diff --git a/CHANGELOG.md b/CHANGELOG.md
index fe003c06..b96488af 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@ Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co
 
 - [#15](https://github.com/nf-core/phaseimpute/pull/15) - Changed test csv files to point to nf-core repository
 - [#16](https://github.com/nf-core/phaseimpute/pull/16) - Removed outdir from test config files
+- [#19](https://github.com/nf-core/phaseimpute/pull/19) - Changed reference panel to accept a csv, update modules and subworkflows (glimpse1/2 and shapeit5)
 
 ### `Fixed`
 
diff --git a/assets/schema_input_panel.json b/assets/schema_input_panel.json
index 49593176..46ce0f7c 100644
--- a/assets/schema_input_panel.json
+++ b/assets/schema_input_panel.json
@@ -15,22 +15,22 @@
             },
             "vcf": {
                 "type": "string",
-                "pattern": "^\\S+\\.vcf$",
+                "pattern": "^\\S+\\.(vcf|bcf)(\\.gz)?$",
                 "errorMessage": "Panel vcf file must be provided, cannot contain spaces and must have extension '.vcf'"
             },
             "index": {
                 "type": "string",
-                "pattern": "^\\S+\\.vcf\\.(tbi|csi)$",
+                "pattern": "^\\S+\\.(vcf|bcf)(\\.gz)?\\.(tbi|csi)$",
                 "errorMessage": "Panel vcf index file must be provided, cannot contain spaces and must have extension '.vcf.tbi' or '.vcf.csi'"
             },
             "sites": {
                 "type": "string",
-                "pattern": "^\\S+\\.sites$",
+                "pattern": "^\\S+\\.sites(\\.bcf)?$",
                 "errorMessage": "Panel sites file must be provided, cannot contain spaces and must have extension '.sites'"
             },
             "tsv": {
                 "type": "string",
-                "pattern": "^\\S+\\.tsv$",
+                "pattern": "^\\S+\\.tsv(\\.gz)?$",
                 "errorMessage": "Panel tsv file must be provided, cannot contain spaces and must have extension '.tsv'"
             },
             "legend": {
diff --git a/conf/test.config b/conf/test.config
index 297d318a..1f046073 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -24,7 +24,7 @@ params {
 
     // Genome references
     fasta    = "https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/reference_genome/21_22/hs38DH.chr21_22.fa"
-    panel    = "https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/panel/21_22/1000GP.chr21_22.s.norel.bcf"
+    panel    = "${projectDir}/tests/csv/panel.csv"
     phased   = true
 
     // Impute parameters
diff --git a/modules.json b/modules.json
index 63f743dd..0a99d93d 100644
--- a/modules.json
+++ b/modules.json
@@ -50,17 +50,17 @@
                     },
                     "glimpse/chunk": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "7e56daae390ff896b292ddc70823447683a79936",
                         "installed_by": ["vcf_impute_glimpse"]
                     },
                     "glimpse/ligate": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "7e56daae390ff896b292ddc70823447683a79936",
                         "installed_by": ["vcf_impute_glimpse"]
                     },
                     "glimpse/phase": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "7e56daae390ff896b292ddc70823447683a79936",
                         "installed_by": ["vcf_impute_glimpse"]
                     },
                     "glimpse2/chunk": {
@@ -70,7 +70,7 @@
                     },
                     "glimpse2/ligate": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "ee7fee68281944b002bd27a8ff3f19200b4d3fad",
                         "installed_by": ["multiple_impute_glimpse2"]
                     },
                     "glimpse2/phase": {
@@ -112,7 +112,7 @@
                     },
                     "shapeit5/ligate": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "dcf17cc0ed8fd5ea57e61a13e0147cddb5c1ee30",
                         "installed_by": ["vcf_phase_shapeit5"]
                     },
                     "shapeit5/phasecommon": {
@@ -136,7 +136,7 @@
                 "nf-core": {
                     "multiple_impute_glimpse2": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {
@@ -156,12 +156,12 @@
                     },
                     "vcf_impute_glimpse": {
                         "branch": "master",
-                        "git_sha": "8dab3bf2aaa912730419080e96d2a7d98911db48",
+                        "git_sha": "7e56daae390ff896b292ddc70823447683a79936",
                         "installed_by": ["subworkflows"]
                     },
                     "vcf_phase_shapeit5": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "dcf17cc0ed8fd5ea57e61a13e0147cddb5c1ee30",
                         "installed_by": ["subworkflows"]
                     }
                 }
diff --git a/modules/nf-core/glimpse/chunk/meta.yml b/modules/nf-core/glimpse/chunk/meta.yml
index 65fa6218..e500d9e9 100644
--- a/modules/nf-core/glimpse/chunk/meta.yml
+++ b/modules/nf-core/glimpse/chunk/meta.yml
@@ -11,7 +11,7 @@ tools:
       documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/glimpse/ligate/meta.yml b/modules/nf-core/glimpse/ligate/meta.yml
index da6066ad..c3b1485c 100644
--- a/modules/nf-core/glimpse/ligate/meta.yml
+++ b/modules/nf-core/glimpse/ligate/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/glimpse/ligate/tests/main.nf.test b/modules/nf-core/glimpse/ligate/tests/main.nf.test
index e86ff231..7289fc91 100644
--- a/modules/nf-core/glimpse/ligate/tests/main.nf.test
+++ b/modules/nf-core/glimpse/ligate/tests/main.nf.test
@@ -3,10 +3,13 @@ nextflow_process {
     name "Test Process GLIMPSE_LIGATE"
     script "../main.nf"
     process "GLIMPSE_LIGATE"
-    tag "glimpse"
-    tag "glimpse/ligate"
+
     tag "modules_nfcore"
     tag "modules"
+    tag "glimpse"
+    tag "glimpse/ligate"
+    tag "glimpse/phase"
+    tag "bcftools/index"
 
     test("test_glimpse_ligate") {
         setup {
@@ -21,15 +24,15 @@ nextflow_process {
                 ])
                 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)
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true)
                 ])
                 ref_panel     = Channel.of([
-                    file("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)
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
                 ])
                 ch_map        = Channel.of([
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true),
                 ])
 
                 input[0]      = input_vcf
@@ -44,7 +47,7 @@ nextflow_process {
                 script "../../../bcftools/index/main.nf"
                 process {
                 """
-                input[0] = GLIMPSE_PHASE.out.phased_variant
+                input[0] = GLIMPSE_PHASE.out.phased_variants
                 """
                 }
             }
@@ -53,7 +56,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = GLIMPSE_PHASE.out.phased_variant
+                input[0] = GLIMPSE_PHASE.out.phased_variants
                     | groupTuple()
                     | join (BCFTOOLS_INDEX.out.csi.groupTuple())
                 """
diff --git a/modules/nf-core/glimpse/phase/main.nf b/modules/nf-core/glimpse/phase/main.nf
index a6f39d15..41004e60 100644
--- a/modules/nf-core/glimpse/phase/main.nf
+++ b/modules/nf-core/glimpse/phase/main.nf
@@ -4,14 +4,14 @@ process GLIMPSE_PHASE {
 
     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':
+        'https://depot.galaxyproject.org/singularity/glimpse-bio:1.1.1--hce55b13_1':
         'biocontainers/glimpse-bio:1.1.1--hce55b13_1' }"
 
     input:
         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
+        tuple val(meta), path("*.{vcf,bcf,vcf.gz,bcf.gz}"), emit: phased_variants
         path "versions.yml"                               , emit: versions
 
     when:
diff --git a/modules/nf-core/glimpse/phase/meta.yml b/modules/nf-core/glimpse/phase/meta.yml
index 696616d3..862033b7 100644
--- a/modules/nf-core/glimpse/phase/meta.yml
+++ b/modules/nf-core/glimpse/phase/meta.yml
@@ -12,7 +12,7 @@ tools:
       documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/glimpse/phase/tests/main.nf.test b/modules/nf-core/glimpse/phase/tests/main.nf.test
index 0009387f..5c92cb1f 100644
--- a/modules/nf-core/glimpse/phase/tests/main.nf.test
+++ b/modules/nf-core/glimpse/phase/tests/main.nf.test
@@ -22,15 +22,15 @@ nextflow_process {
                 ])
                 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)
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true)
                 ])
                 ref_panel     = Channel.of([
-                    file("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)
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
                 ])
                 ch_map        = Channel.of([
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true),
                 ])
 
                 input[0]      = input_vcf
@@ -47,7 +47,7 @@ nextflow_process {
 
         then {
             String targetFileName = "input_present_chr21_16650000-16800000.vcf.gz"
-            File selectedFile = process.out.phased_variant.stream()
+            File selectedFile = process.out.phased_variants.stream()
                 .filter(vector -> vector.size() > 1)
                 .map(vector -> new File(vector.get(1).toString()))
                 .filter(file -> file.getName().equals(targetFileName))
@@ -58,7 +58,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out.versions).match("versions") },
-                { assert process.out.phased_variant.size() == 4},
+                { assert process.out.phased_variants.size() == 4},
                 { assert snapshot(lines).match("imputed") }
             )
         }
diff --git a/modules/nf-core/glimpse2/ligate/meta.yml b/modules/nf-core/glimpse2/ligate/meta.yml
index ffedb344..7c07973f 100644
--- a/modules/nf-core/glimpse2/ligate/meta.yml
+++ b/modules/nf-core/glimpse2/ligate/meta.yml
@@ -14,7 +14,7 @@ tools:
       documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
       tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
       doi: "10.1038/s41588-020-00756-0"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/modules/nf-core/glimpse2/ligate/tests/main.nf.test b/modules/nf-core/glimpse2/ligate/tests/main.nf.test
new file mode 100644
index 00000000..d45c448b
--- /dev/null
+++ b/modules/nf-core/glimpse2/ligate/tests/main.nf.test
@@ -0,0 +1,76 @@
+nextflow_process {
+
+    name "Test Process GLIMPSE2_LIGATE"
+    script "../main.nf"
+
+    process "GLIMPSE2_LIGATE"
+
+    tag "modules_nfcore"
+    tag "modules"
+    tag "glimpse2"
+    tag "glimpse2/ligate"
+    tag "bcftools/index"
+    tag "glimpse2/phase"
+
+    test("Should run glimpse ligate") {
+        setup {
+            run("GLIMPSE2_PHASE") {
+                script "../../phase/main.nf"
+                process {
+                """
+                input_vcf = Channel.of([
+                    [ id:'input' ], // meta map
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true),
+                    [],
+                    "chr21:16600000-16800000",
+                    "chr21:16650000-16750000"
+                ])
+
+                ref_panel = Channel.of([
+                        file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
+                ])
+
+                map_file = Channel.of([
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true)
+                ])
+
+                // [meta, vcf, index, sample_infos, regionin, regionout,ref, index, map] [meta, fasta, fai]
+                input[0] = input_vcf
+                    .combine(ref_panel)
+                    .combine(map_file)
+                input[1] = Channel.of([[],[],[]])
+                """
+                }
+            }
+            run("BCFTOOLS_INDEX") {
+                script "../../../bcftools/index/main.nf"
+                process {
+                """
+                input[0] = GLIMPSE2_PHASE.out.phased_variants
+                """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = GLIMPSE2_PHASE.out.phased_variants
+                    | groupTuple()
+                    | join (BCFTOOLS_INDEX.out.csi.groupTuple())
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match("versions") },
+                { assert file(process.out.merged_variants[0][1]).name == "input.vcf.gz" }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/glimpse2/ligate/tests/main.nf.test.snap b/modules/nf-core/glimpse2/ligate/tests/main.nf.test.snap
new file mode 100644
index 00000000..a1b0b8c8
--- /dev/null
+++ b/modules/nf-core/glimpse2/ligate/tests/main.nf.test.snap
@@ -0,0 +1,14 @@
+{
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,44addcaef4965ff6409a8293c5bcad84"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T15:52:19.469961519"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/glimpse2/ligate/tests/tags.yml b/modules/nf-core/glimpse2/ligate/tests/tags.yml
new file mode 100644
index 00000000..1613896f
--- /dev/null
+++ b/modules/nf-core/glimpse2/ligate/tests/tags.yml
@@ -0,0 +1,2 @@
+glimpse2/ligate:
+  - modules/nf-core/glimpse2/ligate/**
diff --git a/modules/nf-core/shapeit5/ligate/meta.yml b/modules/nf-core/shapeit5/ligate/meta.yml
index ab68274e..ed1e5e9e 100644
--- a/modules/nf-core/shapeit5/ligate/meta.yml
+++ b/modules/nf-core/shapeit5/ligate/meta.yml
@@ -12,8 +12,8 @@ tools:
       homepage: "https://odelaneau.github.io/shapeit5/"
       documentation: "https://odelaneau.github.io/shapeit5/docs/documentation"
       tool_dev_url: "https://github.com/odelaneau/shapeit5"
-      doi: "10.1101/2022.10.19.512867 "
-      licence: "['MIT']"
+      doi: "10.1101/2022.10.19.512867"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 7124fefd..2e36b1c4 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -37,16 +37,9 @@
                     "description": "Path to the reference panel or csv file with the list of panels",
                     "fa_icon": "far fa-file-code",
                     "format": "file-path",
-                    "anyOf": [
-                        {
-                            "pattern": "^\\S+\\.(vcf|bcf)(\\.gz)?$"
-                        },
-                        {
-                            "pattern": "^\\S+\\.(csv|tsv|txt)$",
-                            "mimetype": "text/csv",
-                            "schema": "assets/schema_input_panel.json"
-                        }
-                    ]
+                    "schema": "assets/schema_input_panel.json",
+                    "pattern": "^\\S+\\.(csv|tsv|txt)$",
+                    "mimetype": "text/csv"
                 },
                 "panel_index": {
                     "type": "string",
@@ -90,22 +83,9 @@
                 "input_region": {
                     "type": "string",
                     "description": "Region of the genome to use, can be the entire genome (i.e. 'all') or a specific chromosome or region (e.g. 'chr1', 'chr1:1000-2000'). You can also specify a file containing a list of regions to process, one per line. The file should be a comma-separated file with 3 columns, and a header row.",
-                    "anyOf": [
-                        {
-                            "pattern": "all"
-                        },
-                        {
-                            "pattern": "^(chr)?[0-9XYM]+$"
-                        },
-                        {
-                            "pattern": "^(chr)?[0-9XYM]+:[0-9]+-[0-9]+$"
-                        },
-                        {
-                            "format": "file-path",
-                            "pattern": "^\\S+\\.csv$",
-                            "schema": "assets/schema_input_region.json"
-                        }
-                    ]
+                    "schema": "assets/schema_input_region.json",
+                    "format": "file-path",
+                    "pattern": "^\\S+\\.csv$"
                 },
                 "outdir": {
                     "type": "string",
@@ -175,11 +155,11 @@
                     "type": "string",
                     "format": "file-path",
                     "exists": true,
-                    "mimetype": "text/plain",
-                    "pattern": "^\\S+\\.gmap(sta)?(\\.gz)?$",
                     "description": "Path to gmap genome file.",
                     "help_text": "This parameter is *optional*. This is used to refine the imputation process to match the recombination event rate in your specie.",
-                    "fa_icon": "far fa-file-code"
+                    "fa_icon": "far fa-file-code",
+                    "mimetype": "text/csv",
+                    "schema": "assets/schema_map.json"
                 },
                 "igenomes_ignore": {
                     "type": "boolean",
diff --git a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf
index a443a2a5..164b78d5 100644
--- a/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf
@@ -126,17 +126,12 @@ workflow PIPELINE_INITIALISATION {
     // Create channel for panel
     //
     if (params.panel) {
-        if (params.panel.endsWith("csv|tsv|txt")) {
-            print("Panel file provided as input is a samplesheet")
-            ch_panel = Channel.fromSamplesheet("panel")
-        } else {
-            print("Panel file provided as input is a variant file")
-            ch_panel = Channel.of([
-                [id: file(params.panel, checkIfExists:true).getBaseName()],
-                file(params.panel, checkIfExists:true),
-                params.panel_index ? file(params.panel_index, checkIfExists:true) : file(params.panel + ".csi", checkIfExists:true)
-            ])
-        }
+        ch_panel = Channel
+                .fromSamplesheet("panel")
+                .map {
+                    meta,vcf,index,sites,tsv,legend,phased ->
+                        [ meta, vcf, index ]
+                    }
     }
 
     //
diff --git a/subworkflows/nf-core/vcf_impute_glimpse/main.nf b/subworkflows/nf-core/vcf_impute_glimpse/main.nf
index 5fe26551..94262e34 100644
--- a/subworkflows/nf-core/vcf_impute_glimpse/main.nf
+++ b/subworkflows/nf-core/vcf_impute_glimpse/main.nf
@@ -33,11 +33,11 @@ workflow VCF_IMPUTE_GLIMPSE {
     GLIMPSE_PHASE ( phase_input ) // [meta, vcf, index, sample_infos, regionin, regionout, ref, ref_index, map]
     ch_versions = ch_versions.mix(GLIMPSE_PHASE.out.versions )
 
-    INDEX_PHASE ( GLIMPSE_PHASE.out.phased_variant )
+    INDEX_PHASE ( GLIMPSE_PHASE.out.phased_variants )
     ch_versions = ch_versions.mix( INDEX_PHASE.out.versions )
 
     // Ligate all phased files in one and index it
-    ligate_input = GLIMPSE_PHASE.out.phased_variant
+    ligate_input = GLIMPSE_PHASE.out.phased_variants
         .groupTuple( by: 0 )
         .combine( INDEX_PHASE.out.csi
             .groupTuple( by: 0 ),
diff --git a/subworkflows/nf-core/vcf_impute_glimpse/meta.yml b/subworkflows/nf-core/vcf_impute_glimpse/meta.yml
index 6c9fe223..81b3b4d5 100644
--- a/subworkflows/nf-core/vcf_impute_glimpse/meta.yml
+++ b/subworkflows/nf-core/vcf_impute_glimpse/meta.yml
@@ -30,19 +30,17 @@ output:
       description: |
         Tab delimited output txt file containing buffer and imputation regions.
         Structure: [meta, txt]
-  - phased_variants:
-      type: file
-      description: |
-        Output VCF/BCF file containing genotype probabilities (GP field),
-        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.
+        Output phased 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 output of phased VCF/BCF file for the merged regions.
+        Structure: [ val(meta), csi ]
   - versions:
       type: file
       description: File containing software versions
diff --git a/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test b/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test
index 7931f706..46db4244 100644
--- a/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test
+++ b/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test
@@ -3,13 +3,14 @@ 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 "bcftools/index"
     tag "subworkflows_nfcore"
-    tag "vcf_impute_glimpse"
+    tag "subworkflows/vcf_impute_glimpse"
+    tag "glimpse/phase"
+    tag "glimpse/ligate"
+    tag "glimpse/chunk"
 
     test("Should run without failures") {
         config "./nextflow.config"
@@ -24,14 +25,14 @@ nextflow_workflow {
 
                 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",
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/panel/21_22/1000GP.chr21_22.s.norel.bcf",
                         checkIfExists: true),
-                    file("https://github.com/nf-core/test-datasets/raw/imputation/data/panel/both/1000GP.chr21_22.noNA12878.s.bcf.csi",
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/panel/21_22/1000GP.chr21_22.s.norel.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",
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/panel/21_22/1000GP.chr21_22.s.norel.bcf",
                         checkIfExists: true),
-                    file("https://github.com/nf-core/test-datasets/raw/imputation/data/panel/both/1000GP.chr21_22.noNA12878.s.bcf.csi",
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/panel/21_22/1000GP.chr21_22.s.norel.bcf.csi",
                         checkIfExists: true)]
                 ])
                 region = Channel.fromList([
@@ -40,13 +41,13 @@ nextflow_workflow {
                 ])
 
                 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:'NA12878'], // meta map
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA12878/NA12878.s.1x.bcf", checkIfExists: true),
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA12878/NA12878.s.1x.bcf.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),
+                    [[ id:'NA19401'], // meta map
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA19401/NA19401.s.1x.bcf", checkIfExists: true),
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA19401/NA19401.s.1x.bcf.csi", checkIfExists: true),
                     ]
                 ])
                 input_vcf_multiple = input_vcf
@@ -58,10 +59,10 @@ nextflow_workflow {
 
                 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)
+                        file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/reference_genome/GRCh38.chr21.s.map", checkIfExists: true)
                     ],
                     [[ chr: "chr22"],
-                        file("https://github.com/nf-core/test-datasets/raw/imputation/data/genetic_maps.b38/chr22.b38.gmap.gz", checkIfExists: true)
+                        file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/reference_genome/GRCh38.chr22.s.map", checkIfExists: true)
                     ]
                 ])
 
@@ -85,17 +86,7 @@ nextflow_workflow {
         }
 
         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)
+            def lines = path(workflow.out.merged_variants.get(0).get(1)).linesGzip.last()
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(workflow.out.versions).match("versions") },
diff --git a/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test.snap b/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test.snap
index 9265c429..287930cd 100644
--- a/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/vcf_impute_glimpse/tests/main.nf.test.snap
@@ -4,79 +4,83 @@
             [
                 [
                     {
-                        "id": "input",
+                        "id": "NA12878",
                         "chr": "chr21",
                         "region": "chr21:16600000-16800000",
                         "ref": "ref_panel2"
                     },
-                    "input_chr21:16600000-16800000_chunk.txt:md5,426f0f75efed96818656876116f73b06"
+                    "NA12878_chr21:16600000-16800000_chunk.txt:md5,775240b195e782b3b83adf52e0d17089"
                 ],
                 [
                     {
-                        "id": "input",
+                        "id": "NA12878",
                         "chr": "chr21",
                         "region": "chr21:16600000-16800000",
                         "ref": "ref_panel"
                     },
-                    "input_chr21:16600000-16800000_chunk.txt:md5,426f0f75efed96818656876116f73b06"
+                    "NA12878_chr21:16600000-16800000_chunk.txt:md5,775240b195e782b3b83adf52e0d17089"
                 ],
                 [
                     {
-                        "id": "input",
+                        "id": "NA12878",
                         "chr": "chr22",
                         "region": "chr22:16600000-16800000",
                         "ref": "ref_panel2"
                     },
-                    "input_chr22:16600000-16800000_chunk.txt:md5,4f48d33fd9c1e235ccfd25827a92ddd1"
+                    "NA12878_chr22:16600000-16800000_chunk.txt:md5,f5270ed0faa4f9697618444b267442ce"
                 ],
                 [
                     {
-                        "id": "input",
+                        "id": "NA12878",
                         "chr": "chr22",
                         "region": "chr22:16600000-16800000",
                         "ref": "ref_panel"
                     },
-                    "input_chr22:16600000-16800000_chunk.txt:md5,4f48d33fd9c1e235ccfd25827a92ddd1"
+                    "NA12878_chr22:16600000-16800000_chunk.txt:md5,f5270ed0faa4f9697618444b267442ce"
                 ],
                 [
                     {
-                        "id": "input2",
+                        "id": "NA19401",
                         "chr": "chr21",
                         "region": "chr21:16600000-16800000",
                         "ref": "ref_panel2"
                     },
-                    "input2_chr21:16600000-16800000_chunk.txt:md5,426f0f75efed96818656876116f73b06"
+                    "NA19401_chr21:16600000-16800000_chunk.txt:md5,775240b195e782b3b83adf52e0d17089"
                 ],
                 [
                     {
-                        "id": "input2",
+                        "id": "NA19401",
                         "chr": "chr21",
                         "region": "chr21:16600000-16800000",
                         "ref": "ref_panel"
                     },
-                    "input2_chr21:16600000-16800000_chunk.txt:md5,426f0f75efed96818656876116f73b06"
+                    "NA19401_chr21:16600000-16800000_chunk.txt:md5,775240b195e782b3b83adf52e0d17089"
                 ],
                 [
                     {
-                        "id": "input2",
+                        "id": "NA19401",
                         "chr": "chr22",
                         "region": "chr22:16600000-16800000",
                         "ref": "ref_panel2"
                     },
-                    "input2_chr22:16600000-16800000_chunk.txt:md5,4f48d33fd9c1e235ccfd25827a92ddd1"
+                    "NA19401_chr22:16600000-16800000_chunk.txt:md5,f5270ed0faa4f9697618444b267442ce"
                 ],
                 [
                     {
-                        "id": "input2",
+                        "id": "NA19401",
                         "chr": "chr22",
                         "region": "chr22:16600000-16800000",
                         "ref": "ref_panel"
                     },
-                    "input2_chr22:16600000-16800000_chunk.txt:md5,4f48d33fd9c1e235ccfd25827a92ddd1"
+                    "NA19401_chr22:16600000-16800000_chunk.txt:md5,f5270ed0faa4f9697618444b267442ce"
                 ]
             ]
         ],
-        "timestamp": "2023-10-17T18:20:13.045340135"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T23:16:59.014613786"
     },
     "versions": {
         "content": [
@@ -105,54 +109,38 @@
                 "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"
+                "versions.yml:md5,a802158fea97c36620863658efb7ae68",
+                "versions.yml:md5,a802158fea97c36620863658efb7ae68",
+                "versions.yml:md5,a802158fea97c36620863658efb7ae68",
+                "versions.yml:md5,a802158fea97c36620863658efb7ae68",
+                "versions.yml:md5,a802158fea97c36620863658efb7ae68",
+                "versions.yml:md5,a802158fea97c36620863658efb7ae68",
+                "versions.yml:md5,a802158fea97c36620863658efb7ae68",
+                "versions.yml:md5,a802158fea97c36620863658efb7ae68",
+                "versions.yml:md5,e37bdea2d40f36ce8546f87c3e572c96",
+                "versions.yml:md5,e37bdea2d40f36ce8546f87c3e572c96",
+                "versions.yml:md5,e37bdea2d40f36ce8546f87c3e572c96",
+                "versions.yml:md5,e37bdea2d40f36ce8546f87c3e572c96",
+                "versions.yml:md5,e37bdea2d40f36ce8546f87c3e572c96",
+                "versions.yml:md5,e37bdea2d40f36ce8546f87c3e572c96",
+                "versions.yml:md5,e37bdea2d40f36ce8546f87c3e572c96",
+                "versions.yml:md5,e37bdea2d40f36ce8546f87c3e572c96"
             ]
         ],
-        "timestamp": "2023-10-17T18:20:06.846882518"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T23:16:58.336134471"
     },
     "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"
+            "chr21\t16609998\t21:16609998:A:G\tA\tG\t.\t.\tRAF=0.00125156;AF=0;INFO=1\tGT:DS:GP:HS\t0/0:0:1,0,0:0"
         ],
-        "timestamp": "2023-10-17T18:20:19.789038503"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T23:16:59.786459305"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/vcf_impute_glimpse/tests/tags.yml b/subworkflows/nf-core/vcf_impute_glimpse/tests/tags.yml
index 34d27725..24003ec0 100644
--- a/subworkflows/nf-core/vcf_impute_glimpse/tests/tags.yml
+++ b/subworkflows/nf-core/vcf_impute_glimpse/tests/tags.yml
@@ -1,2 +1,2 @@
-vcf_impute_glimpse:
+subworkflows/vcf_impute_glimpse:
   - subworkflows/nf-core/vcf_impute_glimpse/**
diff --git a/subworkflows/nf-core/vcf_phase_shapeit5/main.nf b/subworkflows/nf-core/vcf_phase_shapeit5/main.nf
index 0ddebcb3..966f9019 100644
--- a/subworkflows/nf-core/vcf_phase_shapeit5/main.nf
+++ b/subworkflows/nf-core/vcf_phase_shapeit5/main.nf
@@ -66,10 +66,9 @@ workflow VCF_PHASE_SHAPEIT5 {
 
     ch_ligate_input = SHAPEIT5_PHASECOMMON.out.phased_variant
         .join(VCF_INDEX1.out.csi, failOnMismatch:true, failOnDuplicate:true)
-        .view()
         .map{ meta, vcf, csi ->
             newmeta = meta + [id: meta.id.split("_")[0..-2].join("_")]
-            [newmeta, vcf, csi]}.view()
+            [newmeta, vcf, csi]}
         .combine(ch_chunks_number, by:0)
         .map{meta, vcf, csi, chunks_num ->
             [groupKey(meta, chunks_num), vcf, csi]}