diff --git a/CHANGELOG.md b/CHANGELOG.md
index 042b1474..bbc71090 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -64,6 +64,7 @@ Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co
 - [#148](https://github.com/nf-core/phaseimpute/pull/148) - Fix awsfulltest github action for manual dispatch
 - [#149](https://github.com/nf-core/phaseimpute/pull/149) - Remove the map file from the awsfulltest
 - [#152](https://github.com/nf-core/phaseimpute/pull/152) - Fix URLs in the documentation and remove tools citation in the README, use a white background for all images in the documentation.
+- [#157](https://github.com/nf-core/phaseimpute/pull/157) - Add `chunk_model` as parameter for better control over `GLIMPSE2_CHUNK` and set window size in `GLIMPSE1_CHUNK` and `GLIMPSE2_chunk` to 4mb to reduce number of chunks (empirical).
 
 ### `Fixed`
 
diff --git a/conf/steps/panel_prep.config b/conf/steps/panel_prep.config
index d578817a..3ab60861 100644
--- a/conf/steps/panel_prep.config
+++ b/conf/steps/panel_prep.config
@@ -41,8 +41,8 @@ process {
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_NORMALIZE_BCFTOOLS:BCFTOOLS_NORM' {
-        ext.args      = ["-m +any", "--no-version", "--output-type z", "--write-index=tbi"].join(' ')
-        ext.prefix    = { "${meta.id}_${meta.chr}_multiallelic" }
+        ext.args   = ["-m +any", "--no-version", "--output-type z", "--write-index=tbi"].join(' ')
+        ext.prefix = { "${meta.id}_${meta.chr}_multiallelic" }
         publishDir = [ enabled: false ]
     }
 
@@ -62,7 +62,7 @@ process {
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_NORMALIZE_BCFTOOLS:VCFLIB_VCFFIXUP' {
-        ext.prefix   = { "${meta.id}_${meta.chr}_fixup" }
+        ext.prefix = { "${meta.id}_${meta.chr}_fixup" }
         publishDir = [
             path: { "${params.outdir}/prep_panel/panel" },
             mode: params.publish_dir_mode,
@@ -72,7 +72,7 @@ process {
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_NORMALIZE_BCFTOOLS:BCFTOOLS_INDEX' {
-        ext.args     = "--tbi"
+        ext.args   = "--tbi"
         publishDir = [
             path: { "${params.outdir}/prep_panel/panel" },
             mode: params.publish_dir_mode,
@@ -88,6 +88,7 @@ process {
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_PHASE_SHAPEIT5:GLIMPSE2_CHUNK' {
+        ext.args   = "--window-mb 4"
         ext.prefix = { "${meta.id}_chunks" }
     }
 
@@ -123,7 +124,7 @@ process {
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_SITES_EXTRACT_BCFTOOLS:BCFTOOLS_CONVERT' {
-        ext.args = {"--haplegendsample ${meta.id}_${meta.chr}"}
+        ext.args   = {"--haplegendsample ${meta.id}_${meta.chr}"}
         publishDir = [
             path: { "${params.outdir}/prep_panel/haplegend/" },
             mode: params.publish_dir_mode,
@@ -184,6 +185,7 @@ process {
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CHUNK_GLIMPSE:GLIMPSE_CHUNK' {
+        ext.args   = "--window-size 4"
         ext.prefix = { "${meta.id}_${meta.chr}_chunks_glimpse1" }
         publishDir = [
             path: { "${params.outdir}/prep_panel/chunks/glimpse1/" },
@@ -194,7 +196,8 @@ process {
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CHUNK_GLIMPSE:GLIMPSE2_CHUNK' {
-        ext.prefix    = { "${meta.id}_${meta.chr}_chunks_glimpse2" }
+        ext.args   = "--window-mb 4"
+        ext.prefix = { "${meta.id}_${meta.chr}_chunks_glimpse2" }
         publishDir = [
             path: { "${params.outdir}/prep_panel/chunks/glimpse2/" },
             mode: params.publish_dir_mode,
diff --git a/conf/test_all.config b/conf/test_all.config
index 854f8664..c16d7904 100644
--- a/conf/test_all.config
+++ b/conf/test_all.config
@@ -33,6 +33,7 @@ params {
     phase        = true
     normalize    = true
     compute_freq = false
+    chunk_model  = "recursive"
 
     // Pipeline steps
     steps = "all"
diff --git a/conf/test_dog.config b/conf/test_dog.config
index 33755994..6ebc015e 100644
--- a/conf/test_dog.config
+++ b/conf/test_dog.config
@@ -32,6 +32,7 @@ params {
     normalize    = false
     compute_freq = false
     rename_chr   = true
+    chunk_model  = "recursive"
 
     // Input data
     input        = params.pipelines_testdata_base_path + "dog_data/csv/sample_dog.csv"
diff --git a/conf/test_panelprep.config b/conf/test_panelprep.config
index 181d81de..f62f2189 100644
--- a/conf/test_panelprep.config
+++ b/conf/test_panelprep.config
@@ -32,6 +32,7 @@ params {
     normalize      = true
     compute_freq   = true
     remove_samples = "HG00096,HG00097,HG00099,HG00100"
+    chunk_model    = "recursive"
 
     // Pipeline steps
     steps   = "panelprep"
diff --git a/main.nf b/main.nf
index a5e3fa05..f5303872 100644
--- a/main.nf
+++ b/main.nf
@@ -43,6 +43,7 @@ workflow NFCORE_PHASEIMPUTE {
     ch_map         // channel: map file for imputation
     ch_posfile     // channel: samplesheet read in from --posfile
     ch_chunks      // channel: samplesheet read in from --chunks
+    chunk_model    // parameter: chunk model
     ch_versions    // channel: versions of software used
 
     main:
@@ -101,6 +102,7 @@ workflow NFCORE_PHASEIMPUTE {
         ch_map,
         ch_posfile,
         ch_chunks,
+        chunk_model,
         ch_versions
     )
     emit:
@@ -141,6 +143,7 @@ workflow {
         PIPELINE_INITIALISATION.out.gmap,
         PIPELINE_INITIALISATION.out.posfile,
         PIPELINE_INITIALISATION.out.chunks,
+        PIPELINE_INITIALISATION.out.chunk_model,
         PIPELINE_INITIALISATION.out.versions
     )
     //
diff --git a/nextflow.config b/nextflow.config
index 14781b4a..3e402c96 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -10,7 +10,7 @@
 params {
 
     // steps
-    steps                        = null
+    steps                       = null
 
     // Input options
     input                       = null
@@ -24,6 +24,7 @@ params {
     normalize                   = true
     compute_freq                = false
     remove_samples              = null
+    chunk_model                 = 'sequential'
 
     // ChrCheck parameters
     rename_chr                  = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index c51892b8..3beb8382 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -132,6 +132,13 @@
                 "binaryref": {
                     "type": "string",
                     "description": "Whether to generate a binary reference file to be used with GLIMPSE2"
+                },
+                "chunk_model": {
+                    "type": "string",
+                    "description": "Model type to use for GLIMPSE2_CHUNK",
+                    "enum": ["recursive", "sequential"],
+                    "default": "sequential",
+                    "hidden": true
                 }
             }
         },
diff --git a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf
index 54fc07d1..21eab92c 100644
--- a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf
@@ -279,6 +279,9 @@ workflow PIPELINE_INITIALISATION {
     // Check that all input files have the correct index
     checkFileIndex(ch_input.mix(ch_input_truth, ch_ref_gen, ch_panel))
 
+    // Chunk model
+    chunk_model = params.chunk_model
+
     emit:
     input                = ch_input         // [ [meta], file, index ]
     input_truth          = ch_input_truth   // [ [meta], file, index ]
@@ -289,6 +292,7 @@ workflow PIPELINE_INITIALISATION {
     gmap                 = ch_map           // [ [map], map ]
     posfile              = ch_posfile       // [ [panel, chr], vcf, index, hap, legend ]
     chunks               = ch_chunks        // [ [chr], txt ]
+    chunk_model          = chunk_model
     versions             = ch_versions
 }
 
@@ -407,6 +411,9 @@ def validateInputParameters() {
             error("To use `--remove_samples` you need to include `--normalize`.")
         }
     }
+
+    // Check that the chunk model is provided
+    assert params.chunk_model : "No chunk model provided"
 }
 
 //
diff --git a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/tests/main.nf.test b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/tests/main.nf.test
index 238bc53c..2c7045c9 100644
--- a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/tests/main.nf.test
+++ b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/tests/main.nf.test
@@ -17,6 +17,7 @@ nextflow_workflow {
                 chunks = "../../../tests/csv/chunks.csv"
                 posfile = "../../../tests/csv/posfile.csv"
                 panel = "../../../tests/csv/panel.csv"
+                chunk_model = "recursive"
             }
             workflow {
                 """
@@ -49,6 +50,7 @@ nextflow_workflow {
                 posfile = "../../../tests/csv/posfile.csv"
                 panel = "../../../tests/csv/panel.csv"
                 input_region = "$moduleTestDir/region.csv"
+                chunk_model = "sequential"
             }
             workflow {
                 """
@@ -80,6 +82,7 @@ nextflow_workflow {
                 chunks = "../../../tests/csv/chunks.csv"
                 panel = "../../../tests/csv/panel.csv"
                 input_region = "$moduleTestDir/region.csv"
+                chunk_model = "recursive"
             }
             workflow {
                 """
diff --git a/subworkflows/local/vcf_chunk_glimpse/main.nf b/subworkflows/local/vcf_chunk_glimpse/main.nf
index 457b0b1b..dad0dcf0 100644
--- a/subworkflows/local/vcf_chunk_glimpse/main.nf
+++ b/subworkflows/local/vcf_chunk_glimpse/main.nf
@@ -7,6 +7,7 @@ workflow VCF_CHUNK_GLIMPSE {
     take:
     ch_reference  // channel: [ [panel, chr], vcf, csi ]
     ch_map        // channel  (optional): [ [chr], map ]
+    chunk_model   // channel : model
 
     main:
 
@@ -36,9 +37,6 @@ workflow VCF_CHUNK_GLIMPSE {
         )
         .map { metaPC, it -> [metaPC, it["RegionIn"], it["RegionOut"]]}
 
-    // Make chunks with Glimpse2 (does not work with "sequential" mode)
-    chunk_model = "recursive"
-
     ch_input_glimpse2 = ch_vcf_csi_chr
         .map{
             metaPC, vcf, csi, chr -> [metaPC.subMap("chr"), metaPC, vcf, csi, chr]
diff --git a/subworkflows/local/vcf_chunk_glimpse/tests/main.nf.test b/subworkflows/local/vcf_chunk_glimpse/tests/main.nf.test
index c222059e..9be51fbf 100644
--- a/subworkflows/local/vcf_chunk_glimpse/tests/main.nf.test
+++ b/subworkflows/local/vcf_chunk_glimpse/tests/main.nf.test
@@ -47,6 +47,7 @@ nextflow_workflow {
                         file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38_21.map", checkIfExist:true)
                     ]
                 )
+                input[2] = "recursive"
                 """
             }
         }
@@ -54,10 +55,12 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(workflow.out).match() },
-                { assert snapshot(workflow.out.chunks.collect{
-                    path(it[1]).readLines()
-                    }).match("chunksWithMap")
+                { assert snapshot(
+                    workflow.out,
+                    workflow.out.chunks.collect{
+                        path(it[1]).readLines()
+                    }
+                ).match()
                 }
             )
         }
@@ -87,6 +90,7 @@ nextflow_workflow {
                     [[chr: "chr22"], []],
                     [[chr: "chr21"], []]
                 )
+                input[2] = "recursive"
                 """
             }
         }
@@ -94,10 +98,55 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(workflow.out).match() },
-                { assert snapshot(workflow.out.chunks.collect{
-                    path(it[1]).readLines()
-                    }).match("chunksWithoutMap")
+                { assert snapshot(
+                    workflow.out,
+                    workflow.out.chunks.collect{
+                        path(it[1]).readLines()
+                    }
+                ).match()
+                }
+            )
+        }
+    }
+
+    test("Chunks with sequential model") {
+        when {
+            params {
+                max_cpus   = 2
+                max_memory = '2.GB'
+            }
+            workflow {
+                """
+                input[0] = Channel.of(
+                    [
+                        [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),
+                    ],
+                    [
+                        [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(
+                    [[chr: "chr22"], []],
+                    [[chr: "chr21"], []]
+                )
+                input[2] = "sequential"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out,
+                    workflow.out.chunks.collect{
+                        path(it[1]).readLines()
+                    }
+                ).match()
                 }
             )
         }
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 c6a21882..90a62932 100644
--- a/subworkflows/local/vcf_chunk_glimpse/tests/main.nf.test.snap
+++ b/subworkflows/local/vcf_chunk_glimpse/tests/main.nf.test.snap
@@ -1,23 +1,4 @@
 {
-    "chunksWithoutMap": {
-        "content": [
-            [
-                [
-                    "0\tchr21\tchr21:16570070-16595525\tchr21:16570070-16590513\t20444\t419",
-                    "1\tchr21\tchr21:16585483-16609998\tchr21:16590521-16609998\t19478\t417"
-                ],
-                [
-                    "0\tchr22\tchr22:16570065-16597215\tchr22:16570065-16592216\t22152\t452",
-                    "1\tchr22\tchr22:16587172-16609999\tchr22:16592229-16609999\t17771\t451"
-                ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-07-18T11:26:35.422657952"
-    },
     "Chunks without Map": {
         "content": [
             {
@@ -289,13 +270,23 @@
                     "versions.yml:md5,1ae67fb38ed979f02f47d5ecb8a85f0d",
                     "versions.yml:md5,7d277747b107043dd31d3aef18045eef"
                 ]
-            }
+            },
+            [
+                [
+                    "0\tchr21\tchr21:16570070-16595525\tchr21:16570070-16590513\t20444\t419",
+                    "1\tchr21\tchr21:16585483-16609998\tchr21:16590521-16609998\t19478\t417"
+                ],
+                [
+                    "0\tchr22\tchr22:16570065-16597215\tchr22:16570065-16592216\t22152\t452",
+                    "1\tchr22\tchr22:16587172-16609999\tchr22:16592229-16609999\t17771\t451"
+                ]
+            ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-07-18T11:26:34.820936365"
+        "timestamp": "2024-11-10T18:36:03.086912114"
     },
     "Chunks with Map": {
         "content": [
@@ -536,16 +527,296 @@
                     "versions.yml:md5,1ae67fb38ed979f02f47d5ecb8a85f0d",
                     "versions.yml:md5,7d277747b107043dd31d3aef18045eef"
                 ]
-            }
+            },
+            [
+                [
+                    "0\tchr21\tchr21:16570070-16595525\tchr21:16570070-16590513\t20444\t419",
+                    "1\tchr21\tchr21:16585483-16609998\tchr21:16590521-16609998\t19478\t417"
+                ],
+                [
+                    "0\tchr22\tchr22:16570065-16597215\tchr22:16570065-16592216\t22152\t452",
+                    "1\tchr22\tchr22:16587172-16609999\tchr22:16592229-16609999\t17771\t451"
+                ]
+            ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-07-18T11:26:24.155279577"
+        "timestamp": "2024-11-10T18:35:46.374947355"
     },
-    "chunksWithMap": {
+    "Chunks with sequential model": {
         "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr21"
+                        },
+                        "1000GP_chr21.txt:md5,64ca4a1655363e4a4e558836e5ac12f9"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr22"
+                        },
+                        "1000GP_chr22.txt:md5,3344e171251722cf58ae31136da223ac"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr21"
+                        },
+                        "chr21",
+                        "16570070",
+                        "16595525"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr21"
+                        },
+                        "chr21",
+                        "16585483",
+                        "16609998"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr22"
+                        },
+                        "chr22",
+                        "16570065",
+                        "16597215"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr22"
+                        },
+                        "chr22",
+                        "16587172",
+                        "16609999"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr21"
+                        },
+                        "chr21:16570070-16595525",
+                        "chr21:16570070-16590513"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr21"
+                        },
+                        "chr21:16585483-16609998",
+                        "chr21:16590521-16609998"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr22"
+                        },
+                        "chr22:16570065-16597215",
+                        "chr22:16570065-16592216"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr22"
+                        },
+                        "chr22:16587172-16609999",
+                        "chr22:16592229-16609999"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr21"
+                        },
+                        "chr21:1-16609998",
+                        "chr21:1-16590145"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr21"
+                        },
+                        "chr21:16570070-1248956422",
+                        "chr21:16590146-1248956422"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr22"
+                        },
+                        "chr22:1-16609999",
+                        "chr22:1-16590520"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr22"
+                        },
+                        "chr22:16570065-1248956422",
+                        "chr22:16590521-1248956422"
+                    ]
+                ],
+                "4": [
+                    [
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "5": [
+                    "versions.yml:md5,1ae67fb38ed979f02f47d5ecb8a85f0d",
+                    "versions.yml:md5,1ae67fb38ed979f02f47d5ecb8a85f0d",
+                    "versions.yml:md5,7d277747b107043dd31d3aef18045eef"
+                ],
+                "binary": [
+                    [
+                        [
+                            
+                        ]
+                    ]
+                ],
+                "chunks": [
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr21"
+                        },
+                        "1000GP_chr21.txt:md5,64ca4a1655363e4a4e558836e5ac12f9"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr22"
+                        },
+                        "1000GP_chr22.txt:md5,3344e171251722cf58ae31136da223ac"
+                    ]
+                ],
+                "chunks_glimpse1": [
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr21"
+                        },
+                        "chr21:16570070-16595525",
+                        "chr21:16570070-16590513"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr21"
+                        },
+                        "chr21:16585483-16609998",
+                        "chr21:16590521-16609998"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr22"
+                        },
+                        "chr22:16570065-16597215",
+                        "chr22:16570065-16592216"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr22"
+                        },
+                        "chr22:16587172-16609999",
+                        "chr22:16592229-16609999"
+                    ]
+                ],
+                "chunks_glimpse2": [
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr21"
+                        },
+                        "chr21:1-16609998",
+                        "chr21:1-16590145"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr21"
+                        },
+                        "chr21:16570070-1248956422",
+                        "chr21:16590146-1248956422"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr22"
+                        },
+                        "chr22:1-16609999",
+                        "chr22:1-16590520"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr22"
+                        },
+                        "chr22:16570065-1248956422",
+                        "chr22:16590521-1248956422"
+                    ]
+                ],
+                "chunks_quilt": [
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr21"
+                        },
+                        "chr21",
+                        "16570070",
+                        "16595525"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr21"
+                        },
+                        "chr21",
+                        "16585483",
+                        "16609998"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr22"
+                        },
+                        "chr22",
+                        "16570065",
+                        "16597215"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr22"
+                        },
+                        "chr22",
+                        "16587172",
+                        "16609999"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,1ae67fb38ed979f02f47d5ecb8a85f0d",
+                    "versions.yml:md5,1ae67fb38ed979f02f47d5ecb8a85f0d",
+                    "versions.yml:md5,7d277747b107043dd31d3aef18045eef"
+                ]
+            },
             [
                 [
                     "0\tchr21\tchr21:16570070-16595525\tchr21:16570070-16590513\t20444\t419",
@@ -558,9 +829,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-07-18T11:26:24.609554836"
+        "timestamp": "2024-11-10T18:36:16.974727308"
     }
 }
\ 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 3f3e8b9e..5a412491 100644
--- a/subworkflows/local/vcf_chunk_glimpse/tests/nextflow.config
+++ b/subworkflows/local/vcf_chunk_glimpse/tests/nextflow.config
@@ -1,4 +1,9 @@
 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 = { "${meta.id}_${meta.chr}" }
diff --git a/subworkflows/local/vcf_phase_shapeit5/main.nf b/subworkflows/local/vcf_phase_shapeit5/main.nf
index af643b14..7bf0e7d2 100644
--- a/subworkflows/local/vcf_phase_shapeit5/main.nf
+++ b/subworkflows/local/vcf_phase_shapeit5/main.nf
@@ -7,19 +7,17 @@ include { BCFTOOLS_INDEX as VCF_BCFTOOLS_INDEX_2 } from '../../../modules/nf-cor
 workflow VCF_PHASE_SHAPEIT5 {
 
     take:
-    ch_vcf        // channel (mandatory): [ [id, chr], vcf, csi, pedigree ]
+    ch_vcf        // channel (mandatory) : [ [id, chr], vcf, csi, pedigree ]
     ch_region     // channel (mandatory) : [ [chr, region], region ]
-    ch_ref        // channel (optional) : [ [id, chr], ref, csi ]
-    ch_scaffold   // channel (optional) : [ [id, chr], scaffold, csi ]
+    ch_ref        // channel (optional)  : [ [id, chr], ref, csi ]
+    ch_scaffold   // channel (optional)  : [ [id, chr], scaffold, csi ]
     ch_map        // channel (mandatory) : [ [chr], map]
+    chunk_model   // channel (mandatory) : [ model ]
 
     main:
 
     ch_versions = Channel.empty()
 
-    // Make chunks with Glimpse2 (does not work with "sequential" mode)
-    chunk_model = "recursive"
-
     // Chunk with Glimpse2
     ch_input_glimpse2 = ch_vcf
         .map{
@@ -43,9 +41,6 @@ workflow VCF_PHASE_SHAPEIT5 {
         )
         .map { metaIC, it -> [metaIC, it["RegionBuf"], it["RegionCnk"]]}
 
-    ch_chunks_number = GLIMPSE2_CHUNK.out.chunk_chr
-        .map { meta, chunk -> [meta.subMap("chr"), chunk.countLines().intValue()]}
-
     ch_phase_input = ch_vcf
         .combine(ch_chunks_glimpse2, by:0)
         .map{
diff --git a/subworkflows/local/vcf_phase_shapeit5/tests/main.nf.test b/subworkflows/local/vcf_phase_shapeit5/tests/main.nf.test
index 4a95348f..a2f855ac 100644
--- a/subworkflows/local/vcf_phase_shapeit5/tests/main.nf.test
+++ b/subworkflows/local/vcf_phase_shapeit5/tests/main.nf.test
@@ -20,7 +20,7 @@ nextflow_workflow {
     tag "bcftools"
     tag "bcftools/index"
 
-    test("Phase vcf with regions, no map, no ref, no scaffold") {
+    test("Phase vcf with regions, no map, no ref, no scaffold, recursive model") {
         when {
             params {
                 max_cpus   = 2
@@ -52,6 +52,7 @@ nextflow_workflow {
                     [[chr: "chr22"],[]],
                     [[chr: "chr21"], []]
                 )
+                input[5] = "recursive"
                 """
             }
         }
@@ -59,10 +60,64 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(workflow.out).match() },
-                { assert snapshot(workflow.out.vcf_tbi.collect{
-                    path(it[1]).vcf.summary
-                    }).match("Phasing content")
+                { assert snapshot(
+                    workflow.out,
+                    workflow.out.vcf_tbi.collect{
+                        path(it[1]).vcf.summary
+                    }).match()
+                },
+                { workflow.out.vcf_tbi.collect{
+                    assert path(it[1]).vcf.phased
+                }}
+            )
+        }
+    }
+
+    test("Phase vcf with regions, no map, no ref, no scaffold, sequential model") {
+        when {
+            params {
+                max_cpus   = 2
+                max_memory = '2.GB'
+            }
+            workflow {
+                """
+                input[0] = Channel.of(
+                    [
+                        [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),
+                        []
+                    ],
+                    [
+                        [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(
+                    [[chr: "chr22", region:"chr22:16570000-16610000"], "chr22:16570000-16610000"],
+                    [[chr: "chr21", region:"chr21:16570000-16610000"], "chr21:16570000-16610000"]
+                )
+                input[2] = Channel.of([[],[],[]]).collect()
+                input[3] = Channel.of([[],[],[]]).collect()
+                input[4] = Channel.of(
+                    [[chr: "chr22"],[]],
+                    [[chr: "chr21"], []]
+                )
+                input[5] = "sequential"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out,
+                    workflow.out.vcf_tbi.collect{
+                        path(it[1]).vcf.summary
+                    }).match()
                 },
                 { workflow.out.vcf_tbi.collect{
                     assert path(it[1]).vcf.phased
@@ -70,6 +125,7 @@ nextflow_workflow {
             )
         }
     }
+
     /* TODO: Fix this test with https://github.com/odelaneau/shapeit5/issues/96
     test("Phase vcf with regions, with map, no ref, no scaffold") {
         when {
@@ -103,6 +159,7 @@ nextflow_workflow {
                     [ [chr: "chr22"], file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38_22.map", checkIfExist:true)],
                     [ [chr: "chr21"], file(params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38_21.map", checkIfExist:true)]
                 )
+                input[5] = "recursive"
                 """
             }
         }
diff --git a/subworkflows/local/vcf_phase_shapeit5/tests/main.nf.test.snap b/subworkflows/local/vcf_phase_shapeit5/tests/main.nf.test.snap
index ffa1c169..bb7e9f9d 100644
--- a/subworkflows/local/vcf_phase_shapeit5/tests/main.nf.test.snap
+++ b/subworkflows/local/vcf_phase_shapeit5/tests/main.nf.test.snap
@@ -1,18 +1,70 @@
 {
-    "Phasing content": {
+    "Phase vcf with regions, no map, no ref, no scaffold, sequential model": {
         "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr21"
+                        },
+                        "1000GP.vcf.gz:md5,4029303e3c083ebb2522fb5c8dc4b63a",
+                        "1000GP.vcf.gz.csi:md5,c57057d136f6c859aac4e6ae28ec793b"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr22"
+                        },
+                        "1000GP.vcf.gz:md5,23d09ba884eda7449702fece3f652d9d",
+                        "1000GP.vcf.gz.csi:md5,281791c87517a6f3e83c3fd736ec704e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,529c03b8d921c72026e91d71c0321811",
+                    "versions.yml:md5,714bb0db6e2d39cf0042359a64915bc6",
+                    "versions.yml:md5,8ffcda8a9d22f60c90d0e4276da3e714",
+                    "versions.yml:md5,cab7592ebcb3d391afcd3191a175723b",
+                    "versions.yml:md5,ed131d2608f28f8ada06ccc42717575e"
+                ],
+                "vcf_tbi": [
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr21"
+                        },
+                        "1000GP.vcf.gz:md5,4029303e3c083ebb2522fb5c8dc4b63a",
+                        "1000GP.vcf.gz.csi:md5,c57057d136f6c859aac4e6ae28ec793b"
+                    ],
+                    [
+                        {
+                            "id": "1000GP",
+                            "chr": "chr22"
+                        },
+                        "1000GP.vcf.gz:md5,23d09ba884eda7449702fece3f652d9d",
+                        "1000GP.vcf.gz.csi:md5,281791c87517a6f3e83c3fd736ec704e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,529c03b8d921c72026e91d71c0321811",
+                    "versions.yml:md5,714bb0db6e2d39cf0042359a64915bc6",
+                    "versions.yml:md5,8ffcda8a9d22f60c90d0e4276da3e714",
+                    "versions.yml:md5,cab7592ebcb3d391afcd3191a175723b",
+                    "versions.yml:md5,ed131d2608f28f8ada06ccc42717575e"
+                ]
+            },
             [
                 "VcfFile [chromosomes=[chr21], sampleCount=3196, variantCount=836, phased=true, phasedAutodetect=true]",
                 "VcfFile [chromosomes=[chr22], sampleCount=3196, variantCount=903, phased=true, phasedAutodetect=true]"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-07-18T15:56:20.067633938"
+        "timestamp": "2024-11-10T19:18:52.508986134"
     },
-    "Phase vcf with regions, no map, no ref, no scaffold": {
+    "Phase vcf with regions, no map, no ref, no scaffold, recursive model": {
         "content": [
             {
                 "0": [
@@ -21,16 +73,16 @@
                             "id": "1000GP",
                             "chr": "chr21"
                         },
-                        "1000GP.vcf.gz:md5,a8af1c991fb1ca9e0919e0d5ddae8968",
-                        "1000GP.vcf.gz.csi:md5,b4c653bd398bb838b496e022705bb562"
+                        "1000GP.vcf.gz:md5,d454c821a71b7c569540e381068fbe03",
+                        "1000GP.vcf.gz.csi:md5,13e80ee9a038a715efd6f97befec28c6"
                     ],
                     [
                         {
                             "id": "1000GP",
                             "chr": "chr22"
                         },
-                        "1000GP.vcf.gz:md5,106157dc553c3c19eebdce0567e69d4f",
-                        "1000GP.vcf.gz.csi:md5,58026cf302bd82382a078c5690429b5c"
+                        "1000GP.vcf.gz:md5,68e488b81ea8ca52a52b20fec603bf3e",
+                        "1000GP.vcf.gz.csi:md5,98037a25e4112f8a4df62eba96d08634"
                     ]
                 ],
                 "1": [
@@ -46,16 +98,16 @@
                             "id": "1000GP",
                             "chr": "chr21"
                         },
-                        "1000GP.vcf.gz:md5,a8af1c991fb1ca9e0919e0d5ddae8968",
-                        "1000GP.vcf.gz.csi:md5,b4c653bd398bb838b496e022705bb562"
+                        "1000GP.vcf.gz:md5,d454c821a71b7c569540e381068fbe03",
+                        "1000GP.vcf.gz.csi:md5,13e80ee9a038a715efd6f97befec28c6"
                     ],
                     [
                         {
                             "id": "1000GP",
                             "chr": "chr22"
                         },
-                        "1000GP.vcf.gz:md5,106157dc553c3c19eebdce0567e69d4f",
-                        "1000GP.vcf.gz.csi:md5,58026cf302bd82382a078c5690429b5c"
+                        "1000GP.vcf.gz:md5,68e488b81ea8ca52a52b20fec603bf3e",
+                        "1000GP.vcf.gz.csi:md5,98037a25e4112f8a4df62eba96d08634"
                     ]
                 ],
                 "versions": [
@@ -65,12 +117,16 @@
                     "versions.yml:md5,cab7592ebcb3d391afcd3191a175723b",
                     "versions.yml:md5,ed131d2608f28f8ada06ccc42717575e"
                 ]
-            }
+            },
+            [
+                "VcfFile [chromosomes=[chr21], sampleCount=3196, variantCount=836, phased=true, phasedAutodetect=true]",
+                "VcfFile [chromosomes=[chr22], sampleCount=3196, variantCount=903, phased=true, phasedAutodetect=true]"
+            ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-07-22T15:46:34.727932091"
+        "timestamp": "2024-11-10T19:18:20.407509527"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/local/vcf_phase_shapeit5/tests/nextflow.config b/subworkflows/local/vcf_phase_shapeit5/tests/nextflow.config
index 8817d417..c0c00d6f 100644
--- a/subworkflows/local/vcf_phase_shapeit5/tests/nextflow.config
+++ b/subworkflows/local/vcf_phase_shapeit5/tests/nextflow.config
@@ -1,7 +1,7 @@
 process {
     withName: GLIMPSE2_CHUNK {
         ext.prefix = { "${meta.id}_chunks" }
-        ext.args = ["--window-mb 0.1", "--window-cm 0.1", "--window-count 2000", "--buffer-mb 0.05", "--buffer-cm 0.05", "--buffer-count 300"].join(' ')
+        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(' ')
     }
 
     withName: SHAPEIT5_PHASECOMMON {
diff --git a/workflows/phaseimpute/main.nf b/workflows/phaseimpute/main.nf
index 5ae079dc..fe4c1fa9 100644
--- a/workflows/phaseimpute/main.nf
+++ b/workflows/phaseimpute/main.nf
@@ -91,6 +91,7 @@ workflow PHASEIMPUTE {
     ch_map                  // channel: genetic map   [ [chr], map]
     ch_posfile              // channel: posfile       [ [id, chr], vcf, index, hap, legend]
     ch_chunks               // channel: chunks        [ [chr], txt]
+    chunk_model             // parameter: chunk model
     ch_versions             // channel: versions of software used
 
     main:
@@ -171,14 +172,15 @@ workflow PHASEIMPUTE {
                 ch_region,
                 [[],[],[]],
                 [[],[],[]],
-                ch_map
+                ch_map,
+                chunk_model
             )
             ch_panel_phased = VCF_PHASE_SHAPEIT5.out.vcf_tbi
             ch_versions = ch_versions.mix(VCF_PHASE_SHAPEIT5.out.versions)
         }
 
         // Create chunks from reference VCF
-        VCF_CHUNK_GLIMPSE(ch_panel_phased, ch_map)
+        VCF_CHUNK_GLIMPSE(ch_panel_phased, ch_map, chunk_model)
         ch_versions = ch_versions.mix(VCF_CHUNK_GLIMPSE.out.versions)
 
         // Assign chunks channels