diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0fe5fccbc..6fe77b9e9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[PR #444](https://github.com/nf-core/chipseq/pull/444)] - Add empty map to ch_gff so that when provided by the user `GFFREAD` works.
 - [[#451](https://github.com/nf-core/chipseq/issues/451)] - Pass `map.single_read` to `SUBREAD_FEATURECOUNTS` as to correctly set parameter `-p`.
 - [[PR #462](https://github.com/nf-core/chipseq/pull/462)] - Updated pipeline template to [nf-core/tools 3.2.1](https://github.com/nf-core/tools/releases/tag/3.2.1)
+- [[#468](https://github.com/nf-core/chipseq/issues/468)] - Changed bigWig generation to use `-bga` option instead of `-bg` in `bedtools genomecov` for lower background levels and better IGV visualization. Users can revert to previous behavior using configuration. See [documentation](https://nf-co.re/chipseq/dev/docs/output/#normalised-bigwig-files) for details.
 
 ### Parameters
 
diff --git a/conf/modules.config b/conf/modules.config
index f53e26c16..8741b7532 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -453,19 +453,28 @@ process {
     }
 
     withName: '.*:BAM_BEDGRAPH_BIGWIG_BEDTOOLS_UCSC:BEDTOOLS_GENOMECOV' {
-        ext.args   = { (meta.single_end && params.fragment_size > 0) ? "-fs ${params.fragment_size}" : '' }
+        ext.args   = {
+            def args = []
+            // Include fragment size only for single-end data
+            if (meta.single_end && params.fragment_size > 0) {
+                args << "-fs ${params.fragment_size}"
+            }
+            // Add paired-end correction for paired-end data
+            if (!meta.single_end) {
+                args << "-pc"
+            }
+            // Use -bga instead of -bg to include zero-coverage bins
+            // This results in lower background levels and better IGV visualization
+            args << "-bga"
+            return args.join(' ')
+        }
         ext.prefix = { "${meta.id}.mLB.clN" }
         publishDir = [
             [
                 path: { "${params.outdir}/${params.aligner}/merged_library/bigwig" },
                 mode: params.publish_dir_mode,
-                pattern: "*.bigWig"
+                pattern: "*.bedGraph"
             ],
-            [
-                path: { "${params.outdir}/${params.aligner}/merged_library/bigwig/scale" },
-                mode: params.publish_dir_mode,
-                pattern: "*.txt"
-            ]
         ]
     }
 
diff --git a/docs/output.md b/docs/output.md
index 0fc9a1784..48142a681 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -147,6 +147,17 @@ The [Preseq](http://smithlabresearch.org/software/preseq/) package is aimed at p
 
 The [bigWig](https://genome.ucsc.edu/goldenpath/help/bigWig.html) format is in an indexed binary format useful for displaying dense, continuous data in Genome Browsers such as the [UCSC](https://genome.ucsc.edu/cgi-bin/hgTracks) and [IGV](http://software.broadinstitute.org/software/igv/). This mitigates the need to load the much larger BAM files for data visualisation purposes which will be slower and result in memory issues. The coverage values represented in the bigWig file can also be normalised in order to be able to compare the coverage across multiple samples - this is not possible with BAM files. The bigWig format is also supported by various bioinformatics software for downstream processing such as meta-profile plotting.
 
+> [!IMPORTANT]
+> As of v2.2.0, the pipeline uses the `-bga` option in `bedtools genomecov` instead of `-bg`. This includes zero-coverage bins in the output, resulting in lower background levels and better visualization in IGV. Users who prefer the previous behavior can override this by adding `-bg` to the `ext.args` parameter in their configuration:
+>
+> ```groovy
+> process {
+>     withName: '.*:BAM_BEDGRAPH_BIGWIG_BEDTOOLS_UCSC:BEDTOOLS_GENOMECOV' {
+>         ext.args = '-bg'
+>     }
+> }
+> ```
+
 ### ChIP-seq QC metrics
 
 <details markdown="1">
diff --git a/modules.json b/modules.json
index dc3d6bd83..3fb8d76b3 100644
--- a/modules.json
+++ b/modules.json
@@ -5,6 +5,11 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
+                    "bedtools/genomecov": {
+                        "branch": "master",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "installed_by": ["modules"]
+                    },
                     "bowtie2/align": {
                         "branch": "master",
                         "git_sha": "9bfc81874554e87740bcb3e5e07acf0a153c9ecb",
@@ -123,8 +128,9 @@
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
-                        "installed_by": ["bam_stats_samtools", "modules"]
+                        "git_sha": "e334e12a1e985adc5ffc3fc78a68be1de711de45",
+                        "installed_by": ["bam_stats_samtools", "modules"],
+                        "patch": "modules/nf-core/samtools/flagstat/samtools-flagstat.diff"
                     },
                     "samtools/idxstats": {
                         "branch": "master",
diff --git a/modules/local/bedtools_genomecov.nf b/modules/local/bedtools_genomecov.nf
deleted file mode 100644
index 23cdf4cbc..000000000
--- a/modules/local/bedtools_genomecov.nf
+++ /dev/null
@@ -1,55 +0,0 @@
-process BEDTOOLS_GENOMECOV {
-    tag "$meta.id"
-    label 'process_medium'
-
-    conda "bioconda::bedtools=2.30.0"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0':
-        'biocontainers/bedtools:2.30.0--hc088bd4_0' }"
-
-    input:
-    tuple val(meta), path(bam), path(flagstat)
-
-    output:
-    tuple val(meta), path("*.bedGraph"), emit: bedgraph
-    tuple val(meta), path("*.txt")     , emit: scale_factor
-    path "versions.yml"                , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args   = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def pe     = meta.single_end ? '' : '-pc'
-    """
-    SCALE_FACTOR=\$(grep '[0-9] mapped (' $flagstat | awk '{print 1000000/\$1}')
-    echo \$SCALE_FACTOR > ${prefix}.scale_factor.txt
-
-    bedtools \\
-        genomecov \\
-        -ibam $bam \\
-        -bg \\
-        -scale \$SCALE_FACTOR \\
-        $pe \\
-        $args \\
-        | sort -T '.' -k1,1 -k2,2n > ${prefix}.bedGraph
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
-    END_VERSIONS
-    """
-
-    stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    """
-    touch ${prefix}.bedGraph
-    touch ${prefix}.scale_factor.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/bedtools/genomecov/environment.yml b/modules/nf-core/bedtools/genomecov/environment.yml
new file mode 100644
index 000000000..45c307b0e
--- /dev/null
+++ b/modules/nf-core/bedtools/genomecov/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::bedtools=2.31.1
diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf
new file mode 100644
index 000000000..35e2ab14b
--- /dev/null
+++ b/modules/nf-core/bedtools/genomecov/main.nf
@@ -0,0 +1,77 @@
+process BEDTOOLS_GENOMECOV {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data':
+        'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b' }"
+
+    input:
+    tuple val(meta), path(intervals), val(scale)
+    path  sizes
+    val   extension
+    val   sort
+
+    output:
+    tuple val(meta), path("*.${extension}"), emit: genomecov
+    path  "versions.yml"                   , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args      = task.ext.args  ?: ''
+    def args_list = args.tokenize()
+    args += (scale > 0 && scale != 1) ? " -scale $scale" : ""
+    if (!args_list.contains('-bg') && (scale > 0 && scale != 1)) {
+        args += " -bg"
+    }
+    // Sorts output file by chromosome and position using additional options for performance and consistency
+    // See https://www.biostars.org/p/66927/ for further details
+    def buffer   = task.memory ? "--buffer-size=${task.memory.toGiga().intdiv(2)}G" : ''
+    def sort_cmd = sort ? "| LC_ALL=C sort --parallel=$task.cpus $buffer -k1,1 -k2,2n" : ''
+
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if (intervals.name =~ /\.bam/) {
+        """
+        bedtools \\
+            genomecov \\
+            -ibam $intervals \\
+            $args \\
+            $sort_cmd \\
+            > ${prefix}.${extension}
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
+        END_VERSIONS
+        """
+    } else {
+        """
+        bedtools \\
+            genomecov \\
+            -i $intervals \\
+            -g $sizes \\
+            $args \\
+            $sort_cmd \\
+            > ${prefix}.${extension}
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
+        END_VERSIONS
+        """
+    }
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch  ${prefix}.${extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/bedtools/genomecov/meta.yml b/modules/nf-core/bedtools/genomecov/meta.yml
new file mode 100644
index 000000000..9be3b3f94
--- /dev/null
+++ b/modules/nf-core/bedtools/genomecov/meta.yml
@@ -0,0 +1,76 @@
+name: bedtools_genomecov
+description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg)
+  summaries of feature coverage (e.g., aligned sequences) for a given genome.
+keywords:
+  - bed
+  - bam
+  - genomecov
+  - bedtools
+  - histogram
+tools:
+  - bedtools:
+      description: |
+        A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
+      documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
+      licence: ["MIT"]
+      identifier: biotools:bedtools
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - intervals:
+        type: file
+        description: BAM/BED/GFF/VCF
+        pattern: "*.{bam|bed|gff|vcf}"
+        ontologies: []
+    - scale:
+        type: integer
+        description: Number containing the scale factor for the output. Set to 1 to
+          disable. Setting to a value other than 1 will also get the -bg bedgraph output
+          format as this is required for this command switch
+  - sizes:
+      type: file
+      description: Tab-delimited table of chromosome names in the first column and chromosome
+        sizes in the second column
+      ontologies: []
+  - extension:
+      type: string
+      description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt",
+        ".tab", etc.) It is set arbitrarily by the user and corresponds to the file
+        format which depends on arguments.
+  - sort:
+      type: boolean
+      description: Sort the output
+output:
+  genomecov:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.${extension}":
+          type: file
+          description: Computed genome coverage file
+          pattern: "*.${extension}"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@edmundmiller"
+  - "@sruthipsuresh"
+  - "@drpatelh"
+  - "@sidorov-si"
+  - "@chris-cheshire"
+maintainers:
+  - "@edmundmiller"
+  - "@sruthipsuresh"
+  - "@drpatelh"
+  - "@sidorov-si"
+  - "@chris-cheshire"
diff --git a/modules/nf-core/bedtools/genomecov/tests/main.nf.test b/modules/nf-core/bedtools/genomecov/tests/main.nf.test
new file mode 100644
index 000000000..16a03492c
--- /dev/null
+++ b/modules/nf-core/bedtools/genomecov/tests/main.nf.test
@@ -0,0 +1,174 @@
+nextflow_process {
+    name "Test Process BEDTOOLS_GENOMECOV"
+    script "../main.nf"
+    process "BEDTOOLS_GENOMECOV"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bedtools"
+    tag "bedtools/genomecov"
+
+    test("sarscov2 - no scale") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.bam", checkIfExists: true),
+                    1
+                ]
+                // sizes
+                input[1] = []
+                // extension
+                input[2] = "txt"
+                input[3] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - dummy sizes") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.bam", checkIfExists: true),
+                    0.5
+                ]
+                // sizes
+                input[1] = file('dummy_chromosome_sizes')
+                // extension
+                input[2] = 'txt'
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - scale") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/baits.bed", checkIfExists: true),
+                    0.5
+                ]
+                // sizes
+                input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.sizes", checkIfExists: true)
+                // extension
+                input[2] = 'txt'
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - no scale - stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.bam", checkIfExists: true),
+                    1
+                ]
+                // sizes
+                input[1] = []
+                // extension
+                input[2] = "txt"
+                input[3] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - dummy sizes - stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.bam", checkIfExists: true),
+                    0.5
+                ]
+                // sizes
+                input[1] = file('dummy_chromosome_sizes')
+                // extension
+                input[2] = 'txt'
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - scale - stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/baits.bed", checkIfExists: true),
+                    0.5
+                ]
+                // sizes
+                input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.sizes", checkIfExists: true)
+                // extension
+                input[2] = 'txt'
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/bedtools/genomecov/tests/main.nf.test.snap b/modules/nf-core/bedtools/genomecov/tests/main.nf.test.snap
new file mode 100644
index 000000000..da6dbe875
--- /dev/null
+++ b/modules/nf-core/bedtools/genomecov/tests/main.nf.test.snap
@@ -0,0 +1,200 @@
+{
+    "sarscov2 - dummy sizes": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,01291b6e1beab72e046653e709eb0e10"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ],
+                "genomecov": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,01291b6e1beab72e046653e709eb0e10"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T11:59:33.898146"
+    },
+    "sarscov2 - no scale - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ],
+                "genomecov": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T11:59:52.483371"
+    },
+    "sarscov2 - scale": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,de3c59c0ea123bcdbbad27bc0a0a601e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ],
+                "genomecov": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,de3c59c0ea123bcdbbad27bc0a0a601e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T11:59:43.69501"
+    },
+    "sarscov2 - scale - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ],
+                "genomecov": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T12:00:09.930036"
+    },
+    "sarscov2 - no scale": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,66083198daca6c001d328ba9616e9b53"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ],
+                "genomecov": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,66083198daca6c001d328ba9616e9b53"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T11:59:25.448817"
+    },
+    "sarscov2 - dummy sizes - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ],
+                "genomecov": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.coverage.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,5fd44452613992a6f71f2c73d2e117f2"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-05T12:00:01.086433"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bedtools/genomecov/tests/nextflow.config b/modules/nf-core/bedtools/genomecov/tests/nextflow.config
new file mode 100644
index 000000000..bdb74ae5a
--- /dev/null
+++ b/modules/nf-core/bedtools/genomecov/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: BEDTOOLS_GENOMECOV {
+        ext.prefix = { "${meta.id}.coverage" }
+    }
+    
+}
diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml
index 68b81558e..89e12a645 100644
--- a/modules/nf-core/samtools/flagstat/environment.yml
+++ b/modules/nf-core/samtools/flagstat/environment.yml
@@ -1,8 +1,10 @@
-name: samtools_flagstat
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::samtools=1.20
-  - bioconda::htslib=1.20
+  # renovate: datasource=conda depName=bioconda/htslib
+  - bioconda::htslib=1.22.1
+  # renovate: datasource=conda depName=bioconda/samtools
+  - bioconda::samtools=1.22.1
diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf
index 754d84b73..f148f56bb 100644
--- a/modules/nf-core/samtools/flagstat/main.nf
+++ b/modules/nf-core/samtools/flagstat/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_FLAGSTAT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
-        'biocontainers/samtools:1.20--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.22.1--h96c455f_0' :
+        'biocontainers/samtools:1.22.1--h96c455f_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
@@ -18,7 +18,6 @@ process SAMTOOLS_FLAGSTAT {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     samtools \\
@@ -36,7 +35,19 @@ process SAMTOOLS_FLAGSTAT {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.flagstat
+    cat <<-END_FLAGSTAT > ${prefix}.flagstat
+    1000000 + 0 in total (QC-passed reads + QC-failed reads)
+    0 + 0 secondary
+    0 + 0 supplementary
+    0 + 0 duplicates
+    900000 + 0 mapped (90.00% : N/A)
+    1000000 + 0 paired in sequencing
+    500000 + 0 read1
+    500000 + 0 read2
+    800000 + 0 properly paired (80.00% : N/A)
+    850000 + 0 with mate mapped to a different chr
+    50000 + 0 with mate mapped to a different chr (mapQ>=5)
+    END_FLAGSTAT
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/samtools/flagstat/meta.yml b/modules/nf-core/samtools/flagstat/meta.yml
index 97991358e..ebbc15f27 100644
--- a/modules/nf-core/samtools/flagstat/meta.yml
+++ b/modules/nf-core/samtools/flagstat/meta.yml
@@ -1,5 +1,6 @@
 name: samtools_flagstat
-description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type
+description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG
+  type
 keywords:
   - stats
   - mapping
@@ -17,34 +18,42 @@ tools:
       documentation: http://www.htslib.org/doc/samtools.html
       doi: 10.1093/bioinformatics/btp352
       licence: ["MIT"]
+      identifier: biotools:samtools
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - bam:
-      type: file
-      description: BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
-  - bai:
-      type: file
-      description: Index for BAM/CRAM/SAM file
-      pattern: "*.{bai,crai,sai}"
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: BAM/CRAM/SAM file
+        pattern: "*.{bam,cram,sam}"
+        ontologies: []
+    - bai:
+        type: file
+        description: Index for BAM/CRAM/SAM file
+        pattern: "*.{bai,crai,sai}"
+        ontologies: []
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - flagstat:
-      type: file
-      description: File containing samtools flagstat output
-      pattern: "*.{flagstat}"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+  flagstat:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.flagstat":
+          type: file
+          description: File containing samtools flagstat output
+          pattern: "*.{flagstat}"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@drpatelh"
 maintainers:
diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap
index 23989c612..0a0a9b15c 100644
--- a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap
@@ -8,11 +8,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2"
+                    "versions.yml:md5,bdc0bfb2b0542580e7cd65e80d8570bc"
                 ],
                 "flagstat": [
                     [
@@ -20,19 +20,19 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2"
+                    "versions.yml:md5,bdc0bfb2b0542580e7cd65e80d8570bc"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-07-22T14:17:28.002887"
+        "timestamp": "2025-09-15T15:02:00.813612"
     },
     "BAM": {
         "content": [
@@ -47,7 +47,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2"
+                    "versions.yml:md5,bdc0bfb2b0542580e7cd65e80d8570bc"
                 ],
                 "flagstat": [
                     [
@@ -59,14 +59,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2"
+                    "versions.yml:md5,bdc0bfb2b0542580e7cd65e80d8570bc"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-07-22T14:17:13.330971"
+        "timestamp": "2025-09-15T15:01:55.232954"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/samtools/flagstat/tests/tags.yml b/modules/nf-core/samtools/flagstat/tests/tags.yml
deleted file mode 100644
index 2d2b7255e..000000000
--- a/modules/nf-core/samtools/flagstat/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-samtools/flagstat:
-  - modules/nf-core/samtools/flagstat/**
diff --git a/subworkflows/local/bam_bedgraph_bigwig_bedtools_ucsc.nf b/subworkflows/local/bam_bedgraph_bigwig_bedtools_ucsc.nf
index 271c3aa3b..1c5df00d3 100644
--- a/subworkflows/local/bam_bedgraph_bigwig_bedtools_ucsc.nf
+++ b/subworkflows/local/bam_bedgraph_bigwig_bedtools_ucsc.nf
@@ -2,7 +2,7 @@
 // Convert BAM to normalised bigWig via bedGraph using BEDTools and UCSC
 //
 
-include { BEDTOOLS_GENOMECOV    } from '../../modules/local/bedtools_genomecov'
+include { BEDTOOLS_GENOMECOV    } from '../../modules/nf-core/bedtools/genomecov/main'
 include { UCSC_BEDGRAPHTOBIGWIG } from '../../modules/nf-core/ucsc/bedgraphtobigwig/main'
 
 workflow BAM_BEDGRAPH_BIGWIG_BEDTOOLS_UCSC {
@@ -14,11 +14,40 @@ workflow BAM_BEDGRAPH_BIGWIG_BEDTOOLS_UCSC {
 
     ch_versions = Channel.empty()
 
+    //
+    // Extract scale factor from flagstat and prepare input for bedtools genomecov
+    //
+    ch_bam_scale = ch_bam_flagstat
+        .map { meta, bam, flagstat ->
+            // Parse flagstat to get mapped reads count
+            def flagstat_content = flagstat.text
+            def match = flagstat_content =~ /(\d+) \+ \d+ mapped/
+            if (match.size() == 0) {
+                // Try alternative pattern for different flagstat formats or stub files
+                match = flagstat_content =~ /(\d+) mapped/
+                if (match.size() == 0) {
+                    // For stub tests, use a default scale factor
+                    log.warn "Could not parse mapped reads from flagstat, using default scale factor of 1.0"
+                    return [meta, bam, 1.0]
+                }
+            }
+            def mapped_reads = match[0][1] as Integer
+            if (mapped_reads == 0) {
+                log.warn "Zero mapped reads found in flagstat file, using default scale factor of 1.0"
+                return [meta, bam, 1.0]
+            }
+            def scale_factor = 1000000 / mapped_reads
+            [meta, bam, scale_factor]
+        }
+
     //
     // Create bedGraph coverage track
     //
     BEDTOOLS_GENOMECOV (
-        ch_bam_flagstat
+        ch_bam_scale,
+        [],
+        'bedGraph',
+        true
     )
     ch_versions = ch_versions.mix(BEDTOOLS_GENOMECOV.out.versions.first())
 
@@ -26,15 +55,13 @@ workflow BAM_BEDGRAPH_BIGWIG_BEDTOOLS_UCSC {
     // Create bigWig coverage tracks
     //
     UCSC_BEDGRAPHTOBIGWIG (
-        BEDTOOLS_GENOMECOV.out.bedgraph,
+        BEDTOOLS_GENOMECOV.out.genomecov,
         ch_chrom_sizes
     )
     ch_versions = ch_versions.mix(UCSC_BEDGRAPHTOBIGWIG.out.versions.first())
 
     emit:
-    bedgraph     = BEDTOOLS_GENOMECOV.out.bedgraph      // channel: [ val(meta), [ bedgraph ] ]
-    scale_factor = BEDTOOLS_GENOMECOV.out.scale_factor  // channel: [ val(meta), [ txt ] ]
-
+    bedgraph     = BEDTOOLS_GENOMECOV.out.genomecov     // channel: [ val(meta), [ bedgraph ] ]
     bigwig       = UCSC_BEDGRAPHTOBIGWIG.out.bigwig     // channel: [ val(meta), [ bigwig ] ]
 
     versions     = ch_versions                          // channel: [ versions.yml ]
diff --git a/tests/.nftignore b/tests/.nftignore
index 6b5473db1..67a3a41d1 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -12,8 +12,9 @@ multiqc/multiqc_data/BETA-multiqc.parquet
 **/multiqc.log
 **/multiqc_data.json
 **/multiqc_report.html
+**/multiqc_software_versions.txt
+**/multiqc_software_versions.yaml
 multiqc/multiqc_data/multiqc_sources.txt
-multiqc/multiqc_data/multiqc_software_versions.txt
 multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
 
 # === QC TOOL OUTPUTS ===
@@ -52,6 +53,8 @@ fastqc/*_fastqc.{html,zip}
 **/*.annotatePeaks.txt
 **/*.boolean.annotatePeaks.txt
 **/macs3_peak.summary.txt
+**/macs3_annotatePeaks.summary.txt
+**/macs3_annotatePeaks.summary_mqc.tsv
 
 # Feature counting
 **/*.featureCounts.txt
diff --git a/tests/bowtie2.nf.test.snap b/tests/bowtie2.nf.test.snap
index 91c2f2284..42a9e46f5 100644
--- a/tests/bowtie2.nf.test.snap
+++ b/tests/bowtie2.nf.test.snap
@@ -14,7 +14,7 @@
                     "samtools": "1.15.1"
                 },
                 "BEDTOOLS_GENOMECOV": {
-                    "bedtools": "2.30.0"
+                    "bedtools": "2.31.1"
                 },
                 "BOWTIE2_ALIGN": {
                     "bowtie2": "2.5.2",
@@ -94,7 +94,7 @@
                     "python": "3.8.3"
                 },
                 "SAMTOOLS_FLAGSTAT": {
-                    "samtools": 1.2
+                    "samtools": "1.22.1"
                 },
                 "SAMTOOLS_IDXSTATS": {
                     "samtools": 1.2
@@ -138,19 +138,18 @@
                 "bowtie2/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam",
                 "bowtie2/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam.bai",
                 "bowtie2/merged_library/bigwig",
+                "bowtie2/merged_library/bigwig/SPT5_INPUT_REP1.mLB.clN.bedGraph",
                 "bowtie2/merged_library/bigwig/SPT5_INPUT_REP1.mLb.clN.bigWig",
+                "bowtie2/merged_library/bigwig/SPT5_INPUT_REP2.mLB.clN.bedGraph",
                 "bowtie2/merged_library/bigwig/SPT5_INPUT_REP2.mLb.clN.bigWig",
+                "bowtie2/merged_library/bigwig/SPT5_T0_REP1.mLB.clN.bedGraph",
                 "bowtie2/merged_library/bigwig/SPT5_T0_REP1.mLb.clN.bigWig",
+                "bowtie2/merged_library/bigwig/SPT5_T0_REP2.mLB.clN.bedGraph",
                 "bowtie2/merged_library/bigwig/SPT5_T0_REP2.mLb.clN.bigWig",
+                "bowtie2/merged_library/bigwig/SPT5_T15_REP1.mLB.clN.bedGraph",
                 "bowtie2/merged_library/bigwig/SPT5_T15_REP1.mLb.clN.bigWig",
+                "bowtie2/merged_library/bigwig/SPT5_T15_REP2.mLB.clN.bedGraph",
                 "bowtie2/merged_library/bigwig/SPT5_T15_REP2.mLb.clN.bigWig",
-                "bowtie2/merged_library/bigwig/scale",
-                "bowtie2/merged_library/bigwig/scale/SPT5_INPUT_REP1.mLB.clN.scale_factor.txt",
-                "bowtie2/merged_library/bigwig/scale/SPT5_INPUT_REP2.mLB.clN.scale_factor.txt",
-                "bowtie2/merged_library/bigwig/scale/SPT5_T0_REP1.mLB.clN.scale_factor.txt",
-                "bowtie2/merged_library/bigwig/scale/SPT5_T0_REP2.mLB.clN.scale_factor.txt",
-                "bowtie2/merged_library/bigwig/scale/SPT5_T15_REP1.mLB.clN.scale_factor.txt",
-                "bowtie2/merged_library/bigwig/scale/SPT5_T15_REP2.mLB.clN.scale_factor.txt",
                 "bowtie2/merged_library/deepTools",
                 "bowtie2/merged_library/deepTools/plotFingerprint",
                 "bowtie2/merged_library/deepTools/plotFingerprint/SPT5_T0_REP1.mLb.clN.plotFingerprint.pdf",
@@ -821,12 +820,12 @@
                 "trimgalore/logs/SPT5_T15_REP2_T1_2.fastq.gz_trimming_report.txt"
             ],
             [
-                "SPT5_INPUT_REP1.mLB.clN.scale_factor.txt:md5,c13c2058440720e5bf7e0aa36a5bc52e",
-                "SPT5_INPUT_REP2.mLB.clN.scale_factor.txt:md5,1073f68a937ee8fc94ba4c01fa1d3e52",
-                "SPT5_T0_REP1.mLB.clN.scale_factor.txt:md5,32e77d7bb4cbdf4c5e3a975b2ced1436",
-                "SPT5_T0_REP2.mLB.clN.scale_factor.txt:md5,b51fd58fad0860b880e3092172320a45",
-                "SPT5_T15_REP1.mLB.clN.scale_factor.txt:md5,af29e9ddc1129a747d363932dd89a11f",
-                "SPT5_T15_REP2.mLB.clN.scale_factor.txt:md5,4ec56e29c2040bba38afce216aa2ad14",
+                "SPT5_INPUT_REP1.mLB.clN.bedGraph:md5,3185527dd339a8dbcca453f97ecc0860",
+                "SPT5_INPUT_REP2.mLB.clN.bedGraph:md5,bdc6ce913840caa034fe12f11dc3f821",
+                "SPT5_T0_REP1.mLB.clN.bedGraph:md5,d50a212ac1477362e6266ebb3aa6c857",
+                "SPT5_T0_REP2.mLB.clN.bedGraph:md5,ac8049a66f664f4f52e55738bb1b8482",
+                "SPT5_T15_REP1.mLB.clN.bedGraph:md5,4dd8e393d018debbb6da34bf8a9b9c65",
+                "SPT5_T15_REP2.mLB.clN.bedGraph:md5,2b646aa9a12ee41987726118058a7e21",
                 "SPT5_T0_REP1_peaks.broadPeak:md5,2cb428b8040f21be839fd18a9a500c4f",
                 "SPT5_T0_REP1_peaks.gappedPeak:md5,4f54b0be097b5c164d401a5a8b7224cc",
                 "SPT5_T0_REP1_peaks.xls:md5,2ae150a4de266fbf8d5c6b678ec2cb0d",
@@ -857,8 +856,6 @@
                 "SPT5_T15_REP1.peak_count_mqc.tsv:md5,b26d81220921415cae94ee5e1be459e5",
                 "SPT5_T15_REP2.FRiP_mqc.tsv:md5,9cb9888d7ff1513fe2fefc6c986c5d48",
                 "SPT5_T15_REP2.peak_count_mqc.tsv:md5,c344e0089dc0455c282bb20647c65ab1",
-                "macs3_annotatePeaks.summary.txt:md5,c57b8733e402217c29a6fa6adad60879",
-                "macs3_annotatePeaks.summary_mqc.tsv:md5,dfe99c8893584f2edeeabda3acf2f1c0",
                 "SPT5_INPUT_REP1.mLb.clN.sorted.bam.flagstat:md5,5789960a9102d6f53433dcdbb9b63940",
                 "SPT5_INPUT_REP1.mLb.clN.sorted.bam.idxstats:md5,20a4ac025979cc12c3e0e6cb0bd9c839",
                 "SPT5_INPUT_REP1.mLb.clN.sorted.bam.stats:md5,c409aed714f13ee1d3dc56682a101849",
@@ -930,7 +927,6 @@
                 "multiqc_samtools_stats.yaml:md5,c1f753728b7d0d969f1de706989508ea",
                 "multiqc_samtools_stats_1.yaml:md5,ac39dbae7578b4fc13bf2753d9f2d2eb",
                 "multiqc_samtools_stats_2.yaml:md5,1bb38f88e3cf993ffd1c1eca67965f48",
-                "multiqc_software_versions.yaml:md5,d7bbeb0e2c28361dbc27a45f060d4dcd",
                 "multiqc_strand_shift_correlation.yaml:md5,87ce7906a3297afe5f5d73fe6e6d86ca",
                 "picard-1_alignment_readlength_plot.yaml:md5,ef8322029669a340b33c3efe78c5df94",
                 "picard-1_alignment_summary_Aligned_Bases.yaml:md5,0f3082cdd9d84f49658e02ab83ecd123",
@@ -973,9 +969,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.3"
         },
-        "timestamp": "2025-09-04T20:18:53.73805"
+        "timestamp": "2025-09-17T13:11:14.489285555"
     },
     "bowtie2 with stub": {
         "content": [
@@ -987,4 +983,4 @@
         },
         "timestamp": "2025-09-04T20:19:29.013062"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/chromap.nf.test.snap b/tests/chromap.nf.test.snap
index 0767d57ed..2fd20e1c5 100644
--- a/tests/chromap.nf.test.snap
+++ b/tests/chromap.nf.test.snap
@@ -14,7 +14,7 @@
                     "samtools": "1.15.1"
                 },
                 "BEDTOOLS_GENOMECOV": {
-                    "bedtools": "2.30.0"
+                    "bedtools": "2.31.1"
                 },
                 "CHROMAP_CHROMAP": {
                     "chromap": "0.2.6-r490",
@@ -93,7 +93,7 @@
                     "python": "3.8.3"
                 },
                 "SAMTOOLS_FLAGSTAT": {
-                    "samtools": 1.2
+                    "samtools": "1.22.1"
                 },
                 "SAMTOOLS_IDXSTATS": {
                     "samtools": 1.2
@@ -137,19 +137,18 @@
                 "chromap/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam",
                 "chromap/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam.bai",
                 "chromap/merged_library/bigwig",
+                "chromap/merged_library/bigwig/SPT5_INPUT_REP1.mLB.clN.bedGraph",
                 "chromap/merged_library/bigwig/SPT5_INPUT_REP1.mLb.clN.bigWig",
+                "chromap/merged_library/bigwig/SPT5_INPUT_REP2.mLB.clN.bedGraph",
                 "chromap/merged_library/bigwig/SPT5_INPUT_REP2.mLb.clN.bigWig",
+                "chromap/merged_library/bigwig/SPT5_T0_REP1.mLB.clN.bedGraph",
                 "chromap/merged_library/bigwig/SPT5_T0_REP1.mLb.clN.bigWig",
+                "chromap/merged_library/bigwig/SPT5_T0_REP2.mLB.clN.bedGraph",
                 "chromap/merged_library/bigwig/SPT5_T0_REP2.mLb.clN.bigWig",
+                "chromap/merged_library/bigwig/SPT5_T15_REP1.mLB.clN.bedGraph",
                 "chromap/merged_library/bigwig/SPT5_T15_REP1.mLb.clN.bigWig",
+                "chromap/merged_library/bigwig/SPT5_T15_REP2.mLB.clN.bedGraph",
                 "chromap/merged_library/bigwig/SPT5_T15_REP2.mLb.clN.bigWig",
-                "chromap/merged_library/bigwig/scale",
-                "chromap/merged_library/bigwig/scale/SPT5_INPUT_REP1.mLB.clN.scale_factor.txt",
-                "chromap/merged_library/bigwig/scale/SPT5_INPUT_REP2.mLB.clN.scale_factor.txt",
-                "chromap/merged_library/bigwig/scale/SPT5_T0_REP1.mLB.clN.scale_factor.txt",
-                "chromap/merged_library/bigwig/scale/SPT5_T0_REP2.mLB.clN.scale_factor.txt",
-                "chromap/merged_library/bigwig/scale/SPT5_T15_REP1.mLB.clN.scale_factor.txt",
-                "chromap/merged_library/bigwig/scale/SPT5_T15_REP2.mLB.clN.scale_factor.txt",
                 "chromap/merged_library/deepTools",
                 "chromap/merged_library/deepTools/plotFingerprint",
                 "chromap/merged_library/deepTools/plotFingerprint/SPT5_T0_REP1.mLb.clN.plotFingerprint.pdf",
@@ -823,12 +822,12 @@
                 "trimgalore/logs/SPT5_T15_REP2_T1_2.fastq.gz_trimming_report.txt"
             ],
             [
-                "SPT5_INPUT_REP1.mLB.clN.scale_factor.txt:md5,d90158cfda036c46894de528819160c6",
-                "SPT5_INPUT_REP2.mLB.clN.scale_factor.txt:md5,75f0ad2d43d1e260ebaa5f8c95c5f5d2",
-                "SPT5_T0_REP1.mLB.clN.scale_factor.txt:md5,c19971de49bf6a5bfc42aaac3e25af9e",
-                "SPT5_T0_REP2.mLB.clN.scale_factor.txt:md5,8a591dfbf664f608fe30958ebf5a6af0",
-                "SPT5_T15_REP1.mLB.clN.scale_factor.txt:md5,ed4560b5e4920a7ba50e2a7fdc296de5",
-                "SPT5_T15_REP2.mLB.clN.scale_factor.txt:md5,4fd74f09b1c744240d2d18a61e04f33d",
+                "SPT5_INPUT_REP1.mLB.clN.bedGraph:md5,e18a171dc9e71782335f2ca933da0773",
+                "SPT5_INPUT_REP2.mLB.clN.bedGraph:md5,3155c2b26db574cfccbb0388dea6617a",
+                "SPT5_T0_REP1.mLB.clN.bedGraph:md5,ede095f77136b5b49310b028dc1f3174",
+                "SPT5_T0_REP2.mLB.clN.bedGraph:md5,15b423419d7d837db69c11f911e11b27",
+                "SPT5_T15_REP1.mLB.clN.bedGraph:md5,df839f1a73260decf2510fbbe038fc04",
+                "SPT5_T15_REP2.mLB.clN.bedGraph:md5,286e56304db30e41a14e0f806b03e9b4",
                 "SPT5_T0_REP1_peaks.broadPeak:md5,cdb63f77da49a06fa941a616a1d55bc8",
                 "SPT5_T0_REP1_peaks.gappedPeak:md5,9f8bb554a7265da0b2fad9437e4d142e",
                 "SPT5_T0_REP1_peaks.xls:md5,98ddc7de15179f2089c4ca7edfd04f54",
@@ -859,8 +858,6 @@
                 "SPT5_T15_REP1.peak_count_mqc.tsv:md5,309dc93e03386dbe39172a3b708c3641",
                 "SPT5_T15_REP2.FRiP_mqc.tsv:md5,ecced7a70b355073d5fb4c11fa8832e7",
                 "SPT5_T15_REP2.peak_count_mqc.tsv:md5,f798ceafbec8d5e9a52ffebae84c71fe",
-                "macs3_annotatePeaks.summary.txt:md5,ee7d3a8e6f2b462ecb424caedef0e458",
-                "macs3_annotatePeaks.summary_mqc.tsv:md5,95a588435ff1b878000bb402a54f2e2b",
                 "SPT5_INPUT_REP1.mLb.clN.sorted.bam.flagstat:md5,e7e595088e284c9bc29cd7198bd54d2c",
                 "SPT5_INPUT_REP1.mLb.clN.sorted.bam.idxstats:md5,0096b9a233e8dda267a26d82e4a38438",
                 "SPT5_INPUT_REP1.mLb.clN.sorted.bam.stats:md5,c06240b832185dc3dd6e6978e77112e6",
@@ -933,7 +930,6 @@
                 "multiqc_samtools_stats.yaml:md5,9d9b24aceea1c649a84fa5bcb35fa6c6",
                 "multiqc_samtools_stats_1.yaml:md5,0e4875a9c9c2bfd78588a3ce04ef5caf",
                 "multiqc_samtools_stats_2.yaml:md5,383b58724b6e90ca35f568ebf6ee8919",
-                "multiqc_software_versions.yaml:md5,e584942418ca3a57c203992e8a930c7d",
                 "multiqc_strand_shift_correlation.yaml:md5,14fa8c729c885eea869abeb465ddc31c",
                 "picard-1_alignment_readlength_plot.yaml:md5,1f645e3a75839bf834fa250fb0e46d91",
                 "picard-1_alignment_summary_Aligned_Bases.yaml:md5,392fec9f38be3feea5b930209544b972",
@@ -976,9 +972,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.3"
         },
-        "timestamp": "2025-09-04T20:45:11.657006"
+        "timestamp": "2025-09-17T13:22:19.456795982"
     },
     "chromap with stub": {
         "content": [
@@ -990,4 +986,4 @@
         },
         "timestamp": "2025-09-04T20:51:25.375669"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 0b7cf4a25..9efc5a4de 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -14,7 +14,7 @@
                     "samtools": "1.15.1"
                 },
                 "BEDTOOLS_GENOMECOV": {
-                    "bedtools": "2.30.0"
+                    "bedtools": "2.31.1"
                 },
                 "BWA_INDEX": {
                     "bwa": "0.7.18-r1243-dirty"
@@ -93,7 +93,7 @@
                     "python": "3.8.3"
                 },
                 "SAMTOOLS_FLAGSTAT": {
-                    "samtools": 1.2
+                    "samtools": "1.22.1"
                 },
                 "SAMTOOLS_IDXSTATS": {
                     "samtools": 1.2
@@ -137,19 +137,18 @@
                 "bwa/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam",
                 "bwa/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam.bai",
                 "bwa/merged_library/bigwig",
+                "bwa/merged_library/bigwig/SPT5_INPUT_REP1.mLB.clN.bedGraph",
                 "bwa/merged_library/bigwig/SPT5_INPUT_REP1.mLb.clN.bigWig",
+                "bwa/merged_library/bigwig/SPT5_INPUT_REP2.mLB.clN.bedGraph",
                 "bwa/merged_library/bigwig/SPT5_INPUT_REP2.mLb.clN.bigWig",
+                "bwa/merged_library/bigwig/SPT5_T0_REP1.mLB.clN.bedGraph",
                 "bwa/merged_library/bigwig/SPT5_T0_REP1.mLb.clN.bigWig",
+                "bwa/merged_library/bigwig/SPT5_T0_REP2.mLB.clN.bedGraph",
                 "bwa/merged_library/bigwig/SPT5_T0_REP2.mLb.clN.bigWig",
+                "bwa/merged_library/bigwig/SPT5_T15_REP1.mLB.clN.bedGraph",
                 "bwa/merged_library/bigwig/SPT5_T15_REP1.mLb.clN.bigWig",
+                "bwa/merged_library/bigwig/SPT5_T15_REP2.mLB.clN.bedGraph",
                 "bwa/merged_library/bigwig/SPT5_T15_REP2.mLb.clN.bigWig",
-                "bwa/merged_library/bigwig/scale",
-                "bwa/merged_library/bigwig/scale/SPT5_INPUT_REP1.mLB.clN.scale_factor.txt",
-                "bwa/merged_library/bigwig/scale/SPT5_INPUT_REP2.mLB.clN.scale_factor.txt",
-                "bwa/merged_library/bigwig/scale/SPT5_T0_REP1.mLB.clN.scale_factor.txt",
-                "bwa/merged_library/bigwig/scale/SPT5_T0_REP2.mLB.clN.scale_factor.txt",
-                "bwa/merged_library/bigwig/scale/SPT5_T15_REP1.mLB.clN.scale_factor.txt",
-                "bwa/merged_library/bigwig/scale/SPT5_T15_REP2.mLB.clN.scale_factor.txt",
                 "bwa/merged_library/deepTools",
                 "bwa/merged_library/deepTools/plotFingerprint",
                 "bwa/merged_library/deepTools/plotFingerprint/SPT5_T0_REP1.mLb.clN.plotFingerprint.pdf",
@@ -820,12 +819,12 @@
                 "trimgalore/logs/SPT5_T15_REP2_T1_2.fastq.gz_trimming_report.txt"
             ],
             [
-                "SPT5_INPUT_REP1.mLB.clN.scale_factor.txt:md5,f7980ab61fb34b0db97506c82a41a9a3",
-                "SPT5_INPUT_REP2.mLB.clN.scale_factor.txt:md5,100f43d477b73fb415f3df3074b6426c",
-                "SPT5_T0_REP1.mLB.clN.scale_factor.txt:md5,732314d7bf803d9d802e869558375897",
-                "SPT5_T0_REP2.mLB.clN.scale_factor.txt:md5,35e93082dd1a1abe9af8c29e2a072695",
-                "SPT5_T15_REP1.mLB.clN.scale_factor.txt:md5,a9fbf5cb0740b352a167dcaeb50c8306",
-                "SPT5_T15_REP2.mLB.clN.scale_factor.txt:md5,45ec3f2793055eba8e20d481098a89a6",
+                "SPT5_INPUT_REP1.mLB.clN.bedGraph:md5,0a93a9e9e1c5c89f62050e0a2c12ca31",
+                "SPT5_INPUT_REP2.mLB.clN.bedGraph:md5,729d6cd9bd4e7a1e8ffc2f1cadc6483e",
+                "SPT5_T0_REP1.mLB.clN.bedGraph:md5,490d0e8ae9d5b64ec5ff8988bc17fc61",
+                "SPT5_T0_REP2.mLB.clN.bedGraph:md5,b6d1bb76e3dcb321d010762ca8046fa6",
+                "SPT5_T15_REP1.mLB.clN.bedGraph:md5,79aa337a5bdf210529e9e97189bc5799",
+                "SPT5_T15_REP2.mLB.clN.bedGraph:md5,e82594c663a3e25539b0c039821df8b7",
                 "SPT5_T0_REP1_peaks.broadPeak:md5,2ce0ad3163d0b2b6f0ee2d310dc3e45a",
                 "SPT5_T0_REP1_peaks.gappedPeak:md5,bdf9295567830a37a1ac36dd5b9ae634",
                 "SPT5_T0_REP1_peaks.xls:md5,f9ee78e3871b340a559f3f2397ef0768",
@@ -856,8 +855,6 @@
                 "SPT5_T15_REP1.peak_count_mqc.tsv:md5,f8ced44d005a1e3ece1afc15679f0bde",
                 "SPT5_T15_REP2.FRiP_mqc.tsv:md5,3755b3f252e26d54af798a2793b415e5",
                 "SPT5_T15_REP2.peak_count_mqc.tsv:md5,9bd63147b11a3502c709c6cf6a034d89",
-                "macs3_annotatePeaks.summary.txt:md5,6955a389d7ef581e857a19fcd6ee0998",
-                "macs3_annotatePeaks.summary_mqc.tsv:md5,85c1fbbf740527708d5f5cb9904e4f7e",
                 "SPT5_INPUT_REP1.mLb.clN.sorted.bam.flagstat:md5,f697eae4421b77f0c98467563e12a7aa",
                 "SPT5_INPUT_REP1.mLb.clN.sorted.bam.idxstats:md5,5aa769ef078f2da2c3891d77bf1398a1",
                 "SPT5_INPUT_REP1.mLb.clN.sorted.bam.stats:md5,97da194b4647a6c730333021f0fff1d3",
@@ -929,7 +926,6 @@
                 "multiqc_samtools_stats.yaml:md5,c75c982cdca8a83186d345bf66b365e0",
                 "multiqc_samtools_stats_1.yaml:md5,33531055d31307925f94f5e6460463fc",
                 "multiqc_samtools_stats_2.yaml:md5,e538f9993283ee9f2a056f279d3a8dca",
-                "multiqc_software_versions.yaml:md5,f1c1f63a7fd92a16ae9ae5659a6ff6c0",
                 "multiqc_strand_shift_correlation.yaml:md5,9a9a859ce75534a8074811ee1ca80f71",
                 "picard-1_alignment_readlength_plot.yaml:md5,fc25da4e9daefd74134d960adde48951",
                 "picard-1_alignment_summary_Aligned_Bases.yaml:md5,c174cd7cabe80cedf2c6e11b0091b7cb",
@@ -972,8 +968,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.3"
         },
-        "timestamp": "2025-09-04T21:19:39.042131"
+        "timestamp": "2025-09-17T12:59:57.48698662"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/skip_consensus_peaks.nf.test.snap b/tests/skip_consensus_peaks.nf.test.snap
index 2354afc6a..25abda32d 100644
--- a/tests/skip_consensus_peaks.nf.test.snap
+++ b/tests/skip_consensus_peaks.nf.test.snap
@@ -21,7 +21,7 @@
                     "samtools": "1.15.1"
                 },
                 "BEDTOOLS_GENOMECOV": {
-                    "bedtools": "2.30.0"
+                    "bedtools": "2.31.1"
                 },
                 "BWA_INDEX": {
                     "bwa": "0.7.18-r1243-dirty"
@@ -92,7 +92,7 @@
                     "python": "3.8.3"
                 },
                 "SAMTOOLS_FLAGSTAT": {
-                    "samtools": 1.2
+                    "samtools": "1.22.1"
                 },
                 "SAMTOOLS_IDXSTATS": {
                     "samtools": 1.2
@@ -133,19 +133,18 @@
                 "bwa/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam",
                 "bwa/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam.bai",
                 "bwa/merged_library/bigwig",
+                "bwa/merged_library/bigwig/SPT5_INPUT_REP1.mLB.clN.bedGraph",
                 "bwa/merged_library/bigwig/SPT5_INPUT_REP1.mLb.clN.bigWig",
+                "bwa/merged_library/bigwig/SPT5_INPUT_REP2.mLB.clN.bedGraph",
                 "bwa/merged_library/bigwig/SPT5_INPUT_REP2.mLb.clN.bigWig",
+                "bwa/merged_library/bigwig/SPT5_T0_REP1.mLB.clN.bedGraph",
                 "bwa/merged_library/bigwig/SPT5_T0_REP1.mLb.clN.bigWig",
+                "bwa/merged_library/bigwig/SPT5_T0_REP2.mLB.clN.bedGraph",
                 "bwa/merged_library/bigwig/SPT5_T0_REP2.mLb.clN.bigWig",
+                "bwa/merged_library/bigwig/SPT5_T15_REP1.mLB.clN.bedGraph",
                 "bwa/merged_library/bigwig/SPT5_T15_REP1.mLb.clN.bigWig",
+                "bwa/merged_library/bigwig/SPT5_T15_REP2.mLB.clN.bedGraph",
                 "bwa/merged_library/bigwig/SPT5_T15_REP2.mLb.clN.bigWig",
-                "bwa/merged_library/bigwig/scale",
-                "bwa/merged_library/bigwig/scale/SPT5_INPUT_REP1.mLB.clN.scale_factor.txt",
-                "bwa/merged_library/bigwig/scale/SPT5_INPUT_REP2.mLB.clN.scale_factor.txt",
-                "bwa/merged_library/bigwig/scale/SPT5_T0_REP1.mLB.clN.scale_factor.txt",
-                "bwa/merged_library/bigwig/scale/SPT5_T0_REP2.mLB.clN.scale_factor.txt",
-                "bwa/merged_library/bigwig/scale/SPT5_T15_REP1.mLB.clN.scale_factor.txt",
-                "bwa/merged_library/bigwig/scale/SPT5_T15_REP2.mLB.clN.scale_factor.txt",
                 "bwa/merged_library/deepTools",
                 "bwa/merged_library/deepTools/plotFingerprint",
                 "bwa/merged_library/deepTools/plotFingerprint/SPT5_T0_REP1.mLb.clN.plotFingerprint.pdf",
@@ -773,12 +772,12 @@
                 "trimgalore/logs/SPT5_T15_REP2_T1_2.fastq.gz_trimming_report.txt"
             ],
             [
-                "SPT5_INPUT_REP1.mLB.clN.scale_factor.txt:md5,f7980ab61fb34b0db97506c82a41a9a3",
-                "SPT5_INPUT_REP2.mLB.clN.scale_factor.txt:md5,100f43d477b73fb415f3df3074b6426c",
-                "SPT5_T0_REP1.mLB.clN.scale_factor.txt:md5,732314d7bf803d9d802e869558375897",
-                "SPT5_T0_REP2.mLB.clN.scale_factor.txt:md5,35e93082dd1a1abe9af8c29e2a072695",
-                "SPT5_T15_REP1.mLB.clN.scale_factor.txt:md5,a9fbf5cb0740b352a167dcaeb50c8306",
-                "SPT5_T15_REP2.mLB.clN.scale_factor.txt:md5,45ec3f2793055eba8e20d481098a89a6",
+                "SPT5_INPUT_REP1.mLB.clN.bedGraph:md5,0a93a9e9e1c5c89f62050e0a2c12ca31",
+                "SPT5_INPUT_REP2.mLB.clN.bedGraph:md5,729d6cd9bd4e7a1e8ffc2f1cadc6483e",
+                "SPT5_T0_REP1.mLB.clN.bedGraph:md5,490d0e8ae9d5b64ec5ff8988bc17fc61",
+                "SPT5_T0_REP2.mLB.clN.bedGraph:md5,b6d1bb76e3dcb321d010762ca8046fa6",
+                "SPT5_T15_REP1.mLB.clN.bedGraph:md5,79aa337a5bdf210529e9e97189bc5799",
+                "SPT5_T15_REP2.mLB.clN.bedGraph:md5,e82594c663a3e25539b0c039821df8b7",
                 "SPT5_T0_REP1_peaks.broadPeak:md5,2ce0ad3163d0b2b6f0ee2d310dc3e45a",
                 "SPT5_T0_REP1_peaks.gappedPeak:md5,bdf9295567830a37a1ac36dd5b9ae634",
                 "SPT5_T0_REP1_peaks.xls:md5,f9ee78e3871b340a559f3f2397ef0768",
@@ -799,8 +798,6 @@
                 "SPT5_T15_REP1.peak_count_mqc.tsv:md5,f8ced44d005a1e3ece1afc15679f0bde",
                 "SPT5_T15_REP2.FRiP_mqc.tsv:md5,3755b3f252e26d54af798a2793b415e5",
                 "SPT5_T15_REP2.peak_count_mqc.tsv:md5,9bd63147b11a3502c709c6cf6a034d89",
-                "macs3_annotatePeaks.summary.txt:md5,6955a389d7ef581e857a19fcd6ee0998",
-                "macs3_annotatePeaks.summary_mqc.tsv:md5,85c1fbbf740527708d5f5cb9904e4f7e",
                 "SPT5_INPUT_REP1.mLb.clN.sorted.bam.flagstat:md5,f697eae4421b77f0c98467563e12a7aa",
                 "SPT5_INPUT_REP1.mLb.clN.sorted.bam.idxstats:md5,5aa769ef078f2da2c3891d77bf1398a1",
                 "SPT5_INPUT_REP1.mLb.clN.sorted.bam.stats:md5,97da194b4647a6c730333021f0fff1d3",
@@ -870,7 +867,6 @@
                 "multiqc_samtools_stats.yaml:md5,c75c982cdca8a83186d345bf66b365e0",
                 "multiqc_samtools_stats_1.yaml:md5,33531055d31307925f94f5e6460463fc",
                 "multiqc_samtools_stats_2.yaml:md5,e538f9993283ee9f2a056f279d3a8dca",
-                "multiqc_software_versions.yaml:md5,86ec45886fd8ca55da7be24e41a70b4b",
                 "multiqc_strand_shift_correlation.yaml:md5,9a9a859ce75534a8074811ee1ca80f71",
                 "picard-1_alignment_readlength_plot.yaml:md5,fc25da4e9daefd74134d960adde48951",
                 "picard-1_alignment_summary_Aligned_Bases.yaml:md5,c174cd7cabe80cedf2c6e11b0091b7cb",
@@ -913,8 +909,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.3"
         },
-        "timestamp": "2025-09-04T21:48:44.371756"
+        "timestamp": "2025-09-17T11:32:05.17980739"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap
index 9cb6070a9..b7704fdcf 100644
--- a/tests/skip_trimming.nf.test.snap
+++ b/tests/skip_trimming.nf.test.snap
@@ -14,7 +14,7 @@
                     "samtools": "1.15.1"
                 },
                 "BEDTOOLS_GENOMECOV": {
-                    "bedtools": "2.30.0"
+                    "bedtools": "2.31.1"
                 },
                 "BWA_INDEX": {
                     "bwa": "0.7.18-r1243-dirty"
@@ -93,7 +93,7 @@
                     "python": "3.8.3"
                 },
                 "SAMTOOLS_FLAGSTAT": {
-                    "samtools": 1.2
+                    "samtools": "1.22.1"
                 },
                 "SAMTOOLS_IDXSTATS": {
                     "samtools": 1.2
@@ -133,19 +133,18 @@
                 "bwa/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam",
                 "bwa/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam.bai",
                 "bwa/merged_library/bigwig",
+                "bwa/merged_library/bigwig/SPT5_INPUT_REP1.mLB.clN.bedGraph",
                 "bwa/merged_library/bigwig/SPT5_INPUT_REP1.mLb.clN.bigWig",
+                "bwa/merged_library/bigwig/SPT5_INPUT_REP2.mLB.clN.bedGraph",
                 "bwa/merged_library/bigwig/SPT5_INPUT_REP2.mLb.clN.bigWig",
+                "bwa/merged_library/bigwig/SPT5_T0_REP1.mLB.clN.bedGraph",
                 "bwa/merged_library/bigwig/SPT5_T0_REP1.mLb.clN.bigWig",
+                "bwa/merged_library/bigwig/SPT5_T0_REP2.mLB.clN.bedGraph",
                 "bwa/merged_library/bigwig/SPT5_T0_REP2.mLb.clN.bigWig",
+                "bwa/merged_library/bigwig/SPT5_T15_REP1.mLB.clN.bedGraph",
                 "bwa/merged_library/bigwig/SPT5_T15_REP1.mLb.clN.bigWig",
+                "bwa/merged_library/bigwig/SPT5_T15_REP2.mLB.clN.bedGraph",
                 "bwa/merged_library/bigwig/SPT5_T15_REP2.mLb.clN.bigWig",
-                "bwa/merged_library/bigwig/scale",
-                "bwa/merged_library/bigwig/scale/SPT5_INPUT_REP1.mLB.clN.scale_factor.txt",
-                "bwa/merged_library/bigwig/scale/SPT5_INPUT_REP2.mLB.clN.scale_factor.txt",
-                "bwa/merged_library/bigwig/scale/SPT5_T0_REP1.mLB.clN.scale_factor.txt",
-                "bwa/merged_library/bigwig/scale/SPT5_T0_REP2.mLB.clN.scale_factor.txt",
-                "bwa/merged_library/bigwig/scale/SPT5_T15_REP1.mLB.clN.scale_factor.txt",
-                "bwa/merged_library/bigwig/scale/SPT5_T15_REP2.mLB.clN.scale_factor.txt",
                 "bwa/merged_library/deepTools",
                 "bwa/merged_library/deepTools/plotFingerprint",
                 "bwa/merged_library/deepTools/plotFingerprint/SPT5_T0_REP1.mLb.clN.plotFingerprint.pdf",
@@ -716,12 +715,12 @@
                 "pipeline_info/samplesheet.valid.csv"
             ],
             [
-                "SPT5_INPUT_REP1.mLB.clN.scale_factor.txt:md5,ae3a22800d1607ca843c86a0690fa1fb",
-                "SPT5_INPUT_REP2.mLB.clN.scale_factor.txt:md5,960da3d217480981efd502b0f2e22c9d",
-                "SPT5_T0_REP1.mLB.clN.scale_factor.txt:md5,318821adbe00ab68e6ce1ae34b9dad0a",
-                "SPT5_T0_REP2.mLB.clN.scale_factor.txt:md5,c5185c9a20651197233dc8f0e4bfb19e",
-                "SPT5_T15_REP1.mLB.clN.scale_factor.txt:md5,6eaf3ed3e9d4ede3712e82d57191bec3",
-                "SPT5_T15_REP2.mLB.clN.scale_factor.txt:md5,d2790d9a773e712436499f823724c14e",
+                "SPT5_INPUT_REP1.mLB.clN.bedGraph:md5,cd382620d1d0b392cc476acb3ee5b64c",
+                "SPT5_INPUT_REP2.mLB.clN.bedGraph:md5,adeb44bad86ea7074ac4900b8d04e1e9",
+                "SPT5_T0_REP1.mLB.clN.bedGraph:md5,9169ca9f49eb70a6d282b00d94e8bbb0",
+                "SPT5_T0_REP2.mLB.clN.bedGraph:md5,0155d0171022e7cef596facf4d4f12f7",
+                "SPT5_T15_REP1.mLB.clN.bedGraph:md5,53acbef45032a4c58766c9d220e1a761",
+                "SPT5_T15_REP2.mLB.clN.bedGraph:md5,d2fbf8ad95d452e738f36081d51e4d22",
                 "SPT5_T0_REP1_peaks.broadPeak:md5,ddf2e346dd0b80bd433c09312d31cb51",
                 "SPT5_T0_REP1_peaks.gappedPeak:md5,8369af877d77ad749cc436da6be1f681",
                 "SPT5_T0_REP1_peaks.xls:md5,a472d7386b44247005ccafb042dfb707",
@@ -752,8 +751,6 @@
                 "SPT5_T15_REP1.peak_count_mqc.tsv:md5,b09a3ab94e85d3950755da82133f0920",
                 "SPT5_T15_REP2.FRiP_mqc.tsv:md5,fedde115002f7270d0857a9df170bdcf",
                 "SPT5_T15_REP2.peak_count_mqc.tsv:md5,d79e410476850feb03c3c7c6742f59e0",
-                "macs3_annotatePeaks.summary.txt:md5,9fecf5b62c8acbd8916dafe6461ec759",
-                "macs3_annotatePeaks.summary_mqc.tsv:md5,5fb7f7788934a9ae75c3b075e9d83402",
                 "SPT5_INPUT_REP1.mLb.clN.sorted.bam.flagstat:md5,b72640ccdf91428002029db2c63c1b6f",
                 "SPT5_INPUT_REP1.mLb.clN.sorted.bam.idxstats:md5,ad58d8f8538233584fd3696b3564e0c9",
                 "SPT5_INPUT_REP1.mLb.clN.sorted.bam.stats:md5,9222fb8d6745ea71276bf89bb7a4d0c8",
@@ -810,7 +807,6 @@
                 "multiqc_samtools_stats.yaml:md5,75a45fdc0dff7bd8e983c26fa1639815",
                 "multiqc_samtools_stats_1.yaml:md5,b1a5b16e9fab0cdb3c81f7ff982e1f23",
                 "multiqc_samtools_stats_2.yaml:md5,0b4e00e27f065e7a056635818735d494",
-                "multiqc_software_versions.yaml:md5,cefd13e976daf8bc4c96170d38930069",
                 "multiqc_strand_shift_correlation.yaml:md5,d07ccd5f89fe50a98a5e6673c938187c",
                 "picard-1_alignment_readlength_plot.yaml:md5,cd5131a2c38d9dc8072c39ee191d7e0b",
                 "picard-1_alignment_summary_Aligned_Bases.yaml:md5,86717ca1bbeef507046dee670543c763",
@@ -853,9 +849,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.3"
         },
-        "timestamp": "2025-09-04T22:14:43.613805"
+        "timestamp": "2025-09-17T13:34:31.102064875"
     },
     "skip_trimming with stub": {
         "content": [
@@ -865,6 +861,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-04T22:18:55.08725"
+        "timestamp": "2025-09-05T10:38:29.093856"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/star.nf.test.snap b/tests/star.nf.test.snap
index f148ae007..5a846cf12 100644
--- a/tests/star.nf.test.snap
+++ b/tests/star.nf.test.snap
@@ -14,7 +14,7 @@
                     "samtools": "1.15.1"
                 },
                 "BEDTOOLS_GENOMECOV": {
-                    "bedtools": "2.30.0"
+                    "bedtools": "2.31.1"
                 },
                 "CUSTOM_GETCHROMSIZES": {
                     "getchromsizes": 1.2
@@ -86,7 +86,7 @@
                     "python": "3.8.3"
                 },
                 "SAMTOOLS_FLAGSTAT": {
-                    "samtools": 1.2
+                    "samtools": "1.22.1"
                 },
                 "SAMTOOLS_IDXSTATS": {
                     "samtools": 1.2
@@ -562,19 +562,18 @@
                 "star/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam",
                 "star/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam.bai",
                 "star/merged_library/bigwig",
+                "star/merged_library/bigwig/SPT5_INPUT_REP1.mLB.clN.bedGraph",
                 "star/merged_library/bigwig/SPT5_INPUT_REP1.mLb.clN.bigWig",
+                "star/merged_library/bigwig/SPT5_INPUT_REP2.mLB.clN.bedGraph",
                 "star/merged_library/bigwig/SPT5_INPUT_REP2.mLb.clN.bigWig",
+                "star/merged_library/bigwig/SPT5_T0_REP1.mLB.clN.bedGraph",
                 "star/merged_library/bigwig/SPT5_T0_REP1.mLb.clN.bigWig",
+                "star/merged_library/bigwig/SPT5_T0_REP2.mLB.clN.bedGraph",
                 "star/merged_library/bigwig/SPT5_T0_REP2.mLb.clN.bigWig",
+                "star/merged_library/bigwig/SPT5_T15_REP1.mLB.clN.bedGraph",
                 "star/merged_library/bigwig/SPT5_T15_REP1.mLb.clN.bigWig",
+                "star/merged_library/bigwig/SPT5_T15_REP2.mLB.clN.bedGraph",
                 "star/merged_library/bigwig/SPT5_T15_REP2.mLb.clN.bigWig",
-                "star/merged_library/bigwig/scale",
-                "star/merged_library/bigwig/scale/SPT5_INPUT_REP1.mLB.clN.scale_factor.txt",
-                "star/merged_library/bigwig/scale/SPT5_INPUT_REP2.mLB.clN.scale_factor.txt",
-                "star/merged_library/bigwig/scale/SPT5_T0_REP1.mLB.clN.scale_factor.txt",
-                "star/merged_library/bigwig/scale/SPT5_T0_REP2.mLB.clN.scale_factor.txt",
-                "star/merged_library/bigwig/scale/SPT5_T15_REP1.mLB.clN.scale_factor.txt",
-                "star/merged_library/bigwig/scale/SPT5_T15_REP2.mLB.clN.scale_factor.txt",
                 "star/merged_library/deepTools",
                 "star/merged_library/deepTools/plotFingerprint",
                 "star/merged_library/deepTools/plotFingerprint/SPT5_T0_REP1.mLb.clN.plotFingerprint.pdf",
@@ -898,7 +897,6 @@
                 "multiqc_samtools_stats.yaml:md5,e6c2a7caf8babb26af5fee07f7a7090d",
                 "multiqc_samtools_stats_1.yaml:md5,ead1283548e02f0f6dc7fab553959dfb",
                 "multiqc_samtools_stats_2.yaml:md5,abdd0b1a5a908fddb05c6c4a4ad2bd4e",
-                "multiqc_software_versions.yaml:md5,8e4f4b3a81ca06aefe4a4d4f6fdc04e4",
                 "multiqc_strand_shift_correlation.yaml:md5,b3300505766eb423380ba48bd8161720",
                 "picard-1_alignment_readlength_plot.yaml:md5,9f96961103f78afcc5e42ab1818d1646",
                 "picard-1_alignment_summary_Aligned_Bases.yaml:md5,64a9971ff2cb4560639a455283127f8c",
@@ -943,12 +941,12 @@
                 "SPT5_T0_REP2_T1.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "SPT5_T15_REP1_T1.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "SPT5_T15_REP2_T1.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "SPT5_INPUT_REP1.mLB.clN.scale_factor.txt:md5,daaed62096aa621ff68cc39909ce110e",
-                "SPT5_INPUT_REP2.mLB.clN.scale_factor.txt:md5,84a5197cfe7335b9c1912992dfa6f7da",
-                "SPT5_T0_REP1.mLB.clN.scale_factor.txt:md5,c345ee159ab3e91f0215e7e51bceee31",
-                "SPT5_T0_REP2.mLB.clN.scale_factor.txt:md5,8668f3a8abfc6b65363e4a9439fe59fb",
-                "SPT5_T15_REP1.mLB.clN.scale_factor.txt:md5,8af6ff0052b0c7e90508c28dfdd8b92f",
-                "SPT5_T15_REP2.mLB.clN.scale_factor.txt:md5,e84dbf9f66668ef6f460173e5d6c1588",
+                "SPT5_INPUT_REP1.mLB.clN.bedGraph:md5,27ec9b3ea78e51a6747f10e87fb28e75",
+                "SPT5_INPUT_REP2.mLB.clN.bedGraph:md5,0f5eaf0b37296d9a39240163d428d3da",
+                "SPT5_T0_REP1.mLB.clN.bedGraph:md5,596f22b3ea72ada620869624f0341d84",
+                "SPT5_T0_REP2.mLB.clN.bedGraph:md5,4e3c18d3683f4e20d9cac82084d517cf",
+                "SPT5_T15_REP1.mLB.clN.bedGraph:md5,4bc854fd64d47ef4e61204ffedbc93eb",
+                "SPT5_T15_REP2.mLB.clN.bedGraph:md5,57953f83dbbbff0b256193835448c73d",
                 "SPT5_T0_REP1_peaks.broadPeak:md5,e1fe25b8c90c7c95d2a51928e85bdd83",
                 "SPT5_T0_REP1_peaks.gappedPeak:md5,760698ecb506b316817d968900833238",
                 "SPT5_T0_REP1_peaks.xls:md5,dc2b6465f427257b51ccd1b111d2eefe",
@@ -979,8 +977,6 @@
                 "SPT5_T15_REP1.peak_count_mqc.tsv:md5,a410be995115d5395bddad58356c9317",
                 "SPT5_T15_REP2.FRiP_mqc.tsv:md5,9c4b15116ad398fbfa7d62772ef8c171",
                 "SPT5_T15_REP2.peak_count_mqc.tsv:md5,7cf04251bb45fa69667e008221cf9574",
-                "macs3_annotatePeaks.summary.txt:md5,b2d5ade5eb5c5a2d98b4929aabbe960b",
-                "macs3_annotatePeaks.summary_mqc.tsv:md5,504c12fa2bdbaf184236fd2dcfda2270",
                 "SPT5_INPUT_REP1.mLb.clN.sorted.bam.flagstat:md5,eab2d557e005abce4fca95f1393d6821",
                 "SPT5_INPUT_REP1.mLb.clN.sorted.bam.idxstats:md5,c35a726fcffa4b526325847aab379cc5",
                 "SPT5_INPUT_REP1.mLb.clN.sorted.bam.stats:md5,5f5db9f3088da6e56584461901877c32",
@@ -1003,9 +999,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.3"
         },
-        "timestamp": "2025-09-04T22:39:17.079904"
+        "timestamp": "2025-09-17T13:50:40.996684387"
     },
     "star with stub": {
         "content": [
@@ -1017,4 +1013,4 @@
         },
         "timestamp": "2025-09-04T22:40:58.444452"
     }
-}
\ No newline at end of file
+}