diff --git a/modules/nf-core/glimpse/chunk/meta.yml b/modules/nf-core/glimpse/chunk/meta.yml
index 65fa6218a4a..e500d9e9715 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/concordance/meta.yml b/modules/nf-core/glimpse/concordance/meta.yml
index c73948f4914..2b2d7195df8 100644
--- a/modules/nf-core/glimpse/concordance/meta.yml
+++ b/modules/nf-core/glimpse/concordance/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/concordance/tests/main.nf.test b/modules/nf-core/glimpse/concordance/tests/main.nf.test
index d6236d35557..7e8505352c6 100644
--- a/modules/nf-core/glimpse/concordance/tests/main.nf.test
+++ b/modules/nf-core/glimpse/concordance/tests/main.nf.test
@@ -3,10 +3,13 @@ nextflow_process {
     name "Test Process GLIMPSE_CONCORDANCE"
     script "../main.nf"
     process "GLIMPSE_CONCORDANCE"
-    tag "glimpse"
-    tag "glimpse/concordance"
+
     tag "modules"
     tag "modules_nfcore"
+    tag "glimpse"
+    tag "glimpse/concordance"
+    tag "glimpse/phase"
+    tag "bcftools/index"
 
     test("test_glimpse_concordance") {
         setup {
@@ -20,15 +23,15 @@ 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
@@ -43,7 +46,7 @@ nextflow_process {
                 script "../../../bcftools/index/main.nf"
                 process {
                 """
-                input[0] = GLIMPSE_PHASE.out.phased_variant
+                input[0] = GLIMPSE_PHASE.out.phased_variants
                 """
                 }
             }
@@ -52,14 +55,14 @@ nextflow_process {
             process {
                 """
                 allele_freq = Channel.fromList([
-                    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)
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz",checkIfExists:true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz.csi",checkIfExists:true)
                 ]).collect()
                 truth = Channel.fromList([
-                    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)
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.bcf",checkIfExists:true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.bcf.csi",checkIfExists:true)
                 ]).collect()
-                estimate = GLIMPSE_PHASE.out.phased_variant
+                estimate = GLIMPSE_PHASE.out.phased_variants
                     | join (BCFTOOLS_INDEX.out.csi)
                 input[0] = estimate
                     | combine (allele_freq)
diff --git a/modules/nf-core/glimpse/concordance/tests/main.nf.test.snap b/modules/nf-core/glimpse/concordance/tests/main.nf.test.snap
index 239db1e48de..c0838446b5e 100644
--- a/modules/nf-core/glimpse/concordance/tests/main.nf.test.snap
+++ b/modules/nf-core/glimpse/concordance/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
                         {
                             "id": "input"
                         },
-                        "input.error.cal.txt.gz:md5,3259370d3a6b16dc6518eb96e64afc8a"
+                        "input.error.cal.txt.gz:md5,15c6a120d9fd3ac8c0ff6a6aedc76571"
                     ]
                 ],
                 "1": [
@@ -15,7 +15,7 @@
                         {
                             "id": "input"
                         },
-                        "input.error.grp.txt.gz:md5,c40e24a68ad099285d3d0f84cefd721e"
+                        "input.error.grp.txt.gz:md5,532bec52c03f16dcd6cc6d2b7c26673b"
                     ]
                 ],
                 "2": [
@@ -23,7 +23,7 @@
                         {
                             "id": "input"
                         },
-                        "input.error.spl.txt.gz:md5,a5c4a09ab52790b33c839ecbbf3ff7ce"
+                        "input.error.spl.txt.gz:md5,35cb463e8db41e2180f21941ab0324e0"
                     ]
                 ],
                 "3": [
@@ -31,7 +31,7 @@
                         {
                             "id": "input"
                         },
-                        "input.rsquare.grp.txt.gz:md5,2139f7d680487379ef38e185d7e6f43d"
+                        "input.rsquare.grp.txt.gz:md5,15bc7bf7980fd63e0f09bd267e548b57"
                     ]
                 ],
                 "4": [
@@ -39,7 +39,7 @@
                         {
                             "id": "input"
                         },
-                        "input.rsquare.spl.txt.gz:md5,ea2beba9d4d0f68061176daa767bef95"
+                        "input.rsquare.spl.txt.gz:md5,55659f466775d828ee1ba723464bb460"
                     ]
                 ],
                 "5": [
@@ -50,7 +50,7 @@
                         {
                             "id": "input"
                         },
-                        "input.error.cal.txt.gz:md5,3259370d3a6b16dc6518eb96e64afc8a"
+                        "input.error.cal.txt.gz:md5,15c6a120d9fd3ac8c0ff6a6aedc76571"
                     ]
                 ],
                 "errors_grp": [
@@ -58,7 +58,7 @@
                         {
                             "id": "input"
                         },
-                        "input.error.grp.txt.gz:md5,c40e24a68ad099285d3d0f84cefd721e"
+                        "input.error.grp.txt.gz:md5,532bec52c03f16dcd6cc6d2b7c26673b"
                     ]
                 ],
                 "errors_spl": [
@@ -66,7 +66,7 @@
                         {
                             "id": "input"
                         },
-                        "input.error.spl.txt.gz:md5,a5c4a09ab52790b33c839ecbbf3ff7ce"
+                        "input.error.spl.txt.gz:md5,35cb463e8db41e2180f21941ab0324e0"
                     ]
                 ],
                 "rsquare_grp": [
@@ -74,7 +74,7 @@
                         {
                             "id": "input"
                         },
-                        "input.rsquare.grp.txt.gz:md5,2139f7d680487379ef38e185d7e6f43d"
+                        "input.rsquare.grp.txt.gz:md5,15bc7bf7980fd63e0f09bd267e548b57"
                     ]
                 ],
                 "rsquare_spl": [
@@ -82,7 +82,7 @@
                         {
                             "id": "input"
                         },
-                        "input.rsquare.spl.txt.gz:md5,ea2beba9d4d0f68061176daa767bef95"
+                        "input.rsquare.spl.txt.gz:md5,55659f466775d828ee1ba723464bb460"
                     ]
                 ],
                 "versions": [
@@ -90,6 +90,10 @@
                 ]
             }
         ],
-        "timestamp": "2023-10-17T17:05:45.177807376"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T23:37:00.537398654"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/glimpse/ligate/meta.yml b/modules/nf-core/glimpse/ligate/meta.yml
index da6066add2b..c3b1485c436 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 e86ff2317a0..7289fc91acc 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 a6f39d15866..41004e60789 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 696616d37b1..862033b7f83 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 0009387f5a2..5c92cb1fc64 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/glimpse/sample/meta.yml b/modules/nf-core/glimpse/sample/meta.yml
index 08e27b60c95..36937ec0c26 100644
--- a/modules/nf-core/glimpse/sample/meta.yml
+++ b/modules/nf-core/glimpse/sample/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
@@ -22,12 +22,6 @@ input:
       type: file
       description: VCF/BCF file generated using GLIMPSE ligate
       pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
-  - sample:
-      type: parameter
-      description: Samples a likely haplotype pair for each sample, use it in combination with --seed. Option not recommended for general usage, use --solve instead
-  - solve:
-      type: parameter
-      description: Get the most likely haplotype pair for each sample (the random number generator is not used)
 output:
   - meta:
       type: map
diff --git a/modules/nf-core/glimpse/sample/tests/main.nf.test b/modules/nf-core/glimpse/sample/tests/main.nf.test
index 9e6139d44bd..494c35296fe 100644
--- a/modules/nf-core/glimpse/sample/tests/main.nf.test
+++ b/modules/nf-core/glimpse/sample/tests/main.nf.test
@@ -3,10 +3,12 @@ nextflow_process {
     name "Test Process GLIMPSE_SAMPLE"
     script "../main.nf"
     process "GLIMPSE_SAMPLE"
-    tag "glimpse"
-    tag "glimpse/sample"
+
     tag "modules"
     tag "modules_nfcore"
+    tag "glimpse"
+    tag "glimpse/sample"
+    tag "glimpse/phase"
 
     test("test_glimpse_sample") {
         config "./nextflow.config"
@@ -21,15 +23,15 @@ 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 +46,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = GLIMPSE_PHASE.out.phased_variant
+                input[0] = GLIMPSE_PHASE.out.phased_variants
                 """
             }
         }
diff --git a/subworkflows/nf-core/vcf_impute_glimpse/main.nf b/subworkflows/nf-core/vcf_impute_glimpse/main.nf
index 5fe265519c8..94262e34ae1 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 6c9fe2235ee..81b3b4d5814 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 7931f706670..46db4244271 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 9265c429f2a..287930cdf35 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 34d277258cb..24003ec0293 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/**