diff --git a/modules/nf-core/shapeit5/ligate/environment.yml b/modules/nf-core/shapeit5/ligate/environment.yml
index 7b8e63bba47..91b87fd02eb 100644
--- a/modules/nf-core/shapeit5/ligate/environment.yml
+++ b/modules/nf-core/shapeit5/ligate/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::shapeit5=1.0.0
+  - bioconda::shapeit5=5.1.1
diff --git a/modules/nf-core/shapeit5/ligate/main.nf b/modules/nf-core/shapeit5/ligate/main.nf
index 5624d7d9870..a45179493fd 100644
--- a/modules/nf-core/shapeit5/ligate/main.nf
+++ b/modules/nf-core/shapeit5/ligate/main.nf
@@ -4,11 +4,11 @@ process SHAPEIT5_LIGATE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/shapeit5:1.0.0--h0c8ee15_0':
-        'biocontainers/shapeit5:1.0.0--h0c8ee15_0'}"
+        'https://depot.galaxyproject.org/singularity/shapeit5:5.1.1--hb60d31d_0':
+        'biocontainers/shapeit5:5.1.1--hb60d31d_0'}"
 
     input:
-    tuple val(meta), path(input_list), path (input_list_index)
+    tuple val(meta), path(input_list), path(input_list_index)
 
     output:
     tuple val(meta), path("*.{vcf,bcf,vcf.gz,bcf.gz}"), emit: merged_variants
@@ -37,11 +37,11 @@ process SHAPEIT5_LIGATE {
     """
 
     stub:
-    def args   = task.ext.args   ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def suffix = task.ext.suffix ?: "vcf.gz"
+    def prefix     = task.ext.prefix        ?: "${meta.id}"
+    def suffix     = task.ext.suffix        ?: "vcf.gz"
+    def create_cmd = suffix.endsWith(".gz") ? "echo '' | gzip >" : "touch"
     """
-    touch ${prefix}.${suffix}
+    ${create_cmd} ${prefix}.${suffix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/shapeit5/ligate/tests/main.nf.test b/modules/nf-core/shapeit5/ligate/tests/main.nf.test
new file mode 100644
index 00000000000..4e3391c5631
--- /dev/null
+++ b/modules/nf-core/shapeit5/ligate/tests/main.nf.test
@@ -0,0 +1,99 @@
+nextflow_process {
+
+    name "Test Process SHAPEIT5_LIGATE"
+    script "../main.nf"
+    process "SHAPEIT5_LIGATE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "shapeit5"
+    tag "shapeit5/ligate"
+    tag "bcftools/view"
+
+    test("homo sapiens - map, [vcf], [tbi]") {
+        config "./nextflow.config"
+        setup {
+            run("BCFTOOLS_VIEW", alias: "BCFTOOLS_VIEW_1") {
+                script "../../../bcftools/view"
+                params {
+                    bcftools_args = "--regions chr22:16570000-16600000 -Ob --write-index=csi -e 'GT=\"./.\"||GT=\".\"'"
+                }
+                process {
+                    """
+                    input[0] = [
+                        [ id:'NA12878_1' ], // meta map
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi", checkIfExists: true),
+                    ]
+                    input[1] = []
+                    input[2] = []
+                    input[3] = []
+                    """
+                }
+            }
+            run("BCFTOOLS_VIEW", alias: "BCFTOOLS_VIEW_2") {
+                script "../../../bcftools/view"
+                params {
+                    bcftools_args = "--regions chr22:16580000-16610000 -Ob --write-index=csi -e 'GT=\"./.\"||GT=\".\"'"
+                }
+                process {
+                    """
+                    input[0] = [
+                        [ id:'NA12878_2' ], // meta map
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi", checkIfExists: true),
+                    ]
+                    input[1] = []
+                    input[2] = []
+                    input[3] = []
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = BCFTOOLS_VIEW_1.out.vcf.join(BCFTOOLS_VIEW_1.out.csi)
+                    .mix(BCFTOOLS_VIEW_2.out.vcf.join(BCFTOOLS_VIEW_2.out.csi))
+                    .map { meta, vcf, csi -> [ [id : "NA12878"], vcf, csi ] }
+                    .groupTuple()
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.merged_variants.collect {meta, vcf -> [ meta, path(vcf).vcf.summary ]},
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("homo sapiens - map, [vcf], [tbi] - stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id: 'NA12878'],
+                    [file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz", checkIfExists: true)],
+                    [file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi", checkIfExists: true)]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/shapeit5/ligate/tests/main.nf.test.snap b/modules/nf-core/shapeit5/ligate/tests/main.nf.test.snap
new file mode 100644
index 00000000000..3caae978dd6
--- /dev/null
+++ b/modules/nf-core/shapeit5/ligate/tests/main.nf.test.snap
@@ -0,0 +1,55 @@
+{
+    "homo sapiens - map, [vcf], [tbi] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "NA12878"
+                        },
+                        "NA12878.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,4b66c655a4fd210ca7bc47b6fe35230b"
+                ],
+                "merged_variants": [
+                    [
+                        {
+                            "id": "NA12878"
+                        },
+                        "NA12878.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,4b66c655a4fd210ca7bc47b6fe35230b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-22T17:22:34.235879155"
+    },
+    "homo sapiens - map, [vcf], [tbi]": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "NA12878"
+                    },
+                    "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=60, phased=false, phasedAutodetect=false]"
+                ]
+            ],
+            [
+                "versions.yml:md5,4b66c655a4fd210ca7bc47b6fe35230b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-12-04T10:07:53.185018802"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/shapeit5/ligate/tests/nextflow.config b/modules/nf-core/shapeit5/ligate/tests/nextflow.config
new file mode 100644
index 00000000000..0dee91a2a0c
--- /dev/null
+++ b/modules/nf-core/shapeit5/ligate/tests/nextflow.config
@@ -0,0 +1,6 @@
+process {
+    withName: "BCFTOOLS_VIEW_*" {
+        ext.args = params.bcftools_args
+        ext.prefix = { "${meta.id}" }
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 22dd0b609c7..ae64cc3bc35 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -507,9 +507,6 @@ sgdemux:
   - modules/nf-core/sgdemux/**
   - modules/nf-core/untar/**
   - tests/modules/nf-core/sgdemux/**
-shapeit5/ligate:
-  - modules/nf-core/shapeit5/ligate/**
-  - tests/modules/nf-core/shapeit5/ligate/**
 shapeit5/phaserare:
   - modules/nf-core/shapeit5/phaserare/**
   - tests/modules/nf-core/shapeit5/phaserare/**
diff --git a/tests/modules/nf-core/shapeit5/ligate/main.nf b/tests/modules/nf-core/shapeit5/ligate/main.nf
deleted file mode 100644
index 1213f7bd3a8..00000000000
--- a/tests/modules/nf-core/shapeit5/ligate/main.nf
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/usr/bin/env nextflow
-nextflow.enable.dsl = 2
-
-include { SHAPEIT5_LIGATE                   } from '../../../../../modules/nf-core/shapeit5/ligate/main.nf'
-include { SHAPEIT5_PHASECOMMON              } from '../../../../../modules/nf-core/shapeit5/phasecommon/main.nf'
-include { BCFTOOLS_VIEW                     } from '../../../../../modules/nf-core/bcftools/view/main.nf'
-include { BCFTOOLS_INDEX                    } from '../../../../../modules/nf-core/bcftools/index/main.nf'
-include { BCFTOOLS_INDEX as BCFTOOLS_INDEX2 } from '../../../../../modules/nf-core/bcftools/index/main.nf'
-
-workflow test_shapeit5_ligate {
-    input_vcf = [
-        [ id:'NA12878_1X', single_end:false ], // meta map
-        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
-        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true),
-    ]
-    
-    ref_panel = Channel.of([
-        [ id:'REF_1000GP', single_end:false ], // meta map
-        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
-        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
-    ]).collect()
-
-    scaffold  = Channel.of([[],[],[]]).collect()
-    map       = Channel.of([[],[]]).collect()
-
-    BCFTOOLS_VIEW ( input_vcf, [], [], [] )
-    BCFTOOLS_INDEX ( BCFTOOLS_VIEW.out.vcf )
-
-    region = Channel.of("chr21:16600000-16750000", "chr21:16650000-16800000")
-    sample = Channel.of([[]])
-
-    phase_input = Channel.of([[ id:'NA12878_1X']])
-                        .combine(BCFTOOLS_VIEW.out.vcf.collect().map{it[1]})
-                        .combine(BCFTOOLS_INDEX.out.csi.collect().map{it[1]})
-                        .combine(sample)
-                        .combine(region)
-                        .map{ meta, vcf, csi, sample, region ->
-                            [meta + [region: region.replace(":","_")],
-                            vcf, csi, sample, region]}
-                        
-
-    SHAPEIT5_PHASECOMMON ( phase_input, ref_panel, scaffold, map )
-    
-    phased_variant = SHAPEIT5_PHASECOMMON.output.phased_variant
-                        .map{ meta, vcf -> [meta.subMap(["id"]), vcf]}
-
-    BCFTOOLS_INDEX2 ( phased_variant )
-
-    ligate_input = phased_variant.groupTuple()
-                        .join(BCFTOOLS_INDEX2.out.csi.groupTuple())
-                        .map { meta, vcf, csi ->
-                            [meta,
-                            vcf.sort{ a, b ->
-                                a.getName() <=> b.getName()},
-                            csi]}
-
-    SHAPEIT5_LIGATE ( ligate_input )
-}
diff --git a/tests/modules/nf-core/shapeit5/ligate/nextflow.config b/tests/modules/nf-core/shapeit5/ligate/nextflow.config
deleted file mode 100644
index f96da6737f4..00000000000
--- a/tests/modules/nf-core/shapeit5/ligate/nextflow.config
+++ /dev/null
@@ -1,17 +0,0 @@
-process {
-    withName: BCFTOOLS_VIEW {
-        ext.args = [
-            "-Oz",
-            "-e 'GT=\"./.\"||GT=\".\"'"
-        ].join(' ')
-        ext.prefix = { "${meta.id}" }
-    }
-    withName: SHAPEIT5_PHASECOMMON {
-        ext.args = [
-        ].join(' ')
-        ext.suffix = "bcf"
-        ext.prefix = { "${meta.id}_${meta.region}" }
-    }
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/shapeit5/ligate/test.yml b/tests/modules/nf-core/shapeit5/ligate/test.yml
deleted file mode 100644
index d60fb8e47f0..00000000000
--- a/tests/modules/nf-core/shapeit5/ligate/test.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-- name: shapeit5 ligate test_shapeit5_ligate
-  command: nextflow run ./tests/modules/nf-core/shapeit5/ligate -entry test_shapeit5_ligate -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shapeit5/ligate/nextflow.config
-  tags:
-    - shapeit5
-    - shapeit5/ligate
-  files:
-    - path: output/bcftools/NA12878_1X.vcf.gz
-    - path: output/bcftools/NA12878_1X.vcf.gz.csi
-    - path: output/bcftools/NA12878_1X_chr21_16600000-16750000.bcf.csi
-    - path: output/bcftools/NA12878_1X_chr21_16650000-16800000.bcf.csi
-    - path: output/bcftools/versions.yml
-    - path: output/shapeit5/NA12878_1X.vcf.gz
-    - path: output/shapeit5/NA12878_1X_chr21_16600000-16750000.bcf
-    - path: output/shapeit5/NA12878_1X_chr21_16650000-16800000.bcf
-    - path: output/shapeit5/versions.yml