diff --git a/modules/nf-core/qualimap/bamqc/main.nf b/modules/nf-core/qualimap/bamqc/main.nf
index 1696fd57184c..7716f61b911b 100644
--- a/modules/nf-core/qualimap/bamqc/main.nf
+++ b/modules/nf-core/qualimap/bamqc/main.nf
@@ -24,37 +24,30 @@ process QUALIMAP_BAMQC {
 
     def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs'
     def memory = (task.memory.mega*0.8).intValue() + 'M'
-    def regions = gff ? "--gff $gff" : ''
+    def regions = gff ? "--gff ${gff}" : ''
 
-    def strandedness = 'non-strand-specific'
-    if (meta.strandedness == 'forward') {
-        strandedness = 'strand-specific-forward'
-    } else if (meta.strandedness == 'reverse') {
-        strandedness = 'strand-specific-reverse'
-    }
     """
     unset DISPLAY
     mkdir -p tmp
     export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp
     qualimap \\
-        --java-mem-size=$memory \\
+        --java-mem-size=${memory} \\
         bamqc \\
-        $args \\
-        -bam $bam \\
-        $regions \\
-        -p $strandedness \\
-        $collect_pairs \\
-        -outdir $prefix \\
-        -nt $task.cpus
+        ${args} \\
+        -bam ${bam} \\
+        ${regions} \\
+        ${collect_pairs} \\
+        -outdir ${prefix} \\
+        -nt ${task.cpus}
     """
 
     stub:
-    prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
-    mkdir -p $prefix/css
-    mkdir $prefix/images_qualimapReport
-    mkdir $prefix/raw_data_qualimapReport
-    cd $prefix/css
+    mkdir -p ${prefix}/css
+    mkdir ${prefix}/images_qualimapReport
+    mkdir ${prefix}/raw_data_qualimapReport
+    cd ${prefix}/css
     touch agogo.css
     touch basic.css
     touch bgtop.png
diff --git a/modules/nf-core/qualimap/bamqc/meta.yml b/modules/nf-core/qualimap/bamqc/meta.yml
index e93a9913702d..c1cc91555d75 100644
--- a/modules/nf-core/qualimap/bamqc/meta.yml
+++ b/modules/nf-core/qualimap/bamqc/meta.yml
@@ -14,7 +14,8 @@ tools:
       homepage: http://qualimap.bioinfo.cipf.es/
       documentation: http://qualimap.conesalab.org/doc_html/index.html
       doi: 10.1093/bioinformatics/bts503
-      licence: ["GPL-2.0-only"]
+      licence:
+        - "GPL-2.0-only"
       identifier: biotools:qualimap
 input:
   - - meta:
diff --git a/modules/nf-core/qualimap/bamqc/tests/main.nf.test b/modules/nf-core/qualimap/bamqc/tests/main.nf.test
index 7deb086dd5ef..ed1eac0e0027 100644
--- a/modules/nf-core/qualimap/bamqc/tests/main.nf.test
+++ b/modules/nf-core/qualimap/bamqc/tests/main.nf.test
@@ -12,13 +12,11 @@ nextflow_process {
         when {
             process {
                 """
-                gff = []
-
-                input[0] = Channel.of([
-                    [ id:'test', single_end:false ], // meta map
+                input[0] = [
+                    [ id:'test', single_end:false ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
-                ])
-                input[1] = gff
+                ]
+                input[1] = []
                 """
             }
         }
@@ -26,11 +24,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(
-                    file("${process.out.results[0][1]}/qualimapReport.html").name,
-                    path("${process.out.results[0][1]}/genome_results.txt"),
-                    process.out.findAll {key, value -> key.startsWith("versions")})
-                    .match() }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys:["results"])).match() }
             )
         }
     }
@@ -40,13 +34,11 @@ nextflow_process {
         when {
             process {
                 """
-                gff = []
-
-                input[0] = Channel.of([
-                    [ id:'test', single_end:false ], // meta map
+                input[0] = [
+                    [ id:'test', single_end:false ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
-                ])
-                input[1] = gff
+                ]
+                input[1] = []
                 """
             }
         }
@@ -54,7 +46,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
diff --git a/modules/nf-core/qualimap/bamqc/tests/main.nf.test.snap b/modules/nf-core/qualimap/bamqc/tests/main.nf.test.snap
index 0f67dee181a1..263f478e2410 100644
--- a/modules/nf-core/qualimap/bamqc/tests/main.nf.test.snap
+++ b/modules/nf-core/qualimap/bamqc/tests/main.nf.test.snap
@@ -2,79 +2,6 @@
     "homo_sapiens [bam] - stub": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        [
-                            [
-                                "agogo.css:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "ajax-loader.gif:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "basic.css:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "bgfooter.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "bgtop.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "comment-bright.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "comment-close.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "comment.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "doctools.js:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "down-pressed.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "down.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "file.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "jquery.js:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "minus.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "plus.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "pygments.css:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "qualimap_logo_small.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "report.css:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "searchtools.js:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "underscore.js:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "up-pressed.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "up.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "websupport.js:md5,d41d8cd98f00b204e9800998ecf8427e"
-                            ],
-                            "genome_results.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            [
-                                "genome_coverage_0to50_histogram.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_coverage_across_reference.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_coverage_histogram.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_coverage_quotes.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_gc_content_per_window.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_homopolymer_indels.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_insert_size_across_reference.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_insert_size_histogram.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_mapping_quality_across_reference.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_mapping_quality_histogram.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_reads_clipping_profile.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_reads_content_per_read_position.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_uniq_read_starts_histogram.png:md5,d41d8cd98f00b204e9800998ecf8427e"
-                            ],
-                            "qualimapReport.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                            [
-                                "coverage_across_reference.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "coverage_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "duplication_rate_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "genome_fraction_coverage.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "homopolymer_indels.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "insert_size_across_reference.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "insert_size_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "mapped_reads_clipping_profile.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "mapped_reads_gc-content_distribution.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "mapped_reads_nucleotide_content.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "mapping_quality_across_reference.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                                "mapping_quality_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                            ]
-                        ]
-                    ]
-                ],
-                "1": [
-                    [
-                        "QUALIMAP_BAMQC",
-                        "qualimap",
-                        "2.3"
-                    ]
-                ],
                 "results": [
                     [
                         {
@@ -150,17 +77,24 @@
                 ]
             }
         ],
+        "timestamp": "2026-08-10T17:20:29.62252359",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
-        },
-        "timestamp": "2026-02-13T22:03:27.280522"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     },
     "homo_sapiens [bam]": {
         "content": [
-            "qualimapReport.html",
-            "genome_results.txt:md5,45103d63ba82df2b905eb04819c32dd3",
             {
+                "results": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test"
+                    ]
+                ],
                 "versions_qualimap": [
                     [
                         "QUALIMAP_BAMQC",
@@ -170,10 +104,10 @@
                 ]
             }
         ],
+        "timestamp": "2026-08-10T17:20:21.098222842",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
-        },
-        "timestamp": "2026-02-13T22:12:46.38879"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/qualimap/bamqccram/main.nf b/modules/nf-core/qualimap/bamqccram/main.nf
index 9c4bb6d48651..40993ece45f9 100644
--- a/modules/nf-core/qualimap/bamqccram/main.nf
+++ b/modules/nf-core/qualimap/bamqccram/main.nf
@@ -15,7 +15,8 @@ process QUALIMAP_BAMQCCRAM {
 
     output:
     tuple val(meta), path("${prefix}"), emit: results
-    path  "versions.yml"              , emit: versions
+    tuple val("${task.process}"), val('qualimap'), eval("qualimap -h | sed -n 's/^QualiMap v.//p'"), topic: versions, emit: versions_qualimap
+    tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,14 +27,8 @@ process QUALIMAP_BAMQCCRAM {
 
     def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs'
     def memory = (task.memory.mega*0.8).intValue() + 'M'
-    def regions = gff ? "--gff $gff" : ''
+    def regions = gff ? "--gff ${gff}" : ''
 
-    def strandedness = 'non-strand-specific'
-    if (meta.strandedness == 'forward') {
-        strandedness = 'strand-specific-forward'
-    } else if (meta.strandedness == 'reverse') {
-        strandedness = 'strand-specific-reverse'
-    }
     """
     unset DISPLAY
     mkdir -p tmp
@@ -41,32 +36,19 @@ process QUALIMAP_BAMQCCRAM {
 
     samtools view -hb -T ${fasta} ${cram} |
     qualimap \\
-        --java-mem-size=$memory \\
+        --java-mem-size=${memory} \\
         bamqc \\
-        $args \\
+        ${args} \\
         -bam /dev/stdin \\
-        $regions \\
-        -p $strandedness \\
-        $collect_pairs \\
-        -outdir $prefix \\
-        -nt $task.cpus
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
+        ${regions} \\
+        ${collect_pairs} \\
+        -outdir ${prefix} \\
+        -nt ${task.cpus}
     """
 
     stub:
-    prefix   = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir ${prefix}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/qualimap/bamqccram/meta.yml b/modules/nf-core/qualimap/bamqccram/meta.yml
index 9cf59bbfc843..729b0cd05719 100644
--- a/modules/nf-core/qualimap/bamqccram/meta.yml
+++ b/modules/nf-core/qualimap/bamqccram/meta.yml
@@ -14,7 +14,8 @@ tools:
       homepage: http://qualimap.bioinfo.cipf.es/
       documentation: http://qualimap.conesalab.org/doc_html/index.html
       doi: 10.1093/bioinformatics/bts503
-      licence: ["GPL-2.0-only"]
+      licence:
+        - "GPL-2.0-only"
       identifier: biotools:qualimap
 input:
   - - meta:
@@ -58,13 +59,50 @@ output:
           type: directory
           description: Qualimap results dir
           pattern: "*/*"
+  versions_qualimap:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - qualimap:
+          type: string
+          description: The name of the tool
+      - qualimap -h | sed -n 's/^QualiMap v.//p':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+  versions_samtools:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - samtools:
+          type: string
+          description: The name of the tool
+      - samtools version | sed '1!d;s/.* //':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - qualimap:
+          type: string
+          description: The name of the tool
+      - qualimap -h | sed -n 's/^QualiMap v.//p':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - samtools:
+          type: string
+          description: The name of the tool
+      - samtools version | sed '1!d;s/.* //':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@FriederikeHanssen"
 maintainers:
diff --git a/modules/nf-core/qualimap/bamqccram/tests/main.nf.test b/modules/nf-core/qualimap/bamqccram/tests/main.nf.test
index da2f300d6710..4387407c3448 100644
--- a/modules/nf-core/qualimap/bamqccram/tests/main.nf.test
+++ b/modules/nf-core/qualimap/bamqccram/tests/main.nf.test
@@ -12,16 +12,14 @@ nextflow_process {
         when {
             process {
                 """
-                gff = []
-
-                input[0] = Channel.of([
-                    [ id:'test', single_end:false ], // meta map
+                input[0] = [
+                    [ id:'test', single_end:false ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true)
-                ])
-                input[1] = gff
-                input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true))
-                input[3] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true))
+                ]
+                input[1] = []
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 """
             }
         }
@@ -29,11 +27,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(
-                    file("${process.out.results[0][1]}/qualimapReport.html").name,
-                    path("${process.out.results[0][1]}/genome_results.txt"),
-                    process.out.versions)
-                    .match() }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys:["results"])).match() }
             )
         }
     }
@@ -45,16 +39,14 @@ nextflow_process {
         when {
             process {
                 """
-                gff = []
-
-                input[0] = Channel.of([
-                    [ id:'test', single_end:false ], // meta map
+                input[0] = [
+                    [ id:'test', single_end:false ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true)
-                ])
-                input[1] = gff
-                input[2] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true))
-                input[3] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true))
+                ]
+                input[1] = []
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
                 """
             }
         }
@@ -62,7 +54,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
diff --git a/modules/nf-core/qualimap/bamqccram/tests/main.nf.test.snap b/modules/nf-core/qualimap/bamqccram/tests/main.nf.test.snap
index 20b6c4b1de57..b48b0b8b47e2 100644
--- a/modules/nf-core/qualimap/bamqccram/tests/main.nf.test.snap
+++ b/modules/nf-core/qualimap/bamqccram/tests/main.nf.test.snap
@@ -1,35 +1,41 @@
 {
     "homo_sapiens [cram]": {
-        "content": [
-            "qualimapReport.html",
-            "genome_results.txt:md5,61d8b36507652fd7d7db9583de708161",
-            [
-                "versions.yml:md5,9aedcf514cb222dc019feb8b25fc4bcb"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
-        },
-        "timestamp": "2024-07-22T13:45:35.586664"
-    },
-    "homo_sapiens [cram] - stub": {
         "content": [
             {
-                "0": [
+                "results": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        [
-                            
-                        ]
+                        "test"
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,9aedcf514cb222dc019feb8b25fc4bcb"
+                "versions_qualimap": [
+                    [
+                        "QUALIMAP_BAMQCCRAM",
+                        "qualimap",
+                        "2.2.2-dev"
+                    ]
                 ],
+                "versions_samtools": [
+                    [
+                        "QUALIMAP_BAMQCCRAM",
+                        "samtools",
+                        "1.16.1"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-08-10T17:22:22.049444007",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
+    },
+    "homo_sapiens [cram] - stub": {
+        "content": [
+            {
                 "results": [
                     [
                         {
@@ -41,15 +47,26 @@
                         ]
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,9aedcf514cb222dc019feb8b25fc4bcb"
+                "versions_qualimap": [
+                    [
+                        "QUALIMAP_BAMQCCRAM",
+                        "qualimap",
+                        "2.2.2-dev"
+                    ]
+                ],
+                "versions_samtools": [
+                    [
+                        "QUALIMAP_BAMQCCRAM",
+                        "samtools",
+                        "1.16.1"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-08-10T17:22:30.987280528",
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
-        },
-        "timestamp": "2024-07-22T14:23:41.250873"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf
index 2f260bf2d458..d6e525aca190 100644
--- a/modules/nf-core/qualimap/rnaseq/main.nf
+++ b/modules/nf-core/qualimap/rnaseq/main.nf
@@ -13,7 +13,7 @@ process QUALIMAP_RNASEQ {
 
     output:
     tuple val(meta), path("${prefix}"), emit: results
-    tuple val("${task.process}"), val('qualimap'), eval("qualimap 2>&1 | sed -n 's/.*QualiMap v.\\(.*\\)/\\1/p'"), emit: versions_qualimap, topic: versions
+    tuple val("${task.process}"), val('qualimap'), eval("qualimap -h | sed -n 's/^QualiMap v.//p'"), topic: versions, emit: versions_qualimap
 
     when:
     task.ext.when == null || task.ext.when
@@ -24,25 +24,18 @@ process QUALIMAP_RNASEQ {
     def paired_end = meta.single_end ? '' : '-pe'
     def memory = (task.memory.mega*0.8).intValue() + 'M'
 
-    def strandedness = 'non-strand-specific'
-    if (meta.strandedness == 'forward') {
-        strandedness = 'strand-specific-forward'
-    } else if (meta.strandedness == 'reverse') {
-        strandedness = 'strand-specific-reverse'
-    }
     """
     unset DISPLAY
     mkdir -p tmp
     export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp
     qualimap \\
-        --java-mem-size=$memory \\
+        --java-mem-size=${memory} \\
         rnaseq \\
-        $args \\
-        -bam $bam \\
-        -gtf $gtf \\
-        -p $strandedness \\
-        $paired_end \\
-        -outdir $prefix
+        ${args} \\
+        -bam ${bam} \\
+        -gtf ${gtf} \\
+        ${paired_end} \\
+        -outdir ${prefix}
     """
 
     stub:
diff --git a/modules/nf-core/qualimap/rnaseq/meta.yml b/modules/nf-core/qualimap/rnaseq/meta.yml
index 28e0f910e3ac..6cc2f33b97ec 100644
--- a/modules/nf-core/qualimap/rnaseq/meta.yml
+++ b/modules/nf-core/qualimap/rnaseq/meta.yml
@@ -14,7 +14,8 @@ tools:
       homepage: http://qualimap.bioinfo.cipf.es/
       documentation: http://qualimap.conesalab.org/doc_html/index.html
       doi: 10.1093/bioinformatics/bts503
-      licence: ["GPL-2.0-only"]
+      licence:
+        - "GPL-2.0-only"
       identifier: biotools:qualimap
 input:
   - - meta:
@@ -55,7 +56,7 @@ output:
       - qualimap:
           type: string
           description: The name of the tool
-      - "qualimap 2>&1 | sed -n 's/.*QualiMap v.\\(.*\\)/\\1/p'":
+      - qualimap -h | sed -n 's/^QualiMap v.//p':
           type: eval
           description: The expression to obtain the version of the tool
 
@@ -67,7 +68,7 @@ topics:
       - qualimap:
           type: string
           description: The name of the tool
-      - "qualimap 2>&1 | sed -n 's/.*QualiMap v.\\(.*\\)/\\1/p'":
+      - qualimap -h | sed -n 's/^QualiMap v.//p':
           type: eval
           description: The expression to obtain the version of the tool
 
diff --git a/modules/nf-core/qualimap/rnaseq/tests/main.nf.test b/modules/nf-core/qualimap/rnaseq/tests/main.nf.test
index 87ddf8a32051..c2b6d7131ac6 100644
--- a/modules/nf-core/qualimap/rnaseq/tests/main.nf.test
+++ b/modules/nf-core/qualimap/rnaseq/tests/main.nf.test
@@ -12,14 +12,14 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
-                    [ id:'test', single_end:false ], // meta map
+                input[0] = [
+                    [ id:'test', single_end:false ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
-                ])
-                input[1] = Channel.of([
-                    [ id:'test_fasta_gtf' ], // meta map
+                ]
+                input[1] = [
+                    [ id:'test_fasta_gtf' ],
                     [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
-                ])
+                ]
                 """
             }
         }
@@ -27,11 +27,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(
-                    file("${process.out.results[0][1]}/qualimapReport.html").name,
-                    path("${process.out.results[0][1]}/rnaseq_qc_results.txt"),
-                    process.out.findAll { key, val -> key.startsWith('versions') }
-                ).match() }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys:["results"])).match() }
             )
         }
     }
@@ -43,14 +39,14 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = Channel.of([
-                    [ id:'test', single_end:false ], // meta map
+                input[0] = [
+                    [ id:'test', single_end:false ],
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
-                ])
-                input[1] = Channel.of([
-                    [ id:'test_fasta_gtf' ], // meta map
+                ]
+                input[1] = [
+                    [ id:'test_fasta_gtf' ],
                     [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
-                ])
+                ]
                 """
             }
         }
@@ -58,7 +54,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
diff --git a/modules/nf-core/qualimap/rnaseq/tests/main.nf.test.snap b/modules/nf-core/qualimap/rnaseq/tests/main.nf.test.snap
index 3f29893ca616..599f48d0d2e0 100644
--- a/modules/nf-core/qualimap/rnaseq/tests/main.nf.test.snap
+++ b/modules/nf-core/qualimap/rnaseq/tests/main.nf.test.snap
@@ -2,24 +2,6 @@
     "homo_sapiens [bam] - stub": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        [
-                            
-                        ]
-                    ]
-                ],
-                "1": [
-                    [
-                        "QUALIMAP_RNASEQ",
-                        "qualimap",
-                        "2.3"
-                    ]
-                ],
                 "results": [
                     [
                         {
@@ -40,17 +22,24 @@
                 ]
             }
         ],
+        "timestamp": "2026-08-07T17:04:26.734359056",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
-        },
-        "timestamp": "2026-02-02T14:37:16.973048807"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     },
     "homo_sapiens [bam]": {
         "content": [
-            "qualimapReport.html",
-            "rnaseq_qc_results.txt:md5,b77878cac45beaa79a892af54aad2da3",
             {
+                "results": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test"
+                    ]
+                ],
                 "versions_qualimap": [
                     [
                         "QUALIMAP_RNASEQ",
@@ -60,10 +49,10 @@
                 ]
             }
         ],
+        "timestamp": "2026-08-07T17:04:19.72589915",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.3"
-        },
-        "timestamp": "2026-02-02T14:37:10.64233656"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     }
 }
\ No newline at end of file