diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf
index c472d711614..dff519ec9f6 100644
--- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf
@@ -13,11 +13,17 @@ include { FASTP                 } from '../../../modules/nf-core/fastp/main'
 import groovy.json.JsonSlurper
 
 def getFastpReadsAfterFiltering(json_file) {
+
+    if ( workflow.stubRun ) { return 0 }
+
     def Map json = (Map) new JsonSlurper().parseText(json_file.text).get('summary')
     return json['after_filtering']['total_reads'].toLong()
 }
 
 def getFastpAdapterSequence(json_file){
+
+    if ( workflow.stubRun ) { return "" }
+
     def Map json = (Map) new JsonSlurper().parseText(json_file.text)
     try{
         adapter = json['adapter_cutting']['read1_adapter_sequence']
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test
index 80e06b98ee1..70fa1641906 100644
--- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test
@@ -559,4 +559,49 @@ nextflow_workflow {
             )
         }
     }
+
+    test("sarscov2 paired-end [fastq] - stub") {
+
+        options '-stub'
+
+        when {
+            workflow {
+                """
+                skip_fastqc       = false
+                with_umi          = false
+                skip_umi_extract  = false
+                umi_discard_read  = 1
+                skip_trimming     = false
+                adapter_fasta     = []
+                save_trimmed_fail = false
+                save_merged       = false
+                min_trimmed_reads = 1
+
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+                ])
+                input[1] = skip_fastqc
+                input[2] = with_umi
+                input[3] = skip_umi_extract
+                input[4] = umi_discard_read
+                input[5] = skip_trimming
+                input[6] = adapter_fasta
+                input[7] = save_trimmed_fail
+                input[8] = save_merged
+                input[9] = min_trimmed_reads
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
 }
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap
index 4a6689f6719..5f804bfbe4e 100644
--- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap
@@ -545,5 +545,186 @@
             "nextflow": "24.04.2"
         },
         "timestamp": "2024-06-10T15:08:32.267769943"
+    },
+    "sarscov2 paired-end [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "10": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        0
+                    ]
+                ],
+                "11": [
+                    
+                ],
+                "12": [
+                    
+                ],
+                "13": [
+                    "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
+                    "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        ""
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
+                    
+                ],
+                "9": [
+                    
+                ],
+                "adapter_seq": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        ""
+                    ]
+                ],
+                "fastqc_raw_html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastqc_raw_zip": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "fastqc_trim_html": [
+                    
+                ],
+                "fastqc_trim_zip": [
+                    
+                ],
+                "reads": [
+                    
+                ],
+                "trim_html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "trim_json": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "trim_log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "trim_read_count": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        0
+                    ]
+                ],
+                "trim_reads_fail": [
+                    
+                ],
+                "trim_reads_merged": [
+                    
+                ],
+                "umi_log": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
+                    "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-21T12:21:48.845872"
     }
 }
\ No newline at end of file