diff --git a/modules/nf-core/chromograph/main.nf b/modules/nf-core/chromograph/main.nf
index e1374e483e7..83db6c96092 100644
--- a/modules/nf-core/chromograph/main.nf
+++ b/modules/nf-core/chromograph/main.nf
@@ -1,11 +1,12 @@
 process CHROMOGRAPH {
-    tag "$meta.id"
+    // $meta.id can be [] because autozyg is not required, so use all ids
+    tag "${[meta, meta2, meta3, meta4, meta5, meta6, meta7].collect { meta_map -> meta_map.id }.findAll().unique().join('_') ?: 'chromograph'}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/chromograph:1.3.1--pyhdfd78af_2':
-        'biocontainers/chromograph:1.3.1--pyhdfd78af_2' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/chromograph:1.3.1--pyhdfd78af_2'
+        : 'biocontainers/chromograph:1.3.1--pyhdfd78af_2'}"
 
     input:
     tuple val(meta), path(autozyg)
@@ -17,79 +18,62 @@ process CHROMOGRAPH {
     tuple val(meta7), path(sites)
 
     output:
-    tuple val(meta), path("${prefix}"), emit: plots
-    path "versions.yml"               , emit: versions
+    tuple val(meta), path("*.png"), emit: plots
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args           = task.ext.args   ?: ''
-    def autozyg_param  = autozyg         ? "--autozyg ${autozyg}"   : ''
-    def coverage_param = coverage        ? "--coverage ${coverage}" : ''
-    def exome_param    = exome           ? "--exom ${exome}"        : ''
-    def fracsnp_param  = fracsnp         ? "--fracsnp ${fracsnp}"   : ''
-    def ideogram_param = ideogram        ? "--ideogram ${ideogram}" : ''
-    def regions_param  = regions         ? "--regions ${regions}"   : ''
-    def sites_param    = sites           ? "--sites ${sites}"       : ''
+    def args           = task.ext.args ?: ''
+    def autozyg_param  = autozyg       ? "--autozyg ${autozyg}"   : ''
+    def coverage_param = coverage      ? "--coverage ${coverage}" : ''
+    def exome_param    = exome         ? "--exom ${exome}"        : ''
+    def fracsnp_param  = fracsnp       ? "--fracsnp ${fracsnp}"   : ''
+    def ideogram_param = ideogram      ? "--ideogram ${ideogram}" : ''
+    def regions_param  = regions       ? "--regions ${regions}"   : ''
+    def sites_param    = sites         ? "--sites ${sites}"       : ''
 
-    if (autozyg) {
-        prefix         = task.ext.prefix ?: "${meta.id}"
-    } else if (coverage) {
-        prefix         = task.ext.prefix ?: "${meta2.id}"
-    } else if (exome) {
-        prefix         = task.ext.prefix ?: "${meta3.id}"
-    } else if (fracsnp) {
-        prefix         = task.ext.prefix ?: "${meta4.id}"
-    } else if (ideogram) {
-        prefix         = task.ext.prefix ?: "${meta5.id}"
-    } else if (regions) {
-        prefix         = task.ext.prefix ?: "${meta6.id}"
-    } else {
-        prefix         = task.ext.prefix ?: "${meta7.id}"
-    }
     """
     chromograph \\
-        $args \\
-        $autozyg_param \\
-        $coverage_param \\
-        $exome_param \\
-        $fracsnp_param \\
-        $ideogram_param \\
-        $regions_param \\
-        $sites_param \\
-        --outd ${prefix}
+        ${args} \\
+        ${autozyg_param} \\
+        ${coverage_param} \\
+        ${exome_param} \\
+        ${fracsnp_param} \\
+        ${ideogram_param} \\
+        ${regions_param} \\
+        ${sites_param} \\
+        --outd .
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        chromograph: \$(echo \$(chromograph --version 2>&1) | sed 's/chromograph //' )
+        chromograph: \$(chromograph --version | sed 's/.* //' )
     END_VERSIONS
     """
 
     stub:
-    def args               = task.ext.args   ?: ''
+    def args = task.ext.args ?: ''
+    euploidy = args.contains('-e') || args.contains('--euploid')
 
-    if (autozyg) {
-        prefix             = task.ext.prefix ?: "${meta.id}"
-    } else if (coverage) {
-        prefix             = task.ext.prefix ?: "${meta2.id}"
-    } else if (exome) {
-        prefix             = task.ext.prefix ?: "${meta3.id}"
-    } else if (fracsnp) {
-        prefix             = task.ext.prefix ?: "${meta4.id}"
-    } else if (ideogram) {
-        prefix             = task.ext.prefix ?: "${meta5.id}"
-    } else if (regions) {
-        prefix             = task.ext.prefix ?: "${meta6.id}"
-    } else {
-        prefix             = task.ext.prefix ?: "${meta7.id}"
-    }
     """
-    mkdir ${prefix}
+    ${touchCmd(euploidy, autozyg)}
+    ${touchCmd(euploidy, coverage)}
+    ${touchCmd(euploidy, exome)}
+    ${touchCmd(euploidy, fracsnp)}
+    ${touchCmd(euploidy, ideogram)}
+    ${touchCmd(euploidy, regions)}
+    ${touchCmd(euploidy, sites)}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        chromograph: \$(echo \$(chromograph --version 2>&1) | sed 's/chromograph //' )
+        chromograph: \$(chromograph --version | sed 's/.* //' )
     END_VERSIONS
     """
 }
+
+// Helper function to generate touch commands
+def touchCmd(euploidy, input_file) {
+    def chrs = euploidy ? (1..22) + ['X', 'Y', 'M'] : [1]
+    input_file ? chrs.collect { chr -> "touch ${input_file}_chr${chr}.png" }.join('\n') : ''
+}
diff --git a/modules/nf-core/chromograph/meta.yml b/modules/nf-core/chromograph/meta.yml
index c6148280760..2d3b97f5e60 100644
--- a/modules/nf-core/chromograph/meta.yml
+++ b/modules/nf-core/chromograph/meta.yml
@@ -1,4 +1,4 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "chromograph"
 description: Chromograph is a python package to create PNG images from genetics data
   such as BED and WIG files.
@@ -88,10 +88,9 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - ${prefix}:
+      - "*.png":
           type: file
-          description: Directory containing the plots in png format
-          pattern: "*.png"
+          description: Plot(s) in PNG format
           ontologies: []
   versions:
     - versions.yml:
diff --git a/modules/nf-core/chromograph/tests/main.nf.test b/modules/nf-core/chromograph/tests/main.nf.test
index 8643afe3a6d..050c470cb24 100644
--- a/modules/nf-core/chromograph/tests/main.nf.test
+++ b/modules/nf-core/chromograph/tests/main.nf.test
@@ -6,33 +6,152 @@ nextflow_process {
     tag "modules"
     tag "modules_nfcore"
     tag "chromograph"
+    config "./nextflow.config"
 
-    test("test_chromograph_sites") {
+    test("test_chromograph_sites_wig") {
+        when {
+            params {
+                module_args = ''
+            }
+            process {
+                """
+                input[0] = [[],[]]
+                input[1] = Channel.of(
+                    'fixedStep chrom=chr3 start=400601 step=100',
+                    '11',
+                    '22',
+                    '33')
+                    .collectFile(name: 'wig_input.wig', newLine: true)
+                    .map { file -> [ [ id: file.name ], file ] }
+                input[2] = [[],[]]
+                input[3] = [[],[]]
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                input[6] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/updsites.bed', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_chromograph_sites_wig_euploid") {
+        when {
+            params {
+                module_args = '--euploid'
+            }
+            process {
+                """
+                input[0] = [[],[]]
+                input[1] = Channel.of(
+                    'fixedStep chrom=chr3 start=400601 step=100',
+                    '11',
+                    '22',
+                    '33')
+                    .collectFile(name: 'wig_input.wig', newLine: true)
+                    .map { file -> [ [ id: file.name ], file ] }
+                input[2] = [[],[]]
+                input[3] = [[],[]]
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                input[6] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/updsites.bed', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test_chromograph_sites_wig_stub") {
+
+        options "-stub"
 
         when {
+            params {
+                module_args = ''
+            }
             process {
                 """
-                input[0] = [[:],[]]
-                input[1] = [[:],[]]
-                input[2] = [[:],[]]
-                input[3] = [[:],[]]
-                input[4] = [[:],[]]
-                input[5] = [[:],[]]
+                input[0] = [[],[]]
+                input[1] = Channel.of(
+                    'fixedStep chrom=chr3 start=400601 step=100',
+                    '11',
+                    '22',
+                    '33')
+                    .collectFile(name: 'wig_input.wig', newLine: true)
+                    .map { file -> [ [ id: file.name ], file ] }
+                input[2] = [[],[]]
+                input[3] = [[],[]]
+                input[4] = [[],[]]
+                input[5] = [[],[]]
                 input[6] = [
-                        [ id:'test', single_end:false ], // meta map
-                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/updsites.bed', checkIfExists: true)
-                            ]
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/updsites.bed', checkIfExists: true)
+                ]
                 """
             }
         }
 
         then {
             assertAll(
-            {assert process.success},
-            {assert process.out.plots.get(0).get(1) ==~ ".*/test"}
+            { assert process.success },
+            { assert snapshot(process.out).match() }
             )
         }
 
     }
 
+    test("test_chromograph_sites_wig_euploid_stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                module_args = '--euploid'
+            }
+            process {
+                """
+                input[0] = [[],[]]
+                input[1] = Channel.of(
+                    'fixedStep chrom=chr3 start=400601 step=100',
+                    '11',
+                    '22',
+                    '33')
+                    .collectFile(name: 'wig_input.wig', newLine: true)
+                    .map { file -> [ [ id: file.name ], file ] }
+                input[2] = [[],[]]
+                input[3] = [[],[]]
+                input[4] = [[],[]]
+                input[5] = [[],[]]
+                input[6] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/updsites.bed', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/chromograph/tests/main.nf.test.snap b/modules/nf-core/chromograph/tests/main.nf.test.snap
new file mode 100644
index 00000000000..a2656d92551
--- /dev/null
+++ b/modules/nf-core/chromograph/tests/main.nf.test.snap
@@ -0,0 +1,350 @@
+{
+    "test_chromograph_sites_wig": {
+        "content": [
+            {
+                "0": [
+                    [
+                        [
+                            
+                        ],
+                        [
+                            "updsites_21.png:md5,819946a2718817268668ee73f5062351",
+                            "wig_input_chr3.png:md5,954482b960865332f37d386da5c9fb75"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,26eebbe7ecf582cbc4197f6ccb14fa18"
+                ],
+                "plots": [
+                    [
+                        [
+                            
+                        ],
+                        [
+                            "updsites_21.png:md5,819946a2718817268668ee73f5062351",
+                            "wig_input_chr3.png:md5,954482b960865332f37d386da5c9fb75"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,26eebbe7ecf582cbc4197f6ccb14fa18"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-11-12T16:50:02.807996516"
+    },
+    "test_chromograph_sites_wig_euploid": {
+        "content": [
+            {
+                "0": [
+                    [
+                        [
+                            
+                        ],
+                        [
+                            "updsites_1.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_10.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_11.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_12.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_13.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_14.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_15.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_16.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_17.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_18.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_19.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_2.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_20.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_21.png:md5,819946a2718817268668ee73f5062351",
+                            "updsites_22.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_3.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_4.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_5.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_6.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_7.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_8.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_9.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_M.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_X.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_Y.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr1.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr10.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr11.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr12.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr13.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr14.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr15.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr16.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr17.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr18.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr19.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr2.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr20.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr21.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr22.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr3.png:md5,954482b960865332f37d386da5c9fb75",
+                            "wig_input_chr4.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr5.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr6.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr7.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr8.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr9.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chrM.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chrX.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chrY.png:md5,33d95212be5bf91fbea53500bcbba19c"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,26eebbe7ecf582cbc4197f6ccb14fa18"
+                ],
+                "plots": [
+                    [
+                        [
+                            
+                        ],
+                        [
+                            "updsites_1.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_10.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_11.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_12.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_13.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_14.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_15.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_16.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_17.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_18.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_19.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_2.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_20.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_21.png:md5,819946a2718817268668ee73f5062351",
+                            "updsites_22.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_3.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_4.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_5.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_6.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_7.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_8.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_9.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_M.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_X.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "updsites_Y.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr1.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr10.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr11.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr12.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr13.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr14.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr15.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr16.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr17.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr18.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr19.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr2.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr20.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr21.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr22.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr3.png:md5,954482b960865332f37d386da5c9fb75",
+                            "wig_input_chr4.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr5.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr6.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr7.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr8.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chr9.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chrM.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chrX.png:md5,33d95212be5bf91fbea53500bcbba19c",
+                            "wig_input_chrY.png:md5,33d95212be5bf91fbea53500bcbba19c"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,26eebbe7ecf582cbc4197f6ccb14fa18"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-11-12T16:50:08.440144719"
+    },
+    "test_chromograph_sites_wig_stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        [
+                            
+                        ],
+                        [
+                            "updsites.bed_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,26eebbe7ecf582cbc4197f6ccb14fa18"
+                ],
+                "plots": [
+                    [
+                        [
+                            
+                        ],
+                        [
+                            "updsites.bed_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,26eebbe7ecf582cbc4197f6ccb14fa18"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-11-12T16:50:12.957082993"
+    },
+    "test_chromograph_sites_wig_euploid_stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        [
+                            
+                        ],
+                        [
+                            "updsites.bed_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr10.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr11.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr12.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr13.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr14.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr15.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr16.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr17.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr18.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr19.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr2.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr20.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr21.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr22.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr3.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr4.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr5.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr6.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr7.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr8.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr9.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chrM.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chrX.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chrY.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr10.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr11.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr12.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr13.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr14.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr15.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr16.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr17.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr18.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr19.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr2.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr20.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr21.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr22.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr3.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr4.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr5.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr6.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr7.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr8.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr9.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chrM.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chrX.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chrY.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,44098e3caf6adc824cc68f03f92c1513"
+                ],
+                "plots": [
+                    [
+                        [
+                            
+                        ],
+                        [
+                            "updsites.bed_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr10.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr11.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr12.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr13.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr14.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr15.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr16.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr17.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr18.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr19.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr2.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr20.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr21.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr22.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr3.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr4.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr5.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr6.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr7.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr8.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chr9.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chrM.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chrX.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "updsites.bed_chrY.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr1.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr10.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr11.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr12.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr13.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr14.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr15.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr16.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr17.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr18.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr19.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr2.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr20.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr21.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr22.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr3.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr4.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr5.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr6.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr7.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr8.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chr9.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chrM.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chrX.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "wig_input.wig_chrY.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,44098e3caf6adc824cc68f03f92c1513"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-11-12T17:19:11.669837666"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/chromograph/tests/nextflow.config b/modules/nf-core/chromograph/tests/nextflow.config
new file mode 100644
index 00000000000..c6c5ef7ea4d
--- /dev/null
+++ b/modules/nf-core/chromograph/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: CHROMOGRAPH {
+        ext.args = params.module_args
+    }
+}
\ No newline at end of file