diff --git a/modules/nf-core/trimmomatic/main.nf b/modules/nf-core/trimmomatic/main.nf
index 31f7ffdd422..13fe8b6ee7a 100644
--- a/modules/nf-core/trimmomatic/main.nf
+++ b/modules/nf-core/trimmomatic/main.nf
@@ -12,8 +12,9 @@ process TRIMMOMATIC {
 
     output:
     tuple val(meta), path("*.paired.trim*.fastq.gz")   , emit: trimmed_reads
-    tuple val(meta), path("*.unpaired.trim_*.fastq.gz"), optional:true, emit: unpaired_reads
-    tuple val(meta), path("*.log")                     , emit: log
+    tuple val(meta), path("*.unpaired.trim_*.fastq.gz"), emit: unpaired_reads, optional:true
+    tuple val(meta), path("*_trim.log")                , emit: trim_log
+    tuple val(meta), path("*_out.log")                 , emit: out_log
     tuple val(meta), path("*.summary")                 , emit: summary
     path "versions.yml"                                , emit: versions
 
@@ -27,22 +28,46 @@ process TRIMMOMATIC {
     def output = meta.single_end ?
         "${prefix}.SE.paired.trim.fastq.gz" // HACK to avoid unpaired and paired in the trimmed_reads output
         : "${prefix}.paired.trim_1.fastq.gz ${prefix}.unpaired.trim_1.fastq.gz ${prefix}.paired.trim_2.fastq.gz ${prefix}.unpaired.trim_2.fastq.gz"
-    // TODO Give better error output
     def qual_trim = task.ext.args2 ?: ''
     """
     trimmomatic \\
         $trimmed \\
         -threads $task.cpus \\
-        -trimlog ${prefix}.log \\
+        -trimlog ${prefix}_trim.log \\
         -summary ${prefix}.summary \\
         $reads \\
         $output \\
         $qual_trim \\
-        $args
+        $args 2> >(tee ${prefix}_out.log >&2)
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         trimmomatic: \$(trimmomatic -version)
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    if (meta.single_end) {
+        output_command = "echo '' | gzip > ${prefix}.SE.paired.trim.fastq.gz"
+    } else {
+        output_command  = "echo '' | gzip > ${prefix}.paired.trim_1.fastq.gz"
+        output_command  = "echo '' | gzip > ${prefix}.paired.trim_2.fastq.gz"
+        output_command += "echo '' | gzip > ${prefix}.unpaired.trim_1.fastq.gz"
+        output_command += "echo '' | gzip > ${prefix}.unpaired.trim_2.fastq.gz"
+    }
+
+    """
+    $output_command
+    touch ${prefix}.summary
+    touch ${prefix}_trim.log
+    touch ${prefix}_out.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        trimmomatic: \$(trimmomatic -version)
+    END_VERSIONS
+    """
+
 }
diff --git a/modules/nf-core/trimmomatic/meta.yml b/modules/nf-core/trimmomatic/meta.yml
index 0486e9f5756..2d38bf50f39 100644
--- a/modules/nf-core/trimmomatic/meta.yml
+++ b/modules/nf-core/trimmomatic/meta.yml
@@ -10,7 +10,7 @@ tools:
       homepage: "http://www.usadellab.org/cms/?page=trimmomatic"
       documentation: "https://github.com/usadellab/Trimmomatic"
       doi: "10.1093/bioinformatics/btu170"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
@@ -36,9 +36,13 @@ output:
       type: file
       description: The trimmed/modified unpaired end fastq reads
       pattern: "*.unpaired.trim_*.fastq.gz"
-  - log:
+  - trim_log:
       type: file
-      description: trimmomatic log file
+      description: trimmomatic log file, from the trim_log parameter
+      pattern: "*.log"
+  - out_log:
+      type: file
+      description: log of output from the standard out
       pattern: "*.log"
   - summary:
       type: file
diff --git a/modules/nf-core/trimmomatic/tests/main.nf.test b/modules/nf-core/trimmomatic/tests/main.nf.test
index fd855f25a65..d835c4c48b9 100644
--- a/modules/nf-core/trimmomatic/tests/main.nf.test
+++ b/modules/nf-core/trimmomatic/tests/main.nf.test
@@ -10,9 +10,6 @@ nextflow_process {
     test("Single-Read") {
         config "./nextflow_SE.config"
         when {
-            params {
-                outdir   = "$outputDir"
-            }
             process {
                 """
                 input[0] = [
@@ -30,8 +27,12 @@ nextflow_process {
                 { assert process.success },
                 { assert process.out.trimmed_reads != null },
                 { assert process.out.trimmed_reads.get(0).get(1) ==~ ".*.SE.paired.trim.fastq.gz" },
-                { assert snapshot(process.out.versions).match("versions") },
-                { assert snapshot(process.out).match() }
+                { assert process.out.out_log.get(0).get(1) ==~ ".*.log" },
+                { assert snapshot(process.out.trimmed_reads,
+                                  process.out.trim_log,
+                                  process.out.summary,
+                                  process.out.versions
+                                  ).match() }
             )
         }
     }
@@ -39,9 +40,6 @@ nextflow_process {
     test("Paired-Reads") {
         config "./nextflow_PE.config"
         when {
-            params {
-                outdir   = "$outputDir"
-            }
             process {
                 """
                 input[0] = [
@@ -61,8 +59,12 @@ nextflow_process {
                 { assert process.out.trimmed_reads != null },
                 { assert process.out.trimmed_reads.get(0).get(1).get(0) ==~ ".*.paired.trim_1.fastq.gz" },
                 { assert process.out.trimmed_reads.get(0).get(1).get(1) ==~ ".*.paired.trim_2.fastq.gz" },
-                { assert snapshot(process.out).match() },
-                { assert snapshot(process.out.versions).match("versions") },
+                { assert process.out.out_log.get(0).get(1) ==~ ".*.log" },
+                { assert snapshot(process.out.trimmed_reads,
+                                  process.out.trim_log,
+                                  process.out.summary,
+                                  process.out.versions
+                                  ).match() }
             )
         }
     }
@@ -70,9 +72,6 @@ nextflow_process {
     test("No Adaptors") {
 
         when {
-            params {
-                outdir   = "$outputDir"
-            }
             process {
                 """
                 input[0] = [
@@ -92,4 +91,28 @@ nextflow_process {
             )
         }
     }
+
+    test("Single-Read - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test', single_end:true ],
+                    [
+                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
 }
\ No newline at end of file
diff --git a/modules/nf-core/trimmomatic/tests/main.nf.test.snap b/modules/nf-core/trimmomatic/tests/main.nf.test.snap
index f1519f0cdfb..5e9ec050b9e 100644
--- a/modules/nf-core/trimmomatic/tests/main.nf.test.snap
+++ b/modules/nf-core/trimmomatic/tests/main.nf.test.snap
@@ -1,13 +1,5 @@
 {
-    "versions": {
-        "content": [
-            [
-                "versions.yml:md5,14413a048f088a147fb04f3d59c6c604"
-            ]
-        ],
-        "timestamp": "2023-10-18T12:15:39.464478"
-    },
-    "Single-Read": {
+    "Single-Read - stub": {
         "content": [
             {
                 "0": [
@@ -16,7 +8,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.SE.paired.trim.fastq.gz:md5,089a57f61d7197566b8a3ce71df79113"
+                        "test.SE.paired.trim.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "1": [
@@ -28,7 +20,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.log:md5,e4c3f619e9b0e26847f8f3e3d9af319b"
+                        "test_trim.log:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "3": [
@@ -37,144 +29,150 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.summary:md5,24c973237557a1439c775ca19a5deaa5"
+                        "test_out.log:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,14413a048f088a147fb04f3d59c6c604"
-                ],
-                "log": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.log:md5,e4c3f619e9b0e26847f8f3e3d9af319b"
-                    ]
-                ],
-                "summary": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.summary:md5,24c973237557a1439c775ca19a5deaa5"
-                    ]
-                ],
-                "trimmed_reads": [
                     [
                         {
                             "id": "test",
                             "single_end": true
                         },
-                        "test.SE.paired.trim.fastq.gz:md5,089a57f61d7197566b8a3ce71df79113"
+                        "test.summary:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "unpaired_reads": [
-                    
-                ],
-                "versions": [
+                "5": [
                     "versions.yml:md5,14413a048f088a147fb04f3d59c6c604"
-                ]
-            }
-        ],
-        "timestamp": "2023-10-18T12:15:39.471788"
-    },
-    "Paired-Reads": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        [
-                            "test.paired.trim_1.fastq.gz:md5,575355b98cb5ef9071fad8014c702f4a",
-                            "test.paired.trim_2.fastq.gz:md5,73fb54874d01b2854640266d12cc534a"
-                        ]
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        [
-                            "test.unpaired.trim_1.fastq.gz:md5,2f7b5a15cc4e73a6fb4af1fa01f575cd",
-                            "test.unpaired.trim_2.fastq.gz:md5,096ad7f876b6b704ef7f9f2c5af3cf74"
-                        ]
-                    ]
-                ],
-                "2": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.log:md5,9629761761a34576b3484bf4174f681f"
-                    ]
                 ],
-                "3": [
+                "out_log": [
                     [
                         {
                             "id": "test",
-                            "single_end": false
+                            "single_end": true
                         },
-                        "test.summary:md5,9698e5e5c060bbe64588998fe35f8d71"
+                        "test_out.log:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "4": [
-                    "versions.yml:md5,14413a048f088a147fb04f3d59c6c604"
-                ],
-                "log": [
+                "summary": [
                     [
                         {
                             "id": "test",
-                            "single_end": false
+                            "single_end": true
                         },
-                        "test.log:md5,9629761761a34576b3484bf4174f681f"
+                        "test.summary:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "summary": [
+                "trim_log": [
                     [
                         {
                             "id": "test",
-                            "single_end": false
+                            "single_end": true
                         },
-                        "test.summary:md5,9698e5e5c060bbe64588998fe35f8d71"
+                        "test_trim.log:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "trimmed_reads": [
                     [
                         {
                             "id": "test",
-                            "single_end": false
+                            "single_end": true
                         },
-                        [
-                            "test.paired.trim_1.fastq.gz:md5,575355b98cb5ef9071fad8014c702f4a",
-                            "test.paired.trim_2.fastq.gz:md5,73fb54874d01b2854640266d12cc534a"
-                        ]
+                        "test.SE.paired.trim.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "unpaired_reads": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        [
-                            "test.unpaired.trim_1.fastq.gz:md5,2f7b5a15cc4e73a6fb4af1fa01f575cd",
-                            "test.unpaired.trim_2.fastq.gz:md5,096ad7f876b6b704ef7f9f2c5af3cf74"
-                        ]
-                    ]
+                    
                 ],
                 "versions": [
                     "versions.yml:md5,14413a048f088a147fb04f3d59c6c604"
                 ]
             }
         ],
-        "timestamp": "2023-10-18T12:15:44.677305"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-26T21:50:12.135007267"
+    },
+    "Single-Read": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.SE.paired.trim.fastq.gz:md5,e68abbd3b88f7ec12940a4f5c2b8bfb9"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test_trim.log:md5,e4c3f619e9b0e26847f8f3e3d9af319b"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.summary:md5,24c973237557a1439c775ca19a5deaa5"
+                ]
+            ],
+            [
+                "versions.yml:md5,14413a048f088a147fb04f3d59c6c604"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-26T21:56:07.085100348"
+    },
+    "Paired-Reads": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test.paired.trim_1.fastq.gz:md5,a866e64f451745f176316d0df7d52b30",
+                        "test.paired.trim_2.fastq.gz:md5,725d4ab909b39291ab56b090cab32075"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_trim.log:md5,9629761761a34576b3484bf4174f681f"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.summary:md5,9698e5e5c060bbe64588998fe35f8d71"
+                ]
+            ],
+            [
+                "versions.yml:md5,14413a048f088a147fb04f3d59c6c604"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-26T21:56:18.779303181"
     }
 }
\ No newline at end of file