diff --git a/modules.json b/modules.json
index dbbf78e3..5ca2f98a 100644
--- a/modules.json
+++ b/modules.json
@@ -8,225 +8,163 @@
                     "annotsv/annotsv": {
                         "branch": "master",
                         "git_sha": "a94ad45fa5b350961c374c46f79bc86cd5853353",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "annotsv/installannotations": {
                         "branch": "master",
                         "git_sha": "a94ad45fa5b350961c374c46f79bc86cd5853353",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bcftools/annotate": {
                         "branch": "master",
                         "git_sha": "2ad29c2aed06d815d9f68ad7ba20b3b1c574ce9c",
-                        "installed_by": [
-                            "modules"
-                        ],
+                        "installed_by": ["modules"],
                         "patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff"
                     },
                     "bcftools/concat": {
                         "branch": "master",
                         "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bcftools/filter": {
                         "branch": "master",
                         "git_sha": "a3893076a76e91b3ff152faddf872f00778fb224",
-                        "installed_by": [
-                            "modules"
-                        ],
+                        "installed_by": ["modules"],
                         "patch": "modules/nf-core/bcftools/filter/bcftools-filter.diff"
                     },
                     "bcftools/sort": {
                         "branch": "master",
                         "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bedgovcf": {
                         "branch": "master",
                         "git_sha": "71a96063a7e09be7ea48f069d134a56ce86c9ba6",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bwa/index": {
                         "branch": "master",
                         "git_sha": "6278bf9afd4a4b2d00fa6052250e73da3d91546f",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "delly/call": {
                         "branch": "master",
                         "git_sha": "92bf2a8afa318a64f9d333cf87b510c662fd4274",
-                        "installed_by": [
-                            "modules"
-                        ],
+                        "installed_by": ["modules"],
                         "patch": "modules/nf-core/delly/call/delly-call.diff"
                     },
                     "ensemblvep/download": {
                         "branch": "master",
                         "git_sha": "3db4f8488315cd7d7cf3fcb64251f6603210e831",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "ensemblvep/vep": {
                         "branch": "master",
                         "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "expansionhunter": {
                         "branch": "master",
                         "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gawk": {
                         "branch": "master",
                         "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gridss/gridss": {
                         "branch": "master",
                         "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": [
-                            "modules"
-                        ],
+                        "installed_by": ["modules"],
                         "patch": "modules/nf-core/gridss/gridss/gridss-gridss.diff"
                     },
                     "jasminesv": {
                         "branch": "master",
                         "git_sha": "92bf2a8afa318a64f9d333cf87b510c662fd4274",
-                        "installed_by": [
-                            "modules"
-                        ],
+                        "installed_by": ["modules"],
                         "patch": "modules/nf-core/jasminesv/jasminesv.diff"
                     },
                     "manta/convertinversion": {
                         "branch": "master",
                         "git_sha": "92bf2a8afa318a64f9d333cf87b510c662fd4274",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "manta/germline": {
                         "branch": "master",
                         "git_sha": "ebc1733b77c702f19fe42076a5edfcbaa0d84f66",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "19ca321db5d8bd48923262c2eca6422359633491",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "ngsbits/samplegender": {
                         "branch": "master",
                         "git_sha": "023e119cfa102f319b6dcfd06abecf7f3c2b8df1",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/convert": {
                         "branch": "master",
                         "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
-                        "installed_by": [
-                            "modules"
-                        ],
+                        "installed_by": ["modules"],
                         "patch": "modules/nf-core/samtools/convert/samtools-convert.diff"
                     },
                     "samtools/faidx": {
                         "branch": "master",
                         "git_sha": "f153f1f10e1083c49935565844cccb7453021682",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
                         "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/merge": {
                         "branch": "master",
                         "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "smoove/call": {
                         "branch": "master",
                         "git_sha": "f2fdc5e81efe36beff213752ce1a8e71fceeacba",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "svync": {
                         "branch": "master",
                         "git_sha": "3df1a372b844c98c31ec3446faac7c75e64518a3",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "tabix/bgziptabix": {
                         "branch": "master",
                         "git_sha": "09d3c8c29b31a2dfd610305b10550f0e1dbcd4a9",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "tabix/tabix": {
                         "branch": "master",
                         "git_sha": "9502adb23c0b97ed8e616bbbdfa73b4585aec9a1",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "vcfanno": {
                         "branch": "master",
                         "git_sha": "b558cd24f8751dcda51f957391f5f9cb83e28586",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "wisecondorx/convert": {
                         "branch": "master",
-                        "git_sha": "dc7e9607d9977555ca1235a51a40d097bc66954c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
                     },
                     "wisecondorx/predict": {
                         "branch": "master",
-                        "git_sha": "dc7e9607d9977555ca1235a51a40d097bc66954c",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
                     }
                 }
             },
@@ -235,26 +173,20 @@
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
                         "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
                         "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
-                        "installed_by": [
-                            "subworkflows"
-                        ]
+                        "installed_by": ["subworkflows"]
                     }
                 }
             }
         }
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/wisecondorx/convert/environment.yml b/modules/nf-core/wisecondorx/convert/environment.yml
index 6b26f79c..90e62a7c 100644
--- a/modules/nf-core/wisecondorx/convert/environment.yml
+++ b/modules/nf-core/wisecondorx/convert/environment.yml
@@ -1,7 +1,5 @@
-name: wisecondorx_convert
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::wisecondorx=1.2.5
+  - bioconda::wisecondorx=1.2.9
diff --git a/modules/nf-core/wisecondorx/convert/main.nf b/modules/nf-core/wisecondorx/convert/main.nf
index e284edb0..c52a6d2d 100644
--- a/modules/nf-core/wisecondorx/convert/main.nf
+++ b/modules/nf-core/wisecondorx/convert/main.nf
@@ -5,8 +5,8 @@ process WISECONDORX_CONVERT {
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/wisecondorx:1.2.7--pyhdfd78af_0':
-        'biocontainers/wisecondorx:1.2.7--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/wisecondorx:1.2.9--pyhdfd78af_0':
+        'biocontainers/wisecondorx:1.2.9--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
@@ -24,7 +24,7 @@ process WISECONDORX_CONVERT {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def reference = fasta ? "--reference ${fasta}" : ""
-    def VERSION = '1.2.7' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '1.2.9' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
     """
     WisecondorX convert \\
@@ -41,7 +41,7 @@ process WISECONDORX_CONVERT {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '1.2.7' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '1.2.9' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
     """
     touch ${prefix}.npz
diff --git a/modules/nf-core/wisecondorx/convert/meta.yml b/modules/nf-core/wisecondorx/convert/meta.yml
index d70d9d69..07233d29 100644
--- a/modules/nf-core/wisecondorx/convert/meta.yml
+++ b/modules/nf-core/wisecondorx/convert/meta.yml
@@ -12,52 +12,56 @@ tools:
       tool_dev_url: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX"
       doi: "10.1093/nar/gky1263"
       licence: ["Attribution-NonCommercial-ShareAlike CC BY-NC-SA"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - bam:
-      type: file
-      description: Reads in BAM/CRAM format
-      pattern: "*.{bam,cram}"
-  - bai:
-      type: file
-      description: index of the BAM/CRAM file
-      pattern: "*.{bai,crai}"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference fasta meta information
-        e.g. [ id:'test' ]
-  - fasta:
-      type: file
-      description: The reference FASTA file (mandatory when using CRAM files)
-      pattern: "*.{fasta,fa,fna}"
-  - meta3:
-      type: map
-      description: |
-        Groovy Map containing reference fasta index meta information
-        e.g. [ id:'test' ]
-  - fasta_fai:
-      type: file
-      description: The index of the reference FASTA file (mandatory when using CRAM files)
-      pattern: "*.fai"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: Reads in BAM/CRAM format
+        pattern: "*.{bam,cram}"
+    - bai:
+        type: file
+        description: index of the BAM/CRAM file
+        pattern: "*.{bai,crai}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference fasta meta information
+          e.g. [ id:'test' ]
+    - fasta:
+        type: file
+        description: The reference FASTA file (mandatory when using CRAM files)
+        pattern: "*.{fasta,fa,fna}"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing reference fasta index meta information
+          e.g. [ id:'test' ]
+    - fasta_fai:
+        type: file
+        description: The index of the reference FASTA file (mandatory when using CRAM
+          files)
+        pattern: "*.fai"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - npz:
-      type: file
-      description: The output NPZ file
-      pattern: "*.npz"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.npz":
+          type: file
+          description: The output NPZ file
+          pattern: "*.npz"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@nvnieuwk"
 maintainers:
diff --git a/modules/nf-core/wisecondorx/convert/tests/main.nf.test b/modules/nf-core/wisecondorx/convert/tests/main.nf.test
index 1e093e9a..d0095513 100644
--- a/modules/nf-core/wisecondorx/convert/tests/main.nf.test
+++ b/modules/nf-core/wisecondorx/convert/tests/main.nf.test
@@ -16,8 +16,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true)
                 ]
                 input[1] = [[], []]
                 input[2] = [[], []]
@@ -28,7 +28,11 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    file(process.out.npz[0][1]).name,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
 
@@ -41,18 +45,18 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true)
                 ]
 
                 input[1] = [
                     [ id:'test' ],
-                    file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 ]
 
                 input[2] = [
                     [ id:'test' ],
-                    file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
                 """
             }
@@ -61,7 +65,11 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    file(process.out.npz[0][1]).name,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
 
@@ -76,8 +84,8 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true)
                 ]
                 input[1] = [[], []]
                 input[2] = [[], []]
@@ -88,7 +96,11 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    file(process.out.npz[0][1]).name,
+                    process.out.versions
+                    ).match()
+                }
             )
         }
 
diff --git a/modules/nf-core/wisecondorx/convert/tests/main.nf.test.snap b/modules/nf-core/wisecondorx/convert/tests/main.nf.test.snap
index aa1f22c2..06f49ac1 100644
--- a/modules/nf-core/wisecondorx/convert/tests/main.nf.test.snap
+++ b/modules/nf-core/wisecondorx/convert/tests/main.nf.test.snap
@@ -1,107 +1,41 @@
 {
     "sarscov2 - cram, crai, fasta, fai": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.npz:md5,154337aa93ceddf15ea7382969588524"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,dc34a4dc3f7c98e236b54d2b58c81e92"
-                ],
-                "npz": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.npz:md5,154337aa93ceddf15ea7382969588524"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,dc34a4dc3f7c98e236b54d2b58c81e92"
-                ]
-            }
+            "test.npz",
+            [
+                "versions.yml:md5,cb3166b8b3fe6664deca2ec198dc34c2"
+            ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.02.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-04-25T10:32:21.089786336"
+        "timestamp": "2024-08-29T13:47:47.027602"
     },
     "sarscov2 - bam, bai, [], []": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.npz:md5,00c8acf1727e9eb78e56bce28b09ee3b"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,dc34a4dc3f7c98e236b54d2b58c81e92"
-                ],
-                "npz": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.npz:md5,00c8acf1727e9eb78e56bce28b09ee3b"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,dc34a4dc3f7c98e236b54d2b58c81e92"
-                ]
-            }
+            "test.npz",
+            [
+                "versions.yml:md5,cb3166b8b3fe6664deca2ec198dc34c2"
+            ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.02.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-04-25T10:32:11.059476585"
+        "timestamp": "2024-08-29T13:47:22.0575"
     },
     "sarscov2 - bam, bai - stub": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.npz:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,dc34a4dc3f7c98e236b54d2b58c81e92"
-                ],
-                "npz": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.npz:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,dc34a4dc3f7c98e236b54d2b58c81e92"
-                ]
-            }
+            "test.npz",
+            [
+                "versions.yml:md5,cb3166b8b3fe6664deca2ec198dc34c2"
+            ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.02.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-04-25T10:32:28.177177149"
+        "timestamp": "2024-08-29T13:48:02.484298"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/wisecondorx/predict/environment.yml b/modules/nf-core/wisecondorx/predict/environment.yml
index 35d6a5e2..90e62a7c 100644
--- a/modules/nf-core/wisecondorx/predict/environment.yml
+++ b/modules/nf-core/wisecondorx/predict/environment.yml
@@ -1,7 +1,5 @@
-name: wisecondorx_predict
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::wisecondorx=1.2.5
+  - bioconda::wisecondorx=1.2.9
diff --git a/modules/nf-core/wisecondorx/predict/main.nf b/modules/nf-core/wisecondorx/predict/main.nf
index 1cba5900..70005fc0 100644
--- a/modules/nf-core/wisecondorx/predict/main.nf
+++ b/modules/nf-core/wisecondorx/predict/main.nf
@@ -5,8 +5,8 @@ process WISECONDORX_PREDICT {
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/wisecondorx:1.2.7--pyhdfd78af_0':
-        'biocontainers/wisecondorx:1.2.7--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/wisecondorx:1.2.9--pyhdfd78af_0':
+        'biocontainers/wisecondorx:1.2.9--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(npz)
@@ -32,7 +32,7 @@ process WISECONDORX_PREDICT {
 
     def plots = args.contains("--plot") ? "mv ${prefix}.plots/* ." : ""
 
-    def VERSION = '1.2.7' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '1.2.9' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
     """
     WisecondorX predict \\
@@ -53,7 +53,7 @@ process WISECONDORX_PREDICT {
     stub:
     def args = task.ext.args ?: '--bed --plot'
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '1.2.7' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '1.2.9' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
     def bed = args.contains("--bed") ? "touch ${prefix}_aberrations.bed && touch ${prefix}_bins.bed && touch ${prefix}_chr_statistics.txt && touch ${prefix}_segments.bed" : ""
     def plot = args.contains("--plot") ? "touch genome_wide.png && touch chr22.png && touch chr1.png" : ""
diff --git a/modules/nf-core/wisecondorx/predict/meta.yml b/modules/nf-core/wisecondorx/predict/meta.yml
index 0f347ee3..ae175545 100644
--- a/modules/nf-core/wisecondorx/predict/meta.yml
+++ b/modules/nf-core/wisecondorx/predict/meta.yml
@@ -13,68 +13,107 @@ tools:
       tool_dev_url: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX"
       doi: "10.1093/nar/gky1263"
       licence: ["Attribution-NonCommercial-ShareAlike CC BY-NC-SA"]
+      identifier: ""
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - npz:
-      type: file
-      description: An NPZ file created with WisecondorX convert
-      pattern: "*.npz"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'test', single_end:false ]
-  - reference:
-      type: file
-      description: A reference NPZ file created with WisecondorX newref
-      pattern: "*.npz"
-  - meta3:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - blacklist:
-      type: file
-      description: OPTIONAL - A BED file containing blacklist regions (used mainly when the reference is small)
-      pattern: "*.bed"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - npz:
+        type: file
+        description: An NPZ file created with WisecondorX convert
+        pattern: "*.npz"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'test', single_end:false ]
+    - reference:
+        type: file
+        description: A reference NPZ file created with WisecondorX newref
+        pattern: "*.npz"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - blacklist:
+        type: file
+        description: OPTIONAL - A BED file containing blacklist regions (used mainly
+          when the reference is small)
+        pattern: "*.bed"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - aberrations_bed:
-      type: file
-      description: OPTIONAL - Output abberations in BED format. This gets created with the `--bed` option
-      pattern: "*_aberrations.bed"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*_aberrations.bed":
+          type: file
+          description: OPTIONAL - Output abberations in BED format. This gets created
+            with the `--bed` option
+          pattern: "*_aberrations.bed"
   - bins_bed:
-      type: file
-      description: OPTIONAL - Output bins in BED format. This gets created with the `--bed` option
-      pattern: "*_bins.bed"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*_bins.bed":
+          type: file
+          description: OPTIONAL - Output bins in BED format. This gets created with the
+            `--bed` option
+          pattern: "*_bins.bed"
   - segments_bed:
-      type: file
-      description: OPTIONAL - Output segments in BED format. This gets created with the `--bed` option
-      pattern: "*_segments.bed"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*_segments.bed":
+          type: file
+          description: OPTIONAL - Output segments in BED format. This gets created with
+            the `--bed` option
+          pattern: "*_segments.bed"
   - chr_statistics:
-      type: file
-      description: OPTIONAL - Statistics per chromosome in TXT format. This gets created with the `--bed` option
-      pattern: "*_chr_statistics.txt"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*_chr_statistics.txt":
+          type: file
+          description: OPTIONAL - Statistics per chromosome in TXT format. This gets created
+            with the `--bed` option
+          pattern: "*_chr_statistics.txt"
   - chr_plots:
-      type: list
-      description: OPTIONAL - A list containing the CNV plots of each chromosome. This gets created with the `--plot` option
-      pattern: "[!genome_wide]*.png"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "[!genome_wide]*.png":
+          type: list
+          description: OPTIONAL - A list containing the CNV plots of each chromosome.
+            This gets created with the `--plot` option
+          pattern: "[!genome_wide]*.png"
   - genome_plot:
-      type: file
-      description: OPTIONAL - A plot containing the CNV information of the whole genome
-      pattern: "genome_wide.png"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - genome_wide.png:
+          type: file
+          description: OPTIONAL - A plot containing the CNV information of the whole genome
+          pattern: "genome_wide.png"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@nvnieuwk"
 maintainers:
diff --git a/modules/nf-core/wisecondorx/predict/tests/main.nf.test b/modules/nf-core/wisecondorx/predict/tests/main.nf.test
index 27b47525..2c8ee4d7 100644
--- a/modules/nf-core/wisecondorx/predict/tests/main.nf.test
+++ b/modules/nf-core/wisecondorx/predict/tests/main.nf.test
@@ -22,8 +22,8 @@ nextflow_process {
                     """
                     input[0] = [
                         [ id:'test' ], // meta map
-                        file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
-                        file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true)
                     ]
                     input[1] = [[], []]
                     input[2] = [[], []]
diff --git a/modules/nf-core/wisecondorx/predict/tests/main.nf.test.snap b/modules/nf-core/wisecondorx/predict/tests/main.nf.test.snap
index 59e9a214..9381ba13 100644
--- a/modules/nf-core/wisecondorx/predict/tests/main.nf.test.snap
+++ b/modules/nf-core/wisecondorx/predict/tests/main.nf.test.snap
@@ -2,7 +2,7 @@
     "sarscov2 - npz, reference, []": {
         "content": [
             [
-                "versions.yml:md5,7760ef13f826776ae67780d937c82729"
+                "versions.yml:md5,55d1ce74d0d17479cdbc51ca5cea485e"
             ],
             [
                 [
@@ -57,9 +57,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.02.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-04-25T10:31:51.830934617"
+        "timestamp": "2024-08-29T13:48:50.058254"
     }
 }
\ No newline at end of file