22 +14,21 @@ nextflow_process {
     tag "modules"
 
     test("test glimpse2 concordance") {
-        config "./nextflow.config"
 
         when {
             params {
-                glimpse2_concordance_args = "--gt-val --af-tag AF"
+                glimpse2_concordance_args = "--gt-val --af-tag AF --seed 1"
             }
             process {
                 """
                 target = Channel.of([
                     [id: "input"],
-                    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)
                 ])
                 truth = Channel.of([
-                    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)
                 ])
                 allele_freq = Channel.of([
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.sites.vcf.gz",checkIfExists:true),
@@ -47,22 +49,13 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out.errors_cal.collect{ file(it[1]).name },
-                    process.out.errors_grp.collect{ file(it[1]).name },
-                    process.out.errors_spl.collect{ file(it[1]).name },
-                    process.out.rsquare_grp.collect{ file(it[1]).name },
-                    process.out.rsquare_spl.collect{ file(it[1]).name },
-                    process.out.versions
-                ).match() }
+                { assert snapshot(process.out).match() }
             )
         }
 
     }
 
     test("test list of region and rsquare per site") {
-        config "./nextflow.config"
-
         when {
             params {
                 glimpse2_concordance_args = "--gt-val --af-tag AF --out-r2-per-site"
@@ -71,12 +64,12 @@ nextflow_process {
                 """
                 target = Channel.of([
                     [id: "input"],
-                    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)
                 ])
                 truth = Channel.of([
-                    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)
                 ])
                 allele_freq = Channel.of([
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.sites.vcf.gz",checkIfExists:true),
@@ -98,15 +91,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out.errors_cal.collect{ file(it[1]).name },
-                    process.out.errors_grp.collect{ file(it[1]).name },
-                    process.out.errors_spl.collect{ file(it[1]).name },
-                    process.out.rsquare_grp.collect{ file(it[1]).name },
-                    process.out.rsquare_spl.collect{ file(it[1]).name },
-                    process.out.rsquare_per_site.collect{ file(it[1]).name },
-                    process.out.versions
-                ).match() }
+                { assert snapshot(process.out).match() }
             )
         }
 
diff --git a/modules/nf-core/glimpse2/concordance/tests/main.nf.test.snap b/modules/nf-core/glimpse2/concordance/tests/main.nf.test.snap
index 5e81d44e2f04..b40e39bc825d 100644
--- a/modules/nf-core/glimpse2/concordance/tests/main.nf.test.snap
+++ b/modules/nf-core/glimpse2/concordance/tests/main.nf.test.snap
@@ -1,59 +1,218 @@
 {
     "test glimpse2 concordance": {
         "content": [
-            [
-                "input.error.cal.txt.gz"
-            ],
-            [
-                "input.error.grp.txt.gz"
-            ],
-            [
-                "input.error.spl.txt.gz"
-            ],
-            [
-                "input.rsquare.grp.txt.gz"
-            ],
-            [
-                "input.rsquare.spl.txt.gz"
-            ],
-            [
-                "versions.yml:md5,ba729289bab6b9fbb8c36a620c86bb82"
-            ]
+            {
+                "0": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.error.cal.txt.gz:md5,605cf14649d768c07a6c5cff15aea26a"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.error.grp.txt.gz:md5,bdbe0131aa4d239de367bbb18e3c3327"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.error.spl.txt.gz:md5,034c0ecc19243d70e9cfda9083472763"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.rsquare.grp.txt.gz:md5,d70d53a5012b161ba4de65cd48dcac67"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.rsquare.spl.txt.gz:md5,9f0f2f13b8ea8597a83c35d578476989"
+                    ]
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    "versions.yml:md5,ba729289bab6b9fbb8c36a620c86bb82"
+                ],
+                "errors_cal": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.error.cal.txt.gz:md5,605cf14649d768c07a6c5cff15aea26a"
+                    ]
+                ],
+                "errors_grp": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.error.grp.txt.gz:md5,bdbe0131aa4d239de367bbb18e3c3327"
+                    ]
+                ],
+                "errors_spl": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.error.spl.txt.gz:md5,034c0ecc19243d70e9cfda9083472763"
+                    ]
+                ],
+                "rsquare_grp": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.rsquare.grp.txt.gz:md5,d70d53a5012b161ba4de65cd48dcac67"
+                    ]
+                ],
+                "rsquare_per_site": [
+                    
+                ],
+                "rsquare_spl": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.rsquare.spl.txt.gz:md5,9f0f2f13b8ea8597a83c35d578476989"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ba729289bab6b9fbb8c36a620c86bb82"
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.1"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-12-03T16:22:35.440086384"
+        "timestamp": "2025-11-27T11:09:00.725735403"
     },
     "test list of region and rsquare per site": {
         "content": [
-            [
-                "input.error.cal.txt.gz"
-            ],
-            [
-                "input.error.grp.txt.gz"
-            ],
-            [
-                "input.error.spl.txt.gz"
-            ],
-            [
-                "input.rsquare.grp.txt.gz"
-            ],
-            [
-                "input.rsquare.spl.txt.gz"
-            ],
-            [
-                "input_r2_sites.txt.gz"
-            ],
-            [
-                "versions.yml:md5,ba729289bab6b9fbb8c36a620c86bb82"
-            ]
+            {
+                "0": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.error.cal.txt.gz:md5,3a4753237fd8174ff46fb91bba712d5c"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.error.grp.txt.gz:md5,382dd127002f43716563a71a2b693de4"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.error.spl.txt.gz:md5,61a1133643ae5b0dc44ba76976b0bcce"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.rsquare.grp.txt.gz:md5,974a8c3188112716482103b8508ed109"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.rsquare.spl.txt.gz:md5,9f0f2f13b8ea8597a83c35d578476989"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input_r2_sites.txt.gz:md5,f65d7df3b887a4aade33a0b7b60bcca4"
+                    ]
+                ],
+                "6": [
+                    "versions.yml:md5,ba729289bab6b9fbb8c36a620c86bb82"
+                ],
+                "errors_cal": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.error.cal.txt.gz:md5,3a4753237fd8174ff46fb91bba712d5c"
+                    ]
+                ],
+                "errors_grp": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.error.grp.txt.gz:md5,382dd127002f43716563a71a2b693de4"
+                    ]
+                ],
+                "errors_spl": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.error.spl.txt.gz:md5,61a1133643ae5b0dc44ba76976b0bcce"
+                    ]
+                ],
+                "rsquare_grp": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.rsquare.grp.txt.gz:md5,974a8c3188112716482103b8508ed109"
+                    ]
+                ],
+                "rsquare_per_site": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input_r2_sites.txt.gz:md5,f65d7df3b887a4aade33a0b7b60bcca4"
+                    ]
+                ],
+                "rsquare_spl": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.rsquare.spl.txt.gz:md5,9f0f2f13b8ea8597a83c35d578476989"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ba729289bab6b9fbb8c36a620c86bb82"
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.10.1"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-12-03T16:26:35.009071185"
+        "timestamp": "2025-11-27T11:21:10.279509256"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/glimpse2/ligate/tests/main.nf.test b/modules/nf-core/glimpse2/ligate/tests/main.nf.test
index 1298e7b91c97..1ca94473aaa9 100644
--- a/modules/nf-core/glimpse2/ligate/tests/main.nf.test
+++ b/modules/nf-core/glimpse2/ligate/tests/main.nf.test
@@ -18,14 +18,15 @@ nextflow_process {
                 script "../../phase/main.nf"
                 process {
                 """
-                input_vcf = Channel.of([
+                input_vcf = channel.of([
                     [ id:'input' ],
-                    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),
-                    [], [],
-                    "chr22:16600000-16800000",
-                    "chr22:16650000-16750000"
-                ])
+                    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),
+                    [], []
+                ]).combine(channel.of(
+                    ["chr22:16570065-16597215", "chr22:16570065-16592216"],
+                    ["chr22:16587172-16609999", "chr22:16592229-16609999"]
+                ))
 
                 ref_panel = Channel.of([
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz", checkIfExists:true),
@@ -36,9 +37,12 @@ nextflow_process {
 
                 // [meta, vcf, index, sample_infos, regionin, regionout,ref, index, map] [meta, fasta, fai]
                 input[0] = input_vcf
+                    .map { meta, vcf, index, list, sample, regionI, regionO ->
+                        [[id: meta.id, region : regionI], vcf, index, list, sample, regionI, regionO]
+                    }
                     .combine(ref_panel)
                     .combine(map_file)
-                input[1] = Channel.of([[],[],[]])
+                input[1] = Channel.of([[],[],[]]).collect()
                 """
                 }
             }
@@ -56,8 +60,9 @@ nextflow_process {
             process {
                 """
                 input[0] = GLIMPSE2_PHASE.out.phased_variants
-                    | groupTuple()
-                    | join (BCFTOOLS_INDEX.out.csi.groupTuple())
+                    .join(BCFTOOLS_INDEX.out.csi)
+                    .map{ meta, vcf, index -> [meta.subMap("id"), vcf, index]}
+                    .groupTuple()
                 """
             }
         }
@@ -67,7 +72,12 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     process.out.versions,
-                    process.out.merged_variants.collect{ path(it[1]).vcf.variantsMD5}
+                    process.out.merged_variants.collect{ meta, vcf -> [
+                        meta,
+                        file(vcf).name,
+                        path(vcf).vcf.summary,
+                        path(vcf).vcf.variantsMD5
+                    ] }
                 ).match() },
             )
         }
@@ -80,8 +90,8 @@ nextflow_process {
                 """
                 input[0] = Channel.of([
                     [ id:'input' ],
-                    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),
                 ])
                 """
             }
@@ -90,10 +100,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml,
-                ).match() },
+                { assert snapshot(process.out).match() },
             )
         }
     }
diff --git a/modules/nf-core/glimpse2/ligate/tests/main.nf.test.snap b/modules/nf-core/glimpse2/ligate/tests/main.nf.test.snap
index 995bcfb0eb5b..4422e31d2a5a 100644
--- a/modules/nf-core/glimpse2/ligate/tests/main.nf.test.snap
+++ b/modules/nf-core/glimpse2/ligate/tests/main.nf.test.snap
@@ -5,14 +5,21 @@
                 "versions.yml:md5,44addcaef4965ff6409a8293c5bcad84"
             ],
             [
-                "8730c5450f0c32d72c6d5cb4eb02b38b"
+                [
+                    {
+                        "id": "input"
+                    },
+                    "input.vcf.gz",
+                    "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=903, phased=true, phasedAutodetect=true]",
+                    "bfeec64e4bbd1211d3dd284aff482995"
+                ]
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-19T23:17:50.793909707"
+        "timestamp": "2025-11-26T20:54:57.8806397"
     },
     "Should run glimpse ligate -- stub": {
         "content": [
@@ -39,17 +46,12 @@
                 "versions": [
                     "versions.yml:md5,44addcaef4965ff6409a8293c5bcad84"
                 ]
-            },
-            {
-                "GLIMPSE2_LIGATE": {
-                    "glimpse2": "2.0.0"
-                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-19T23:19:24.515887682"
+        "timestamp": "2025-11-26T20:46:48.337059937"
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/glimpse2/phase/tests/main.nf.test b/modules/nf-core/glimpse2/phase/tests/main.nf.test
index c7b2d46a2d47..c7dfcd7ed827 100644
--- a/modules/nf-core/glimpse2/phase/tests/main.nf.test
+++ b/modules/nf-core/glimpse2/phase/tests/main.nf.test
@@ -17,27 +17,27 @@ nextflow_process {
         when {
             process {
                 """
-                input_vcf = Channel.of([
+                input_vcf = channel.of([
                     [ id:'input' ],
-                    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),
                     [], [],
                     "chr22:16600000-16800000",
                     "chr22:16650000-16750000"
                 ])
 
-                ref_panel = Channel.of([
+                ref_panel = channel.of([
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz", checkIfExists:true),
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz.csi", checkIfExists:true),
                 ])
 
-                map_file = Channel.of([[]])
+                map_file = channel.of([[]])
 
                 // [meta, vcf, index, sample_infos, regionin, regionout,ref, index, map] [meta, fasta, fai]
                 input[0] = input_vcf
                     .combine(ref_panel)
                     .combine(map_file)
-                input[1] = Channel.of([[],[],[]])
+                input[1] = channel.of([[],[],[]])
                 """
             }
         }
@@ -46,7 +46,13 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    path(process.out.phased_variants[0][1]).vcf.variantsMD5,
+                    process.out.phased_variants.collect{ meta, vcf -> [
+                        meta,
+                        file(vcf).name,
+                        path(vcf).vcf.summary,
+                        path(vcf).vcf.variantsMD5
+                    ]},
+                    process.out.stats_coverage,
                     process.out.versions
                 ).match()}
             )
@@ -58,27 +64,27 @@ nextflow_process {
         when {
             process {
                 """
-                input_bam = Channel.of([
+                input_bam = channel.of([
                     [id:'input'],
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA12878.chr22.1X.bam", checkIfExists: true),
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA12878.chr22.1X.bam.bai", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA12878.chr21_22.1X.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA12878.chr21_22.1X.bam.bai", checkIfExists: true),
                     [], [],
                     "chr22:16600000-16800000",
                     "chr22:16650000-16750000",
                 ])
 
-                ref_panel = Channel.of([
+                ref_panel = channel.of([
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz", checkIfExists:true),
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz.csi", checkIfExists:true),
                 ])
 
-                map_file = Channel.of([[]])
+                map_file = channel.of([[]])
 
                 // [meta, vcf, index, sample_infos, regionin, regionout,ref, index, map] [meta, fasta, fai]
                 input[0] = input_bam
                     .combine(ref_panel)
                     .combine(map_file)
-                input[1] = Channel.of([[],[],[]])
+                input[1] = channel.of([[],[],[]])
                 """
             }
         }
@@ -87,7 +93,12 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    path(process.out.phased_variants[0][1]).vcf.variantsMD5,
+                    process.out.phased_variants.collect{ meta, vcf -> [
+                        meta,
+                        file(vcf).name,
+                        path(vcf).vcf.summary,
+                        path(vcf).vcf.variantsMD5
+                    ]},
                     process.out.stats_coverage,
                     process.out.versions
                 ).match()}
@@ -102,14 +113,14 @@ nextflow_process {
                 script "../../../samtools/view"
                 process {
                     """
-                    input[0] = Channel.of([
+                    input[0] = channel.of([
                         [id:'input'],
-                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA12878.chr22.1X.bam", checkIfExists: true),
-                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA12878.chr22.1X.bam.bai", checkIfExists: true)
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA12878.chr21_22.1X.bam", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA12878.chr21_22.1X.bam.bai", checkIfExists: true)
                     ])
-                    input[1] = Channel.of([
+                    input[1] = channel.of([
                         [id: 'Hg38'],
-                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/GRCh37_chr22.fasta.gz", checkIfExists: true)
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genomeGRCh38_chr21_22.fa.gz", checkIfExists: true)
                     ])
                     input[2] = []
                     input[3] = "crai"
@@ -123,22 +134,22 @@ nextflow_process {
                 """
                 input_cram = SAMTOOLS_VIEW.out.cram
                     .join(SAMTOOLS_VIEW.out.crai)
-                    .combine(Channel.of([
+                    .combine(channel.of([
                         [], [],
                         "chr22:16600000-16800000",
                         "chr22:16650000-16750000",
                     ]))
-                ref_panel = Channel.of([
+                ref_panel = channel.of([
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz", checkIfExists:true),
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz.csi", checkIfExists:true)
                 ])
 
-                map_file = Channel.of([[]])
+                map_file = channel.of([[]])
 
-                reference_genome = Channel.of([
+                reference_genome = channel.of([
                     [id: 'Hg38'],
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/GRCh37_chr22.fasta.gz", checkIfExists: true),
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta.fai", checkIfExists: true)
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genomeGRCh38_chr21_22.fa.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genomeGRCh38_chr21_22.fa.gz.fai", checkIfExists: true)
                 ])
 
                 // [meta, vcf, index, sample_infos, regionin, regionout,ref, index, map] [meta, fasta, fai]
@@ -154,7 +165,12 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    path(process.out.phased_variants[0][1]).vcf.variantsMD5,
+                    process.out.phased_variants.collect{ meta, vcf -> [
+                        meta,
+                        file(vcf).name,
+                        path(vcf).vcf.summary,
+                        path(vcf).vcf.variantsMD5
+                    ]},
                     process.out.stats_coverage,
                     process.out.versions
                 ).match()}
@@ -163,35 +179,36 @@ nextflow_process {
     }
 
     test("homo_sapiens - [bam, bam] region - panel") {
+        tag "test"
         when {
             process {
                 """
-                input_bam = Channel.of([
+                input_bam = channel.of([
                     [id:'input'],
                     [
-                        file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/individuals/NA12878/NA12878.s.bam", checkIfExists: true),
-                        file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/individuals/NA19401/NA19401.s.bam", checkIfExists: true)
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA12878.chr21_22.1X.bam", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA19401.chr21_22.1X.bam", checkIfExists: true)
                     ],
                     [
-                        file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/individuals/NA12878/NA12878.s.bam.bai", checkIfExists: true),
-                        file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/individuals/NA19401/NA19401.s.bam.bai", checkIfExists: true)
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA12878.chr21_22.1X.bam.bai", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA19401.chr21_22.1X.bam.bai", checkIfExists: true)
                     ],
                     [], [],
                     "chr22:16600000-16800000",
                     "chr22:16650000-16750000",
                 ])
-                ref_panel = Channel.of([
+                ref_panel = channel.of([
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz", checkIfExists:true),
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz.csi", checkIfExists:true)
                 ])
 
-                map_file = Channel.of([[]])
+                map_file = channel.of([[]])
 
                 // [meta, vcf, index, sample_infos, regionin, regionout,ref, index, map] [meta, fasta, fai]
                 input[0] = input_bam
                     .combine(ref_panel)
                     .combine(map_file)
-                input[1] = Channel.of([[],[],[]])
+                input[1] = channel.of([[],[],[]])
                 """
                 }
         }
@@ -200,8 +217,12 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    // path(process.out.phased_variants[0][1]).vcf.variantsMD5, // MD5 sum not stable for the AF infos of 1 variant at the 5th decimals
-                    process.out.phased_variants.collect{ path(it[1]).vcf.summary.replaceAll(", phasedAutodetect=(false|true)", "") },
+                    process.out.phased_variants.collect{ meta, vcf -> [
+                        meta,
+                        file(vcf).name,
+                        path(vcf).vcf.summary,
+                        path(vcf).vcf.variantsMD5
+                    ]},
                     process.out.stats_coverage,
                     process.out.versions
                 ).match()}
@@ -213,15 +234,15 @@ nextflow_process {
         when {
             process {
                 """
-                input_bam = Channel.of([
+                input_bam = channel.of([
                     [id:'input'],
                     [
-                        file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/individuals/NA12878/NA12878.s.bam", checkIfExists: true),
-                        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/bam/NA12878.chr21_22.1X.bam", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz", checkIfExists: true)
                     ],
                     [
-                        file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/individuals/NA12878/NA12878.s.bam.bai", 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/bam/NA12878.chr21_22.1X.bam.bai", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878.chr21_22.1X.glimpse2.vcf.gz.csi", checkIfExists: true)
                     ],
                     [], [],
                     "chr22:16600000-16800000",
@@ -231,7 +252,7 @@ nextflow_process {
 
                 // [meta, vcf, index, sample_infos, regionin, regionout,ref, index, map] [meta, fasta, fai]
                 input[0] = input_bam
-                input[1] = Channel.of([[],[],[]])
+                input[1] = channel.of([[],[],[]])
                 """
                 }
         }
@@ -248,15 +269,15 @@ nextflow_process {
         when {
             process {
                 """
-                input_bam = Channel.of([
+                input_bam = channel.of([
                     [id:'input'],
                     [
-                        file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/individuals/NA12878/NA12878.s.1x.bcf", checkIfExists: true),
-                        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/NA19401.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", checkIfExists: true),
                     ],
                     [
-                        file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/individuals/NA12878/NA12878.s.1x.bcf.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/NA19401.chr21_22.1X.glimpse2.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),
                     ],
                     [], [],
                     "chr21:16600000-16800000",
@@ -266,7 +287,7 @@ nextflow_process {
 
                 // [meta, vcf, index, sample_infos, regionin, regionout,ref, index, map] [meta, fasta, fai]
                 input[0] = input_bam
-                input[1] = Channel.of([[],[],[]])
+                input[1] = channel.of([[],[],[]])
                 """
                 }
         }
@@ -280,23 +301,24 @@ nextflow_process {
     }
 
     test("homo_sapiens - [bam, bam] region sample rename - panel") {
+        tag "test"
         when {
             process {
                 """
-                bamlist = Channel.of(
-                    "NA12878.s.bam\tNA12878",
-                    "NA19401.s.bam\tNA19401"
+                bamlist = channel.of(
+                    "NA12878.chr21_22.1X.bam\tSample1",
+                    "NA19401.chr21_22.1X.bam\tSample2"
                 ).collectFile(name: 'bamlist.txt', newLine: true)
 
-                input_bam = Channel.of([
+                input_bam = channel.of([
                     [id:'input'],
                     [
-                        file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/individuals/NA12878/NA12878.s.bam", checkIfExists: true),
-                        file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/individuals/NA19401/NA19401.s.bam", checkIfExists: true)
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA12878.chr21_22.1X.bam", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA19401.chr21_22.1X.bam", checkIfExists: true)
                     ],
                     [
-                        file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/individuals/NA12878/NA12878.s.bam.bai", checkIfExists: true),
-                        file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/individuals/NA19401/NA19401.s.bam.bai", checkIfExists: true)
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA12878.chr21_22.1X.bam.bai", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA19401.chr21_22.1X.bam.bai", checkIfExists: true)
                     ],
                 ]).combine(bamlist)
                 .map{ map, bam, bai, bamlist -> [
@@ -305,17 +327,17 @@ nextflow_process {
                     "chr22:16650000-16750000",
                 ]}
 
-                ref_panel = Channel.of([
+                ref_panel = channel.of([
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz", checkIfExists:true),
                     file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz.csi", checkIfExists:true)
                 ])
 
-                map_file = Channel.of([[]])
+                map_file = channel.of([[]])
                 // [meta, vcf, index, sample_infos, regionin, regionout,ref, index, map] [meta, fasta, fai]
                 input[0] = input_bam
                     .combine(ref_panel)
                     .combine(map_file)
-                input[1] = Channel.of([[],[],[]])
+                input[1] = channel.of([[],[],[]])
                 """
                 }
         }
@@ -324,8 +346,14 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.phased_variants.collect{ path(it[1]).vcf.header.getGenotypeSamples().sort() },
-                    process.out.phased_variants.collect{ path(it[1]).vcf.summary.replaceAll(", phasedAutodetect=(false|true)", "") }
+                    process.out.phased_variants.collect{ meta, vcf -> [
+                        meta,
+                        file(vcf).name,
+                        path(vcf).vcf.summary,
+                        path(vcf).vcf.variantsMD5
+                    ]},
+                    process.out.stats_coverage,
+                    process.out.versions
                 ).match()}
             )
         }
@@ -336,10 +364,10 @@ nextflow_process {
         when {
             process {
                 """
-                input_vcf = Channel.of([
+                input_vcf = channel.of([
                     [ id:'input' ],
-                    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),
                     [], [],
                     "chr22:16600000-16800000",
                     "chr22:16650000-16750000",
@@ -348,7 +376,7 @@ nextflow_process {
 
                 // [meta, vcf, index, sample_infos, regionin, regionout,ref, index, map] [meta, fasta, fai]
                 input[0] = input_vcf
-                input[1] = Channel.of([[],[],[]])
+                input[1] = channel.of([[],[],[]])
                 """
             }
         }
@@ -356,10 +384,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml
-                ).match()}
+                { assert snapshot(process.out).match()}
             )
         }
 
diff --git a/modules/nf-core/glimpse2/phase/tests/main.nf.test.snap b/modules/nf-core/glimpse2/phase/tests/main.nf.test.snap
index 52fe9b37acca..143504524b83 100644
--- a/modules/nf-core/glimpse2/phase/tests/main.nf.test.snap
+++ b/modules/nf-core/glimpse2/phase/tests/main.nf.test.snap
@@ -1,13 +1,22 @@
 {
     "homo_sapiens - bam region - panel": {
         "content": [
-            "b84087788284d7ca02e23a0a24da2cff",
             [
                 [
                     {
                         "id": "input"
                     },
-                    "input_chr22_16650000-16750000_stats_coverage.txt.gz:md5,5682c97193f6cd8041f3bc4ef81e7252"
+                    "input_chr22_16650000-16750000.vcf",
+                    "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=266, phased=true, phasedAutodetect=false]",
+                    "23026b2111d5b93194ebbb5de09d654d"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "input"
+                    },
+                    "input_chr22_16650000-16750000_stats_coverage.txt.gz:md5,39bf5e7c67e377207656104f64fea657"
                 ]
             ],
             [
@@ -15,22 +24,29 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-19T22:59:18.246884827"
+        "timestamp": "2025-11-26T20:59:49.43898101"
     },
     "homo_sapiens - [bam, bam] region - panel": {
         "content": [
             [
-                "VcfFile [chromosomes=[chr22], sampleCount=2, variantCount=266, phased=true]"
+                [
+                    {
+                        "id": "input"
+                    },
+                    "input_chr22_16650000-16750000.vcf",
+                    "VcfFile [chromosomes=[chr22], sampleCount=2, variantCount=266, phased=true, phasedAutodetect=false]",
+                    "f06d12e3c16a8edc313ad564836008"
+                ]
             ],
             [
                 [
                     {
                         "id": "input"
                     },
-                    "input_chr22_16650000-16750000_stats_coverage.txt.gz:md5,ce67a9fd6944b74e65ab6f401b1b9bb0"
+                    "input_chr22_16650000-16750000_stats_coverage.txt.gz:md5,fa1b295b071c1b8670c013577a982139"
                 ]
             ],
             [
@@ -38,27 +54,48 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-19T23:09:13.67984812"
+        "timestamp": "2025-11-26T21:03:14.8627618"
     },
     "homo_sapiens - vcf region - panel": {
         "content": [
-            "d8e9e1ec4d9d229536a23f2f69a469de",
+            [
+                [
+                    {
+                        "id": "input"
+                    },
+                    "input_chr22_16650000-16750000.vcf",
+                    "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=266, phased=true, phasedAutodetect=false]",
+                    "d8e9e1ec4d9d229536a23f2f69a469de"
+                ]
+            ],
+            [
+                
+            ],
             [
                 "versions.yml:md5,c68de03046a6503cdbcf3a1495fc512f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-19T22:59:11.310995509"
+        "timestamp": "2025-11-26T20:58:13.192800596"
     },
     "homo_sapiens - cram region - panel - fasta": {
         "content": [
-            "d8e9e1ec4d9d229536a23f2f69a469de",
+            [
+                [
+                    {
+                        "id": "input"
+                    },
+                    "input_chr22_16650000-16750000.vcf",
+                    "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=266, phased=true, phasedAutodetect=false]",
+                    "d8e9e1ec4d9d229536a23f2f69a469de"
+                ]
+            ],
             [
                 [
                     {
@@ -72,28 +109,40 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-19T22:59:28.11190592"
+        "timestamp": "2025-11-26T21:00:40.288219943"
     },
     "homo_sapiens - [bam, bam] region sample rename - panel": {
         "content": [
             [
                 [
-                    "NA12878",
-                    "NA19401"
+                    {
+                        "id": "input"
+                    },
+                    "input_chr22_16650000-16750000.vcf",
+                    "VcfFile [chromosomes=[chr22], sampleCount=2, variantCount=266, phased=true, phasedAutodetect=false]",
+                    "f2aff70c52df2f69d9bc1f4bf63fcb5c"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "input"
+                    },
+                    "input_chr22_16650000-16750000_stats_coverage.txt.gz:md5,b21fbf77322b281c5cf4822edadd844c"
                 ]
             ],
             [
-                "VcfFile [chromosomes=[chr22], sampleCount=2, variantCount=266, phased=true]"
+                "versions.yml:md5,c68de03046a6503cdbcf3a1495fc512f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-19T22:59:55.383590515"
+        "timestamp": "2025-11-26T21:05:13.564441099"
     },
     "homo_sapiens - vcf region - panel -- stub": {
         "content": [
@@ -126,17 +175,12 @@
                 "versions": [
                     "versions.yml:md5,c68de03046a6503cdbcf3a1495fc512f"
                 ]
-            },
-            {
-                "GLIMPSE2_PHASE": {
-                    "glimpse2": "2.0.0"
-                }
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-19T23:19:50.900935094"
+        "timestamp": "2025-11-26T21:01:07.257765596"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/glimpse2/phase/tests/nextflow.config b/modules/nf-core/glimpse2/phase/tests/nextflow.config
index 820e20151921..310c7f220dd7 100644
--- a/modules/nf-core/glimpse2/phase/tests/nextflow.config
+++ b/modules/nf-core/glimpse2/phase/tests/nextflow.config
@@ -1,5 +1,6 @@
 process {
     withName: GLIMPSE2_PHASE {
+        cpus = 1
         ext.args = "--seed 1"
         ext.suffix = "vcf"
     }
diff --git a/modules/nf-core/glimpse2/splitreference/tests/main.nf.test b/modules/nf-core/glimpse2/splitreference/tests/main.nf.test
index d10648c40e1e..e95febde9a3c 100644
--- a/modules/nf-core/glimpse2/splitreference/tests/main.nf.test
+++ b/modules/nf-core/glimpse2/splitreference/tests/main.nf.test
@@ -52,7 +52,7 @@ nextflow_process {
                 ]
                 input[1]= [
                     [ id:'map'],
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.GRCh38.glimpse.chr22.map.gz", checkIfExists:true)
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr22.glimpse.map", checkIfExists:true)
                 ]
                 """
             }
diff --git a/subworkflows/nf-core/multiple_impute_glimpse2/main.nf b/subworkflows/nf-core/multiple_impute_glimpse2/main.nf
index 47fb600f3c23..c9c0022beacc 100644
--- a/subworkflows/nf-core/multiple_impute_glimpse2/main.nf
+++ b/subworkflows/nf-core/multiple_impute_glimpse2/main.nf
@@ -10,13 +10,13 @@ workflow MULTIPLE_IMPUTE_GLIMPSE2 {
     take:
     ch_input    // channel (mandatory): [ meta, vcf, csi, infos ]
     ch_ref      // channel (mandatory): [ meta, vcf, csi, region ]
-    ch_map      // channel (optional): [ meta, map ]
-    ch_fasta    // channel  (optional): [ meta, fasta, index ]
+    ch_map      // channel (optional) : [ meta, map ]
+    ch_fasta    // channel (optional) : [ meta, fasta, index ]
     chunk_model // string: model used to chunk the reference panel
 
     main:
 
-    ch_versions = Channel.empty()
+    ch_versions = channel.empty()
 
     // Chunk reference panel
     ch_ref_map = ch_ref.combine(ch_map, by: 0)
@@ -48,10 +48,10 @@ workflow MULTIPLE_IMPUTE_GLIMPSE2 {
 
     // Phase input files for each reference bin files + indexing
     GLIMPSE2_PHASE ( phase_input, ch_fasta ) // [meta, vcf, index, sample_infos, regionin, regionout, regionindex, ref, ref_index, map], [ meta, fasta, index ]
-    ch_versions = ch_versions.mix( GLIMPSE2_PHASE.out.versions)
+    ch_versions = ch_versions.mix( GLIMPSE2_PHASE.out.versions.first() )
 
     INDEX_PHASE ( GLIMPSE2_PHASE.out.phased_variants )
-    ch_versions = ch_versions.mix( INDEX_PHASE.out.versions )
+    ch_versions = ch_versions.mix( INDEX_PHASE.out.versions.first() )
 
     // Ligate all phased files in one and index it
     ligate_input = GLIMPSE2_PHASE.out.phased_variants
@@ -61,10 +61,10 @@ workflow MULTIPLE_IMPUTE_GLIMPSE2 {
                 .collect(), by: 0 )
 
     GLIMPSE2_LIGATE ( ligate_input )
-    ch_versions = ch_versions.mix( GLIMPSE2_LIGATE.out.versions )
+    ch_versions = ch_versions.mix( GLIMPSE2_LIGATE.out.versions.first() )
 
     INDEX_LIGATE ( GLIMPSE2_LIGATE.out.merged_variants )
-    ch_versions = ch_versions.mix( INDEX_LIGATE.out.versions )
+    ch_versions = ch_versions.mix( INDEX_LIGATE.out.versions.first() )
 
     emit:
     chunk_chr              = GLIMPSE2_CHUNK.out.chunk_chr           // channel: [ val(meta), txt ]
diff --git a/subworkflows/nf-core/multiple_impute_glimpse2/tests/main.nf.test b/subworkflows/nf-core/multiple_impute_glimpse2/tests/main.nf.test
index 43f17ec771d7..989bdb8a1ca7 100644
--- a/subworkflows/nf-core/multiple_impute_glimpse2/tests/main.nf.test
+++ b/subworkflows/nf-core/multiple_impute_glimpse2/tests/main.nf.test
@@ -24,8 +24,8 @@ nextflow_workflow {
                 """
                 input[0] = Channel.of([
                     [id:'input_vcf'],
-                    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] = Channel.of([
@@ -63,8 +63,8 @@ nextflow_workflow {
                     .collectFile(name: 'sampleinfos.txt')
                 input[0] = Channel.of([
                     [id:'input_vcf'],
-                    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),
                 ]).combine(sample)
                 input[1] = Channel.of([
                     [id:'ref_panel', chr: "22"],
@@ -103,8 +103,8 @@ nextflow_workflow {
                 """
                 input[0] = Channel.of([
                     [id:'input_bam'],
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA12878.chr22.1X.bam", checkIfExists: true),
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA12878.chr22.1X.bam.bai", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA12878.chr21_22.1X.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA12878.chr21_22.1X.bam.bai", checkIfExists: true),
                     []
                 ])
                 input[1] = Channel.of([
@@ -142,8 +142,8 @@ nextflow_workflow {
                 """
                 input[0] = input[0] = Channel.of([
                     [id:'input_bam'],
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA12878.chr22.1X.bam", checkIfExists: true),
-                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA12878.chr22.1X.bam.bai", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA12878.chr21_22.1X.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/NA12878.chr21_22.1X.bam.bai", checkIfExists: true),
                     []
                 ])
                 input[1] = Channel.of([
diff --git a/subworkflows/nf-core/multiple_impute_glimpse2/tests/main.nf.test.snap b/subworkflows/nf-core/multiple_impute_glimpse2/tests/main.nf.test.snap
index c75e08a02aee..232c67643f96 100644
--- a/subworkflows/nf-core/multiple_impute_glimpse2/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/multiple_impute_glimpse2/tests/main.nf.test.snap
@@ -17,19 +17,17 @@
             [
                 "versions.yml:md5,048d5415737cdc568fcc4fbdc5df11e2",
                 "versions.yml:md5,1301ab7e8d92b232e306aef24d94e252",
-                "versions.yml:md5,1301ab7e8d92b232e306aef24d94e252",
                 "versions.yml:md5,1362d3f6834c21239d705f550b11c2af",
                 "versions.yml:md5,2373902d5432eba6898c90d4c4685f90",
                 "versions.yml:md5,642ed64b13825472557113ba2e4b1566",
-                "versions.yml:md5,e81cfbe9cf12832b8312f966b6c9beb1",
                 "versions.yml:md5,e81cfbe9cf12832b8312f966b6c9beb1"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-15T07:30:09.139160775"
+        "timestamp": "2025-11-27T11:11:34.893641629"
     },
     "homo_sapiens - bam [] - panel vcf - [] - [] - sequential": {
         "content": [
@@ -43,7 +41,7 @@
                 ]
             ],
             [
-                "11558863c409ca2d6278e699cd5fde1a"
+                "49df7da6c9745ba9a86112193ff172a9"
             ],
             "input_bam.vcf.gz.csi",
             [
@@ -56,10 +54,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-15T07:30:25.249656096"
+        "timestamp": "2025-11-26T21:19:09.9592341"
     },
     "homo_sapiens - bam [] - panel vcf - [] - [] - sequential -- stub": {
         "content": [
diff --git a/subworkflows/nf-core/vcf_impute_glimpse/main.nf b/subworkflows/nf-core/vcf_impute_glimpse/main.nf
index 94262e34ae14..9b6884df3e1c 100644
--- a/subworkflows/nf-core/vcf_impute_glimpse/main.nf
+++ b/subworkflows/nf-core/vcf_impute_glimpse/main.nf
@@ -11,30 +11,30 @@ workflow VCF_IMPUTE_GLIMPSE {
 
     main:
 
-    ch_versions = Channel.empty()
+    ch_versions = channel.empty()
 
     input_chunk = ch_input.map{
-                    meta, vcf, csi, sample, region, ref, ref_index, map ->
+                    meta, vcf, csi, _sample, region, _ref, _ref_index, _map ->
                     [ meta, vcf, csi, region]
                 }
 
     GLIMPSE_CHUNK ( input_chunk )
-    ch_versions = ch_versions.mix( GLIMPSE_CHUNK.out.versions )
+    ch_versions = ch_versions.mix( GLIMPSE_CHUNK.out.versions.first() )
 
     chunk_output = GLIMPSE_CHUNK.out.chunk_chr
                                 .splitCsv(header: ['ID', 'Chr', 'RegionIn', 'RegionOut', 'Size1', 'Size2'], sep: "\t", skip: 0)
                                 .map { meta, it -> [meta, it["RegionIn"], it["RegionOut"]]}
 
-    phase_input = ch_input.map{ meta, vcf, csi, sample, region, ref, ref_index, map -> [meta, vcf, csi, sample, ref, ref_index, map]}
+    phase_input = ch_input.map{ meta, vcf, csi, sample, _region, ref, ref_index, map -> [meta, vcf, csi, sample, ref, ref_index, map]}
                         .combine(chunk_output, by: 0)
                         .map{meta, vcf, csi, sample, ref, ref_index, map, regionin, regionout ->
                             [meta, vcf, csi, sample, regionin, regionout, ref, ref_index, map]}
 
     GLIMPSE_PHASE ( phase_input ) // [meta, vcf, index, sample_infos, regionin, regionout, ref, ref_index, map]
-    ch_versions = ch_versions.mix(GLIMPSE_PHASE.out.versions )
+    ch_versions = ch_versions.mix(GLIMPSE_PHASE.out.versions.first() )
 
     INDEX_PHASE ( GLIMPSE_PHASE.out.phased_variants )
-    ch_versions = ch_versions.mix( INDEX_PHASE.out.versions )
+    ch_versions = ch_versions.mix( INDEX_PHASE.out.versions.first() )
 
     // Ligate all phased files in one and index it
     ligate_input = GLIMPSE_PHASE.out.phased_variants
@@ -45,10 +45,10 @@ workflow VCF_IMPUTE_GLIMPSE {
         )
 
     GLIMPSE_LIGATE ( ligate_input )
-    ch_versions = ch_versions.mix(GLIMPSE_LIGATE.out.versions )
+    ch_versions = ch_versions.mix(GLIMPSE_LIGATE.out.versions.first() )
 
     INDEX_LIGATE ( GLIMPSE_LIGATE.out.merged_variants )
-    ch_versions = ch_versions.mix( INDEX_LIGATE.out.versions )
+    ch_versions = ch_versions.mix( INDEX_LIGATE.out.versions.first() )
 
     emit:
     chunk_chr              = GLIMPSE_CHUNK.out.chunk_chr           // channel: [ val(meta), txt ]
diff --git a/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test b/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test
index 29b71c982273..a7dfec8a7ccc 100644
--- a/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test
+++ b/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test
@@ -18,7 +18,6 @@ nextflow_workflow {
         when {
             params {
                 outdir = "tests/results"
-                impute_dataset = "https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/"
             }
             workflow {
                 """
@@ -26,11 +25,11 @@ nextflow_workflow {
 
                 ch_panel = Channel.fromList([
                     [[ chr:"chr21"],
-                    file(params.impute_dataset + "panel/chr21/1000GP.chr21.s.norel.vcf.gz", checkIfExists: true),
-                    file(params.impute_dataset + "panel/chr21/1000GP.chr21.s.norel.vcf.gz.csi", checkIfExists: true)],
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr21.vcf.gz", checkIfExists:true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr21.vcf.gz.csi", checkIfExists:true)],
                     [[ chr:"chr22"],
-                    file(params.impute_dataset + "panel/chr22/1000GP.chr22.s.norel.vcf.gz", checkIfExists: true),
-                    file(params.impute_dataset + "panel/chr22/1000GP.chr22.s.norel.vcf.gz.csi", checkIfExists: true)]
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz", checkIfExists:true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.vcf.gz.csi", checkIfExists:true)]
                 ])
                 region = Channel.fromList([
                     [[chr: "chr21", region: "chr21:16600000-16800000"], "chr21:16600000-16800000"],
@@ -39,12 +38,12 @@ nextflow_workflow {
 
                 input_vcf = Channel.fromList([
                     [[ id:'NA12878'], // meta map
-                    file(params.impute_dataset + "individuals/NA12878/NA12878.s.1x.bcf", checkIfExists: true),
-                    file(params.impute_dataset + "individuals/NA12878/NA12878.s.1x.bcf.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),
                     ],
                     [[ id:'NA19401'], // meta map
-                    file(params.impute_dataset + "individuals/NA19401/NA19401.s.1x.bcf", checkIfExists: true),
-                    file(params.impute_dataset + "individuals/NA19401/NA19401.s.1x.bcf.csi", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA19401.chr21_22.1X.glimpse2.vcf.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA19401.chr21_22.1X.glimpse2.vcf.gz.csi", checkIfExists: true),
                     ]
                 ])
                 input_vcf_multiple = input_vcf
@@ -56,10 +55,10 @@ nextflow_workflow {
 
                 ch_map = Channel.fromList([
                     [[ chr: "chr21"],
-                        file(params.impute_dataset + "reference_genome/GRCh38_chr21.glimpse.map", checkIfExists: true)
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr21.glimpse.map", checkIfExists: true)
                     ],
                     [[ chr: "chr22"],
-                        file(params.impute_dataset + "reference_genome/GRCh38_chr21.glimpse.map", checkIfExists: true)
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr22.glimpse.map", checkIfExists: true)
                     ]
                 ])
 
@@ -78,13 +77,18 @@ nextflow_workflow {
         }
 
         then {
-            def lines = path(workflow.out.merged_variants.get(0).get(1)).linesGzip.last()
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(workflow.out.versions).match("versions") },
-                { assert snapshot(workflow.out.chunk_chr).match("chunk_chr") },
-                { assert workflow.out.merged_variants.size() == 4},
-                { assert snapshot(lines).match("merged") }
+                { assert snapshot(
+                    workflow.out.versions,
+                    workflow.out.chunk_chr,
+                    workflow.out.merged_variants.collect{ meta, vcf -> [
+                        meta,
+                        file(vcf).name,
+                        path(vcf).vcf.summary,
+                        path(vcf).vcf.variantsMD5
+                    ]}
+                ).match() }
             )
         }
 
diff --git a/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test.snap b/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test.snap
index e1e48f2e30f6..d0174f8cacc8 100644
--- a/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test.snap
@@ -1,6 +1,13 @@
 {
-    "chunk_chr": {
+    "Should run without failures": {
         "content": [
+            [
+                "versions.yml:md5,21a662d09502bd6516ec62b72e4fb182",
+                "versions.yml:md5,227d8e960e4382d8a615e040b874fc27",
+                "versions.yml:md5,4c01309242fd8da3ddbde9fab54aae4c",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,c7bdac5a09390d02a95e5042a2fd133e"
+            ],
             [
                 [
                     {
@@ -16,7 +23,7 @@
                         "chr": "chr22",
                         "region": "chr22:16600000-16800000"
                     },
-                    "NA12878_chr22:16600000-16800000_chunk.txt:md5,f5270ed0faa4f9697618444b267442ce"
+                    "NA12878_chr22:16600000-16800000_chunk.txt:md5,7ac5d116bc3357a154946576c21060cd"
                 ],
                 [
                     {
@@ -32,55 +39,56 @@
                         "chr": "chr22",
                         "region": "chr22:16600000-16800000"
                     },
-                    "NA19401_chr22:16600000-16800000_chunk.txt:md5,f5270ed0faa4f9697618444b267442ce"
+                    "NA19401_chr22:16600000-16800000_chunk.txt:md5,7ac5d116bc3357a154946576c21060cd"
                 ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
-        },
-        "timestamp": "2025-03-01T13:00:44.904715825"
-    },
-    "versions": {
-        "content": [
+            ],
             [
-                "versions.yml:md5,227d8e960e4382d8a615e040b874fc27",
-                "versions.yml:md5,227d8e960e4382d8a615e040b874fc27",
-                "versions.yml:md5,227d8e960e4382d8a615e040b874fc27",
-                "versions.yml:md5,227d8e960e4382d8a615e040b874fc27",
-                "versions.yml:md5,4c01309242fd8da3ddbde9fab54aae4c",
-                "versions.yml:md5,4c01309242fd8da3ddbde9fab54aae4c",
-                "versions.yml:md5,4c01309242fd8da3ddbde9fab54aae4c",
-                "versions.yml:md5,4c01309242fd8da3ddbde9fab54aae4c",
-                "versions.yml:md5,73621eae1bfd89c2ceb009524fe680d4",
-                "versions.yml:md5,73621eae1bfd89c2ceb009524fe680d4",
-                "versions.yml:md5,73621eae1bfd89c2ceb009524fe680d4",
-                "versions.yml:md5,73621eae1bfd89c2ceb009524fe680d4",
-                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
-                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
-                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
-                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
-                "versions.yml:md5,c7bdac5a09390d02a95e5042a2fd133e",
-                "versions.yml:md5,c7bdac5a09390d02a95e5042a2fd133e",
-                "versions.yml:md5,c7bdac5a09390d02a95e5042a2fd133e",
-                "versions.yml:md5,c7bdac5a09390d02a95e5042a2fd133e"
+                [
+                    {
+                        "id": "NA12878",
+                        "chr": "chr21",
+                        "region": "chr21:16600000-16800000"
+                    },
+                    "NA12878_chr21_null_ligate.vcf.gz",
+                    "VcfFile [chromosomes=[chr21], sampleCount=1, variantCount=211, phased=false, phasedAutodetect=false]",
+                    "66d0bfb31b037fb57d6b56e65b7cd6a7"
+                ],
+                [
+                    {
+                        "id": "NA12878",
+                        "chr": "chr22",
+                        "region": "chr22:16600000-16800000"
+                    },
+                    "NA12878_chr22_null_ligate.vcf.gz",
+                    "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=266, phased=false, phasedAutodetect=false]",
+                    "58751684e0168ad0485ba3510e0cfd3e"
+                ],
+                [
+                    {
+                        "id": "NA19401",
+                        "chr": "chr21",
+                        "region": "chr21:16600000-16800000"
+                    },
+                    "NA19401_chr21_null_ligate.vcf.gz",
+                    "VcfFile [chromosomes=[chr21], sampleCount=1, variantCount=211, phased=false, phasedAutodetect=false]",
+                    "66d0bfb31b037fb57d6b56e65b7cd6a7"
+                ],
+                [
+                    {
+                        "id": "NA19401",
+                        "chr": "chr22",
+                        "region": "chr22:16600000-16800000"
+                    },
+                    "NA19401_chr22_null_ligate.vcf.gz",
+                    "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=266, phased=false, phasedAutodetect=false]",
+                    "58751684e0168ad0485ba3510e0cfd3e"
+                ]
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-09-15T09:04:33.581167"
-    },
-    "merged": {
-        "content": [
-            "chr21\t16609998\tchr21:16609998:A:G\tA\tG\t.\t.\tRAF=0.00125156;AF=0;INFO=1\tGT:DS:GP:HS\t0/0:0:1,0,0:0"
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-03-01T13:00:44.91963315"
+        "timestamp": "2025-11-27T11:10:39.309436558"
     }
 }
\ No newline at end of file