diff --git a/modules.json b/modules.json
index c2e28076ab..1b00aac7e4 100644
--- a/modules.json
+++ b/modules.json
@@ -392,7 +392,7 @@
                     },
                     "samtools/mpileup": {
                         "branch": "master",
-                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
+                        "git_sha": "13e7d1046922381df90cd8fe9bee8c3e57ae8457",
                         "installed_by": ["modules"]
                     },
                     "samtools/stats": {
diff --git a/modules/local/create_intervals_bed/main.nf b/modules/local/create_intervals_bed/main.nf
index 2bf36190e4..ad42e6ad53 100644
--- a/modules/local/create_intervals_bed/main.nf
+++ b/modules/local/create_intervals_bed/main.nf
@@ -79,7 +79,7 @@ process CREATE_INTERVALS_BED {
     // def prefix_basename = prefix.substring(0, prefix.lastIndexOf("."))
 
     """
-    touch ${prefix}.bed
+    touch ${prefix}.stub.bed
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/samtools/mpileup/main.nf b/modules/nf-core/samtools/mpileup/main.nf
index a45c6045b1..925c8244e0 100644
--- a/modules/nf-core/samtools/mpileup/main.nf
+++ b/modules/nf-core/samtools/mpileup/main.nf
@@ -6,13 +6,14 @@ process SAMTOOLS_MPILEUP {
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
         'biocontainers/samtools:1.21--h50ea8bc_0' }"
+
     input:
     tuple val(meta), path(input), path(intervals)
     path  fasta
 
     output:
     tuple val(meta), path("*.mpileup.gz"), emit: mpileup
-    path  "versions.yml"                           , emit: versions
+    path  "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -20,15 +21,29 @@ process SAMTOOLS_MPILEUP {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def intervals = intervals ? "-l ${intervals}" : ""
+    def intervals_arg = intervals ? "-l ${intervals}" : ""
     """
     samtools mpileup \\
         --fasta-ref $fasta \\
         --output ${prefix}.mpileup \\
         $args \\
-        $intervals \\
+        $intervals_arg \\
         $input
     bgzip ${prefix}.mpileup
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def intervals_arg = intervals ? "-l ${intervals}" : ""
+    """
+    touch ${prefix}.mpileup.gz
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
diff --git a/tests/variant_calling_controlfreec.nf.test b/tests/variant_calling_controlfreec.nf.test
index 163cdde918..934cf97c4c 100644
--- a/tests/variant_calling_controlfreec.nf.test
+++ b/tests/variant_calling_controlfreec.nf.test
@@ -94,4 +94,94 @@ nextflow_pipeline {
             )
         }
     }
+
+    test("Run with profile test | --tools controlfreec --no_intervals | somatic | stub") {
+        options "-stub"
+        when {
+            params {
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+                chr_dir = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz'
+                dbsnp = params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz'
+                dbsnp_tbi = params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi'
+                fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta'
+                fasta_fai = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai'
+                input = "${projectDir}/tests/csv/3.0/recalibrated_somatic.csv"
+                no_intervals = true
+                outdir = "$outputDir"
+                step = "variant_calling"
+                tools = 'controlfreec'
+                wes = true
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // cram_files: All cram files
+            def cram_files  = getAllFilesFromDir(params.outdir, include: ['**/*.cram'])
+            def fasta       = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta'
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path,
+                    // All cram files
+                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] }
+                ).match() }
+            )
+        }
+    }
+
+    test("Run with profile test | --tools controlfreec | tumoronly | stub") {
+        options "-stub"
+        when {
+            params {
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+                chr_dir = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz'
+                dbsnp = params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz'
+                dbsnp_tbi = params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi'
+                fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta'
+                fasta_fai = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai'
+                input = "${projectDir}/tests/csv/3.0/recalibrated_tumoronly.csv"
+                intervals = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed'
+                outdir = "$outputDir"
+                step = "variant_calling"
+                tools = 'controlfreec'
+                wes = true
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // cram_files: All cram files
+            def cram_files  = getAllFilesFromDir(params.outdir, include: ['**/*.cram'])
+            def fasta       = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta'
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path,
+                    // All cram files
+                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] }
+                ).match() }
+            )
+        }
+    }
 }
diff --git a/tests/variant_calling_controlfreec.nf.test.snap b/tests/variant_calling_controlfreec.nf.test.snap
index 8f3ce080f8..5fe28a6577 100644
--- a/tests/variant_calling_controlfreec.nf.test.snap
+++ b/tests/variant_calling_controlfreec.nf.test.snap
@@ -1,4 +1,284 @@
 {
+    "Run with profile test | --tools controlfreec --no_intervals | somatic": {
+        "content": [
+            8,
+            {
+                "SAMTOOLS_MPILEUP": {
+                    "samtools": 1.21
+                },
+                "Workflow": {
+                    "nf-core/sarek": "v3.5.0dev"
+                }
+            },
+            [
+                "csv",
+                "no_intervals.bed",
+                "no_intervals.bed.gz",
+                "no_intervals.bed.gz.tbi",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+                "reference",
+                "reports",
+                "reports/mosdepth",
+                "reports/mosdepth/sample3",
+                "reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt",
+                "reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt",
+                "reports/mosdepth/sample3/sample3.recal.per-base.bed.gz",
+                "reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi",
+                "reports/mosdepth/sample4",
+                "reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt",
+                "reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt",
+                "reports/mosdepth/sample4/sample4.recal.per-base.bed.gz",
+                "reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi",
+                "reports/samtools",
+                "reports/samtools/sample3",
+                "reports/samtools/sample3/sample3.recal.cram.stats",
+                "reports/samtools/sample4",
+                "reports/samtools/sample4/sample4.recal.cram.stats"
+            ],
+            [
+                "sample3.recal.mosdepth.global.dist.txt:md5,69e29702ef01fd8f6c7a5468fc35a16a",
+                "sample3.recal.mosdepth.summary.txt:md5,d2775eb102acc5950f7f53883dcb503d",
+                "sample3.recal.per-base.bed.gz:md5,297f96648928d0ca5184223fb9941e7c",
+                "sample3.recal.per-base.bed.gz.csi:md5,519cc5bf84da0d71b87a88c76f83194e",
+                "sample4.recal.mosdepth.global.dist.txt:md5,f2dcd00a64947c49e8e4b93c2f4fbf27",
+                "sample4.recal.mosdepth.summary.txt:md5,0a7300e56eda6fba7c7564f00aa000f0",
+                "sample4.recal.per-base.bed.gz:md5,39a1bc436aa8546c26faedbe94cb676c",
+                "sample4.recal.per-base.bed.gz.csi:md5,aaa7bed9e7ef873b23bca249b8b58eb9",
+                "sample3.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
+                "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03"
+            ],
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-10T09:46:49.516904333"
+    },
+    "Run with profile test | --tools controlfreec | tumoronly": {
+        "content": [
+            11,
+            {
+                "FREEC2BED": {
+                    "controlfreec": "11.6b"
+                },
+                "FREEC2CIRCOS": {
+                    "controlfreec": "11.6b"
+                },
+                "FREEC_TUMORONLY": {
+                    "controlfreec": "11.6b"
+                },
+                "SAMTOOLS_MPILEUP": {
+                    "samtools": 1.21
+                },
+                "Workflow": {
+                    "nf-core/sarek": "v3.5.0dev"
+                }
+            },
+            [
+                "csv",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+                "reference",
+                "reports",
+                "reports/mosdepth",
+                "reports/mosdepth/sample2",
+                "reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt",
+                "reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt",
+                "reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt",
+                "reports/mosdepth/sample2/sample2.recal.per-base.bed.gz",
+                "reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi",
+                "reports/mosdepth/sample2/sample2.recal.regions.bed.gz",
+                "reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi",
+                "reports/samtools",
+                "reports/samtools/sample2",
+                "reports/samtools/sample2/sample2.recal.cram.stats",
+                "variant_calling",
+                "variant_calling/controlfreec",
+                "variant_calling/controlfreec/sample2",
+                "variant_calling/controlfreec/sample2/config.txt",
+                "variant_calling/controlfreec/sample2/sample2.bed",
+                "variant_calling/controlfreec/sample2/sample2.circos.txt",
+                "variant_calling/controlfreec/sample2/sample2.p.value.txt",
+                "variant_calling/controlfreec/sample2/sample2.tumor.mpileup.gz_BAF.txt",
+                "variant_calling/controlfreec/sample2/sample2.tumor.mpileup.gz_CNVs",
+                "variant_calling/controlfreec/sample2/sample2.tumor.mpileup.gz_info.txt",
+                "variant_calling/controlfreec/sample2/sample2.tumor.mpileup.gz_ratio.BedGraph",
+                "variant_calling/controlfreec/sample2/sample2.tumor.mpileup.gz_ratio.txt",
+                "variant_calling/controlfreec/sample2/sample2.tumor.mpileup.gz_sample.cpn"
+            ],
+            [
+                "sample2.recal.mosdepth.global.dist.txt:md5,f2dcd00a64947c49e8e4b93c2f4fbf27",
+                "sample2.recal.mosdepth.region.dist.txt:md5,39005ffaac22871ffaaf19656fe69c5b",
+                "sample2.recal.mosdepth.summary.txt:md5,68d4b98f17361fddf73052ead34fa370",
+                "sample2.recal.per-base.bed.gz:md5,39a1bc436aa8546c26faedbe94cb676c",
+                "sample2.recal.per-base.bed.gz.csi:md5,aaa7bed9e7ef873b23bca249b8b58eb9",
+                "sample2.recal.regions.bed.gz:md5,b7561bc56a955f7db0f11e67e2ec0386",
+                "sample2.recal.regions.bed.gz.csi:md5,538cb5d244411a670a4b041691f8825b",
+                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
+                "sample2.bed:md5,480eb7f5467f7496c0c96da382563fed",
+                "sample2.circos.txt:md5,83b313af17990145404e4a98d59b98b2",
+                "sample2.p.value.txt:md5,a5baccb0b7e35c93848fc7d3f586bc98",
+                "sample2.tumor.mpileup.gz_BAF.txt:md5,c7f0d18d66988fe2938a8f5691772bcb",
+                "sample2.tumor.mpileup.gz_CNVs:md5,29d1456ae74a2a07c87dfae5dd1bf4a9",
+                "sample2.tumor.mpileup.gz_info.txt:md5,da8f48d99b48e85c2aac89f143e20e5b",
+                "sample2.tumor.mpileup.gz_ratio.BedGraph:md5,869661a75d7ec23f6cf1192b4c6f8512",
+                "sample2.tumor.mpileup.gz_ratio.txt:md5,cc7f5e1ae29196cc1f4052eebc03b65c",
+                "sample2.tumor.mpileup.gz_sample.cpn:md5,1b53d73a6f04b29c9693ecbffe8dc3a2"
+            ],
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-10T09:55:52.492595419"
+    },
+    "Run with profile test | --tools controlfreec --no_intervals | somatic | stub": {
+        "content": [
+            14,
+            {
+                "ASSESS_SIGNIFICANCE": {
+                    "controlfreec": 11.6
+                },
+                "FREEC2BED": {
+                    "controlfreec": "11.6b"
+                },
+                "FREEC2CIRCOS": {
+                    "controlfreec": "11.6b"
+                },
+                "FREEC_SOMATIC": {
+                    "controlfreec": "11.6b"
+                },
+                "MAKEGRAPH2": {
+                    "controlfreec": "11.6b"
+                },
+                "SAMTOOLS_MPILEUP": {
+                    "samtools": 1.21
+                },
+                "Workflow": {
+                    "nf-core/sarek": "v3.5.0dev"
+                }
+            },
+            [
+                "csv",
+                "multiqc",
+                "multiqc/multiqc_data",
+                "multiqc/multiqc_plots",
+                "multiqc/multiqc_report.html",
+                "no_intervals.bed",
+                "no_intervals.bed.gz",
+                "no_intervals.bed.gz.tbi",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+                "reference",
+                "reports",
+                "reports/mosdepth",
+                "reports/mosdepth/sample3",
+                "reports/mosdepth/sample3/sample3.recal.global.dist.txt",
+                "reports/mosdepth/sample3/sample3.recal.per-base.bed.gz",
+                "reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi",
+                "reports/mosdepth/sample3/sample3.recal.per-base.d4",
+                "reports/mosdepth/sample3/sample3.recal.quantized.bed.gz",
+                "reports/mosdepth/sample3/sample3.recal.quantized.bed.gz.csi",
+                "reports/mosdepth/sample3/sample3.recal.region.dist.txt",
+                "reports/mosdepth/sample3/sample3.recal.regions.bed.gz",
+                "reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi",
+                "reports/mosdepth/sample3/sample3.recal.summary.txt",
+                "reports/mosdepth/sample3/sample3.recal.thresholds.bed.gz",
+                "reports/mosdepth/sample3/sample3.recal.thresholds.bed.gz.csi",
+                "reports/mosdepth/sample4",
+                "reports/mosdepth/sample4/sample4.recal.global.dist.txt",
+                "reports/mosdepth/sample4/sample4.recal.per-base.bed.gz",
+                "reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi",
+                "reports/mosdepth/sample4/sample4.recal.per-base.d4",
+                "reports/mosdepth/sample4/sample4.recal.quantized.bed.gz",
+                "reports/mosdepth/sample4/sample4.recal.quantized.bed.gz.csi",
+                "reports/mosdepth/sample4/sample4.recal.region.dist.txt",
+                "reports/mosdepth/sample4/sample4.recal.regions.bed.gz",
+                "reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi",
+                "reports/mosdepth/sample4/sample4.recal.summary.txt",
+                "reports/mosdepth/sample4/sample4.recal.thresholds.bed.gz",
+                "reports/mosdepth/sample4/sample4.recal.thresholds.bed.gz.csi",
+                "reports/samtools",
+                "reports/samtools/sample3",
+                "reports/samtools/sample3/sample3.recal.cram.stats",
+                "reports/samtools/sample4",
+                "reports/samtools/sample4/sample4.recal.cram.stats",
+                "variant_calling",
+                "variant_calling/controlfreec",
+                "variant_calling/controlfreec/sample4_vs_sample3",
+                "variant_calling/controlfreec/sample4_vs_sample3/GC_profile.sample4_vs_sample3.cpn",
+                "variant_calling/controlfreec/sample4_vs_sample3/config.txt",
+                "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.bed",
+                "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.circos.txt",
+                "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.p.value.txt",
+                "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_BAF.png",
+                "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_BAF.txt",
+                "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_CNVs",
+                "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_info.txt",
+                "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.BedGraph",
+                "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.log2.png",
+                "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.png",
+                "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.txt",
+                "variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_sample.cpn"
+            ],
+            [
+                "sample3.recal.global.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample3.recal.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "sample3.recal.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample3.recal.per-base.d4:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample3.recal.quantized.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "sample3.recal.quantized.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample3.recal.region.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample3.recal.regions.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "sample3.recal.regions.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample3.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample3.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "sample3.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4.recal.global.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4.recal.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "sample4.recal.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4.recal.per-base.d4:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4.recal.quantized.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "sample4.recal.quantized.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4.recal.region.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4.recal.regions.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "sample4.recal.regions.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "sample4.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample3.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "GC_profile.sample4_vs_sample3.cpn:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4_vs_sample3.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4_vs_sample3.circos.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4_vs_sample3.p.value.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4_vs_sample3_BAF.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4_vs_sample3_BAF.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4_vs_sample3_CNVs:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4_vs_sample3_info.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4_vs_sample3_ratio.BedGraph:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4_vs_sample3_ratio.log2.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4_vs_sample3_ratio.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4_vs_sample3_ratio.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample4_vs_sample3_sample.cpn:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-10T10:14:32.674251218"
+    },
     "Run with profile test | --tools controlfreec | somatic": {
         "content": [
             16,
@@ -112,7 +392,7 @@
                 "sample4_vs_sample3_ratio.png:md5,6ac35ba93babc019c2d863f7e06b49b1"
             ],
             [
-
+                
             ]
         ],
         "meta": {
@@ -121,6 +401,115 @@
         },
         "timestamp": "2024-11-14T16:46:15.872055864"
     },
+    "Run with profile test | --tools controlfreec | tumoronly | stub": {
+        "content": [
+            13,
+            {
+                "ASSESS_SIGNIFICANCE": {
+                    "controlfreec": 11.6
+                },
+                "FREEC2BED": {
+                    "controlfreec": "11.6b"
+                },
+                "FREEC2CIRCOS": {
+                    "controlfreec": "11.6b"
+                },
+                "FREEC_TUMORONLY": {
+                    "controlfreec": "11.6b"
+                },
+                "MAKEGRAPH2": {
+                    "controlfreec": "11.6b"
+                },
+                "SAMTOOLS_MPILEUP": {
+                    "samtools": 1.21
+                },
+                "Workflow": {
+                    "nf-core/sarek": "v3.5.0dev"
+                }
+            },
+            [
+                "csv",
+                "multiqc",
+                "multiqc/multiqc_data",
+                "multiqc/multiqc_plots",
+                "multiqc/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+                "reference",
+                "reports",
+                "reports/mosdepth",
+                "reports/mosdepth/sample2",
+                "reports/mosdepth/sample2/sample2.recal.global.dist.txt",
+                "reports/mosdepth/sample2/sample2.recal.per-base.bed.gz",
+                "reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi",
+                "reports/mosdepth/sample2/sample2.recal.per-base.d4",
+                "reports/mosdepth/sample2/sample2.recal.quantized.bed.gz",
+                "reports/mosdepth/sample2/sample2.recal.quantized.bed.gz.csi",
+                "reports/mosdepth/sample2/sample2.recal.region.dist.txt",
+                "reports/mosdepth/sample2/sample2.recal.regions.bed.gz",
+                "reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi",
+                "reports/mosdepth/sample2/sample2.recal.summary.txt",
+                "reports/mosdepth/sample2/sample2.recal.thresholds.bed.gz",
+                "reports/mosdepth/sample2/sample2.recal.thresholds.bed.gz.csi",
+                "reports/samtools",
+                "reports/samtools/sample2",
+                "reports/samtools/sample2/sample2.recal.cram.stats",
+                "variant_calling",
+                "variant_calling/controlfreec",
+                "variant_calling/controlfreec/sample2",
+                "variant_calling/controlfreec/sample2/GC_profile.sample2.cpn",
+                "variant_calling/controlfreec/sample2/config.txt",
+                "variant_calling/controlfreec/sample2/sample2.bed",
+                "variant_calling/controlfreec/sample2/sample2.circos.txt",
+                "variant_calling/controlfreec/sample2/sample2.p.value.txt",
+                "variant_calling/controlfreec/sample2/sample2_BAF.png",
+                "variant_calling/controlfreec/sample2/sample2_BAF.txt",
+                "variant_calling/controlfreec/sample2/sample2_CNVs",
+                "variant_calling/controlfreec/sample2/sample2_info.txt",
+                "variant_calling/controlfreec/sample2/sample2_ratio.BedGraph",
+                "variant_calling/controlfreec/sample2/sample2_ratio.log2.png",
+                "variant_calling/controlfreec/sample2/sample2_ratio.png",
+                "variant_calling/controlfreec/sample2/sample2_ratio.txt",
+                "variant_calling/controlfreec/sample2/sample2_sample.cpn"
+            ],
+            [
+                "sample2.recal.global.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.recal.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "sample2.recal.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.recal.per-base.d4:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.recal.quantized.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "sample2.recal.quantized.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.recal.region.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.recal.regions.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "sample2.recal.regions.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "sample2.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "GC_profile.sample2.cpn:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.circos.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.p.value.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2_BAF.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2_BAF.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2_CNVs:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2_info.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2_ratio.BedGraph:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2_ratio.log2.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2_ratio.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2_ratio.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2_sample.cpn:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-10T10:33:44.36063821"
+    },
     "Run with profile test | --tools controlfreec --no_intervals | tumoronly": {
         "content": [
             11,
@@ -211,7 +600,7 @@
                 "sample2_ratio.png:md5,47fce58116c63d6cad34f80575e34e43"
             ],
             [
-
+                
             ]
         ],
         "meta": {
@@ -220,4 +609,4 @@
         },
         "timestamp": "2024-11-14T16:47:40.762784422"
     }
-}
+}
\ No newline at end of file