diff --git a/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test b/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test
index afdd1cec2429..5f3499da00ef 100644
--- a/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test
+++ b/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test
@@ -9,6 +9,7 @@ nextflow_process {
     tag "modkit"
     tag "modkit/bedmethyltobigwig"
     tag "modkit/pileup"
+    tag "tabix/bgzip"
 
     setup {
         run("MODKIT_PILEUP"){
@@ -25,6 +26,15 @@ nextflow_process {
                 """
             }
         }
+
+        run("TABIX_BGZIP"){
+            script "../../../tabix/bgzip/main.nf"
+            process {
+                """
+                input[0] = MODKIT_PILEUP.out.bedgz
+                """
+            }
+        }
     }
 
     test("homo sapiens - bedmethyl, fai, list") {
@@ -32,7 +42,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = MODKIT_PILEUP.out.bed
+                input[0] = TABIX_BGZIP.out.output
                 input[1] = [
                     [ id : 'hg38' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
@@ -55,7 +65,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = MODKIT_PILEUP.out.bed
+                input[0] = TABIX_BGZIP.out.output
                 input[1] = [
                     [ id : 'hg38' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
@@ -78,7 +88,7 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = MODKIT_PILEUP.out.bed
+                input[0] = TABIX_BGZIP.out.output
                 input[1] = [
                     [ id : 'hg38' ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
diff --git a/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap b/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap
index d3ebb75cfbcd..48c989060696 100644
--- a/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap
+++ b/modules/nf-core/modkit/bedmethyltobigwig/tests/main.nf.test.snap
@@ -30,7 +30,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-11T09:38:52.912687858"
+        "timestamp": "2025-12-11T14:18:11.382889943"
     },
     "homo sapiens - bedmethyl, fai, list": {
         "content": [
@@ -63,7 +63,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-11T09:38:35.894897541"
+        "timestamp": "2025-12-11T14:17:52.811754475"
     },
     "homo sapiens - bedmethyl, fai, string": {
         "content": [
@@ -96,6 +96,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-11T09:38:44.647742811"
+        "timestamp": "2025-12-11T14:18:02.079953932"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/modkit/pileup/environment.yml b/modules/nf-core/modkit/pileup/environment.yml
index c7c61cdfe973..67c67438a94d 100644
--- a/modules/nf-core/modkit/pileup/environment.yml
+++ b/modules/nf-core/modkit/pileup/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - ont-modkit=0.5.0
+  - ont-modkit=0.6.0
diff --git a/modules/nf-core/modkit/pileup/main.nf b/modules/nf-core/modkit/pileup/main.nf
index a3ef3bf14607..fc4068cc125d 100644
--- a/modules/nf-core/modkit/pileup/main.nf
+++ b/modules/nf-core/modkit/pileup/main.nf
@@ -4,8 +4,8 @@ process MODKIT_PILEUP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ont-modkit:0.5.0--hcdda2d0_2':
-        'biocontainers/ont-modkit:0.5.0--hcdda2d0_2' }"
+        'https://depot.galaxyproject.org/singularity/ont-modkit:0.6.0--hcdda2d0_0':
+        'biocontainers/ont-modkit:0.6.0--hcdda2d0_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
@@ -13,8 +13,7 @@ process MODKIT_PILEUP {
     tuple val(meta3), path(bed)
 
     output:
-    tuple val(meta), path("*.bed")     , emit: bed     , optional: true
-    tuple val(meta), path("*.bedgraph"), emit: bedgraph, optional: true
+    tuple val(meta), path("*.bed.gz")  , emit: bedgz   , optional: true
     tuple val(meta), path("*.log")     , emit: log     , optional: true
     path "versions.yml"                , emit: versions
 
@@ -31,6 +30,8 @@ process MODKIT_PILEUP {
     modkit \\
         pileup \\
         $args \\
+        --bgzf \\
+        --bgzf-threads ${task.cpus} \\
         --threads ${task.cpus} \\
         --prefix ${prefix} \\
         $reference \\
@@ -45,7 +46,7 @@ process MODKIT_PILEUP {
             fi
         done
     else
-        mv ${prefix}.tmp ${prefix}.bed
+        mv ${prefix}.tmp ${prefix}.bed.gz
     fi
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/modkit/pileup/meta.yml b/modules/nf-core/modkit/pileup/meta.yml
index 32aba6add7fc..3d7d9fd5b8ee 100644
--- a/modules/nf-core/modkit/pileup/meta.yml
+++ b/modules/nf-core/modkit/pileup/meta.yml
@@ -6,8 +6,8 @@ keywords:
   - long-read
 tools:
   - "modkit":
-      description: A bioinformatics tool for working with modified bases in Oxford Nanopore
-        sequencing data
+      description: A bioinformatics tool for working with modified bases in Oxford
+        Nanopore sequencing data
       homepage: https://github.com/nanoporetech/modkit
       documentation: https://github.com/nanoporetech/modkit
       tool_dev_url: https://github.com/nanoporetech/modkit
@@ -36,8 +36,8 @@ input:
           e.g. `[ id:'hg38' ]`
     - fasta:
         type: file
-        description: Reference sequence in FASTA format. Required for motif (e.g. CpG)
-          filtering
+        description: Reference sequence in FASTA format. Required for motif (e.g.
+          CpG) filtering
         pattern: "*.fasta"
         ontologies: []
     - fai:
@@ -52,33 +52,22 @@ input:
           e.g. `[ id:'regions' ]`
     - bed:
         type: file
-        description: BED file that will restrict threshold estimation and pileup results
-          to positions overlapping intervals in the file
+        description: BED file that will restrict threshold estimation and pileup
+          results to positions overlapping intervals in the file
         pattern: "*.bed"
         ontologies: []
 output:
-  bed:
+  bedgz:
     - - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'test', single_end:false ]`
-      - "*.bed":
+      - "*.bed.gz":
           type: file
-          description: bedMethyl output file(s)
+          description: bgzf-compressed bedMethyl output file(s)
           pattern: "*.bed"
           ontologies: []
-  bedgraph:
-    - - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. `[ id:'test', single_end:false ]`
-      - "*.bedgraph":
-          type: file
-          description: bedgraph output files
-          pattern: "*.bedgraph"
-          ontologies: []
   log:
     - - meta:
           type: map
@@ -102,3 +91,4 @@ authors:
   - "@fellen31"
 maintainers:
   - "@fellen31"
+  - "@jkh00"
diff --git a/modules/nf-core/modkit/pileup/tests/main.nf.test b/modules/nf-core/modkit/pileup/tests/main.nf.test
index 030d28ba1d1f..652b725ae556 100644
--- a/modules/nf-core/modkit/pileup/tests/main.nf.test
+++ b/modules/nf-core/modkit/pileup/tests/main.nf.test
@@ -7,10 +7,14 @@ nextflow_process {
     tag "modkit"
     tag "modkit/pileup"
     process "MODKIT_PILEUP"
+    config "./nextflow.config"
 
     test("[bam, bai], [], []") {
 
         when {
+            params {
+                module_args = ''
+            }
             process {
                 """
                 input[0] = [
@@ -36,6 +40,9 @@ nextflow_process {
     test("[bam, bai], [fasta, fai], []") {
 
         when {
+            params {
+                module_args = ''
+            }
             process {
                 """
                 input[0] = [
@@ -65,6 +72,9 @@ nextflow_process {
     test("[bam, bai], [fasta, fai], bed") {
 
         when {
+            params {
+                module_args = '--modified-bases 5mC 5hmC'
+                }
             process {
                 """
                 input[0] = [
@@ -93,11 +103,12 @@ nextflow_process {
 
     }
 
-    test("[bam, bai], [fasta, fai], bed - traditional") {
-
-        config "./nextflow.traditional.config"
+    test("[bam, bai], [fasta, fai], [], phased") {
 
         when {
+            params {
+                module_args = '--phased --modified-bases 5mC 5hmC'
+                }
             process {
                 """
                 input[0] = [
@@ -110,42 +121,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
-                input[2] = Channel.of('chr22\t0\t1000')
-                    .collectFile(name: 'chr22.bed', newLine: true)
-                    .map { file -> [ [ id:'chr22' ], file ] }
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-    test("[bam, bai], [fasta, fai], bed - traditional, HP") {
-
-        config "./nextflow.traditional_hp.config"
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id: 'test' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam.bai', checkIfExists: true)
-                ]
-                input[1] = [
-                    [ id: 'test_ref' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
-                ]
-                input[2] = Channel.of('chr22\t0\t1000')
-                    .collectFile(name: 'chr22.bed', newLine: true)
-                    .map { file -> [ [ id:'chr22' ], file ] }
+                input[2] = [[],[]]
                 """
             }
         }
@@ -159,11 +135,12 @@ nextflow_process {
 
     }
 
-    test("[bam, bai], [fasta, fai], bed - traditional, HP, bedgraph") {
-
-        config "./nextflow.traditional_hp_bedgraph.config"
+    test("[bam, bai], [fasta, fai], bed, phased") {
 
         when {
+            params {
+                module_args = '--phased --modified-bases 5mC 5hmC'
+                }
             process {
                 """
                 input[0] = [
@@ -197,6 +174,9 @@ nextflow_process {
         options "-stub"
 
         when {
+            params {
+                module_args = ''
+            }
             process {
                 """
                 input[0] = [
@@ -224,6 +204,9 @@ nextflow_process {
         options "-stub"
 
         when {
+            params {
+                module_args = ''
+            }
             process {
                 """
                 input[0] = [
@@ -251,10 +234,12 @@ nextflow_process {
     }
 
     test("[bam, bai], [fasta, fai], bed - stub") {
-
         options "-stub"
 
         when {
+            params {
+                module_args = '--modified-bases 5mC 5hmC'
+                }
             process {
                 """
                 input[0] = [
@@ -283,12 +268,14 @@ nextflow_process {
 
     }
 
-    test("[bam, bai], [fasta, fai], bed - traditional - stub") {
+    test("[bam, bai], [fasta, fai], [], phased - stub") {
 
-        config "./nextflow.traditional.config"
         options "-stub"
 
         when {
+            params {
+                module_args = '--phased --modified-bases 5mC 5hmC'
+                }
             process {
                 """
                 input[0] = [
@@ -301,43 +288,7 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 ]
-                input[2] = Channel.of('chr22\t0\t1000')
-                    .collectFile(name: 'chr22.bed', newLine: true)
-                    .map { file -> [ [ id:'chr22' ], file ] }
-                """
-            }
-        }
-
-        then {
-            assertAll (
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-    test("[bam, bai], [fasta, fai], bed - traditional, HP - stub") {
-
-        config "./nextflow.traditional_hp.config"
-        options "-stub"
-
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id: 'test' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.phased.bam.bai', checkIfExists: true)
-                ]
-                input[1] = [
-                    [ id: 'test_ref' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
-                ]
-                input[2] = Channel.of('chr22\t0\t1000')
-                    .collectFile(name: 'chr22.bed', newLine: true)
-                    .map { file -> [ [ id:'chr22' ], file ] }
+                input[2] = [[],[]]
                 """
             }
         }
@@ -351,12 +302,14 @@ nextflow_process {
 
     }
 
-    test("[bam, bai], [fasta, fai], bed - traditional, HP, bedgraph - stub") {
+    test("[bam, bai], [fasta, fai], bed, phased - stub") {
 
-        config "./nextflow.traditional_hp_bedgraph.config"
         options "-stub"
 
         when {
+            params {
+                module_args = '--phased --modified-bases 5mC 5hmC'
+                }
             process {
                 """
                 input[0] = [
diff --git a/modules/nf-core/modkit/pileup/tests/main.nf.test.snap b/modules/nf-core/modkit/pileup/tests/main.nf.test.snap
index 3ed08d3655dd..2011be7c9e03 100644
--- a/modules/nf-core/modkit/pileup/tests/main.nf.test.snap
+++ b/modules/nf-core/modkit/pileup/tests/main.nf.test.snap
@@ -7,63 +7,44 @@
                         {
                             "id": "test"
                         },
-                        "test.bed:md5,ac38ce3bed1f8aa770d1e1a9f332e170"
+                        "test.bed.gz:md5,e60263a72bb1cfdca8eb12028cfe1472"
                     ]
                 ],
                 "1": [
                     
                 ],
                 "2": [
-                    
-                ],
-                "3": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
+                    "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ],
-                "bed": [
+                "bedgz": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.bed:md5,ac38ce3bed1f8aa770d1e1a9f332e170"
+                        "test.bed.gz:md5,e60263a72bb1cfdca8eb12028cfe1472"
                     ]
-                ],
-                "bedgraph": [
-                    
                 ],
                 "log": [
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
+                    "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.04.2"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-10-29T13:33:40.323944879"
+        "timestamp": "2025-12-11T14:18:34.613472799"
     },
     "[bam, bai], [fasta, fai], [] - stub": {
         "content": [
             {
                 "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
                     [
                         {
                             "id": "test"
@@ -71,24 +52,11 @@
                         "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "3": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
-                ],
-                "bed": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                "2": [
+                    "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ],
-                "bedgraph": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                "bedgz": [
+                    
                 ],
                 "log": [
                     [
@@ -99,50 +67,46 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
+                    "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.04.2"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-10-29T13:34:25.818328219"
+        "timestamp": "2025-12-11T14:19:04.629490834"
     },
-    "[bam, bai], [fasta, fai], bed - traditional, HP, bedgraph": {
+    "[bam, bai], [fasta, fai], [], phased": {
         "content": [
             {
                 "0": [
-                    
-                ],
-                "1": [
                     [
                         {
                             "id": "test"
                         },
                         [
-                            "test_1_m_CG0_combined.bedgraph:md5,af55904c9acbafa17ff35ee3239152d0",
-                            "test_2_m_CG0_combined.bedgraph:md5,13554927fb35b71a98c0e6bcdc3945c9"
+                            "test_combined.bed.gz:md5,2ade8f1d8c163ff61698d828d0ef3fb0",
+                            "test_hp1.bed.gz:md5,e8e8c00005127492fd5610a9fa0cd098",
+                            "test_hp2.bed.gz:md5,b211935a2e88b0ebeee987abc3a622e2"
                         ]
                     ]
                 ],
-                "2": [
+                "1": [
                     
                 ],
-                "3": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
-                ],
-                "bed": [
-                    
+                "2": [
+                    "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ],
-                "bedgraph": [
+                "bedgz": [
                     [
                         {
                             "id": "test"
                         },
                         [
-                            "test_1_m_CG0_combined.bedgraph:md5,af55904c9acbafa17ff35ee3239152d0",
-                            "test_2_m_CG0_combined.bedgraph:md5,13554927fb35b71a98c0e6bcdc3945c9"
+                            "test_combined.bed.gz:md5,2ade8f1d8c163ff61698d828d0ef3fb0",
+                            "test_hp1.bed.gz:md5,e8e8c00005127492fd5610a9fa0cd098",
+                            "test_hp2.bed.gz:md5,b211935a2e88b0ebeee987abc3a622e2"
                         ]
                     ]
                 ],
@@ -150,66 +114,54 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
+                    "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.04.2"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-10-29T13:34:09.480034362"
+        "timestamp": "2025-12-11T14:18:42.290304403"
     },
-    "[bam, bai], [fasta, fai], bed - traditional, HP": {
+    "[bam, bai], [fasta, fai], [], phased - stub": {
         "content": [
             {
                 "0": [
+                    
+                ],
+                "1": [
                     [
                         {
                             "id": "test"
                         },
-                        [
-                            "test_1.bed:md5,464a9870774c340753e79639aeaf76c2",
-                            "test_2.bed:md5,118de4b653dd082d76faa8802df493eb"
-                        ]
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
-                ],
-                "1": [
-                    
                 ],
                 "2": [
-                    
+                    "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ],
-                "3": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
+                "bedgz": [
+                    
                 ],
-                "bed": [
+                "log": [
                     [
                         {
                             "id": "test"
                         },
-                        [
-                            "test_1.bed:md5,464a9870774c340753e79639aeaf76c2",
-                            "test_2.bed:md5,118de4b653dd082d76faa8802df493eb"
-                        ]
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
-                ],
-                "bedgraph": [
-                    
-                ],
-                "log": [
-                    
                 ],
                 "versions": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
+                    "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.04.2"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-10-29T13:34:01.652042889"
+        "timestamp": "2025-12-11T14:19:19.17467827"
     },
     "[bam, bai], [fasta, fai], []": {
         "content": [
@@ -219,44 +171,38 @@
                         {
                             "id": "test"
                         },
-                        "test.bed:md5,f973de342df883efc1656c82a3a3978d"
+                        "test.bed.gz:md5,f973de342df883efc1656c82a3a3978d"
                     ]
                 ],
                 "1": [
                     
                 ],
                 "2": [
-                    
-                ],
-                "3": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
+                    "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ],
-                "bed": [
+                "bedgz": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.bed:md5,f973de342df883efc1656c82a3a3978d"
+                        "test.bed.gz:md5,f973de342df883efc1656c82a3a3978d"
                     ]
-                ],
-                "bedgraph": [
-                    
                 ],
                 "log": [
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
+                    "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.04.2"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-10-29T13:33:30.820830386"
+        "timestamp": "2025-12-11T14:18:26.964056871"
     },
-    "[bam, bai], [fasta, fai], bed - traditional, HP - stub": {
+    "[bam, bai], [], []": {
         "content": [
             {
                 "0": [
@@ -264,64 +210,38 @@
                         {
                             "id": "test"
                         },
-                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.bed.gz:md5,f973de342df883efc1656c82a3a3978d"
                     ]
                 ],
                 "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "2": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ],
-                "3": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
-                ],
-                "bed": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "bedgraph": [
+                "bedgz": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.bed.gz:md5,f973de342df883efc1656c82a3a3978d"
                     ]
                 ],
                 "log": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "versions": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
+                    "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.04.2"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-10-29T13:34:51.355845894"
+        "timestamp": "2025-12-11T14:18:19.273553787"
     },
-    "[bam, bai], [], []": {
+    "[bam, bai], [fasta, fai], bed, phased": {
         "content": [
             {
                 "0": [
@@ -329,63 +249,52 @@
                         {
                             "id": "test"
                         },
-                        "test.bed:md5,f973de342df883efc1656c82a3a3978d"
+                        [
+                            "test_combined.bed.gz:md5,e60263a72bb1cfdca8eb12028cfe1472",
+                            "test_hp1.bed.gz:md5,8125fff82b626811d73c6a09c292ed31",
+                            "test_hp2.bed.gz:md5,6438ea42b16a21db197ddf73ec665685"
+                        ]
                     ]
                 ],
                 "1": [
                     
                 ],
                 "2": [
-                    
+                    "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ],
-                "3": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
-                ],
-                "bed": [
+                "bedgz": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.bed:md5,f973de342df883efc1656c82a3a3978d"
+                        [
+                            "test_combined.bed.gz:md5,e60263a72bb1cfdca8eb12028cfe1472",
+                            "test_hp1.bed.gz:md5,8125fff82b626811d73c6a09c292ed31",
+                            "test_hp2.bed.gz:md5,6438ea42b16a21db197ddf73ec665685"
+                        ]
                     ]
-                ],
-                "bedgraph": [
-                    
                 ],
                 "log": [
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
+                    "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.04.2"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-10-29T13:33:22.654774712"
+        "timestamp": "2025-12-11T14:18:50.043853179"
     },
-    "[bam, bai], [fasta, fai], bed - traditional, HP, bedgraph - stub": {
+    "[bam, bai], [fasta, fai], bed, phased - stub": {
         "content": [
             {
                 "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
                     [
                         {
                             "id": "test"
@@ -393,24 +302,11 @@
                         "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "3": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
-                ],
-                "bed": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                "2": [
+                    "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ],
-                "bedgraph": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                "bedgz": [
+                    
                 ],
                 "log": [
                     [
@@ -421,36 +317,23 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
+                    "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.04.2"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-10-29T13:35:00.477494397"
+        "timestamp": "2025-12-11T14:19:26.675056899"
     },
     "[bam, bai], [], [] - stub": {
         "content": [
             {
                 "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
                     [
                         {
                             "id": "test"
@@ -458,89 +341,11 @@
                         "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "3": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
-                ],
-                "bed": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "bedgraph": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "log": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.2"
-        },
-        "timestamp": "2025-10-29T13:34:17.906798987"
-    },
-    "[bam, bai], [fasta, fai], bed - traditional - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
                 "2": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "3": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
+                    "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ],
-                "bed": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "bedgraph": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                "bedgz": [
+                    
                 ],
                 "log": [
                     [
@@ -551,36 +356,23 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
+                    "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.04.2"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-10-29T13:34:42.242953279"
+        "timestamp": "2025-12-11T14:18:56.962234621"
     },
     "[bam, bai], [fasta, fai], bed - stub": {
         "content": [
             {
                 "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
                     [
                         {
                             "id": "test"
@@ -588,24 +380,11 @@
                         "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "3": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
-                ],
-                "bed": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                "2": [
+                    "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ],
-                "bedgraph": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bedgraph:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                "bedgz": [
+                    
                 ],
                 "log": [
                     [
@@ -616,59 +395,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.2"
-        },
-        "timestamp": "2025-10-29T13:34:34.378006702"
-    },
-    "[bam, bai], [fasta, fai], bed - traditional": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed:md5,db6333f714a8ea4aa33902404a8d4812"
-                    ]
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
-                ],
-                "bed": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.bed:md5,db6333f714a8ea4aa33902404a8d4812"
-                    ]
-                ],
-                "bedgraph": [
-                    
-                ],
-                "log": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,3c84f12b2a56c95c51a1d0b6b07fb33a"
+                    "versions.yml:md5,e6cca757b0a2786ae34eaa213d95edc3"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.04.2"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-10-29T13:33:48.061931781"
+        "timestamp": "2025-12-11T14:19:11.953321139"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/modkit/pileup/tests/nextflow.config b/modules/nf-core/modkit/pileup/tests/nextflow.config
new file mode 100644
index 000000000000..62521d0b5fe2
--- /dev/null
+++ b/modules/nf-core/modkit/pileup/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+  withName: 'MODKIT_PILEUP' {
+    ext.args = params.module_args
+  }
+}
diff --git a/modules/nf-core/modkit/pileup/tests/nextflow.traditional.config b/modules/nf-core/modkit/pileup/tests/nextflow.traditional.config
deleted file mode 100644
index 672598d51332..000000000000
--- a/modules/nf-core/modkit/pileup/tests/nextflow.traditional.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-    withName: 'MODKIT_PILEUP' {
-        ext.args = '--preset traditional'
-    }
-}
diff --git a/modules/nf-core/modkit/pileup/tests/nextflow.traditional_hp.config b/modules/nf-core/modkit/pileup/tests/nextflow.traditional_hp.config
deleted file mode 100644
index c0e0d79a5264..000000000000
--- a/modules/nf-core/modkit/pileup/tests/nextflow.traditional_hp.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-    withName: 'MODKIT_PILEUP' {
-        ext.args = '--preset traditional --partition-tag HP'
-    }
-}
diff --git a/modules/nf-core/modkit/pileup/tests/nextflow.traditional_hp_bedgraph.config b/modules/nf-core/modkit/pileup/tests/nextflow.traditional_hp_bedgraph.config
deleted file mode 100644
index 4f456dcd9fb2..000000000000
--- a/modules/nf-core/modkit/pileup/tests/nextflow.traditional_hp_bedgraph.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-    withName: 'MODKIT_PILEUP' {
-        ext.args = '--preset traditional --partition-tag HP --bedgraph'
-    }
-}