diff --git a/modules.json b/modules.json
index 8e361457..dff640fa 100644
--- a/modules.json
+++ b/modules.json
@@ -12,13 +12,8 @@
                     },
                     "bcftools/index": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "multiple_impute_glimpse2",
-                            "modules",
-                            "vcf_impute_glimpse",
-                            "vcf_phase_shapeit5"
-                        ]
+                        "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
+                        "installed_by": ["multiple_impute_glimpse2", "vcf_impute_glimpse", "vcf_phase_shapeit5"]
                     },
                     "bcftools/norm": {
                         "branch": "master",
@@ -52,17 +47,17 @@
                     },
                     "glimpse/chunk": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["vcf_impute_glimpse", "modules"]
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "installed_by": ["vcf_impute_glimpse"]
                     },
                     "glimpse/ligate": {
                         "branch": "master",
-                        "git_sha": "36cfa4c2a7e538832c50f40cb16d159e84cd3305",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["vcf_impute_glimpse"]
                     },
                     "glimpse/phase": {
                         "branch": "master",
-                        "git_sha": "36cfa4c2a7e538832c50f40cb16d159e84cd3305",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["vcf_impute_glimpse"]
                     },
                     "glimpse2/chunk": {
@@ -140,29 +135,29 @@
                         "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
                         "installed_by": ["subworkflows"]
                     },
-                    "vcf_impute_glimpse": {
+                    "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "74d79f1853c9ff2961e6061aad3c68d728d5c20d",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     },
-                    "vcf_phase_shapeit5": {
+                    "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     },
-                    "utils_nextflow_pipeline": {
+                    "utils_nfvalidation_plugin": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["subworkflows"]
                     },
-                    "utils_nfcore_pipeline": {
+                    "vcf_impute_glimpse": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "8dab3bf2aaa912730419080e96d2a7d98911db48",
                         "installed_by": ["subworkflows"]
                     },
-                    "utils_nfvalidation_plugin": {
+                    "vcf_phase_shapeit5": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/bcftools/index/environment.yml b/modules/nf-core/bcftools/index/environment.yml
new file mode 100644
index 00000000..bbee37ad
--- /dev/null
+++ b/modules/nf-core/bcftools/index/environment.yml
@@ -0,0 +1,7 @@
+name: bcftools_index
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::bcftools=1.18
diff --git a/modules/nf-core/bcftools/index/main.nf b/modules/nf-core/bcftools/index/main.nf
index 43360aab..4cd0dcbb 100644
--- a/modules/nf-core/bcftools/index/main.nf
+++ b/modules/nf-core/bcftools/index/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_INDEX {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::bcftools=1.17"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0':
-        'biocontainers/bcftools:1.17--haef29d1_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0':
+        'biocontainers/bcftools:1.18--h8b25389_0' }"
 
     input:
     tuple val(meta), path(vcf)
@@ -34,4 +34,18 @@ process BCFTOOLS_INDEX {
         bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def extension = args.contains("--tsi") || args.contains("-t") ? "tbi" :
+                    "csi"
+    """
+    touch ${vcf}.${extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/bcftools/index/meta.yml b/modules/nf-core/bcftools/index/meta.yml
index b883fa5f..fc340cbc 100644
--- a/modules/nf-core/bcftools/index/meta.yml
+++ b/modules/nf-core/bcftools/index/meta.yml
@@ -14,7 +14,6 @@ tools:
       tool_dev_url: https://github.com/samtools/bcftools
       doi: "10.1093/gigascience/giab008"
       licence: ["MIT", "GPL-3.0-or-later"]
-
 input:
   - meta:
       type: map
@@ -25,7 +24,6 @@ input:
       type: file
       description: VCF file (optionally GZIPPED)
       pattern: "*.{vcf,vcf.gz}"
-
 output:
   - meta:
       type: map
@@ -44,6 +42,7 @@ output:
       type: file
       description: Alternative VCF file index file for larger files (activated with -t parameter)
       pattern: "*.tbi"
-
 authors:
   - "@jfy133"
+maintainers:
+  - "@jfy133"
diff --git a/modules/nf-core/glimpse/chunk/environment.yml b/modules/nf-core/glimpse/chunk/environment.yml
new file mode 100644
index 00000000..8d71aa91
--- /dev/null
+++ b/modules/nf-core/glimpse/chunk/environment.yml
@@ -0,0 +1,7 @@
+name: glimpse_chunk
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::glimpse-bio=1.1.1
diff --git a/modules/nf-core/glimpse/chunk/main.nf b/modules/nf-core/glimpse/chunk/main.nf
index f2ffed2f..94779846 100644
--- a/modules/nf-core/glimpse/chunk/main.nf
+++ b/modules/nf-core/glimpse/chunk/main.nf
@@ -2,7 +2,7 @@ process GLIMPSE_CHUNK {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::glimpse-bio=1.1.1"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--h2ce4488_2':
         'biocontainers/glimpse-bio:1.1.1--hce55b13_1' }"
@@ -31,7 +31,19 @@ process GLIMPSE_CHUNK {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        glimpse: "\$(GLIMPSE_phase --help | sed -nr '/Version/p' | grep -o -E '([0-9]+.){1,2}[0-9]')"
+        glimpse: "\$(GLIMPSE_chunk --help | sed -nr '/Version/p' | grep -o -E '([0-9]+.){1,2}[0-9]')"
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix  = task.ext.prefix ?: "${meta.id}"
+    def args    = task.ext.args   ?: ""
+    """
+    touch ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        glimpse: "\$(GLIMPSE_chunk --help | sed -nr '/Version/p' | grep -o -E '([0-9]+.){1,2}[0-9]')"
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/glimpse/chunk/meta.yml b/modules/nf-core/glimpse/chunk/meta.yml
index 9ac840a6..65fa6218 100644
--- a/modules/nf-core/glimpse/chunk/meta.yml
+++ b/modules/nf-core/glimpse/chunk/meta.yml
@@ -12,21 +12,18 @@ tools:
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
       licence: "['MIT']"
-
 input:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-
   - input:
       type: file
       description: |
         Target dataset in VCF/BCF format defined at all variable positions.
         The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).
       pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
-
   - region:
       type: string
       description: |
@@ -38,16 +35,15 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-
   - txt:
       type: file
       description: Tab delimited output txt file containing buffer and imputation regions.
       pattern: "*.{txt}"
-
 authors:
   - "@louislenezet"
+maintainers:
+  - "@louislenezet"
diff --git a/modules/nf-core/glimpse/chunk/tests/main.nf.test b/modules/nf-core/glimpse/chunk/tests/main.nf.test
new file mode 100644
index 00000000..4c278af1
--- /dev/null
+++ b/modules/nf-core/glimpse/chunk/tests/main.nf.test
@@ -0,0 +1,36 @@
+nextflow_process {
+
+    name "Test Process GLIMPSE_CHUNK"
+    script "../main.nf"
+    process "GLIMPSE_CHUNK"
+    tag "glimpse"
+    tag "glimpse/chunk"
+    tag "modules_nfcore"
+    tag "modules"
+
+    test("Should run without failures") {
+        config "modules/nf-core/glimpse/chunk/tests/nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'input' ], // meta map
+                    file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true),
+                    "chr21"
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/glimpse/chunk/tests/main.nf.test.snap b/modules/nf-core/glimpse/chunk/tests/main.nf.test.snap
new file mode 100644
index 00000000..0490a8e4
--- /dev/null
+++ b/modules/nf-core/glimpse/chunk/tests/main.nf.test.snap
@@ -0,0 +1,31 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.txt:md5,9e5562b3f94857b8189b59849ce65cfb"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a523ef8d6391ddeff47bfd30b606d628"
+                ],
+                "chunk_chr": [
+                    [
+                        {
+                            "id": "input"
+                        },
+                        "input.txt:md5,9e5562b3f94857b8189b59849ce65cfb"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a523ef8d6391ddeff47bfd30b606d628"
+                ]
+            }
+        ],
+        "timestamp": "2023-10-16T15:55:52.457257547"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/glimpse/chunk/tests/nextflow.config b/modules/nf-core/glimpse/chunk/tests/nextflow.config
new file mode 100644
index 00000000..c945152e
--- /dev/null
+++ b/modules/nf-core/glimpse/chunk/tests/nextflow.config
@@ -0,0 +1,9 @@
+process {
+    withName: GLIMPSE_CHUNK {
+        ext.args = [
+            "--window-size 2000000",
+            "--buffer-size 200000"
+        ].join(' ')
+        ext.prefix = { "${meta.id}" }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/glimpse/chunk/tests/tags.yml b/modules/nf-core/glimpse/chunk/tests/tags.yml
new file mode 100644
index 00000000..bd846dfd
--- /dev/null
+++ b/modules/nf-core/glimpse/chunk/tests/tags.yml
@@ -0,0 +1,2 @@
+glimpse/chunk:
+  - modules/nf-core/glimpse/chunk/**
diff --git a/modules/nf-core/glimpse/ligate/environment.yml b/modules/nf-core/glimpse/ligate/environment.yml
new file mode 100644
index 00000000..0f9e9a33
--- /dev/null
+++ b/modules/nf-core/glimpse/ligate/environment.yml
@@ -0,0 +1,7 @@
+name: glimpse_ligate
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::glimpse-bio=1.1.1
diff --git a/modules/nf-core/glimpse/ligate/main.nf b/modules/nf-core/glimpse/ligate/main.nf
index f9775bbf..65425fd5 100644
--- a/modules/nf-core/glimpse/ligate/main.nf
+++ b/modules/nf-core/glimpse/ligate/main.nf
@@ -2,7 +2,7 @@ process GLIMPSE_LIGATE {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::glimpse-bio=1.1.1"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--hce55b13_1':
         'biocontainers/glimpse-bio:1.1.1--hce55b13_1' }"
diff --git a/modules/nf-core/glimpse/ligate/meta.yml b/modules/nf-core/glimpse/ligate/meta.yml
index 9a2a8daa..da6066ad 100644
--- a/modules/nf-core/glimpse/ligate/meta.yml
+++ b/modules/nf-core/glimpse/ligate/meta.yml
@@ -13,42 +13,37 @@ tools:
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
       licence: "['MIT']"
-
 input:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-
   - input_list:
       type: file
       description: VCF/BCF file containing genotype probabilities (GP field).
       pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
-
   - input_index:
       type: file
       description: Index file of the input VCF/BCF file containing genotype likelihoods.
       pattern: "*.{vcf.gz.csi,bcf.gz.csi}"
-
 output:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-
   - merged_variants:
       type: file
       description: |
         Output VCF/BCF file for the merged regions.
         Phased information (HS field) is updated accordingly for the full region.
       pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
-
 authors:
   - "@louislenezet"
+maintainers:
+  - "@louislenezet"
diff --git a/modules/nf-core/glimpse/ligate/tests/main.nf.test b/modules/nf-core/glimpse/ligate/tests/main.nf.test
new file mode 100644
index 00000000..e86ff231
--- /dev/null
+++ b/modules/nf-core/glimpse/ligate/tests/main.nf.test
@@ -0,0 +1,73 @@
+nextflow_process {
+
+    name "Test Process GLIMPSE_LIGATE"
+    script "../main.nf"
+    process "GLIMPSE_LIGATE"
+    tag "glimpse"
+    tag "glimpse/ligate"
+    tag "modules_nfcore"
+    tag "modules"
+
+    test("test_glimpse_ligate") {
+        setup {
+            run("GLIMPSE_PHASE") {
+                script "../../phase/main.nf"
+                process {
+                """
+                ch_sample     = Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt')
+                region        = Channel.fromList([
+                    ["chr21:16600000-16750000","chr21:16650000-16700000"],
+                    ["chr21:16650000-16800000","chr21:16700000-16750000"]
+                ])
+                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)
+                ])
+                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),
+                ])
+
+                input[0]      = input_vcf
+                    | combine(ch_sample)
+                    | combine(region)
+                    | combine(ref_panel)
+                    | combine(ch_map)
+                """
+                }
+            }
+            run("BCFTOOLS_INDEX") {
+                script "../../../bcftools/index/main.nf"
+                process {
+                """
+                input[0] = GLIMPSE_PHASE.out.phased_variant
+                """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = GLIMPSE_PHASE.out.phased_variant
+                    | groupTuple()
+                    | join (BCFTOOLS_INDEX.out.csi.groupTuple())
+                """
+            }
+        }
+
+        then {
+            def lines = path(process.out.merged_variants.get(0).get(1)).linesGzip.last()
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match("versions") },
+                { assert snapshot(lines).match("ligate") }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/glimpse/ligate/tests/main.nf.test.snap b/modules/nf-core/glimpse/ligate/tests/main.nf.test.snap
new file mode 100644
index 00000000..8eec1328
--- /dev/null
+++ b/modules/nf-core/glimpse/ligate/tests/main.nf.test.snap
@@ -0,0 +1,16 @@
+{
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,0cc9dfe9c9c1087666c418aa3379cf85"
+            ]
+        ],
+        "timestamp": "2023-10-17T11:56:25.087453677"
+    },
+    "ligate": {
+        "content": [
+            "chr21\t16799989\t21:16799989:T:C\tT\tC\t.\t.\tRAF=0.000468897;AF=0;INFO=1\tGT:DS:GP:HS\t0/0:0:1,0,0:0"
+        ],
+        "timestamp": "2023-10-17T11:56:25.116120487"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/glimpse/ligate/tests/tags.yml b/modules/nf-core/glimpse/ligate/tests/tags.yml
new file mode 100644
index 00000000..f15d8121
--- /dev/null
+++ b/modules/nf-core/glimpse/ligate/tests/tags.yml
@@ -0,0 +1,2 @@
+glimpse/ligate:
+  - modules/nf-core/glimpse/ligate/**
diff --git a/modules/nf-core/glimpse/phase/environment.yml b/modules/nf-core/glimpse/phase/environment.yml
new file mode 100644
index 00000000..fc79765a
--- /dev/null
+++ b/modules/nf-core/glimpse/phase/environment.yml
@@ -0,0 +1,7 @@
+name: glimpse_phase
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::glimpse-bio=1.1.1
diff --git a/modules/nf-core/glimpse/phase/main.nf b/modules/nf-core/glimpse/phase/main.nf
index e2c73ea2..a6f39d15 100644
--- a/modules/nf-core/glimpse/phase/main.nf
+++ b/modules/nf-core/glimpse/phase/main.nf
@@ -2,7 +2,7 @@ process GLIMPSE_PHASE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::glimpse-bio=1.1.1"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--h2ce4488_2':
         'biocontainers/glimpse-bio:1.1.1--hce55b13_1' }"
diff --git a/modules/nf-core/glimpse/phase/meta.yml b/modules/nf-core/glimpse/phase/meta.yml
index 47da4de6..696616d3 100644
--- a/modules/nf-core/glimpse/phase/meta.yml
+++ b/modules/nf-core/glimpse/phase/meta.yml
@@ -5,7 +5,6 @@ keywords:
   - imputation
   - low-coverage
   - glimpse
-
 tools:
   - "glimpse":
       description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies."
@@ -14,24 +13,20 @@ tools:
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
       licence: "['MIT']"
-
 input:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-
   - input:
       type: file
       description: Input VCF/BCF file containing genotype likelihoods.
       pattern: "*.{vcf.gz,bcf.gz}"
-
   - input_index:
       type: file
       description: Index file of the input VCF/BCF file containing genotype likelihoods.
       pattern: "*.{vcf.gz.csi,bcf.gz.csi}"
-
   - samples_file:
       type: file
       description: |
@@ -40,44 +35,36 @@ input:
         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).
       pattern: "chrXX:leftBufferPosition-rightBufferPosition"
-
   - output_region:
       type: string
       description: Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).
       pattern: "chrXX:leftBufferPosition-rightBufferPosition"
-
   - reference:
       type: file
       description: Reference panel of haplotypes in VCF/BCF format.
       pattern: "*.{vcf.gz,bcf.gz}"
-
   - reference_index:
       type: file
       description: Index file of the Reference panel file.
       pattern: "*.{vcf.gz.csi,bcf.gz.csi}"
-
   - map:
       type: file
       description: File containing the genetic map.
       pattern: "*.gmap"
-
 output:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-
   - phased_variants:
       type: file
       description: |
@@ -85,6 +72,7 @@ output:
         imputed dosages (DS field), best guess genotypes (GT field),
         sampled haplotypes in the last (max 16) main iterations (HS field) and info-score.
       pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
-
 authors:
   - "@louislenezet"
+maintainers:
+  - "@louislenezet"
diff --git a/modules/nf-core/glimpse/phase/tests/main.nf.test b/modules/nf-core/glimpse/phase/tests/main.nf.test
new file mode 100644
index 00000000..0009387f
--- /dev/null
+++ b/modules/nf-core/glimpse/phase/tests/main.nf.test
@@ -0,0 +1,67 @@
+nextflow_process {
+
+    name "Test Process GLIMPSE_PHASE"
+    script "../main.nf"
+    process "GLIMPSE_PHASE"
+    tag "glimpse"
+    tag "glimpse/phase"
+    tag "modules_nfcore"
+    tag "modules"
+
+    test("test_glimpse_phase") {
+
+        when {
+            process {
+                """
+                ch_sample = Channel.of([sample:'present'])
+                    | combine(Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt'))
+                    | concat(Channel.of([[sample: 'absent'], []]))
+                region        = Channel.fromList([
+                    ["chr21:16600000-16750000","chr21:16650000-16700000"],
+                    ["chr21:16650000-16800000","chr21:16700000-16750000"]
+                ])
+                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([
+                    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),
+                ])
+
+                input[0]      = input_vcf
+                    | combine(ch_sample)
+                    | combine(region)
+                    | map { meta, vcf, index, metaS, sample, regionI, regionO ->
+                        [[id: meta.id + "_" + metaS.sample, region : regionI], vcf, index, sample, regionI, regionO]
+                    }
+                    | combine(ref_panel)
+                    | combine(ch_map)
+                """
+            }
+        }
+
+        then {
+            String targetFileName = "input_present_chr21_16650000-16800000.vcf.gz"
+            File selectedFile = process.out.phased_variant.stream()
+                .filter(vector -> vector.size() > 1)
+                .map(vector -> new File(vector.get(1).toString()))
+                .filter(file -> file.getName().equals(targetFileName))
+                .findFirst()
+                .orElse(null)
+            String selectedFilename = selectedFile != null ? selectedFile.getPath() : null
+            def lines = path(selectedFilename).linesGzip.last()
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match("versions") },
+                { assert process.out.phased_variant.size() == 4},
+                { assert snapshot(lines).match("imputed") }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/glimpse/phase/tests/main.nf.test.snap b/modules/nf-core/glimpse/phase/tests/main.nf.test.snap
new file mode 100644
index 00000000..d61cf86e
--- /dev/null
+++ b/modules/nf-core/glimpse/phase/tests/main.nf.test.snap
@@ -0,0 +1,19 @@
+{
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,b24f49b2f5989a1f7da32c195334e96b",
+                "versions.yml:md5,b24f49b2f5989a1f7da32c195334e96b",
+                "versions.yml:md5,b24f49b2f5989a1f7da32c195334e96b",
+                "versions.yml:md5,b24f49b2f5989a1f7da32c195334e96b"
+            ]
+        ],
+        "timestamp": "2023-10-17T15:27:55.512415434"
+    },
+    "imputed": {
+        "content": [
+            "chr21\t16799989\t21:16799989:T:C\tT\tC\t.\t.\tRAF=0.000468897;AF=0;INFO=1;BUF=1\tGT:DS:GP:HS\t0/0:0:1,0,0:0"
+        ],
+        "timestamp": "2023-10-17T15:27:55.99820664"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/glimpse/phase/tests/tags.yml b/modules/nf-core/glimpse/phase/tests/tags.yml
new file mode 100644
index 00000000..61c28281
--- /dev/null
+++ b/modules/nf-core/glimpse/phase/tests/tags.yml
@@ -0,0 +1,2 @@
+glimpse/phase:
+  - modules/nf-core/glimpse/phase/**
diff --git a/subworkflows/nf-core/vcf_impute_glimpse/meta.yml b/subworkflows/nf-core/vcf_impute_glimpse/meta.yml
index 598b6888..6c9fe223 100644
--- a/subworkflows/nf-core/vcf_impute_glimpse/meta.yml
+++ b/subworkflows/nf-core/vcf_impute_glimpse/meta.yml
@@ -6,13 +6,11 @@ keywords:
   - chunk
   - phase
   - ligate
-
 components:
   - glimpse/chunk
   - glimpse/phase
   - glimpse/ligate
   - bcftools/index
-
 input:
   - ch_input:
       type: file
@@ -26,14 +24,12 @@ input:
         File containing the genetic map.
         The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).
         Structure: [ meta, vcf, csi, txt, region, ref_vcf, ref_csi, gmap ]
-
 output:
   - chunk_chr:
       type: file
       description: |
         Tab delimited output txt file containing buffer and imputation regions.
         Structure: [meta, txt]
-
   - phased_variants:
       type: file
       description: |
@@ -41,18 +37,17 @@ output:
         imputed dosages (DS field), best guess genotypes (GT field),
         sampled haplotypes in the last (max 16) main iterations (HS field) and info-score.
         Structure: [ val(meta), bcf ]
-
   - 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 ]
-
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-
 authors:
   - "@LouisLeNezet"
+maintainers:
+  - "@LouisLeNezet"
diff --git a/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test b/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test
new file mode 100644
index 00000000..7931f706
--- /dev/null
+++ b/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test
@@ -0,0 +1,110 @@
+nextflow_workflow {
+
+    name "Test Workflow VCF_IMPUTE_GLIMPSE"
+    script "../main.nf"
+    workflow "VCF_IMPUTE_GLIMPSE"
+    tag "glimpse"
+    tag "glimpse/chunk"
+    tag "glimpse/phase"
+    tag "glimpse/ligate"
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "vcf_impute_glimpse"
+
+    test("Should run without failures") {
+        config "./nextflow.config"
+
+        when {
+            params {
+                outdir = "tests/results"
+            }
+            workflow {
+                """
+                samples_infos = Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt')
+
+                ch_panel = Channel.fromList([
+                    [[ ref:'ref_panel'],
+                    file("https://github.com/nf-core/test-datasets/raw/imputation/data/panel/both/1000GP.chr21_22.noNA12878.s.bcf",
+                        checkIfExists: true),
+                    file("https://github.com/nf-core/test-datasets/raw/imputation/data/panel/both/1000GP.chr21_22.noNA12878.s.bcf.csi",
+                        checkIfExists: true)],
+                    [[ ref:'ref_panel2'],
+                    file("https://github.com/nf-core/test-datasets/raw/imputation/data/panel/both/1000GP.chr21_22.noNA12878.s.bcf",
+                        checkIfExists: true),
+                    file("https://github.com/nf-core/test-datasets/raw/imputation/data/panel/both/1000GP.chr21_22.noNA12878.s.bcf.csi",
+                        checkIfExists: true)]
+                ])
+                region = Channel.fromList([
+                    [[chr: "chr21", region: "chr21:16600000-16800000"], "chr21:16600000-16800000"],
+                    [[chr: "chr22", region: "chr22:16600000-16800000"], "chr22:16600000-16800000"]
+                ])
+
+                input_vcf = Channel.fromList([
+                    [[ id:'input'], // meta map
+                    file("https://github.com/nf-core/test-datasets/raw/imputation/data/NA12878/both/NA12878.chr21_22.s.1x.vcf.gz", checkIfExists: true),
+                    file("https://github.com/nf-core/test-datasets/raw/imputation/data/NA12878/both/NA12878.chr21_22.s.1x.vcf.gz.csi", checkIfExists: true),
+                    ],
+                    [[ id:'input2'], // meta map
+                    file("https://github.com/nf-core/test-datasets/raw/imputation/data/NA12878/both/NA12878.chr21_22.s.1x.vcf.gz", checkIfExists: true),
+                    file("https://github.com/nf-core/test-datasets/raw/imputation/data/NA12878/both/NA12878.chr21_22.s.1x.vcf.gz.csi", checkIfExists: true),
+                    ]
+                ])
+                input_vcf_multiple = input_vcf
+                    .combine( samples_infos )
+                    .combine( region )
+                    .map{ metaI, vcf, index, sample, metaCR, region ->
+                        [metaI + metaCR, vcf, index, sample, region ]
+                    }
+
+                ch_map = Channel.fromList([
+                    [[ chr: "chr21"],
+                        file("https://github.com/nf-core/test-datasets/raw/imputation/data/genetic_maps.b38/chr21.b38.gmap.gz", checkIfExists: true)
+                    ],
+                    [[ chr: "chr22"],
+                        file("https://github.com/nf-core/test-datasets/raw/imputation/data/genetic_maps.b38/chr22.b38.gmap.gz", checkIfExists: true)
+                    ]
+                ])
+
+                // Combine input and map depending on chromosome name
+                ch_input_map = input_vcf_multiple
+                    .map{ metaIRC, vcf, index, sample, region ->
+                        [metaIRC.subMap(["chr"]), metaIRC, vcf, index, sample, region]
+                    }
+                    .combine(ch_map, by: 0)
+                    .map{ metaC, metaIRC, vcf, index, sample, region, map ->
+                        [metaIRC, vcf, index, sample, region, map] }
+
+                // Combine input and map to reference panel could also be done by chromosome
+                input[0] = ch_input_map
+                    .combine(ch_panel)
+                    .map{ metaIRC, vcf, index, sample, region, map, metaP, ref, ref_index ->
+                        [ metaIRC + metaP, vcf, index, sample, region, ref, ref_index, map ]
+                    }
+                """
+            }
+        }
+
+        then {
+            println(workflow.out.merged_variants)
+            String targetFileName = "input_chr21_ref_panel2_ligate.vcf.gz"
+            File selectedFile = workflow.out.merged_variants.stream()
+                .filter(vector -> vector.size() > 1)
+                .map(vector -> new File(vector.get(1).toString()))
+                .filter(file -> file.getName().equals(targetFileName))
+                .findFirst()
+                .orElse(null)
+            String selectedFilename = selectedFile != null ? selectedFile.getPath() : null
+            def lines = path(selectedFilename).linesGzip.last()
+            print(lines)
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out.versions).match("versions") },
+                { assert snapshot(workflow.out.chunk_chr).match("chunk_chr") },
+                { assert workflow.out.merged_variants.size() == 8},
+                { assert snapshot(lines).match("merged") }
+            )
+        }
+
+    }
+
+}
diff --git a/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test.snap b/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test.snap
new file mode 100644
index 00000000..9265c429
--- /dev/null
+++ b/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test.snap
@@ -0,0 +1,158 @@
+{
+    "chunk_chr": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "input",
+                        "chr": "chr21",
+                        "region": "chr21:16600000-16800000",
+                        "ref": "ref_panel2"
+                    },
+                    "input_chr21:16600000-16800000_chunk.txt:md5,426f0f75efed96818656876116f73b06"
+                ],
+                [
+                    {
+                        "id": "input",
+                        "chr": "chr21",
+                        "region": "chr21:16600000-16800000",
+                        "ref": "ref_panel"
+                    },
+                    "input_chr21:16600000-16800000_chunk.txt:md5,426f0f75efed96818656876116f73b06"
+                ],
+                [
+                    {
+                        "id": "input",
+                        "chr": "chr22",
+                        "region": "chr22:16600000-16800000",
+                        "ref": "ref_panel2"
+                    },
+                    "input_chr22:16600000-16800000_chunk.txt:md5,4f48d33fd9c1e235ccfd25827a92ddd1"
+                ],
+                [
+                    {
+                        "id": "input",
+                        "chr": "chr22",
+                        "region": "chr22:16600000-16800000",
+                        "ref": "ref_panel"
+                    },
+                    "input_chr22:16600000-16800000_chunk.txt:md5,4f48d33fd9c1e235ccfd25827a92ddd1"
+                ],
+                [
+                    {
+                        "id": "input2",
+                        "chr": "chr21",
+                        "region": "chr21:16600000-16800000",
+                        "ref": "ref_panel2"
+                    },
+                    "input2_chr21:16600000-16800000_chunk.txt:md5,426f0f75efed96818656876116f73b06"
+                ],
+                [
+                    {
+                        "id": "input2",
+                        "chr": "chr21",
+                        "region": "chr21:16600000-16800000",
+                        "ref": "ref_panel"
+                    },
+                    "input2_chr21:16600000-16800000_chunk.txt:md5,426f0f75efed96818656876116f73b06"
+                ],
+                [
+                    {
+                        "id": "input2",
+                        "chr": "chr22",
+                        "region": "chr22:16600000-16800000",
+                        "ref": "ref_panel2"
+                    },
+                    "input2_chr22:16600000-16800000_chunk.txt:md5,4f48d33fd9c1e235ccfd25827a92ddd1"
+                ],
+                [
+                    {
+                        "id": "input2",
+                        "chr": "chr22",
+                        "region": "chr22:16600000-16800000",
+                        "ref": "ref_panel"
+                    },
+                    "input2_chr22:16600000-16800000_chunk.txt:md5,4f48d33fd9c1e235ccfd25827a92ddd1"
+                ]
+            ]
+        ],
+        "timestamp": "2023-10-17T18:20:13.045340135"
+    },
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,227d8e960e4382d8a615e040b874fc27",
+                "versions.yml:md5,227d8e960e4382d8a615e040b874fc27",
+                "versions.yml:md5,227d8e960e4382d8a615e040b874fc27",
+                "versions.yml:md5,227d8e960e4382d8a615e040b874fc27",
+                "versions.yml:md5,227d8e960e4382d8a615e040b874fc27",
+                "versions.yml:md5,227d8e960e4382d8a615e040b874fc27",
+                "versions.yml:md5,227d8e960e4382d8a615e040b874fc27",
+                "versions.yml:md5,227d8e960e4382d8a615e040b874fc27",
+                "versions.yml:md5,73621eae1bfd89c2ceb009524fe680d4",
+                "versions.yml:md5,73621eae1bfd89c2ceb009524fe680d4",
+                "versions.yml:md5,73621eae1bfd89c2ceb009524fe680d4",
+                "versions.yml:md5,73621eae1bfd89c2ceb009524fe680d4",
+                "versions.yml:md5,73621eae1bfd89c2ceb009524fe680d4",
+                "versions.yml:md5,73621eae1bfd89c2ceb009524fe680d4",
+                "versions.yml:md5,73621eae1bfd89c2ceb009524fe680d4",
+                "versions.yml:md5,73621eae1bfd89c2ceb009524fe680d4",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,7ae4d2b0252f9382dd08d783b7a234d2",
+                "versions.yml:md5,86d1ec939ded96a4ed3fb73ff83c240b",
+                "versions.yml:md5,86d1ec939ded96a4ed3fb73ff83c240b",
+                "versions.yml:md5,86d1ec939ded96a4ed3fb73ff83c240b",
+                "versions.yml:md5,86d1ec939ded96a4ed3fb73ff83c240b",
+                "versions.yml:md5,86d1ec939ded96a4ed3fb73ff83c240b",
+                "versions.yml:md5,86d1ec939ded96a4ed3fb73ff83c240b",
+                "versions.yml:md5,86d1ec939ded96a4ed3fb73ff83c240b",
+                "versions.yml:md5,86d1ec939ded96a4ed3fb73ff83c240b",
+                "versions.yml:md5,a17a10f6eb5e140e388b92d5f19680ae",
+                "versions.yml:md5,a17a10f6eb5e140e388b92d5f19680ae",
+                "versions.yml:md5,a17a10f6eb5e140e388b92d5f19680ae",
+                "versions.yml:md5,a17a10f6eb5e140e388b92d5f19680ae",
+                "versions.yml:md5,a17a10f6eb5e140e388b92d5f19680ae",
+                "versions.yml:md5,a17a10f6eb5e140e388b92d5f19680ae",
+                "versions.yml:md5,a17a10f6eb5e140e388b92d5f19680ae",
+                "versions.yml:md5,a17a10f6eb5e140e388b92d5f19680ae",
+                "versions.yml:md5,a17a10f6eb5e140e388b92d5f19680ae",
+                "versions.yml:md5,a17a10f6eb5e140e388b92d5f19680ae",
+                "versions.yml:md5,a17a10f6eb5e140e388b92d5f19680ae",
+                "versions.yml:md5,a17a10f6eb5e140e388b92d5f19680ae",
+                "versions.yml:md5,a17a10f6eb5e140e388b92d5f19680ae",
+                "versions.yml:md5,a17a10f6eb5e140e388b92d5f19680ae",
+                "versions.yml:md5,a17a10f6eb5e140e388b92d5f19680ae",
+                "versions.yml:md5,a17a10f6eb5e140e388b92d5f19680ae",
+                "versions.yml:md5,a17a10f6eb5e140e388b92d5f19680ae",
+                "versions.yml:md5,a17a10f6eb5e140e388b92d5f19680ae",
+                "versions.yml:md5,a17a10f6eb5e140e388b92d5f19680ae",
+                "versions.yml:md5,a17a10f6eb5e140e388b92d5f19680ae"
+            ]
+        ],
+        "timestamp": "2023-10-17T18:20:06.846882518"
+    },
+    "merged": {
+        "content": [
+            "chr21\t16799989\t21:16799989:T:C\tT\tC\t.\t.\tRAF=0.000468897;AF=0;INFO=1\tGT:DS:GP:HS\t0/0:0:1,0,0:0"
+        ],
+        "timestamp": "2023-10-17T18:20:19.789038503"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/vcf_impute_glimpse/tests/nextflow.config b/subworkflows/nf-core/vcf_impute_glimpse/tests/nextflow.config
new file mode 100644
index 00000000..09ab6858
--- /dev/null
+++ b/subworkflows/nf-core/vcf_impute_glimpse/tests/nextflow.config
@@ -0,0 +1,12 @@
+process {
+    withName: GLIMPSE_CHUNK {
+        ext.prefix = { "${meta.id}_${meta.region}_chunk" }
+        ext.args = "--window-size 50000 --buffer-size 1000"
+    }
+    withName: GLIMPSE_PHASE {
+        ext.prefix = { "${meta.id}_${meta.region}_${meta.ref}_phase_${input_region.replace(":","_")}" }
+    }
+    withName: GLIMPSE_LIGATE {
+        ext.prefix = { "${meta.id}_${meta.chr}_${meta.ref}_ligate" }
+    }
+}
diff --git a/subworkflows/nf-core/vcf_impute_glimpse/tests/tags.yml b/subworkflows/nf-core/vcf_impute_glimpse/tests/tags.yml
new file mode 100644
index 00000000..34d27725
--- /dev/null
+++ b/subworkflows/nf-core/vcf_impute_glimpse/tests/tags.yml
@@ -0,0 +1,2 @@
+vcf_impute_glimpse:
+  - subworkflows/nf-core/vcf_impute_glimpse/**
diff --git a/workflows/phaseimpute.nf b/workflows/phaseimpute.nf
index c7835ac0..69e1755d 100644
--- a/workflows/phaseimpute.nf
+++ b/workflows/phaseimpute.nf
@@ -7,13 +7,13 @@
 //
 // MODULE: Installed directly from nf-core/modules
 //
-include { MULTIQC                     } from '../modules/nf-core/multiqc/main'
+include { MULTIQC                } from '../modules/nf-core/multiqc/main'
 include { paramsSummaryMap       } from 'plugin/nf-validation'
 include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_phaseimpute_pipeline'
-include { SAMTOOLS_FAIDX              } from '../modules/nf-core/samtools/faidx/main'
-include { BAM_REGION                  } from '../subworkflows/local/bam_region'
+include { SAMTOOLS_FAIDX         } from '../modules/nf-core/samtools/faidx/main'
+include { BAM_REGION             } from '../subworkflows/local/bam_region'
 
 //
 // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
@@ -153,8 +153,8 @@ workflow PHASEIMPUTE {
             VCF_IMPUTE_GLIMPSE(impute_input,
                 GET_PANEL.out.panel_phased,
                 ch_map)
-            
-            ch_impute_output = ch_impute_output.mix(VCF_IMPUTE_GLIMPSE.out.)
+
+            ch_impute_output = ch_impute_output.mix(VCF_IMPUTE_GLIMPSE.out.merged_variants)
         }
         if (params.tools.contains("glimpse2")){
             print("Impute with Glimpse2")