diff --git a/CHANGELOG.md b/CHANGELOG.md
index 23f93f12..4adec731 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#248](https://github.com/nf-core/phaseimpute/pull/248) - Add chromosomes concatenation to `BAM_GL_BCFTOOLS`
 - [#259](https://github.com/nf-core/phaseimpute/pull/259) - Add `publish_all` arguments to all workflow level nf-test.
 - [#272](https://github.com/nf-core/phaseimpute/pull/272) - Add genetic map detection and convertion for all phasing and imputation tools. Update usage.
+- [#](https://github.com/nf-core/phaseimpute/pull/) - Add `chunk_version` parameter to control which Glimpse version to use to chunk.
 
 ### `Changed`
 
diff --git a/conf/test_full.config b/conf/test_full.config
index 00ab556d..62455864 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -33,6 +33,7 @@ params {
     normalize      = true
     compute_freq   = false
     phase          = false
+    chunk_version  = "V2"
 
     // Validation optional args
     min_val_gl = 0
diff --git a/main.nf b/main.nf
index 99ea537d..4a3228a7 100644
--- a/main.nf
+++ b/main.nf
@@ -60,7 +60,7 @@ workflow NFCORE_PHASEIMPUTE {
     rename_chr       // parameter: rename chromosome prefix
     max_chr_names    // parameter: max number of chr to show in message
     params_simulate  // map: parameters use for simulation step [depth: float, genotype: path]
-    params_panelprep // map: parameters use for panelprep step  [normalize: boolean, remove_samples: string, compute_freq: boolean, phase: boolean, chunk_model: string ]
+    params_panelprep // map: parameters use for panelprep step  [normalize: boolean, remove_samples: string, compute_freq: boolean, phase: boolean, chunk_model: string, chunk_version: string ]
     params_impute    // map: parameters use for imputation step [batch_size: integer, k_val: integer, n_gen: integer, buffer: integer]
     params_validate  // map: parameters use for validation step [bins: string, min_val_gl: float, min_val_dp: integer]
     params_multiqc   // map: parameters use for multiqc report  [config: path, logo: path, methods_description: string]
@@ -166,7 +166,8 @@ workflow {
         remove_samples: params.remove_samples,
         compute_freq  : params.compute_freq,
         phase         : params.phase,
-        chunk_model   : params.chunk_model
+        chunk_model   : params.chunk_model,
+        chunk_version : params.chunk_version
     ]
 
     def params_impute = [
diff --git a/nextflow.config b/nextflow.config
index af23ed99..5d00fe2f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -25,6 +25,7 @@ params {
     compute_freq                = false
     remove_samples              = null
     chunk_model                 = 'sequential'
+    chunk_version               = 'V1'
 
     // ChrCheck parameters
     rename_chr                  = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index cee82d7c..a7b661b7 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -144,6 +144,13 @@
                     "enum": ["recursive", "sequential"],
                     "default": "sequential",
                     "hidden": true
+                },
+                "chunk_version": {
+                    "type": "string",
+                    "description": "Glimpse version to use for chunking",
+                    "enum": ["V1", "V2"],
+                    "default": "V1",
+                    "hidden": true
                 }
             }
         },
diff --git a/subworkflows/local/vcf_chunk_glimpse/main.nf b/subworkflows/local/vcf_chunk_glimpse/main.nf
index d2bbffaa..3bd09a9e 100644
--- a/subworkflows/local/vcf_chunk_glimpse/main.nf
+++ b/subworkflows/local/vcf_chunk_glimpse/main.nf
@@ -6,7 +6,8 @@ workflow VCF_CHUNK_GLIMPSE {
     take:
     ch_reference  // channel (mandatory): [ [panel_id, chr], vcf, csi ]
     ch_map        // channel (optional) : [ [panel_id, chr], map ]
-    chunk_model   // channel : model
+    chunk_model   // value : model
+    chunk_version // value : glimpse version to use
 
     main:
 
@@ -14,44 +15,21 @@ workflow VCF_CHUNK_GLIMPSE {
     ch_vcf_csi_chr = ch_reference
         .map{metaPC, vcf, csi -> [metaPC, vcf, csi, metaPC.chr]}
 
-    // Make chunks with Glimpse1
-    GLIMPSE_CHUNK(ch_vcf_csi_chr)
-
-    // Rearrange chunks into channel for QUILT
-    ch_chunks_quilt = GLIMPSE_CHUNK.out.chunk_chr
-        .splitText()
-        .map { metaPC, line ->
-            def fields = line.split("\t")
-            def startEnd = fields[2].split(':')[1].split('-')
-            [metaPC, metaPC.chr, startEnd[0], startEnd[1]]
-        }
-
-    // Rearrange chunks into channel for GLIMPSE1 and GLIMPSE2
-    ch_chunks_glimpse1 = GLIMPSE_CHUNK.out.chunk_chr
-        .splitCsv(
-            header: ['ID', 'Chr', 'RegionIn', 'RegionOut', 'Size1', 'Size2'],
-            sep: "\t", skip: 0
-        )
-        .map { metaPC, it -> [metaPC, it["RegionIn"], it["RegionOut"]]}
-
-    ch_input_glimpse2 = ch_vcf_csi_chr
-        .combine(ch_map, by:0)
-
-    GLIMPSE2_CHUNK(ch_input_glimpse2, chunk_model)
-
-    // Rearrange channels
-    ch_chunks_glimpse2 = GLIMPSE2_CHUNK.out.chunk_chr
-        .splitCsv(
-            header: [
-                'ID', 'Chr', 'RegionBuf', 'RegionCnk', 'WindowCm',
-                'WindowMb', 'NbTotVariants', 'NbComVariants'
-            ], sep: "\t", skip: 0
-        )
-        .map { metaPC, it -> [metaPC, it["RegionBuf"], it["RegionCnk"]]}
+    if (chunk_version == "V1") {
+        // Make chunks with Glimpse1
+        GLIMPSE_CHUNK(ch_vcf_csi_chr)
+
+        ch_chunks = GLIMPSE_CHUNK.out.chunk_chr
+    } else if (chunk_version == "V2") {
+        ch_input_glimpse2 = ch_vcf_csi_chr
+            .combine(ch_map, by:0)
+
+        GLIMPSE2_CHUNK(ch_input_glimpse2, chunk_model)
+        ch_chunks = GLIMPSE2_CHUNK.out.chunk_chr
+    } else {
+        error ("Parameter chunk_version should be V1 or V2, found: ${chunk_version}.")
+    }
 
     emit:
-    chunks                    = GLIMPSE_CHUNK.out.chunk_chr           // channel:  [ [panel_id, chr], txt ]
-    chunks_quilt              = ch_chunks_quilt                       // channel:  [ [panel_id, chr], chr,  start, end ]
-    chunks_glimpse1           = ch_chunks_glimpse1                    // channel:  [ [panel_id, chr], chr,  region1, region2 ]
-    chunks_glimpse2           = ch_chunks_glimpse2                    // channel:  [ [panel_id, chr], chr,  region1, region2 ]
+    chunks         = ch_chunks         // channel:  [ [panel_id, chr], txt ]
 }
diff --git a/subworkflows/local/vcf_chunk_glimpse/meta.yml b/subworkflows/local/vcf_chunk_glimpse/meta.yml
index 57282572..4b6349cb 100644
--- a/subworkflows/local/vcf_chunk_glimpse/meta.yml
+++ b/subworkflows/local/vcf_chunk_glimpse/meta.yml
@@ -43,6 +43,12 @@ input:
         - recursive
         - sequential
         - uniform-number-variants
+  - chunk_version:
+      description: Glimpse version to chunk
+      type: string
+      enum:
+        - V1
+        - V2
 output:
   - chunks:
       description: Channel with chunks files
diff --git a/subworkflows/local/vcf_chunk_glimpse/tests/main.nf.test b/subworkflows/local/vcf_chunk_glimpse/tests/main.nf.test
index e654a8e7..4f895bfc 100644
--- a/subworkflows/local/vcf_chunk_glimpse/tests/main.nf.test
+++ b/subworkflows/local/vcf_chunk_glimpse/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_workflow {
     tag "glimpse2"
     tag "glimpse2/chunk"
 
-    test("Chunks with Map") {
+    test("Chunks with Map - V1") {
         when {
             workflow {
                 """
@@ -36,14 +36,15 @@ nextflow_workflow {
                 input[1] = channel.of(
                     [
                         [panel_id: "1000GP", chr: "chr22"],
-                        file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38_chr22.glimpse.map", checkIfExist:true)
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr22.glimpse.map", checkIfExist:true)
                     ],
                     [
                         [panel_id: "1000GP", chr: "chr21"],
-                        file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38_chr21.glimpse.map", checkIfExist:true)
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr21.glimpse.map", checkIfExist:true)
                     ]
                 )
                 input[2] = "recursive"
+                input[3] = "V1"
                 """
             }
         }
@@ -52,7 +53,7 @@ nextflow_workflow {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    workflow.out,
+                    workflow.out.chunks,
                     workflow.out.chunks.collect{
                         path(it[1]).readLines()
                     }
@@ -62,7 +63,53 @@ nextflow_workflow {
         }
     }
 
-    test("Chunks without Map") {
+    test("Chunks with Map - V2") {
+        when {
+            workflow {
+                """
+                input[0] = channel.of(
+                    [
+                        [panel_id: "1000GP", chr: "chr22"],
+                        file(params.pipelines_testdata_base_path + "hum_data/panel/chr22/1000GP.chr22.s.norel.vcf.gz", checkIfExist:true),
+                        file(params.pipelines_testdata_base_path + "hum_data/panel/chr22/1000GP.chr22.s.norel.vcf.gz.csi", checkIfExist:true),
+                    ],
+                    [
+                        [panel_id: "1000GP", chr: "chr21"],
+                        file(params.pipelines_testdata_base_path + "hum_data/panel/chr21/1000GP.chr21.s.norel.vcf.gz", checkIfExist:true),
+                        file(params.pipelines_testdata_base_path + "hum_data/panel/chr21/1000GP.chr21.s.norel.vcf.gz.csi", checkIfExist:true),
+                    ]
+                )
+                input[1] = channel.of(
+                    [
+                        [panel_id: "1000GP", chr: "chr22"],
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr22.glimpse.map", checkIfExist:true)
+                    ],
+                    [
+                        [panel_id: "1000GP", chr: "chr21"],
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr21.glimpse.map", checkIfExist:true)
+                    ]
+                )
+                input[2] = "recursive"
+                input[3] = "V2"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.chunks,
+                    workflow.out.chunks.collect{
+                        path(it[1]).readLines()
+                    }
+                ).match()
+                }
+            )
+        }
+    }
+
+    test("Chunks without Map - V1") {
         when {
             workflow {
                 """
@@ -83,6 +130,7 @@ nextflow_workflow {
                     [[panel_id: "1000GP", chr: "chr21"], []]
                 )
                 input[2] = "recursive"
+                input[3] = "V1"
                 """
             }
         }
@@ -91,7 +139,7 @@ nextflow_workflow {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    workflow.out,
+                    workflow.out.chunks,
                     workflow.out.chunks.collect{
                         path(it[1]).readLines()
                     }
@@ -101,7 +149,7 @@ nextflow_workflow {
         }
     }
 
-    test("Chunks with sequential model") {
+    test("Chunks with sequential model - V2") {
         when {
             workflow {
                 """
@@ -122,6 +170,7 @@ nextflow_workflow {
                     [[panel_id: "1000GP", chr: "chr21"], []]
                 )
                 input[2] = "sequential"
+                input[3] = "V2"
                 """
             }
         }
@@ -130,7 +179,7 @@ nextflow_workflow {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    workflow.out,
+                    workflow.out.chunks,
                     workflow.out.chunks.collect{
                         path(it[1]).readLines()
                     }
diff --git a/subworkflows/local/vcf_chunk_glimpse/tests/main.nf.test.snap b/subworkflows/local/vcf_chunk_glimpse/tests/main.nf.test.snap
index 660098eb..d7913e06 100644
--- a/subworkflows/local/vcf_chunk_glimpse/tests/main.nf.test.snap
+++ b/subworkflows/local/vcf_chunk_glimpse/tests/main.nf.test.snap
@@ -1,252 +1,22 @@
 {
-    "Chunks without Map": {
+    "Chunks without Map - V1": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "1000GP_chr21.txt:md5,64ca4a1655363e4a4e558836e5ac12f9"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "1000GP_chr22.txt:md5,3344e171251722cf58ae31136da223ac"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21",
-                        "16570070",
-                        "16595525"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21",
-                        "16585483",
-                        "16609998"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22",
-                        "16570065",
-                        "16597215"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22",
-                        "16587172",
-                        "16609999"
-                    ]
-                ],
-                "2": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16570070-16595525",
-                        "chr21:16570070-16590513"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16585483-16609998",
-                        "chr21:16590521-16609998"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16570065-16597215",
-                        "chr22:16570065-16592216"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16587172-16609999",
-                        "chr22:16592229-16609999"
-                    ]
-                ],
-                "3": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16570070-16609998",
-                        "chr21:16570070-16590517"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16570070-16609998",
-                        "chr21:16590518-16609998"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16570065-16609999",
-                        "chr22:16570065-16592222"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16570065-16609999",
-                        "chr22:16592223-16609999"
-                    ]
-                ],
-                "chunks": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "1000GP_chr21.txt:md5,64ca4a1655363e4a4e558836e5ac12f9"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "1000GP_chr22.txt:md5,3344e171251722cf58ae31136da223ac"
-                    ]
-                ],
-                "chunks_glimpse1": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16570070-16595525",
-                        "chr21:16570070-16590513"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16585483-16609998",
-                        "chr21:16590521-16609998"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16570065-16597215",
-                        "chr22:16570065-16592216"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16587172-16609999",
-                        "chr22:16592229-16609999"
-                    ]
-                ],
-                "chunks_glimpse2": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16570070-16609998",
-                        "chr21:16570070-16590517"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16570070-16609998",
-                        "chr21:16590518-16609998"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16570065-16609999",
-                        "chr22:16570065-16592222"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16570065-16609999",
-                        "chr22:16592223-16609999"
-                    ]
+            [
+                [
+                    {
+                        "panel_id": "1000GP",
+                        "chr": "chr21"
+                    },
+                    "1000GP_chr21.txt:md5,64ca4a1655363e4a4e558836e5ac12f9"
                 ],
-                "chunks_quilt": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21",
-                        "16570070",
-                        "16595525"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21",
-                        "16585483",
-                        "16609998"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22",
-                        "16570065",
-                        "16597215"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22",
-                        "16587172",
-                        "16609999"
-                    ]
+                [
+                    {
+                        "panel_id": "1000GP",
+                        "chr": "chr22"
+                    },
+                    "1000GP_chr22.txt:md5,3344e171251722cf58ae31136da223ac"
                 ]
-            },
+            ],
             [
                 [
                     "0\tchr21\tchr21:16570070-16595525\tchr21:16570070-16590513\t20444\t419",
@@ -258,260 +28,65 @@
                 ]
             ]
         ],
-        "timestamp": "2026-03-03T11:23:28.044105102",
+        "timestamp": "2026-09-01T18:58:22.306561207",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     },
-    "Chunks with Map": {
+    "Chunks with Map - V2": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "1000GP_chr21.txt:md5,64ca4a1655363e4a4e558836e5ac12f9"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "1000GP_chr22.txt:md5,3344e171251722cf58ae31136da223ac"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21",
-                        "16570070",
-                        "16595525"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21",
-                        "16585483",
-                        "16609998"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22",
-                        "16570065",
-                        "16597215"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22",
-                        "16587172",
-                        "16609999"
-                    ]
-                ],
-                "2": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16570070-16595525",
-                        "chr21:16570070-16590513"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16585483-16609998",
-                        "chr21:16590521-16609998"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16570065-16597215",
-                        "chr22:16570065-16592216"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16587172-16609999",
-                        "chr22:16592229-16609999"
-                    ]
-                ],
-                "3": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16570070-16609998",
-                        "chr21:16570070-16590517"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16570070-16609998",
-                        "chr21:16590518-16609998"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16570065-16609999",
-                        "chr22:16570065-16592222"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16570065-16609999",
-                        "chr22:16592223-16609999"
-                    ]
-                ],
-                "chunks": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "1000GP_chr21.txt:md5,64ca4a1655363e4a4e558836e5ac12f9"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "1000GP_chr22.txt:md5,3344e171251722cf58ae31136da223ac"
-                    ]
+            [
+                [
+                    {
+                        "panel_id": "1000GP",
+                        "chr": "chr21"
+                    },
+                    "1000GP_chr21.txt:md5,9f516b111710d22969aab9ad46850fdf"
                 ],
-                "chunks_glimpse1": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16570070-16595525",
-                        "chr21:16570070-16590513"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16585483-16609998",
-                        "chr21:16590521-16609998"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16570065-16597215",
-                        "chr22:16570065-16592216"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16587172-16609999",
-                        "chr22:16592229-16609999"
-                    ]
+                [
+                    {
+                        "panel_id": "1000GP",
+                        "chr": "chr22"
+                    },
+                    "1000GP_chr22.txt:md5,3bfef0fe24564dd3f759ee390345970a"
+                ]
+            ],
+            [
+                [
+                    "0\tchr21\tchr21:16570070-16609998\tchr21:16570070-16590517\t0.0566807\t20443\t419\t201",
+                    "1\tchr21\tchr21:16570070-16609998\tchr21:16590518-16609998\t0.0107975\t19477\t417\t220"
                 ],
-                "chunks_glimpse2": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16570070-16609998",
-                        "chr21:16570070-16590517"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16570070-16609998",
-                        "chr21:16590518-16609998"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16570065-16609999",
-                        "chr22:16570065-16592222"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16570065-16609999",
-                        "chr22:16592223-16609999"
-                    ]
+                [
+                    "0\tchr22\tchr22:16570065-16609999\tchr22:16570065-16592222\t0.0598867\t22151\t452\t218",
+                    "1\tchr22\tchr22:16570065-16609999\tchr22:16592223-16609999\t0.0331761\t17770\t451\t200"
+                ]
+            ]
+        ],
+        "timestamp": "2026-09-01T18:58:14.220996698",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
+        }
+    },
+    "Chunks with Map - V1": {
+        "content": [
+            [
+                [
+                    {
+                        "panel_id": "1000GP",
+                        "chr": "chr21"
+                    },
+                    "1000GP_chr21.txt:md5,64ca4a1655363e4a4e558836e5ac12f9"
                 ],
-                "chunks_quilt": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21",
-                        "16570070",
-                        "16595525"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21",
-                        "16585483",
-                        "16609998"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22",
-                        "16570065",
-                        "16597215"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22",
-                        "16587172",
-                        "16609999"
-                    ]
+                [
+                    {
+                        "panel_id": "1000GP",
+                        "chr": "chr22"
+                    },
+                    "1000GP_chr22.txt:md5,3344e171251722cf58ae31136da223ac"
                 ]
-            },
+            ],
             [
                 [
                     "0\tchr21\tchr21:16570070-16595525\tchr21:16570070-16590513\t20444\t419",
@@ -523,275 +98,45 @@
                 ]
             ]
         ],
-        "timestamp": "2026-03-03T11:23:15.791547471",
+        "timestamp": "2026-09-01T18:58:04.139816463",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     },
-    "Chunks with sequential model": {
+    "Chunks with sequential model - V2": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "1000GP_chr21.txt:md5,64ca4a1655363e4a4e558836e5ac12f9"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "1000GP_chr22.txt:md5,3344e171251722cf58ae31136da223ac"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21",
-                        "16570070",
-                        "16595525"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21",
-                        "16585483",
-                        "16609998"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22",
-                        "16570065",
-                        "16597215"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22",
-                        "16587172",
-                        "16609999"
-                    ]
-                ],
-                "2": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16570070-16595525",
-                        "chr21:16570070-16590513"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16585483-16609998",
-                        "chr21:16590521-16609998"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16570065-16597215",
-                        "chr22:16570065-16592216"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16587172-16609999",
-                        "chr22:16592229-16609999"
-                    ]
-                ],
-                "3": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:1-16609998",
-                        "chr21:1-16590145"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16570070-1248956422",
-                        "chr21:16590146-1248956422"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:1-16609999",
-                        "chr22:1-16590520"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16570065-1248956422",
-                        "chr22:16590521-1248956422"
-                    ]
-                ],
-                "chunks": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "1000GP_chr21.txt:md5,64ca4a1655363e4a4e558836e5ac12f9"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "1000GP_chr22.txt:md5,3344e171251722cf58ae31136da223ac"
-                    ]
-                ],
-                "chunks_glimpse1": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16570070-16595525",
-                        "chr21:16570070-16590513"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16585483-16609998",
-                        "chr21:16590521-16609998"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16570065-16597215",
-                        "chr22:16570065-16592216"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16587172-16609999",
-                        "chr22:16592229-16609999"
-                    ]
-                ],
-                "chunks_glimpse2": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:1-16609998",
-                        "chr21:1-16590145"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21:16570070-1248956422",
-                        "chr21:16590146-1248956422"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:1-16609999",
-                        "chr22:1-16590520"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22:16570065-1248956422",
-                        "chr22:16590521-1248956422"
-                    ]
+            [
+                [
+                    {
+                        "panel_id": "1000GP",
+                        "chr": "chr21"
+                    },
+                    "1000GP_chr21.txt:md5,e6156c3f8f0273b4d5c49784300ecc86"
                 ],
-                "chunks_quilt": [
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21",
-                        "16570070",
-                        "16595525"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr21"
-                        },
-                        "chr21",
-                        "16585483",
-                        "16609998"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22",
-                        "16570065",
-                        "16597215"
-                    ],
-                    [
-                        {
-                            "panel_id": "1000GP",
-                            "chr": "chr22"
-                        },
-                        "chr22",
-                        "16587172",
-                        "16609999"
-                    ]
+                [
+                    {
+                        "panel_id": "1000GP",
+                        "chr": "chr22"
+                    },
+                    "1000GP_chr22.txt:md5,4714831df331b665e634eb1a86a84156"
                 ]
-            },
+            ],
             [
                 [
-                    "0\tchr21\tchr21:16570070-16595525\tchr21:16570070-16590513\t20444\t419",
-                    "1\tchr21\tchr21:16585483-16609998\tchr21:16590521-16609998\t19478\t417"
+                    "0\tchr21\tchr21:1-16609998\tchr21:1-16590145\t0.0199917\t19992\t414\t201",
+                    "1\tchr21\tchr21:16570070-1248956422\tchr21:16590146-1248956422\t0.019769\t19769\t422\t221"
                 ],
                 [
-                    "0\tchr22\tchr22:16570065-16597215\tchr22:16570065-16592216\t22152\t452",
-                    "1\tchr22\tchr22:16587172-16609999\tchr22:16592229-16609999\t17771\t451"
+                    "0\tchr22\tchr22:1-16609999\tchr22:1-16590520\t0.0204135\t20413\t410\t201",
+                    "1\tchr22\tchr22:16570065-1248956422\tchr22:16590521-1248956422\t0.019437\t19437\t493\t219"
                 ]
             ]
         ],
-        "timestamp": "2026-03-03T11:23:40.295298786",
+        "timestamp": "2026-09-01T18:58:30.252352768",
         "meta": {
-            "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
         }
     }
 }
\ No newline at end of file
diff --git a/subworkflows/local/vcf_chunk_glimpse/tests/nextflow.config b/subworkflows/local/vcf_chunk_glimpse/tests/nextflow.config
index 7191780d..43696b73 100644
--- a/subworkflows/local/vcf_chunk_glimpse/tests/nextflow.config
+++ b/subworkflows/local/vcf_chunk_glimpse/tests/nextflow.config
@@ -1,9 +1,4 @@
 process {
-    resourceLimits = [
-        memory : "2.GB",
-        cpus : 2,
-        time : "1h"
-    ]
     withName: GLIMPSE2_CHUNK {
         ext.args = ["--window-mb 0.01", "--window-cm 0.01", "--window-count 200", "--buffer-mb 0.005", "--buffer-cm 0.005", "--buffer-count 30"].join(' ')
         ext.prefix = { "${meta.panel_id}_${meta.chr}" }
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index d514c9c9..7e4f0887 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -3,7 +3,8 @@
 
 params {
     // Base directory for test data
-    test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/modules"
+    test_data_base             = "https://raw.githubusercontent.com/nf-core/test-datasets/modules"
+    modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
 
     test_data {
         'sarscov2' {
diff --git a/tests/csv/map_glimpse.csv b/tests/csv/map_glimpse.csv
index 830f4d20..e81e0e4d 100644
--- a/tests/csv/map_glimpse.csv
+++ b/tests/csv/map_glimpse.csv
@@ -1,3 +1,3 @@
 chr,map
-chr21,https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/reference_genome/GRCh38_chr21.glimpse.map
-chr22,https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/reference_genome/GRCh38_chr22.glimpse.map
+chr21,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr21.plink.map
+chr22,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr22.plink.map
diff --git a/tests/csv/map_plink.csv b/tests/csv/map_plink.csv
index b8f8fb3c..e81e0e4d 100644
--- a/tests/csv/map_plink.csv
+++ b/tests/csv/map_plink.csv
@@ -1,3 +1,3 @@
 chr,map
-chr21,https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/reference_genome/GRCh38_chr21.plink.map
-chr22,https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/reference_genome/GRCh38_chr22.plink.map
+chr21,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr21.plink.map
+chr22,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genetic_map/genome.GRCh38.chr22.plink.map
diff --git a/tests/function.nf.test b/tests/function.nf.test
index 801f435b..38a2c0ab 100644
--- a/tests/function.nf.test
+++ b/tests/function.nf.test
@@ -110,6 +110,62 @@ nextflow_function {
         }
     }
 
+    test("Prepare chunks channel Glimpse - input Glimpse V2 - with chunks") {
+        function "chunkPrepareChannel"
+        tag "chunkPrepareChannel"
+        when {
+            function {
+                """
+                input[0] = channel.of([
+                    [id: "1000GP", chr: "chr21"],
+                    file(params.pipelines_testdata_base_path + "hum_data/panel/chr21/1000GP.chr21_chunks_v2.txt", checkIfExist:true)
+                ])
+                input[1] = channel.of([
+                    [chr: "chr21", region: "chr21:16570000-16610000"],
+                    "chr21:16570000-16610000"
+                ])
+                input[2] = "glimpse1"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.success },
+                { assert snapshot(function.result).match()}
+            )
+        }
+    }
+
+    test("Prepare chunks channel Glimpse - input wrong format") {
+        function "chunkPrepareChannel"
+        tag "chunkPrepareChannel"
+        when {
+            function {
+                """
+                ch_chunks = channel.of([
+                    "0\tchr22\tchr22:16570065-16597215\tchr22:16570065-16592216\t22152\t452\textrafield",
+                    "1\tchr22\tchr22:16587172-16609999\tchr22:16592229-16609999\t17771\t451\textrafield"
+                ]).collectFile(name: 'chunks.txt', newLine: true)
+                input[0] = channel.of([
+                    [id: "1000GP", chr: "chr21"]
+                ]).combine(ch_chunks)
+                input[1] = channel.of([
+                    [chr: "chr21", region: "chr21:16570000-16610000"],
+                    "chr21:16570000-16610000"
+                ])
+                input[2] = "glimpse1"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert function.failed }
+            )
+        }
+    }
+
     test("Prepare chunks channel error tool") {
         function "chunkPrepareChannel"
         tag "chunkPrepareChannel"
diff --git a/tests/function.nf.test.snap b/tests/function.nf.test.snap
index 23448808..e7c56948 100644
--- a/tests/function.nf.test.snap
+++ b/tests/function.nf.test.snap
@@ -11,6 +11,18 @@
             "nextflow": "25.10.0"
         }
     },
+    "Prepare chunks channel Glimpse - input Glimpse V2 - with chunks": {
+        "content": [
+            {
+                
+            }
+        ],
+        "timestamp": "2026-09-01T19:04:57.436505706",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
+        }
+    },
     "Prepare chunks channel Glimpse - no chunks": {
         "content": [
             {
diff --git a/tests/test_all.nf.test.snap b/tests/test_all.nf.test.snap
index e6b4655c..0ca9515b 100644
--- a/tests/test_all.nf.test.snap
+++ b/tests/test_all.nf.test.snap
@@ -2,7 +2,7 @@
     "Check test_all - no map - no chunks": {
         "content": [
             {
-                "workflow size": 240,
+                "workflow size": 238,
                 "versions": {
                     "ADDCOLUMNS": {
                         "gawk": "5.3.1"
@@ -89,9 +89,6 @@
                     "GAWK_TRUTH": {
                         "gawk": "5.3.1"
                     },
-                    "GLIMPSE2_CHUNK": {
-                        "glimpse2": "2.0.0"
-                    },
                     "GLIMPSE2_CONCORDANCE": {
                         "glimpse2": "2.0.0"
                     },
@@ -431,9 +428,6 @@
                     "prep_panel/chunks/glimpse1",
                     "prep_panel/chunks/glimpse1/1000GP_chr21_chunks_glimpse1.txt",
                     "prep_panel/chunks/glimpse1/1000GP_chr22_chunks_glimpse1.txt",
-                    "prep_panel/chunks/glimpse2",
-                    "prep_panel/chunks/glimpse2/1000GP_chr21_chunks_glimpse2.txt",
-                    "prep_panel/chunks/glimpse2/1000GP_chr22_chunks_glimpse2.txt",
                     "prep_panel/concat",
                     "prep_panel/concat/1000GP.panel.vcf.gz",
                     "prep_panel/concat/1000GP.panel.vcf.gz.tbi",
@@ -603,8 +597,6 @@
                     "samtools-coverage_Reads.txt:md5,b4d9f56aedae09971ff3353eea5a9451",
                     "1000GP_chr21_chunks_glimpse1.txt:md5,64ca4a1655363e4a4e558836e5ac12f9",
                     "1000GP_chr22_chunks_glimpse1.txt:md5,3344e171251722cf58ae31136da223ac",
-                    "1000GP_chr21_chunks_glimpse2.txt:md5,834dea86a63b5a49d36f53c0ac7e01a2",
-                    "1000GP_chr22_chunks_glimpse2.txt:md5,c363e235162ca0f7d22e5604c192e256",
                     "1000GP_chr21.hap.gz:md5,64d7fdfc96ce79848cf9c3c220e6774f",
                     "1000GP_chr21.legend.gz:md5,3f7edc4c153521a0871c9d51f7da2372",
                     "1000GP_chr21.samples:md5,d8ca3e8336976001de8df6be7ae236cb",
@@ -952,16 +944,16 @@
                 }
             }
         ],
-        "timestamp": "2026-06-21T19:28:15.252414691",
+        "timestamp": "2026-09-02T15:11:35.015117606",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.0"
+            "nextflow": "26.04.6"
         }
     },
     "Check test_all - with map - no chunks": {
         "content": [
             {
-                "workflow size": 242,
+                "workflow size": 240,
                 "versions": {
                     "ADDCOLUMNS": {
                         "gawk": "5.3.1"
@@ -1054,9 +1046,6 @@
                     "GAWK_TRUTH": {
                         "gawk": "5.3.1"
                     },
-                    "GLIMPSE2_CHUNK": {
-                        "glimpse2": "2.0.0"
-                    },
                     "GLIMPSE2_CONCORDANCE": {
                         "glimpse2": "2.0.0"
                     },
@@ -1405,9 +1394,6 @@
                     "prep_panel/chunks/glimpse1",
                     "prep_panel/chunks/glimpse1/1000GP_chr21_chunks_glimpse1.txt",
                     "prep_panel/chunks/glimpse1/1000GP_chr22_chunks_glimpse1.txt",
-                    "prep_panel/chunks/glimpse2",
-                    "prep_panel/chunks/glimpse2/1000GP_chr21_chunks_glimpse2.txt",
-                    "prep_panel/chunks/glimpse2/1000GP_chr22_chunks_glimpse2.txt",
                     "prep_panel/concat",
                     "prep_panel/concat/1000GP.panel.vcf.gz",
                     "prep_panel/concat/1000GP.panel.vcf.gz.tbi",
@@ -1585,8 +1571,6 @@
                     "samtools-coverage_Reads.txt:md5,b4d9f56aedae09971ff3353eea5a9451",
                     "1000GP_chr21_chunks_glimpse1.txt:md5,64ca4a1655363e4a4e558836e5ac12f9",
                     "1000GP_chr22_chunks_glimpse1.txt:md5,3344e171251722cf58ae31136da223ac",
-                    "1000GP_chr21_chunks_glimpse2.txt:md5,5d68b3816a4cf607be3728237d2cfa2e",
-                    "1000GP_chr22_chunks_glimpse2.txt:md5,3bfef0fe24564dd3f759ee390345970a",
                     "1000GP_chr21.hap.gz:md5,64d7fdfc96ce79848cf9c3c220e6774f",
                     "1000GP_chr21.legend.gz:md5,3f7edc4c153521a0871c9d51f7da2372",
                     "1000GP_chr21.samples:md5,d8ca3e8336976001de8df6be7ae236cb",
@@ -1934,10 +1918,10 @@
                 }
             }
         ],
-        "timestamp": "2026-06-21T19:31:43.527166058",
+        "timestamp": "2026-09-02T15:09:59.329236171",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.0"
+            "nextflow": "26.04.6"
         }
     }
 }
\ No newline at end of file
diff --git a/tests/test_dog.nf.test.snap b/tests/test_dog.nf.test.snap
index 00f2e7fe..00e888b7 100644
--- a/tests/test_dog.nf.test.snap
+++ b/tests/test_dog.nf.test.snap
@@ -2,7 +2,7 @@
     "Check test_dog - no map - no chunk": {
         "content": [
             {
-                "workflow size": 91,
+                "workflow size": 89,
                 "versions": {
                     "BAMCHREXTRACT": {
                         "samtools": "1.23"
@@ -53,9 +53,6 @@
                     "GAWK_POSFILE_IMPUTE": {
                         "gawk": "5.3.1"
                     },
-                    "GLIMPSE2_CHUNK": {
-                        "glimpse2": "2.0.0"
-                    },
                     "GLIMPSE2_LIGATE": {
                         "glimpse2": "2.0.0"
                     },
@@ -226,9 +223,6 @@
                     "prep_panel/chunks/glimpse1",
                     "prep_panel/chunks/glimpse1/658Dog_chr21_chunks_glimpse1.txt",
                     "prep_panel/chunks/glimpse1/658Dog_chr22_chunks_glimpse1.txt",
-                    "prep_panel/chunks/glimpse2",
-                    "prep_panel/chunks/glimpse2/658Dog_chr21_chunks_glimpse2.txt",
-                    "prep_panel/chunks/glimpse2/658Dog_chr22_chunks_glimpse2.txt",
                     "prep_panel/csv",
                     "prep_panel/csv/chunks_glimpse1.csv",
                     "prep_panel/csv/panel.csv",
@@ -287,8 +281,6 @@
                     "multiqc_general_stats.txt:md5,308b31e233de70b3e1e7b9c093e58093",
                     "658Dog_chr21_chunks_glimpse1.txt:md5,fc93d5f473c8bff30c1244c968be6b8c",
                     "658Dog_chr22_chunks_glimpse1.txt:md5,846073f9a512a680f7e7155cc4ac1f70",
-                    "658Dog_chr21_chunks_glimpse2.txt:md5,76a5a9b772ce2f8e6f5bef47743a24aa",
-                    "658Dog_chr22_chunks_glimpse2.txt:md5,087f226af57448b5777a0fac6806a776",
                     "658Dog_chr21.hap.gz:md5,0730a032b058730d6abdbf836bb57ba7",
                     "658Dog_chr21.legend.gz:md5,3eaa371bdf51f74f9749fd35e9e834a6",
                     "658Dog_chr21.samples:md5,92a2aa1d024ca2001cfec04671082eff",
@@ -450,10 +442,10 @@
                 }
             }
         ],
-        "timestamp": "2026-06-21T18:08:14.707538039",
+        "timestamp": "2026-09-02T15:21:12.966406137",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.0"
+            "nextflow": "26.04.6"
         }
     }
 }
\ No newline at end of file
diff --git a/tests/test_panelprep.nf.test.snap b/tests/test_panelprep.nf.test.snap
index da41889d..bf6dddf5 100644
--- a/tests/test_panelprep.nf.test.snap
+++ b/tests/test_panelprep.nf.test.snap
@@ -2,7 +2,7 @@
     "Check test_panelprep - no map - no chunks": {
         "content": [
             {
-                "workflow size": 34,
+                "workflow size": 32,
                 "versions": {
                     "BCFTOOLS_CONVERT": {
                         "bcftools": "1.23.1"
@@ -25,9 +25,6 @@
                     "GAWK": {
                         "gawk": "5.3.1"
                     },
-                    "GLIMPSE2_CHUNK": {
-                        "glimpse2": "2.0.0"
-                    },
                     "GLIMPSE_CHUNK": {
                         "glimpse": "1.1.1"
                     },
@@ -73,9 +70,6 @@
                     "prep_panel/chunks/glimpse1",
                     "prep_panel/chunks/glimpse1/1000GP_chr21_chunks_glimpse1.txt",
                     "prep_panel/chunks/glimpse1/1000GP_chr22_chunks_glimpse1.txt",
-                    "prep_panel/chunks/glimpse2",
-                    "prep_panel/chunks/glimpse2/1000GP_chr21_chunks_glimpse2.txt",
-                    "prep_panel/chunks/glimpse2/1000GP_chr22_chunks_glimpse2.txt",
                     "prep_panel/csv",
                     "prep_panel/csv/chunks_glimpse1.csv",
                     "prep_panel/csv/panel.csv",
@@ -129,8 +123,6 @@
                     "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
                     "1000GP_chr21_chunks_glimpse1.txt:md5,64ca4a1655363e4a4e558836e5ac12f9",
                     "1000GP_chr22_chunks_glimpse1.txt:md5,3344e171251722cf58ae31136da223ac",
-                    "1000GP_chr21_chunks_glimpse2.txt:md5,834dea86a63b5a49d36f53c0ac7e01a2",
-                    "1000GP_chr22_chunks_glimpse2.txt:md5,c363e235162ca0f7d22e5604c192e256",
                     "1000GP_chr21.hap.gz:md5,d18ac86ed7080c6527aade3b6717ebb0",
                     "1000GP_chr21.legend.gz:md5,3f7edc4c153521a0871c9d51f7da2372",
                     "1000GP_chr21.samples:md5,ba53fdcb71cd6dbd218e0e932555086c",
@@ -191,10 +183,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-06-21T18:16:13.344773591",
+        "timestamp": "2026-09-02T15:28:40.592623143",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "26.04.0"
+            "nextflow": "26.04.6"
         }
     },
     "Check test_panelprep - with map - with chunks": {
diff --git a/workflows/phaseimpute/function.nf b/workflows/phaseimpute/function.nf
index 4078957b..1717b4a2 100644
--- a/workflows/phaseimpute/function.nf
+++ b/workflows/phaseimpute/function.nf
@@ -12,27 +12,34 @@ def chunkPrepareChannel(ch_chunks, ch_region, tool) {
             empty: true
                 return [metaPC, region]
         }
+
+    def ch_chunks_in_out = channel.of()
+
+    ch_chunks_in_out = ch_chunks_branched.txt.map { metaPC, txt -> [metaPC, file(txt)]}
+        .splitCsv(sep:"\t", skip:0)
+        .map{ meta, row ->
+            if (row.size() == 6 ) {
+                return [ meta, row[2], row[3] ] // header is 'ID', 'Chr', 'RegionIn', 'RegionOut', 'Size1', 'Size2'
+            }
+            if (row.size() == 8) {
+                return [ meta, row[3], row[2] ] // header is 'ID', 'Chr', 'RegionBuff', 'RegionCnk', 'WindowCm', 'WindowMb', 'NbTotVariants', 'NbComVariants'
+            }
+            error "Chunks csv should have either 6 columns (glimpse V1 format) or 8 columns (glimpse V2 format)"
+        }
+
     if(tool == "glimpse1"){
-        def ch_chunks_txt = ch_chunks_branched.txt.map { metaPC, txt -> [metaPC, file(txt)]}
-            .splitCsv(header: ['ID', 'Chr', 'RegionIn', 'RegionOut', 'Size1', 'Size2'], sep: "\t", skip: 0)
-            .map { meta, it -> [meta, it["RegionIn"], it["RegionOut"]]}
         def ch_chunks_region = ch_chunks_branched.empty.map{
             metaPC, region -> [ metaPC, region, region ]
         }
-        return ch_chunks_txt.mix(ch_chunks_region)
+        return ch_chunks_in_out.mix(ch_chunks_region)
     } else if(tool == "quilt") {
-        def ch_chunks_txt = ch_chunks_branched.txt.map { metaC, txt -> [metaC, file(txt)]}
-            .splitCsv(header: ['ID', 'Chr', 'RegionIn', 'RegionOut', 'Size1', 'Size2'], sep: "\t", skip: 0)
-            .map { metaC, it ->
-                def startEnd = it["RegionIn"].split(':')[1].split('-')
-                [ metaC, metaC.chr, startEnd[0], startEnd[1] ]
+        return ch_chunks_in_out
+            .map{meta, region_in, _region_out -> [meta, region_in] }
+            .mix(ch_chunks_branched.empty)
+            .map { meta, it ->
+                def startEnd = it.split(':')[1].split('-')
+                [ meta, meta.chr, startEnd[0], startEnd[1] ]
             }
-        def ch_chunks_region = ch_chunks_branched.empty.map{
-            metaPC, region ->
-            def startEnd = region.split(':')[1].split('-')
-            [ metaPC, metaPC.chr, startEnd[0], startEnd[1] ]
-        }
-        return ch_chunks_txt.mix(ch_chunks_region)
     } else {
         error "ERROR: Only 'glimpse1' and 'quilt' output format are supported. Got ${tool}"
     }
diff --git a/workflows/phaseimpute/main.nf b/workflows/phaseimpute/main.nf
index 7595a1be..76212102 100644
--- a/workflows/phaseimpute/main.nf
+++ b/workflows/phaseimpute/main.nf
@@ -251,7 +251,8 @@ workflow PHASEIMPUTE {
             VCF_CHUNK_GLIMPSE(
                 VCF_NORMALIZE_BCFTOOLS.out.vcf_index,
                 ch_map_glimpse,
-                params_panelprep["chunk_model"]
+                params_panelprep["chunk_model"],
+                params_panelprep["chunk_version"]
             )
             ch_chunks  = VCF_CHUNK_GLIMPSE.out.chunks