diff --git a/modules/nf-core/glimpse/chunk/meta.yml b/modules/nf-core/glimpse/chunk/meta.yml
index 9e77ddeb1da..9ac840a6e39 100644
--- a/modules/nf-core/glimpse/chunk/meta.yml
+++ b/modules/nf-core/glimpse/chunk/meta.yml
@@ -3,6 +3,7 @@ description: Defines chunks where to run imputation
 keywords:
   - chunk
   - imputation
+  - low coverage
 tools:
   - "glimpse":
       description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies."
diff --git a/modules/nf-core/glimpse/phase/main.nf b/modules/nf-core/glimpse/phase/main.nf
index b936f0bd08c..894d8f1ec6a 100644
--- a/modules/nf-core/glimpse/phase/main.nf
+++ b/modules/nf-core/glimpse/phase/main.nf
@@ -8,7 +8,7 @@ process GLIMPSE_PHASE {
         'quay.io/biocontainers/glimpse-bio:1.1.1--hce55b13_1' }"
 
     input:
-        tuple val(meta) , path(input), path(input_index), val(input_region), val(output_region), path(reference), path(reference_index), path(map), path(samples_file)
+        tuple val(meta) , path(input), path(input_index), path(samples_file), val(input_region), val(output_region), path(reference), path(reference_index), path(map)
 
     output:
         tuple val(meta), path("*.{vcf,bcf,vcf.gz,bcf.gz}"), emit: phased_variant
diff --git a/modules/nf-core/glimpse/phase/meta.yml b/modules/nf-core/glimpse/phase/meta.yml
index b17567de76d..47da4de6ec6 100644
--- a/modules/nf-core/glimpse/phase/meta.yml
+++ b/modules/nf-core/glimpse/phase/meta.yml
@@ -3,6 +3,9 @@ description: main GLIMPSE algorithm, performs phasing and imputation refining ge
 keywords:
   - phase
   - imputation
+  - low-coverage
+  - glimpse
+
 tools:
   - "glimpse":
       description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies."
@@ -29,6 +32,15 @@ input:
       description: Index file of the input VCF/BCF file containing genotype likelihoods.
       pattern: "*.{vcf.gz.csi,bcf.gz.csi}"
 
+  - samples_file:
+      type: file
+      description: |
+        File with sample names and ploidy information.
+        One sample per line with a mandatory second column indicating ploidy (1 or 2).
+        Sample names that are not present are assumed to have ploidy 2 (diploids).
+        GLIMPSE does NOT handle the use of sex (M/F) instead of ploidy.
+      pattern: "*.{txt,tsv}"
+
   - input_region:
       type: string
       description: Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).
@@ -54,15 +66,6 @@ input:
       description: File containing the genetic map.
       pattern: "*.gmap"
 
-  - samples_file:
-      type: file
-      description: |
-        File with sample names and ploidy information.
-        One sample per line with a mandatory second column indicating ploidy (1 or 2).
-        Sample names that are not present are assumed to have ploidy 2 (diploids).
-        GLIMPSE does NOT handle the use of sex (M/F) instead of ploidy.
-      pattern: "*.{txt,tsv}"
-
 output:
   - meta:
       type: map
diff --git a/modules/nf-core/glimpse2/chunk/main.nf b/modules/nf-core/glimpse2/chunk/main.nf
index bfb7e440bd4..a6b0011d51f 100644
--- a/modules/nf-core/glimpse2/chunk/main.nf
+++ b/modules/nf-core/glimpse2/chunk/main.nf
@@ -17,7 +17,8 @@ process GLIMPSE2_CHUNK {
         'quay.io/biocontainers/glimpse-bio:2.0.0--hf340a29_0' }"
 
     input:
-    tuple val(meta), path(input), path(input_index), val(region), path(map)
+    tuple val(meta) , path(input), path(input_index), val(region)
+    tuple val(meta2), path(map)
     val(model)
 
     output:
diff --git a/modules/nf-core/glimpse2/phase/main.nf b/modules/nf-core/glimpse2/phase/main.nf
index 03e6803a3ed..97c332afaaf 100644
--- a/modules/nf-core/glimpse2/phase/main.nf
+++ b/modules/nf-core/glimpse2/phase/main.nf
@@ -18,8 +18,9 @@ process GLIMPSE2_PHASE {
         'quay.io/biocontainers/glimpse-bio:2.0.0--hf340a29_0' }"
 
     input:
-        tuple val(meta), path(input), path(input_index), val(input_region), val(output_region), path(reference), path(reference_index), path(map), path(samples_file)
+        tuple val(meta) , path(input), path(input_index), path(samples_file), val(input_region), val(output_region), path(reference), path(reference_index), path(map)
         tuple val(meta2), path(fasta_reference), path(fasta_reference_index)
+
     output:
         tuple val(meta), path("*.{vcf,bcf,bgen}"), emit: phased_variant
         tuple val(meta), path("*.txt.gz")        , emit: stats_coverage, optional: true
@@ -29,13 +30,17 @@ process GLIMPSE2_PHASE {
         task.ext.when == null || task.ext.when
 
     script:
+    def region = input_region    ? "${output_region.replace(":","_")}" : "${reference}"
     def args   = task.ext.args   ?: ""
-    def prefix = task.ext.prefix ?: "${meta.id}_${input_region.replace(":","_")}"
+    def prefix = task.ext.prefix ?: "${meta.id}_${region}"
     def suffix = task.ext.suffix ?: "bcf"
 
     def map_command           = map                 ? "--map $map"                    : ""
     def samples_file_command  = samples_file        ? "--samples-file $samples_file"  : ""
     def fasta_command         = fasta_reference     ? "--fasta $fasta_reference"      : ""
+    def input_region_cmd      = input_region        ? "--input-region $input_region"  : ""
+    def output_region_cmd     = output_region       ? "--output-region $output_region": ""
+
     def input_bam             = input.any { it.extension in ["cram","bam"]}
 
     """
@@ -54,14 +59,14 @@ process GLIMPSE2_PHASE {
         $map_command \\
         $fasta_command \\
         $samples_file_command \\
-        --input-region $input_region \\
-        --output-region $output_region \\
+        $input_region_cmd \\
+        $output_region_cmd \\
         --thread $task.cpus \\
         --output ${prefix}.${suffix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        glimpse2: "\$(GLIMPSE2_split_reference --help | sed -nr '/Version/p' | grep -o -E '([0-9]+.){1,2}[0-9]' | head -1)"
+        glimpse2: "\$(GLIMPSE2_phase --help | sed -nr '/Version/p' | grep -o -E '([0-9]+.){1,2}[0-9]' | head -1)"
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/glimpse2/phase/meta.yml b/modules/nf-core/glimpse2/phase/meta.yml
index 6ba4933e3bf..5e5e88cbbbc 100644
--- a/modules/nf-core/glimpse2/phase/meta.yml
+++ b/modules/nf-core/glimpse2/phase/meta.yml
@@ -22,9 +22,10 @@ input:
         e.g. [ id:'test', single_end:false ]
 
   - input:
-      type: files
+      type: file
       description: |
-        Either multiple BAM/CRAM files containing low-coverage sequencing reads or one VCF/BCF file containing the genotype likelihoods. When using BAM/CRAM the name of the file is used as samples name.
+        Either multiple BAM/CRAM files containing low-coverage sequencing reads or one VCF/BCF file containing the genotype likelihoods.
+        When using BAM/CRAM the name of the file is used as samples name.
       pattern: "*.{bam,cram,vcf,vcf.gz,bcf,bcf.gz}"
 
   - input_index:
@@ -32,14 +33,27 @@ input:
       description: Index file of the input BAM/CRAM/VCF/BCF file.
       pattern: "*.{bam.bai,cram.crai,vcf.gz.csi,bcf.gz.csi}"
 
+  - samples_file:
+      type: file
+      description: |
+        File with sample names and ploidy information.
+        One sample per line with a mandatory second column indicating ploidy (1 or 2).
+        Sample names that are not present are assumed to have ploidy 2 (diploids).
+        GLIMPSE does NOT handle the use of sex (M/F) instead of ploidy.
+      pattern: "*.{txt,tsv}"
+
   - input_region:
       type: string
-      description: Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).
+      description: |
+        Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).
+        Optional if reference panel is in bin format.
       pattern: "chrXX:leftBufferPosition-rightBufferPosition"
 
   - output_region:
       type: string
-      description: Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).
+      description: |
+        Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).
+        Optional if reference panel is in bin format.
       pattern: "chrXX:leftBufferPosition-rightBufferPosition"
 
   - reference:
@@ -53,27 +67,24 @@ input:
       pattern: "*.{vcf.gz.csi,bcf.gz.csi}"
 
   - map:
-      type: file
-      description: File containing the genetic map.
-      pattern: "*.gmap"
-
-  - samples_file:
       type: file
       description: |
-        File with sample names and ploidy information. One sample per line with a mandatory second column indicating ploidy (1 or 2). Sample names that are not present are assumed to have ploidy 2 (diploids). GLIMPSE does NOT handle the use of sex (M/F) instead of ploidy.
-      pattern: "*.{txt,tsv}"
+        File containing the genetic map.
+        Optional if reference panel is in bin format.
+      pattern: "*.gmap"
 
   - fasta_reference:
       type: file
       description: |
         Faidx-indexed reference sequence file in the appropriate genome build.
-        Necessary for CRAM files
+        Necessary for CRAM files.
       pattern: "*.fasta"
 
   - fasta_reference_index:
       type: file
       description: |
         Faidx index of the reference sequence file in the appropriate genome build.
+        Necessary for CRAM files.
       pattern: "*.fai"
 
 output:
diff --git a/modules/nf-core/glimpse2/splitreference/main.nf b/modules/nf-core/glimpse2/splitreference/main.nf
index a86061d47d1..45c6a812cf7 100644
--- a/modules/nf-core/glimpse2/splitreference/main.nf
+++ b/modules/nf-core/glimpse2/splitreference/main.nf
@@ -31,7 +31,7 @@ process GLIMPSE2_SPLITREFERENCE {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}_${output_region.replace(":","_")}"
     def map_command = map ? "--map $map" : ""
 
     """
diff --git a/subworkflows/nf-core/multiple_impute_glimpse2/main.nf b/subworkflows/nf-core/multiple_impute_glimpse2/main.nf
new file mode 100644
index 00000000000..b300f771246
--- /dev/null
+++ b/subworkflows/nf-core/multiple_impute_glimpse2/main.nf
@@ -0,0 +1,73 @@
+include { GLIMPSE2_CHUNK                 } from '../../../modules/nf-core/glimpse2/chunk/main'
+include { GLIMPSE2_SPLITREFERENCE        } from '../../../modules/nf-core/glimpse2/splitreference/main'
+include { GLIMPSE2_PHASE                 } from '../../../modules/nf-core/glimpse2/phase/main'
+include { GLIMPSE2_LIGATE                } from '../../../modules/nf-core/glimpse2/ligate/main'
+include { BCFTOOLS_INDEX as INDEX_PHASE  } from '../../../modules/nf-core/bcftools/index/main.nf'
+include { BCFTOOLS_INDEX as INDEX_LIGATE } from '../../../modules/nf-core/bcftools/index/main.nf'
+
+workflow MULTIPLE_IMPUTE_GLIMPSE2 {
+
+    take:
+    ch_input    // channel (mandatory): [ meta, vcf, csi, infos ]
+    ch_ref      // channel (mandatory): [ meta, vcf, csi, region ]
+    ch_map      // channel  (optional): [ meta, map ]
+    ch_fasta    // channel  (optional): [ meta, fasta, index ]
+    chunk_model // string: model used to chunk the reference panel
+
+    main:
+
+    ch_versions = Channel.empty()
+
+    // Chunk reference panel
+    GLIMPSE2_CHUNK ( ch_ref, ch_map, chunk_model )
+    ch_versions = ch_versions.mix( GLIMPSE2_CHUNK.out.versions.first() )
+
+    chunk_output = GLIMPSE2_CHUNK.out.chunk_chr
+                                .splitCsv(header: ['ID', 'Chr', 'RegionBuf', 'RegionCnk', 'WindowCm',
+                                            'WindowMb', 'NbTotVariants', 'NbComVariants'],
+                                        sep: "\t", skip: 0)
+                                .map { meta, it -> [meta, it["RegionBuf"], it["RegionCnk"]]}
+
+    // Split reference panel in bin files
+    split_input = ch_ref.map{ meta, ref, index, region -> [meta, ref, index]}
+                        .combine(chunk_output, by: 0)
+
+    GLIMPSE2_SPLITREFERENCE( split_input, ch_map )
+    ch_versions = ch_versions.mix( GLIMPSE2_SPLITREFERENCE.out.versions.first() )
+
+    phase_input = ch_input.combine( GLIMPSE2_SPLITREFERENCE.out.bin_ref )
+                        .map{ input_meta, input_file, input_index, input_infos,
+                            panel_meta, panel_bin ->
+                            [input_meta, input_file, input_index, input_infos,
+                            [], [], panel_bin, [], []]
+                    }/* Remove unnecessary meta maps
+                        add null index as we use a bin file,
+                        add null value for input and output region as we use a bin file */
+
+    // Phase input files for each reference bin files + indexing
+    GLIMPSE2_PHASE ( phase_input, ch_fasta ) // [meta, vcf, index, sample_infos, regionin, regionout, regionindex, ref, ref_index, map], [ meta, fasta, index ]
+    ch_versions = ch_versions.mix( GLIMPSE2_PHASE.out.versions.first() )
+
+    INDEX_PHASE ( GLIMPSE2_PHASE.out.phased_variant )
+    ch_versions = ch_versions.mix( INDEX_PHASE.out.versions.first() )
+
+    // Ligate all phased files in one and index it
+    ligate_input = GLIMPSE2_PHASE.out.phased_variant
+                                    .groupTuple()
+                                    .combine( INDEX_PHASE.out.csi
+                                            .groupTuple()
+                                            .collect(), by: 0 )
+
+    GLIMPSE2_LIGATE ( ligate_input )
+    ch_versions = ch_versions.mix( GLIMPSE2_LIGATE.out.versions.first() )
+
+    INDEX_LIGATE ( GLIMPSE2_LIGATE.out.merged_variants )
+    ch_versions = ch_versions.mix( INDEX_LIGATE.out.versions.first() )
+
+    emit:
+    chunk_chr              = GLIMPSE2_CHUNK.out.chunk_chr           // channel: [ val(meta), txt ]
+    merged_variants        = GLIMPSE2_LIGATE.out.merged_variants    // channel: [ val(meta), bcf ]
+    merged_variants_index  = INDEX_LIGATE.out.csi                   // channel: [ val(meta), csi ]
+
+    versions               = ch_versions                            // channel: [ versions.yml ]
+}
diff --git a/subworkflows/nf-core/multiple_impute_glimpse2/meta.yml b/subworkflows/nf-core/multiple_impute_glimpse2/meta.yml
new file mode 100644
index 00000000000..4f233281b1e
--- /dev/null
+++ b/subworkflows/nf-core/multiple_impute_glimpse2/meta.yml
@@ -0,0 +1,72 @@
+name: "multiple_imputation_glimpse2"
+description: Impute VCF/BCF files, but also CRAM and BAM files with Glimpse2
+keywords:
+  - glimpse
+  - chunk
+  - phase
+  - ligate
+  - split_reference
+
+modules:
+  - glimpse2/chunk
+  - glimpse/2phase
+  - glimpse2/ligate
+  - glimpse2/split_reference
+  - bcftools/index
+
+input:
+  - ch_input:
+      type: file
+      description: |
+        Target dataset in CRAM, BAM or VCF/BCF format.
+        Index file of the input file.
+        File with sample names and ploidy information.
+        Structure: [ meta, file, index, txt ]
+
+  - ch_ref:
+      type: file
+      description: |
+        Reference panel of haplotypes in VCF/BCF format.
+        Index file of the Reference panel file.
+        Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).
+        The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).
+        Structure: [ meta, vcf, csi, region ]
+
+  - ch_map:
+      type: file
+      description: |
+        File containing the genetic map.
+        Structure: [ meta, gmap ]
+
+  - ch_fasta:
+      type: file
+      description: |
+        Reference genome in fasta format.
+        Reference genome index in fai format
+        Structure: [ meta, fasta, fai ]
+
+output:
+  - chunk_chr:
+      type: file
+      description: |
+        Tab delimited output txt file containing buffer and imputation regions.
+        Structure: [meta, txt]
+
+  - merged_variants:
+      type: file
+      description: |
+        Output VCF/BCF file for the merged regions.
+        Phased information (HS field) is updated accordingly for the full region.
+        Structure: [ val(meta), bcf ]
+
+  - merged_variants_index:
+      type: file
+      description: Index file of the ligated phased variants files.
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@LouisLeNezet"
diff --git a/subworkflows/nf-core/vcf_impute_glimpse/main.nf b/subworkflows/nf-core/vcf_impute_glimpse/main.nf
index ce3ce7eedc4..d5d9b032220 100644
--- a/subworkflows/nf-core/vcf_impute_glimpse/main.nf
+++ b/subworkflows/nf-core/vcf_impute_glimpse/main.nf
@@ -1,46 +1,65 @@
-include { GLIMPSE_CHUNK      } from '../../../modules/nf-core/glimpse/chunk/main'
-include { GLIMPSE_PHASE      } from '../../../modules/nf-core/glimpse/phase/main'
-include { GLIMPSE_LIGATE     } from '../../../modules/nf-core/glimpse/ligate/main'
-include { BCFTOOLS_INDEX     } from '../../../modules/nf-core/bcftools/index/main.nf'
+include { GLIMPSE_CHUNK                  } from '../../../modules/nf-core/glimpse/chunk/main'
+include { GLIMPSE_PHASE                  } from '../../../modules/nf-core/glimpse/phase/main'
+include { GLIMPSE_LIGATE                 } from '../../../modules/nf-core/glimpse/ligate/main'
+include { BCFTOOLS_INDEX as INDEX_PHASE  } from '../../../modules/nf-core/bcftools/index/main.nf'
+include { BCFTOOLS_INDEX as INDEX_LIGATE } from '../../../modules/nf-core/bcftools/index/main.nf'
 
 workflow VCF_IMPUTE_GLIMPSE {
 
     take:
-    ch_vcf      // channel (mandatory): [ meta, vcf, csi, region, sample ]
+    ch_vcf      // channel (mandatory): [ meta, vcf, csi, sample, region ]
     ch_ref      // channel (mandatory): [ meta, vcf, csi ]
-    ch_map      // channel  (optional): path to map
-    ch_infos    // channel  (optional): sample infos
+    ch_map      // channel  (optional): [meta, map ]
 
     main:
 
     ch_versions = Channel.empty()
 
-    GLIMPSE_CHUNK ( ch_vcf )
+    input_chunk = ch_vcf.map{
+                    meta, vcf, csi, sample, region ->
+                    [ meta, vcf, csi, region]
+                }
+
+    GLIMPSE_CHUNK ( input_chunk )
     ch_versions = ch_versions.mix(GLIMPSE_CHUNK.out.versions)
 
     chunk_output = GLIMPSE_CHUNK.out.chunk_chr
                                 .splitCsv(header: ['ID', 'Chr', 'RegionIn', 'RegionOut', 'Size1', 'Size2'], sep: "\t", skip: 0)
-                                .map { metamap, it -> [metamap, it["RegionIn"], it["RegionOut"]]}
-    phase_input = ch_vcf.map{[it[0], it[1], it[2]]}
+                                .map { meta, it -> [meta, it["RegionIn"], it["RegionOut"]]}
+
+    phase_input = ch_vcf.map{meta, vcf, csi, sample, region -> [meta, vcf, csi, sample]}
                             .join(chunk_output)
-                            .join(ch_ref)
-                            .join(ch_map)
-                            .join(ch_infos)
+                            .combine(ch_ref)
+                            .combine(ch_map)
+                            .map{meta, vcf, csi, sample,
+                                regionin, regionout,
+                                meta_ref, ref, ref_index,
+                                meta_map, map ->
+                                [meta, vcf, csi, sample, regionin, regionout, ref, ref_index, map]}
 
-    GLIMPSE_PHASE ( phase_input ) // [meta, vcf, index, regionin, regionout, regionindex, ref, ref_index, map, sample_infos]
+    GLIMPSE_PHASE ( phase_input ) // [meta, vcf, index, sample_infos, regionin, regionout, ref, ref_index, map]
     ch_versions = ch_versions.mix(GLIMPSE_PHASE.out.versions.first())
 
-    ligate_input  = GLIMPSE_PHASE.out.phased_variant.groupTuple()
+    INDEX_PHASE ( GLIMPSE_PHASE.out.phased_variant )
+    ch_versions = ch_versions.mix( INDEX_PHASE.out.versions.first() )
 
-    BCFTOOLS_INDEX ( ligate_input )
-    GLIMPSE_LIGATE ( ligate_input.join(BCFTOOLS_INDEX.out.csi.groupTuple()) )
+    // Ligate all phased files in one and index it
+    ligate_input = GLIMPSE_PHASE.out.phased_variant
+                                    .groupTuple()
+                                    .combine( INDEX_PHASE.out.csi
+                                            .groupTuple()
+                                            .collect(), by: 0 )
 
+    GLIMPSE_LIGATE ( ligate_input )
     ch_versions = ch_versions.mix(GLIMPSE_LIGATE.out.versions.first())
 
+    INDEX_LIGATE ( GLIMPSE_LIGATE.out.merged_variants )
+    ch_versions = ch_versions.mix( INDEX_LIGATE.out.versions.first() )
+
     emit:
-    chunk_chr        = GLIMPSE_CHUNK.out.chunk_chr           // channel: [ val(meta), txt ]
-    merged_variants  = GLIMPSE_LIGATE.out.merged_variants    // channel: [ val(meta), bcf ]
-    phased_variants  = GLIMPSE_PHASE.out.phased_variant      // channel: [ val(meta), bcf ]
+    chunk_chr              = GLIMPSE_CHUNK.out.chunk_chr           // channel: [ val(meta), txt ]
+    merged_variants        = GLIMPSE_LIGATE.out.merged_variants    // channel: [ val(meta), bcf ]
+    merged_variants_index  = INDEX_LIGATE.out.csi                  // channel: [ val(meta), csi ]
 
-    versions         = ch_versions                           // channel: [ versions.yml ]
+    versions               = ch_versions                           // channel: [ versions.yml ]
 }
diff --git a/subworkflows/nf-core/vcf_impute_glimpse/meta.yml b/subworkflows/nf-core/vcf_impute_glimpse/meta.yml
index 9e0ea49ecfd..3dd30d9313f 100644
--- a/subworkflows/nf-core/vcf_impute_glimpse/meta.yml
+++ b/subworkflows/nf-core/vcf_impute_glimpse/meta.yml
@@ -11,6 +11,7 @@ modules:
   - glimpse/chunk
   - glimpse/phase
   - glimpse/ligate
+  - bcftools/index
 
 input:
   - ch_vcf:
@@ -18,9 +19,10 @@ input:
       description: |
         Target dataset in VCF/BCF format defined at all variable positions.
         Index file of the input VCF/BCF file containing genotype likelihoods.
+        File with sample names and ploidy information.
         Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).
         The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).
-        Structure: [ meta, vcf, csi, region ]
+        Structure: [ meta, vcf, csi, txt, region ]
 
   - ch_ref:
       type: file
@@ -35,15 +37,6 @@ input:
         File containing the genetic map.
         Structure: [gmap]
 
-  - ch_infos:
-      type: file
-      description: |
-        File with sample names and ploidy information.
-        One sample per line with a mandatory second column indicating ploidy (1 or 2).
-        Sample names that are not present are assumed to have ploidy 2 (diploids).
-        GLIMPSE does NOT handle the use of sex (M/F) instead of ploidy.
-        Structure: [ txt ]
-
 output:
   - chunk_chr:
       type: file
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 5c6af0b59d3..b3020dddda5 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -3464,6 +3464,10 @@ subworkflows/homer/groseq:
   - subworkflows/nf-core/homer/groseq/**
   - tests/subworkflows/nf-core/homer/groseq/**
 
+subworkflows/multiple_impute_glimpse2:
+  - subworkflows/nf-core/multiple_impute_glimpse2/**
+  - tests/subworkflows/nf-core/multiple_impute_glimpse2/**
+
 subworkflows/vcf_annotate_ensemblvep:
   - subworkflows/nf-core/vcf_annotate_ensemblvep/**
   - tests/subworkflows/nf-core/vcf_annotate_ensemblvep/**
diff --git a/tests/modules/nf-core/glimpse/chunk/main.nf b/tests/modules/nf-core/glimpse/chunk/main.nf
index cb1610e18b0..a481fca8ae7 100644
--- a/tests/modules/nf-core/glimpse/chunk/main.nf
+++ b/tests/modules/nf-core/glimpse/chunk/main.nf
@@ -6,7 +6,7 @@ include { GLIMPSE_CHUNK } from '../../../../../modules/nf-core/glimpse/chunk/mai
 
 workflow test_glimpse_chunk {
     input = [
-        [ id:'test', single_end:false ], // meta map
+        [ id:'input' ], // meta map
         file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true),
         file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true),
         "chr21"]
diff --git a/tests/modules/nf-core/glimpse/chunk/test.yml b/tests/modules/nf-core/glimpse/chunk/test.yml
index dfe3f7bc294..bce2b34bc48 100644
--- a/tests/modules/nf-core/glimpse/chunk/test.yml
+++ b/tests/modules/nf-core/glimpse/chunk/test.yml
@@ -4,6 +4,6 @@
     - glimpse
     - glimpse/chunk
   files:
-    - path: output/glimpse/test.txt
+    - path: output/glimpse/input.txt
       md5sum: 9e5562b3f94857b8189b59849ce65cfb
     - path: output/glimpse/versions.yml
diff --git a/tests/modules/nf-core/glimpse/concordance/main.nf b/tests/modules/nf-core/glimpse/concordance/main.nf
index ad361cf41be..fe25e6874c6 100644
--- a/tests/modules/nf-core/glimpse/concordance/main.nf
+++ b/tests/modules/nf-core/glimpse/concordance/main.nf
@@ -9,13 +9,15 @@ include { BCFTOOLS_INDEX      } from '../../../../../modules/nf-core/bcftools/in
 
 workflow test_glimpse_concordance {
     
-   input_vcf = Channel.of([
-        [ id:'input', single_end:false ], // meta map
+    samples_infos = Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt')
+    region        = Channel.of(["chr21:16600000-16800000","chr21:16650000-16750000"])
+    input_vcf     = Channel.of([
+        [ id:'input' ], // meta map
         file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
-        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true),
-        "chr21:16600000-16800000",
-        "chr21:16650000-16750000"
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true)        
     ])
+
+    input_vcf_with_samples_infos = input_vcf.combine(samples_infos).combine(region)
     
     ref_panel = Channel.of([
             file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
@@ -26,31 +28,34 @@ workflow test_glimpse_concordance {
             file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true),
     ])
 
-    samples_file = Channel.of('NA12878 2')
-                    .collectFile(name: 'sampleinfos.txt')
-
     GLIMPSE_PHASE (
-        input_vcf.combine(ref_panel)
-                .combine(ch_map)
-                .combine(samples_file)
-    ) // [meta, vcf, index, regionin, regionout, regionindex, ref, ref_index, map, sample_infos]
+        input_vcf_with_samples_infos.combine(ref_panel)
+                                    .combine(ch_map)
+    ) // [meta, vcf, sample_infos, index, regionin, regionout, regionindex, ref, ref_index, map]
 
     ligate_input = GLIMPSE_PHASE.output.phased_variant
                                 .groupTuple()
 
     BCFTOOLS_INDEX ( ligate_input )
+
     GLIMPSE_LIGATE ( ligate_input.join(BCFTOOLS_INDEX.out.csi.groupTuple()) )
     
-    allele_freq = [file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz",checkIfExists:true),
-                   file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz.csi",checkIfExists:true)]
+    allele_freq = [
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz",checkIfExists:true),
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz.csi",checkIfExists:true)
+    ]
     
-    truth = [file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf",checkIfExists:true),
-                  file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf.csi",checkIfExists:true)]
+    truth = [
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf",checkIfExists:true),
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf.csi",checkIfExists:true)
+    ]
     
     list_inputs = Channel.of(["chr21", allele_freq[0], truth[0]])
                     .combine(GLIMPSE_LIGATE.out.merged_variants.map{it[1]}.collect().map{it[0]})
                     .collect()
+
     concordance_input = Channel.of([[ id:'input', single_end:false ]]).combine(list_inputs)
 
     GLIMPSE_CONCORDANCE ( concordance_input, [], [], []) // meta, Region, Frequencies, Truth, Estimate, minPROB, minDP, bins
+
 }
diff --git a/tests/modules/nf-core/glimpse/ligate/main.nf b/tests/modules/nf-core/glimpse/ligate/main.nf
index 2862f53212a..7ffb7dbbd53 100644
--- a/tests/modules/nf-core/glimpse/ligate/main.nf
+++ b/tests/modules/nf-core/glimpse/ligate/main.nf
@@ -2,35 +2,40 @@
 
 nextflow.enable.dsl = 2
 
-include { GLIMPSE_LIGATE } from '../../../../../modules/nf-core/glimpse/ligate/main.nf'
-include { GLIMPSE_PHASE  } from '../../../../../modules/nf-core/glimpse/phase/main.nf'
+include { GLIMPSE_LIGATE  } from '../../../../../modules/nf-core/glimpse/ligate/main.nf'
+include { GLIMPSE_PHASE   } from '../../../../../modules/nf-core/glimpse/phase/main.nf'
 include { BCFTOOLS_INDEX  } from '../../../../../modules/nf-core/bcftools/index/main.nf'
 
 workflow test_glimpse_ligate {
-    input_vcf = Channel.of([
-        [ id:'input', single_end:false ], // meta map
+
+    samples_infos = Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt')
+    region        = Channel.of(["chr21:16600000-16800000","chr21:16650000-16750000"])
+    input_vcf     = Channel.of([
+        [ id:'input'], // meta map
         file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
-        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true),
-        "chr21:16600000-16800000",
-        "chr21:16650000-16750000",
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true)        
     ])
+
+    input_vcf_with_samples_infos = input_vcf.combine(samples_infos).combine(region)
+
     ref_panel = Channel.of([
         file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
         file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
     ])
+
     ch_map = Channel.of([
         file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true),
     ])
-    samples_file = Channel.of('NA12878 2')
-                        .collectFile(name: 'sampleinfos.txt')
+
     GLIMPSE_PHASE (
-       input_vcf.combine(ref_panel)
-                .combine(ch_map)
-                .combine(samples_file)
-    ) // [meta, vcf, index, regionin, regionout, regionindex, ref, ref_index, map, sample_infos]
+        input_vcf_with_samples_infos.combine(ref_panel)
+                                    .combine(ch_map)
+    ) // [meta, vcf, index, sample_infos, regionin, regionout, regionindex, ref, ref_index, map]
 
     ligate_input = GLIMPSE_PHASE.output.phased_variant
                                 .groupTuple()
+
     BCFTOOLS_INDEX ( ligate_input )
+
     GLIMPSE_LIGATE ( ligate_input.join(BCFTOOLS_INDEX.out.csi.groupTuple()) )
 }
diff --git a/tests/modules/nf-core/glimpse/phase/main.nf b/tests/modules/nf-core/glimpse/phase/main.nf
index 152cb332273..bfe5ea37b5f 100644
--- a/tests/modules/nf-core/glimpse/phase/main.nf
+++ b/tests/modules/nf-core/glimpse/phase/main.nf
@@ -4,14 +4,18 @@ nextflow.enable.dsl = 2
 
 include { GLIMPSE_PHASE } from '../../../../../modules/nf-core/glimpse/phase/main.nf'
 
-    input_vcf = Channel.of([
-        [ id:'input', single_end:false ], // meta map
+    samples_infos = Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt')
+    empty_channel = Channel.of([[]])
+    region        = Channel.of(["chr21:16600000-16800000","chr21:16650000-16750000"])
+    input_vcf     = Channel.of([
+        [ id:'input'], // meta map
         file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
-        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true),
-        "chr21:16600000-16800000",
-        "chr21:16650000-16750000",
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true)        
     ])
 
+    input_vcf_with_samples_infos    = input_vcf.combine(samples_infos).combine(region)
+    input_vcf_without_samples_infos = input_vcf.combine(empty_channel).combine(region)
+
     ref_panel = Channel.of([
             file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
             file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
@@ -21,20 +25,16 @@ include { GLIMPSE_PHASE } from '../../../../../modules/nf-core/glimpse/phase/mai
         file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true),
     ])
 
-    samples_file = Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt')
-
 workflow test_glimpse_phase_nosampleinfos {
     GLIMPSE_PHASE (
-        input_vcf.combine(ref_panel)
-                .combine(ch_map)
-                .combine(Channel.of([[]]))
-    ) // [meta, vcf, index, regionin, regionout, regionindex, ref, ref_index, map, sample_infos]
+        input_vcf_without_samples_infos.combine(ref_panel)
+                                        .combine(ch_map)
+    ) // [meta, vcf, index, sample_infos, regionin, regionout, regionindex, ref, ref_index, map]
 }
 
 workflow test_glimpse_phase_withsampleinfos {
     GLIMPSE_PHASE (
-        input_vcf.combine(ref_panel)
-                .combine(ch_map)
-                .combine(samples_file)
-    ) // [meta, vcf, index, regionin, regionout, regionindex, ref, ref_index, map, sample_infos]
+        input_vcf_with_samples_infos.combine(ref_panel)
+                                    .combine(ch_map)
+    ) // [meta, vcf, index, sample_infos, regionin, regionout, regionindex, ref, ref_index, map]
 }
diff --git a/tests/modules/nf-core/glimpse/sample/main.nf b/tests/modules/nf-core/glimpse/sample/main.nf
index 029ace0c191..093fd16036d 100644
--- a/tests/modules/nf-core/glimpse/sample/main.nf
+++ b/tests/modules/nf-core/glimpse/sample/main.nf
@@ -8,15 +8,17 @@ include { GLIMPSE_SAMPLE } from '../../../../../modules/nf-core/glimpse/sample/m
 include { BCFTOOLS_INDEX  } from '../../../../../modules/nf-core/bcftools/index/main.nf'
 
 workflow test_glimpse_sample {
-    
-    input_vcf = Channel.of([
-        [ id:'input', single_end:false ], // meta map
+
+    samples_infos = Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt')
+    region        = Channel.of(["chr21:16600000-16800000","chr21:16650000-16750000"])
+    input_vcf     = Channel.of([
+        [ id:'input'], // meta map
         file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
-        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true),
-        "chr21:16600000-16800000",
-        "chr21:16650000-16750000",
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true)        
     ])
 
+    input_vcf_with_samples_infos = input_vcf.combine(samples_infos).combine(region)
+
     ref_panel = Channel.of([
             file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
             file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
@@ -26,13 +28,10 @@ workflow test_glimpse_sample {
         file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true),
     ])
 
-    samples_file = Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt')
-
-   GLIMPSE_PHASE (
-        input_vcf.combine(ref_panel)
-                .combine(ch_map)
-                .combine(Channel.of([[]]))
-    ) // [meta, vcf, index, regionin, regionout, regionindex, ref, ref_index, map, sample_infos]
+    GLIMPSE_PHASE (
+        input_vcf_with_samples_infos.combine(ref_panel)
+                                    .combine(ch_map)
+    ) // [meta, vcf, index, sample_infos, regionin, regionout, regionindex, ref, ref_index, map]
 
     ligate_input = GLIMPSE_PHASE.output.phased_variant
                                 .groupTuple()
diff --git a/tests/modules/nf-core/glimpse2/chunk/main.nf b/tests/modules/nf-core/glimpse2/chunk/main.nf
index 607d6bca23c..177beb1f6d4 100644
--- a/tests/modules/nf-core/glimpse2/chunk/main.nf
+++ b/tests/modules/nf-core/glimpse2/chunk/main.nf
@@ -4,27 +4,28 @@ nextflow.enable.dsl = 2
 
 include { GLIMPSE2_CHUNK } from '../../../../../modules/nf-core/glimpse2/chunk/main.nf'
 
-workflow test_glimpse2_chunk {
-    
-    input = [
+input = [
         [ id:'test', single_end:false ], // meta map
         file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
         file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true),
-        "chr21",
-        []]
-    GLIMPSE2_CHUNK (input, "recursive")
+        "chr21"]
+
+workflow test_glimpse2_chunk {
+    ch_map_empty = Channel.of([
+        [ id:'map'],
+        []
+    ]).collect()
+
+    GLIMPSE2_CHUNK (input, ch_map_empty, "recursive")
 
 }
 
 workflow test_glimpse2_chunk_withmap {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
-        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true),
-        "chr21",
-        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true)]
-    GLIMPSE2_CHUNK (input, "recursive")
+    ch_map = Channel.of([
+        [ id:'map'],
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true)
+    ]).collect()
 
+    GLIMPSE2_CHUNK (input,ch_map,"recursive")
 }
 
diff --git a/tests/modules/nf-core/glimpse2/concordance/main.nf b/tests/modules/nf-core/glimpse2/concordance/main.nf
index 4d2508d3a74..ad78ce739d3 100644
--- a/tests/modules/nf-core/glimpse2/concordance/main.nf
+++ b/tests/modules/nf-core/glimpse2/concordance/main.nf
@@ -3,20 +3,23 @@
 nextflow.enable.dsl = 2
 
 include { GLIMPSE2_PHASE       } from '../../../../../modules/nf-core/glimpse2/phase/main.nf'
-include { GLIMPSE_LIGATE      } from '../../../../../modules/nf-core/glimpse/ligate/main.nf'
+include { GLIMPSE_LIGATE       } from '../../../../../modules/nf-core/glimpse/ligate/main.nf'
 include { GLIMPSE2_CONCORDANCE } from '../../../../../modules/nf-core/glimpse2/concordance/main.nf'
-include { BCFTOOLS_INDEX  } from '../../../../../modules/nf-core/bcftools/index/main.nf'
+include { BCFTOOLS_INDEX       } from '../../../../../modules/nf-core/bcftools/index/main.nf'
 
 workflow test_glimpse2_concordance {
-    
-   input_vcf = Channel.of([
-        [ id:'input', single_end:false ], // meta map
+
+    samples_infos = Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt')
+    region        = Channel.of(["chr21:16600000-16800000","chr21:16650000-16750000"])
+    input_vcf     = Channel.of([
+        [ id:'input'], // meta map
         file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
-        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true),
-        "chr21:16600000-16800000",
-        "chr21:16650000-16750000"
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true)        
     ])
-    
+
+    input_vcf_with_samples_infos = input_vcf.combine(samples_infos).combine(region)
+
+
     ref_panel = Channel.of([
             file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
             file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
@@ -26,32 +29,34 @@ workflow test_glimpse2_concordance {
             file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true),
     ])
 
-    samples_file = Channel.of('NA12878 2')
-                    .collectFile(name: 'sampleinfos.txt')
-
     GLIMPSE2_PHASE (
-        input_vcf.combine(ref_panel)
-                .combine(ch_map)
-                .combine(samples_file),
+        input_vcf_with_samples_infos.combine( ref_panel )
+                                    .combine( ch_map ),
         Channel.of([[],[],[]])
-    ) // [meta, vcf, index, regionin, regionout, regionindex, ref, ref_index, map, sample_infos]
-   
-    allele_freq = Channel.of([file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz",checkIfExists:true),
-                   file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz.csi",checkIfExists:true)])
-    
-    truth = Channel.of([file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf",checkIfExists:true),
-                  file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf.csi",checkIfExists:true)])
-    
-    BCFTOOLS_INDEX(GLIMPSE2_PHASE.output.phased_variant)
+    ) // [meta, vcf, index, sample_infos, regionin, regionout, regionindex, ref, ref_index, map]
+
+    allele_freq = Channel.of([
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz",checkIfExists:true),
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz.csi",checkIfExists:true)
+    ])
+
+    truth = Channel.of([
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf",checkIfExists:true),
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf.csi",checkIfExists:true)
+    ])
+
+    BCFTOOLS_INDEX ( GLIMPSE2_PHASE.output.phased_variant )
+
     list_inputs = GLIMPSE2_PHASE.output.phased_variant
-                        .join(BCFTOOLS_INDEX.out.csi)
-                        .combine(truth)
-                        .combine(allele_freq)
-                        .combine(Channel.of([[]]))
-                        .combine(Channel.of(["chr21"]))
+                        .join( BCFTOOLS_INDEX.out.csi )
+                        .combine( truth )
+                        .combine( allele_freq )
+                        .combine( Channel.of([[]]) )
+                        .combine( Channel.of(["chr21"]) )
 
     GLIMPSE2_CONCORDANCE ( list_inputs,
                         Channel.of([[id:"params"],[],"0 0.01 0.05 0.1 0.2 0.5",[],[]]),
                         0.9999,
                         8) // [meta, Region, Frequencies, Truth, Estimate], [meta, group, bins, ac_bins, allele_count], min-val-gl, min-val-dp
+
 }
diff --git a/tests/modules/nf-core/glimpse2/concordance/test.yml b/tests/modules/nf-core/glimpse2/concordance/test.yml
index 9999229c3e0..f62cb36fcbc 100644
--- a/tests/modules/nf-core/glimpse2/concordance/test.yml
+++ b/tests/modules/nf-core/glimpse2/concordance/test.yml
@@ -4,12 +4,12 @@
     - glimpse2
     - glimpse2/concordance
   files:
-    - path: output/bcftools/input_chr21_16600000-16800000.bcf.csi
+    - path: output/bcftools/input_chr21_16650000-16750000.bcf.csi
     - path: output/bcftools/versions.yml
     - path: output/glimpse2/input.error.cal.txt.gz
     - path: output/glimpse2/input.error.grp.txt.gz
     - path: output/glimpse2/input.error.spl.txt.gz
     - path: output/glimpse2/input.rsquare.grp.txt.gz
     - path: output/glimpse2/input.rsquare.spl.txt.gz
-    - path: output/glimpse2/input_chr21_16600000-16800000.bcf
+    - path: output/glimpse2/input_chr21_16650000-16750000.bcf
     - path: output/glimpse2/versions.yml
diff --git a/tests/modules/nf-core/glimpse2/ligate/main.nf b/tests/modules/nf-core/glimpse2/ligate/main.nf
index 20f1c2bfde3..82e885243ac 100644
--- a/tests/modules/nf-core/glimpse2/ligate/main.nf
+++ b/tests/modules/nf-core/glimpse2/ligate/main.nf
@@ -7,31 +7,37 @@ include { GLIMPSE2_PHASE  } from '../../../../../modules/nf-core/glimpse2/phase/
 include { BCFTOOLS_INDEX  } from '../../../../../modules/nf-core/bcftools/index/main.nf'
 
 workflow test_glimpse2_ligate {
-    input_vcf = Channel.of([
-        [ id:'input', single_end:false ], // meta map
+
+    samples_infos = Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt')
+    region        = Channel.of(["chr21:16600000-16800000","chr21:16650000-16750000"])
+    input_vcf     = Channel.of([
+        [ id:'input'], // meta map
         file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
-        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true),
-        "chr21:16600000-16800000",
-        "chr21:16650000-16750000",
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true)        
     ])
+
+    input_vcf_with_samples_infos = input_vcf.combine(samples_infos).combine(region)
+
     ref_panel = Channel.of([
         file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
         file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
     ])
+
     ch_map = Channel.of([
         file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true),
     ])
-    samples_file = Channel.of('NA12878 2')
-                        .collectFile(name: 'sampleinfos.txt')
+
     GLIMPSE2_PHASE (
-       input_vcf.combine(ref_panel)
-                .combine(ch_map)
-                .combine(samples_file),
+        input_vcf_with_samples_infos.combine( ref_panel )
+                                    .combine( ch_map ),
         Channel.of([[],[],[]])
-    ) // [meta, vcf, index, regionin, regionout, regionindex, ref, ref_index, map, sample_infos]
+    ) // [meta, vcf, index, sample_infos, regionin, regionout, regionindex, ref, ref_index, map]
 
     ligate_input = GLIMPSE2_PHASE.output.phased_variant
                                 .groupTuple()
+
     BCFTOOLS_INDEX ( ligate_input )
+
     GLIMPSE2_LIGATE ( ligate_input.join(BCFTOOLS_INDEX.out.csi.groupTuple()) )
+
 }
diff --git a/tests/modules/nf-core/glimpse2/ligate/test.yml b/tests/modules/nf-core/glimpse2/ligate/test.yml
index d8518751b98..c18143cd298 100644
--- a/tests/modules/nf-core/glimpse2/ligate/test.yml
+++ b/tests/modules/nf-core/glimpse2/ligate/test.yml
@@ -4,8 +4,8 @@
     - glimpse2
     - glimpse2/ligate
   files:
-    - path: output/bcftools/input_chr21_16600000-16800000.bcf.csi
+    - path: output/bcftools/input_chr21_16650000-16750000.bcf.csi
     - path: output/bcftools/versions.yml
     - path: output/glimpse2/input.vcf.gz
-    - path: output/glimpse2/input_chr21_16600000-16800000.bcf
+    - path: output/glimpse2/input_chr21_16650000-16750000.bcf
     - path: output/glimpse2/versions.yml
diff --git a/tests/modules/nf-core/glimpse2/phase/main.nf b/tests/modules/nf-core/glimpse2/phase/main.nf
index bff99e53ba6..36219c4e92e 100644
--- a/tests/modules/nf-core/glimpse2/phase/main.nf
+++ b/tests/modules/nf-core/glimpse2/phase/main.nf
@@ -4,11 +4,12 @@ nextflow.enable.dsl = 2
 
 include { GLIMPSE2_PHASE } from '../../../../../modules/nf-core/glimpse2/phase/main.nf'
 
- 
+
 input_vcf = Channel.of([
     [ id:'input' ], // meta map
     file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
     file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true),
+    [],
     "chr21:16600000-16800000",
     "chr21:16650000-16750000"
     ])
@@ -16,15 +17,17 @@ input_bam = Channel.of([
     [id:'input'],
     file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.bam", checkIfExists: true),
     file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.bam.bai", checkIfExists: true),
+    [],
     "chr21:16600000-16800000",
-    "chr21:16650000-16750000",    
+    "chr21:16650000-16750000",
 ])
 input_cram = Channel.of([
     [id:'input'],
     file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.cram", checkIfExists: true),
     file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.cram.crai", checkIfExists: true),
+    [],
     "chr21:16600000-16800000",
-    "chr21:16650000-16750000",    
+    "chr21:16650000-16750000",
 ])
 ref_panel = Channel.of([
         file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
@@ -35,10 +38,6 @@ map_file = Channel.of([
     file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true)
     ])
 
-samples_file = Channel.of([
-    []
-    ])
-
 reference_genome = Channel.of([
                     [id:'refHG38_chr21'],
                     file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/hs38DH.chr21.fa.gz", checkIfExists: true),
@@ -48,26 +47,23 @@ reference_genome = Channel.of([
 workflow test_glimpse2_phase_vcf {
     GLIMPSE2_PHASE (
         input_vcf.combine(ref_panel)
-                .combine(map_file)
-                .combine(samples_file),
+                .combine(map_file),
         Channel.of([[],[],[]])
-        ) // [meta, vcf, index, regionin, regionout, regionindex, sample_infos], map, sample, [meta, ref, index]
+        ) // [meta, vcf, index, sample_infos, regionin, regionout,ref, index, map] [meta, fasta, fai]
 }
 
 workflow test_glimpse2_phase_bam {
     GLIMPSE2_PHASE (
         input_bam.combine(ref_panel)
-                .combine(map_file)
-                .combine(samples_file),
+                .combine(map_file),
         Channel.of([[],[],[]])
-        ) // [meta, vcf, index, regionin, regionout, regionindex, sample_infos], map, sample, [meta, ref, index]
+        ) // [meta, vcf, index, sample_infos, regionin, regionout,ref, index, map] [meta, fasta, fai]
 }
 
 workflow test_glimpse2_phase_cram {
     GLIMPSE2_PHASE (
         input_cram.combine(ref_panel)
-                .combine(map_file)
-                .combine(samples_file),
+                .combine(map_file),
         reference_genome
-        ) // [meta, vcf, index, regionin, regionout, regionindex, sample_infos], map, sample, [meta, ref, index]
-}
\ No newline at end of file
+        ) // [meta, vcf, index, sample_infos, regionin, regionout,ref, index, map] [meta, fasta, fai]
+}
diff --git a/tests/modules/nf-core/glimpse2/phase/test.yml b/tests/modules/nf-core/glimpse2/phase/test.yml
index 17d8e3e8ad0..d23a02903db 100644
--- a/tests/modules/nf-core/glimpse2/phase/test.yml
+++ b/tests/modules/nf-core/glimpse2/phase/test.yml
@@ -4,7 +4,7 @@
     - glimpse2
     - glimpse2/phase
   files:
-    - path: output/glimpse2/input_chr21_16600000-16800000.bcf
+    - path: output/glimpse2/input_chr21_16650000-16750000.bcf
     - path: output/glimpse2/versions.yml
 
 - name: glimpse2 phase test_glimpse2_phase_bam
@@ -13,8 +13,8 @@
     - glimpse2
     - glimpse2/phase
   files:
-    - path: output/glimpse2/input_chr21_16600000-16800000.bcf
-    - path: output/glimpse2/input_chr21_16600000-16800000_stats_coverage.txt.gz
+    - path: output/glimpse2/input_chr21_16650000-16750000.bcf
+    - path: output/glimpse2/input_chr21_16650000-16750000_stats_coverage.txt.gz
       md5sum: 632f4bf08bed0870192933a0a32b95c8
     - path: output/glimpse2/versions.yml
 
@@ -24,7 +24,7 @@
     - glimpse2
     - glimpse2/phase
   files:
-    - path: output/glimpse2/input_chr21_16600000-16800000.bcf
-    - path: output/glimpse2/input_chr21_16600000-16800000_stats_coverage.txt.gz
+    - path: output/glimpse2/input_chr21_16650000-16750000.bcf
+    - path: output/glimpse2/input_chr21_16650000-16750000_stats_coverage.txt.gz
       md5sum: a2d58d6fcd1918f649a4eb19d0ee68c3
     - path: output/glimpse2/versions.yml
diff --git a/tests/subworkflows/nf-core/multiple_impute_glimpse2/main.nf b/tests/subworkflows/nf-core/multiple_impute_glimpse2/main.nf
new file mode 100644
index 00000000000..df0c9fb0a00
--- /dev/null
+++ b/tests/subworkflows/nf-core/multiple_impute_glimpse2/main.nf
@@ -0,0 +1,73 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MULTIPLE_IMPUTE_GLIMPSE2 } from '../../../../subworkflows/nf-core/multiple_impute_glimpse2/main.nf'
+
+    ch_input_vcf = Channel.of([
+        [ id:'input_vcf'], // meta map
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz",
+            checkIfExists: true),
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi",
+            checkIfExists: true),
+    ])
+    sample = Channel.of('NA12878 2')
+            .collectFile(name: 'sampleinfos.txt')
+    ch_input_vcf_with_sample = ch_input_vcf.combine(sample)
+    ch_input_vcf_without_sample = ch_input_vcf.combine(Channel.of([[]]))
+
+    ch_ref_panel = Channel.of([
+        [ id:'ref_panel'],
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf",
+            checkIfExists: true),
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi",
+            checkIfExists: true),
+        "chr21"
+    ])
+    ch_map = Channel.of([
+        [ id:'map'],
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true)
+    ]).collect()
+
+    ch_fasta_empty = Channel.of([
+        [ id:'ref_fasta'],
+        [],
+        []
+    ]).collect()
+
+workflow test_multiple_impute_glimpse2_without_sample {
+    MULTIPLE_IMPUTE_GLIMPSE2 ( ch_input_vcf_without_sample,
+                        ch_ref_panel, ch_map, ch_fasta_empty, "recursive" )
+}
+
+workflow test_multiple_impute_glimpse2_with_sample {
+    MULTIPLE_IMPUTE_GLIMPSE2 ( ch_input_vcf_with_sample,
+                        ch_ref_panel, ch_map, ch_fasta_empty, "recursive" )
+}
+
+workflow test_multiple_impute_glimpse2_bam {
+
+    input_bam = Channel.of([
+        [id:'input'],
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.bam", checkIfExists: true),
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.bam.bai", checkIfExists: true),
+        []
+    ])
+
+    MULTIPLE_IMPUTE_GLIMPSE2 ( input_bam, ch_ref_panel, ch_map, ch_fasta_empty, "recursive" )
+}
+
+workflow test_multiple_impute_glimpse2_cram {
+    input_cram = Channel.of([
+        [id:'input'],
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.cram", checkIfExists: true),
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.cram.crai", checkIfExists: true),
+        []
+    ])
+    ch_fasta = Channel.of([
+                    [id:'refHG38_chr21'],
+                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/hs38DH.chr21.fa.gz", checkIfExists: true),
+                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/hs38DH.chr21.fa.gz.fai", checkIfExists: true)
+                ]).collect()
+    MULTIPLE_IMPUTE_GLIMPSE2 ( input_cram, ch_ref_panel, ch_map, ch_fasta, "recursive" )
+}
diff --git a/tests/subworkflows/nf-core/multiple_impute_glimpse2/nextflow.config b/tests/subworkflows/nf-core/multiple_impute_glimpse2/nextflow.config
new file mode 100644
index 00000000000..15fff1d62f5
--- /dev/null
+++ b/tests/subworkflows/nf-core/multiple_impute_glimpse2/nextflow.config
@@ -0,0 +1,13 @@
+process {
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: GLIMPSE2_CHUNK {
+        ext.args = [
+            "--window-cm 0.05",
+            "--buffer-cm 0.02",
+            "--window-mb 0.05",
+            "--buffer-mb 0.02",
+            "--window-count 50",
+            "--buffer-count 25"
+        ].join(' ')
+    }
+}
diff --git a/tests/subworkflows/nf-core/multiple_impute_glimpse2/test.yml b/tests/subworkflows/nf-core/multiple_impute_glimpse2/test.yml
new file mode 100644
index 00000000000..ead3a4648a9
--- /dev/null
+++ b/tests/subworkflows/nf-core/multiple_impute_glimpse2/test.yml
@@ -0,0 +1,103 @@
+- name: multiple_impute_glimpse2 test_multiple_impute_glimpse2_without_sample
+  command: nextflow run ./tests/subworkflows/nf-core/multiple_impute_glimpse2 -entry test_multiple_impute_glimpse2_without_sample -c ./tests/config/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/index
+    - glimpse2
+    - glimpse2/chunk
+    - glimpse2/ligate
+    - glimpse2/phase
+    - glimpse2/splitreference
+    - subworkflows
+    - subworkflows/multiple_impute_glimpse2
+  files:
+    - path: output/glimpse2/input_vcf.vcf.gz
+    - path: output/glimpse2/input_vcf_ref_panel_chr21_16600115-16696345_chr21_16600115_16799989.bin.bcf
+    - path: output/glimpse2/input_vcf_ref_panel_chr21_16696369-16799989_chr21_16600115_16799989.bin.bcf
+    - path: output/glimpse2/ref_panel.txt
+      md5sum: 129913c63dbe586de143b8062bd1119d
+    - path: output/glimpse2/ref_panel_chr21_16600115-16696345_chr21_16600115_16799989.bin
+    - path: output/glimpse2/ref_panel_chr21_16696369-16799989_chr21_16600115_16799989.bin
+    - path: output/index/input_vcf.vcf.gz.csi
+    - path: output/index/input_vcf_ref_panel_chr21_16600115-16696345_chr21_16600115_16799989.bin.bcf.csi
+    - path: output/index/input_vcf_ref_panel_chr21_16696369-16799989_chr21_16600115_16799989.bin.bcf.csi
+
+- name: multiple_impute_glimpse2 test_multiple_impute_glimpse2_with_sample
+  command: nextflow run ./tests/subworkflows/nf-core/multiple_impute_glimpse2 -entry test_multiple_impute_glimpse2_with_sample -c ./tests/config/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/index
+    - glimpse2
+    - glimpse2/chunk
+    - glimpse2/ligate
+    - glimpse2/phase
+    - glimpse2/splitreference
+    - subworkflows
+    - subworkflows/multiple_impute_glimpse2
+  files:
+    - path: output/glimpse2/input_vcf.vcf.gz
+    - path: output/glimpse2/input_vcf_ref_panel_chr21_16600115-16696345_chr21_16600115_16799989.bin.bcf
+    - path: output/glimpse2/input_vcf_ref_panel_chr21_16696369-16799989_chr21_16600115_16799989.bin.bcf
+    - path: output/glimpse2/ref_panel.txt
+      md5sum: 129913c63dbe586de143b8062bd1119d
+    - path: output/glimpse2/ref_panel_chr21_16600115-16696345_chr21_16600115_16799989.bin
+    - path: output/glimpse2/ref_panel_chr21_16696369-16799989_chr21_16600115_16799989.bin
+    - path: output/index/input_vcf.vcf.gz.csi
+    - path: output/index/input_vcf_ref_panel_chr21_16600115-16696345_chr21_16600115_16799989.bin.bcf.csi
+    - path: output/index/input_vcf_ref_panel_chr21_16696369-16799989_chr21_16600115_16799989.bin.bcf.csi
+
+- name: multiple_impute_glimpse2 test_multiple_impute_glimpse2_bam
+  command: nextflow run ./tests/subworkflows/nf-core/multiple_impute_glimpse2 -entry test_multiple_impute_glimpse2_bam -c ./tests/config/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/index
+    - glimpse2
+    - glimpse2/chunk
+    - glimpse2/ligate
+    - glimpse2/phase
+    - glimpse2/splitreference
+    - subworkflows
+    - subworkflows/multiple_impute_glimpse2
+  files:
+    - path: output/glimpse2/input.vcf.gz
+    - path: output/glimpse2/input_ref_panel_chr21_16600115-16696345_chr21_16600115_16799989.bin.bcf
+    - path: output/glimpse2/input_ref_panel_chr21_16600115-16696345_chr21_16600115_16799989.bin_stats_coverage.txt.gz
+      md5sum: 632f4bf08bed0870192933a0a32b95c8
+    - path: output/glimpse2/input_ref_panel_chr21_16696369-16799989_chr21_16600115_16799989.bin.bcf
+    - path: output/glimpse2/input_ref_panel_chr21_16696369-16799989_chr21_16600115_16799989.bin_stats_coverage.txt.gz
+      md5sum: 632f4bf08bed0870192933a0a32b95c8
+    - path: output/glimpse2/ref_panel.txt
+      md5sum: 129913c63dbe586de143b8062bd1119d
+    - path: output/glimpse2/ref_panel_chr21_16600115-16696345_chr21_16600115_16799989.bin
+    - path: output/glimpse2/ref_panel_chr21_16696369-16799989_chr21_16600115_16799989.bin
+    - path: output/index/input.vcf.gz.csi
+    - path: output/index/input_ref_panel_chr21_16600115-16696345_chr21_16600115_16799989.bin.bcf.csi
+    - path: output/index/input_ref_panel_chr21_16696369-16799989_chr21_16600115_16799989.bin.bcf.csi
+
+- name: multiple_impute_glimpse2 test_multiple_impute_glimpse2_cram
+  command: nextflow run ./tests/subworkflows/nf-core/multiple_impute_glimpse2 -entry test_multiple_impute_glimpse2_cram -c ./tests/config/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/index
+    - glimpse2
+    - glimpse2/chunk
+    - glimpse2/ligate
+    - glimpse2/phase
+    - glimpse2/splitreference
+    - subworkflows
+    - subworkflows/multiple_impute_glimpse2
+  files:
+    - path: output/glimpse2/input.vcf.gz
+    - path: output/glimpse2/input_ref_panel_chr21_16600115-16696345_chr21_16600115_16799989.bin.bcf
+    - path: output/glimpse2/input_ref_panel_chr21_16600115-16696345_chr21_16600115_16799989.bin_stats_coverage.txt.gz
+      md5sum: a2d58d6fcd1918f649a4eb19d0ee68c3
+    - path: output/glimpse2/input_ref_panel_chr21_16696369-16799989_chr21_16600115_16799989.bin.bcf
+    - path: output/glimpse2/input_ref_panel_chr21_16696369-16799989_chr21_16600115_16799989.bin_stats_coverage.txt.gz
+      md5sum: a2d58d6fcd1918f649a4eb19d0ee68c3
+    - path: output/glimpse2/ref_panel.txt
+      md5sum: 129913c63dbe586de143b8062bd1119d
+    - path: output/glimpse2/ref_panel_chr21_16600115-16696345_chr21_16600115_16799989.bin
+    - path: output/glimpse2/ref_panel_chr21_16696369-16799989_chr21_16600115_16799989.bin
+    - path: output/index/input.vcf.gz.csi
+    - path: output/index/input_ref_panel_chr21_16600115-16696345_chr21_16600115_16799989.bin.bcf.csi
+    - path: output/index/input_ref_panel_chr21_16696369-16799989_chr21_16600115_16799989.bin.bcf.csi
diff --git a/tests/subworkflows/nf-core/vcf_impute_glimpse/main.nf b/tests/subworkflows/nf-core/vcf_impute_glimpse/main.nf
index befb4e4ad45..f6cf80c20d7 100644
--- a/tests/subworkflows/nf-core/vcf_impute_glimpse/main.nf
+++ b/tests/subworkflows/nf-core/vcf_impute_glimpse/main.nf
@@ -4,35 +4,35 @@ nextflow.enable.dsl = 2
 
 include { VCF_IMPUTE_GLIMPSE } from '../../../../subworkflows/nf-core/vcf_impute_glimpse/main.nf'
 
-    input_vcf = Channel.of([
-        [ id:'input1'], // meta map
-        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz",
-            checkIfExists: true),
-        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi",
-            checkIfExists: true),
-        "chr21"
+    samples_infos = Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt')
+    empty_channel = Channel.of([[]])
+    region        = Channel.of(["chr21"])
+    input_vcf     = Channel.of([
+        [ id:'input'], // meta map
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
+        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true)        
     ])
-    ref_panel = Channel.of([
-        [ id:'input1'],
+
+    input_vcf_with_samples_infos    = input_vcf.combine(samples_infos).combine(region)
+    input_vcf_without_samples_infos = input_vcf.combine(empty_channel).combine(region)
+
+    ch_ref_panel = Channel.of([
+        [ id:'ref_panel'],
         file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf",
             checkIfExists: true),
         file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi",
             checkIfExists: true)
     ])
+
     ch_map = Channel.of([
-        [ id:'input1'],
+        [ id:'map'],
         file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true)
     ])
 
 workflow test_vcf_impute_glimpse_without_sample {
-    sample = Channel.of([[ id:'input1'],[]])
-    VCF_IMPUTE_GLIMPSE ( input_vcf, ref_panel, ch_map, sample )
+    VCF_IMPUTE_GLIMPSE ( input_vcf_without_samples_infos, ch_ref_panel, ch_map )
 }
 
 workflow test_vcf_impute_glimpse_with_sample {
-    sample = Channel.of([[ id:'input1']])
-                    .combine(Channel.of('NA12878 2')
-                                .collectFile(name: 'sampleinfos.txt')
-                    )
-    VCF_IMPUTE_GLIMPSE ( input_vcf, ref_panel, ch_map, sample )
+    VCF_IMPUTE_GLIMPSE ( input_vcf_with_samples_infos, ch_ref_panel, ch_map )
 }
diff --git a/tests/subworkflows/nf-core/vcf_impute_glimpse/test.yml b/tests/subworkflows/nf-core/vcf_impute_glimpse/test.yml
index f950fe3df1f..0dd90f6b903 100644
--- a/tests/subworkflows/nf-core/vcf_impute_glimpse/test.yml
+++ b/tests/subworkflows/nf-core/vcf_impute_glimpse/test.yml
@@ -8,10 +8,10 @@
     - subworkflows
     - subworkflows/vcf_impute_glimpse
   files:
-    - path: output/glimpse/input1.txt
+    - path: output/glimpse/input.txt
       md5sum: 75bff56f26d8a590c429afee74df5110
-    - path: output/glimpse/input1.vcf.gz
-    - path: output/glimpse/input1_chr21_16600115-16799989.vcf.gz
+    - path: output/glimpse/input.vcf.gz
+    - path: output/glimpse/input_chr21_16600115-16799989.vcf.gz
 
 - name: vcf_impute_glimpse test_vcf_impute_glimpse_with_sample
   command: nextflow run ./tests/subworkflows/nf-core/vcf_impute_glimpse -entry test_vcf_impute_glimpse_with_sample -c ./tests/config/nextflow.config
@@ -23,7 +23,7 @@
     - subworkflows
     - subworkflows/vcf_impute_glimpse
   files:
-    - path: output/glimpse/input1.txt
+    - path: output/glimpse/input.txt
       md5sum: 75bff56f26d8a590c429afee74df5110
-    - path: output/glimpse/input1.vcf.gz
-    - path: output/glimpse/input1_chr21_16600115-16799989.vcf.gz
+    - path: output/glimpse/input.vcf.gz
+    - path: output/glimpse/input_chr21_16600115-16799989.vcf.gz