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 bc9b84fc5cc..1addaba39ab 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
@@ -28,7 +28,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.fastp.json:md5,47a1bbd79b21721d81eb457e44fa3e3b"
+                    "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd"
                 ]
             ],
             [
@@ -57,9 +57,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-12T14:23:56.776685218"
+        "timestamp": "2024-12-20T14:49:55.964438399"
     },
     "sarscov2 paired-end [fastq] | with_umi": {
         "content": [
@@ -87,7 +87,7 @@
                         "id": "test",
                         "single_end": true
                     },
-                    "test.fastp.json:md5,0ed43f6b2e5361e7ed6bc3c0b5d6e89a"
+                    "test.fastp.json:md5,d39c5c6d9a2e35fb60d26ced46569af6"
                 ]
             ],
             [
@@ -114,133 +114,11 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
-        },
-        "timestamp": "2024-12-12T14:23:44.160061128"
-    },
-    "sarscov2 paired-end [fastq] | skip_trimming - stub": {
-        "content": [
-            [
-                
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
-                ]
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
-            [
-                "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-12T14:32:15.355312216"
+        "timestamp": "2024-12-20T14:49:32.102996566"
     },
-    "sarscov2 paired-end [fastq] | umi_discard_read = 2": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "unspecified"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    [
-                        "test_1.fastp.fastq.gz:md5,67b2bbae47f073e05a97a9c2edce23c7",
-                        "test_2.fastp.fastq.gz:md5,25cbdca08e2083dbd4f0502de6b62f39"
-                    ]
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.fastp.json:md5,47a1bbd79b21721d81eb457e44fa3e3b"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    198
-                ]
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
-            [
-                "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
-                "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
-                "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
-        },
-        "timestamp": "2024-12-12T14:24:09.203612468"
-    },
-    "sarscov2 paired-end [fastq] | min_trimmed_reads = 26 - stub": {
+    "sarscov2 paired-end [fastq] | umi_discard_read = 2 - stub": {
         "content": [
             {
                 "0": [
@@ -270,7 +148,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        26
+                        1
                     ]
                 ],
                 "11": [
@@ -348,13 +226,7 @@
                     
                 ],
                 "9": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                    ]
+                    
                 ],
                 "adapter_seq": [
                     [
@@ -446,20 +318,14 @@
                             "id": "test",
                             "single_end": false
                         },
-                        26
+                        1
                     ]
                 ],
                 "trim_reads_fail": [
                     
                 ],
                 "trim_reads_merged": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                    ]
+                    
                 ],
                 "umi_log": [
                     
@@ -475,9 +341,103 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-12T14:32:39.987530839"
+        "timestamp": "2024-12-12T14:32:07.840128843"
     },
-    "sarscov2 paired-end [fastq] | skip_fastqc": {
+    "sarscov2 paired-end [fastq] | skip_trimming - stub": {
+        "content": [
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-12T14:32:15.355312216"
+    },
+    "sarscov2 paired-end [fastq] | skip_trimming": {
+        "content": [
+            [
+                
+            ],
+            {
+                "id": "test",
+                "single_end": false
+            },
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-12T14:24:19.774510678"
+    },
+    "sarscov2 paired-end [fastq] | umi_discard_read = 2": {
         "content": [
             [
                 [
@@ -506,7 +466,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.fastp.json:md5,47a1bbd79b21721d81eb457e44fa3e3b"
+                    "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd"
                 ]
             ],
             [
@@ -528,16 +488,18 @@
                 
             ],
             [
-                "versions.yml:md5,85bd0117e5778fff18e3920972a296ad"
+                "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
+                "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
+                "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-12T14:23:28.044081844"
+        "timestamp": "2024-12-20T14:50:21.346654157"
     },
-    "sarscov2 paired-end [fastq] | skip_fastqc - stub": {
+    "sarscov2 paired-end [fastq] | min_trimmed_reads = 26 - stub": {
         "content": [
             {
                 "0": [
@@ -553,7 +515,13 @@
                     ]
                 ],
                 "1": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "10": [
                     [
@@ -561,20 +529,40 @@
                             "id": "test",
                             "single_end": false
                         },
-                        1
+                        26
                     ]
                 ],
                 "11": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "12": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "13": [
-                    "versions.yml:md5,85bd0117e5778fff18e3920972a296ad"
+                    "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
+                    "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
+                    "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
                 ],
                 "2": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "3": [
                     
@@ -619,7 +607,13 @@
                     
                 ],
                 "9": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
                 ],
                 "adapter_seq": [
                     [
@@ -631,16 +625,40 @@
                     ]
                 ],
                 "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": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "fastqc_trim_zip": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "reads": [
                     [
@@ -687,20 +705,28 @@
                             "id": "test",
                             "single_end": false
                         },
-                        1
+                        26
                     ]
                 ],
                 "trim_reads_fail": [
                     
                 ],
                 "trim_reads_merged": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
                 ],
                 "umi_log": [
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,85bd0117e5778fff18e3920972a296ad"
+                    "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
+                    "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
+                    "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
                 ]
             }
         ],
@@ -708,9 +734,141 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-12T14:31:39.612937297"
+        "timestamp": "2024-12-12T14:32:39.987530839"
     },
-    "sarscov2 paired-end [fastq] | save_merged - stub": {
+    "sarscov2 paired-end [fastq] | save_trimmed_fail": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "unspecified"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test_1.fastp.fastq.gz:md5,6ff32a64c5188b9a9192be1398c262c7",
+                        "test_2.fastp.fastq.gz:md5,db0cb7c9977e94ac2b4b446ebd017a8a"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.fastp.json:md5,4c3268ddb50ea5b33125984776aa3519"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    162
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test.paired.fail.fastq.gz:md5,409b687c734cedd7a1fec14d316e1366",
+                        "test_1.fail.fastq.gz:md5,4f273cf3159c13f79e8ffae12f5661f6",
+                        "test_2.fail.fastq.gz:md5,f97b9edefb5649aab661fbc9e71fc995"
+                    ]
+                ]
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
+                "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
+                "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2024-12-20T14:51:03.282629859"
+    },
+    "sarscov2 paired-end [fastq] | skip_fastqc": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "unspecified"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test_1.fastp.fastq.gz:md5,67b2bbae47f073e05a97a9c2edce23c7",
+                        "test_2.fastp.fastq.gz:md5,25cbdca08e2083dbd4f0502de6b62f39"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    198
+                ]
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,85bd0117e5778fff18e3920972a296ad"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2024-12-20T14:48:39.414996952"
+    },
+    "sarscov2 paired-end [fastq] | save_trimmed_fail - stub": {
         "content": [
             {
                 "0": [
@@ -815,16 +973,20 @@
                     ]
                 ],
                 "8": [
-                    
-                ],
-                "9": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        [
+                            "test.paired.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_1.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
                     ]
+                ],
+                "9": [
+                    
                 ],
                 "adapter_seq": [
                     [
@@ -920,16 +1082,20 @@
                     ]
                 ],
                 "trim_reads_fail": [
-                    
-                ],
-                "trim_reads_merged": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        [
+                            "test.paired.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_1.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test_2.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
                     ]
+                ],
+                "trim_reads_merged": [
+                    
                 ],
                 "umi_log": [
                     
@@ -945,9 +1111,9 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-12T14:32:31.825964203"
+        "timestamp": "2024-12-12T14:32:23.571618376"
     },
-    "sarscov2 paired-end [fastq] - stub": {
+    "sarscov2 paired-end [fastq] | skip_fastqc - stub": {
         "content": [
             {
                 "0": [
@@ -963,13 +1129,7 @@
                     ]
                 ],
                 "1": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "10": [
                     [
@@ -981,36 +1141,16 @@
                     ]
                 ],
                 "11": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "12": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "13": [
-                    "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
-                    "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
-                    "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
+                    "versions.yml:md5,85bd0117e5778fff18e3920972a296ad"
                 ],
                 "2": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "3": [
                     
@@ -1067,40 +1207,16 @@
                     ]
                 ],
                 "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": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "fastqc_trim_zip": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "reads": [
                     [
@@ -1160,19 +1276,17 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
-                    "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
-                    "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
+                    "versions.yml:md5,85bd0117e5778fff18e3920972a296ad"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-07-22T16:58:29.296468"
+        "timestamp": "2024-12-12T14:31:39.612937297"
     },
-    "sarscov2 paired-end [fastq] | umi_discard_read = 2 - stub": {
+    "sarscov2 paired-end [fastq] | save_merged - stub": {
         "content": [
             {
                 "0": [
@@ -1280,7 +1394,13 @@
                     
                 ],
                 "9": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
                 ],
                 "adapter_seq": [
                     [
@@ -1379,7 +1499,13 @@
                     
                 ],
                 "trim_reads_merged": [
-                    
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
                 ],
                 "umi_log": [
                     
@@ -1395,43 +1521,77 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-12T14:32:07.840128843"
+        "timestamp": "2024-12-12T14:32:31.825964203"
     },
-    "sarscov2 paired-end [fastq] | skip_trimming": {
+    "sarscov2 paired-end [fastq] | min_trimmed_reads = 26": {
         "content": [
             [
-                
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "unspecified"
+                ]
             ],
-            {
-                "id": "test",
-                "single_end": false
-            },
             [
-                
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    [
+                        "test_1.fastp.fastq.gz:md5,54b726a55e992a869fd3fa778afe1672",
+                        "test_2.fastp.fastq.gz:md5,29d3b33b869f7b63417b8ff07bb128ba"
+                    ]
+                ]
             ],
             [
-                
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.fastp.json:md5,b712fd68ed0322f4bec49ff2a5237fcc"
+                ]
             ],
             [
-                
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    75
+                ]
             ],
             [
                 
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.merged.fastq.gz:md5,c873bb1ab3fa859dcc47306465e749d5"
+                ]
             ],
             [
                 
             ],
             [
+                "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
+                "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
                 "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-12T14:24:19.774510678"
+        "timestamp": "2024-12-20T14:52:01.390925061"
     },
-    "sarscov2 paired-end [fastq] | save_trimmed_fail": {
+    "sarscov2 paired-end [fastq]": {
         "content": [
             [
                 [
@@ -1449,8 +1609,8 @@
                         "single_end": false
                     },
                     [
-                        "test_1.fastp.fastq.gz:md5,6ff32a64c5188b9a9192be1398c262c7",
-                        "test_2.fastp.fastq.gz:md5,db0cb7c9977e94ac2b4b446ebd017a8a"
+                        "test_1.fastp.fastq.gz:md5,67b2bbae47f073e05a97a9c2edce23c7",
+                        "test_2.fastp.fastq.gz:md5,25cbdca08e2083dbd4f0502de6b62f39"
                     ]
                 ]
             ],
@@ -1460,7 +1620,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.fastp.json:md5,21fdf3cfd611a7959b93318f25d126e9"
+                    "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd"
                 ]
             ],
             [
@@ -1469,21 +1629,11 @@
                         "id": "test",
                         "single_end": false
                     },
-                    162
+                    198
                 ]
             ],
             [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    [
-                        "test.paired.fail.fastq.gz:md5,409b687c734cedd7a1fec14d316e1366",
-                        "test_1.fail.fastq.gz:md5,4f273cf3159c13f79e8ffae12f5661f6",
-                        "test_2.fail.fastq.gz:md5,f97b9edefb5649aab661fbc9e71fc995"
-                    ]
-                ]
+                
             ],
             [
                 
@@ -1499,11 +1649,11 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-12T14:24:32.09683126"
+        "timestamp": "2024-12-20T14:48:22.223898663"
     },
-    "sarscov2 paired-end [fastq] | save_trimmed_fail - stub": {
+    "sarscov2 paired-end [fastq] - stub": {
         "content": [
             {
                 "0": [
@@ -1608,17 +1758,7 @@
                     ]
                 ],
                 "8": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        [
-                            "test.paired.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                            "test_1.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                            "test_2.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                        ]
-                    ]
+                    
                 ],
                 "9": [
                     
@@ -1717,17 +1857,7 @@
                     ]
                 ],
                 "trim_reads_fail": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        [
-                            "test.paired.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                            "test_1.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
-                            "test_2.fail.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
-                        ]
-                    ]
+                    
                 ],
                 "trim_reads_merged": [
                     
@@ -1743,140 +1873,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
-        },
-        "timestamp": "2024-12-12T14:32:23.571618376"
-    },
-    "sarscov2 paired-end [fastq] | min_trimmed_reads = 26": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "unspecified"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    [
-                        "test_1.fastp.fastq.gz:md5,54b726a55e992a869fd3fa778afe1672",
-                        "test_2.fastp.fastq.gz:md5,29d3b33b869f7b63417b8ff07bb128ba"
-                    ]
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.fastp.json:md5,b913b6f0faf64d208ecc009eb765ada6"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    75
-                ]
-            ],
-            [
-                
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.merged.fastq.gz:md5,c873bb1ab3fa859dcc47306465e749d5"
-                ]
-            ],
-            [
-                
-            ],
-            [
-                "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
-                "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
-                "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
-        },
-        "timestamp": "2024-12-12T14:24:56.36378285"
-    },
-    "sarscov2 paired-end [fastq]": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "unspecified"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    [
-                        "test_1.fastp.fastq.gz:md5,67b2bbae47f073e05a97a9c2edce23c7",
-                        "test_2.fastp.fastq.gz:md5,25cbdca08e2083dbd4f0502de6b62f39"
-                    ]
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.fastp.json:md5,47a1bbd79b21721d81eb457e44fa3e3b"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    198
-                ]
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
-            [
-                
-            ],
-            [
-                "versions.yml:md5,85bd0117e5778fff18e3920972a296ad",
-                "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0",
-                "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-12-12T14:14:48.625336841"
+        "timestamp": "2024-07-22T16:58:29.296468"
     },
     "sarscov2 paired-end [fastq] | save_merged": {
         "content": [
@@ -1907,7 +1907,7 @@
                         "id": "test",
                         "single_end": false
                     },
-                    "test.fastp.json:md5,b913b6f0faf64d208ecc009eb765ada6"
+                    "test.fastp.json:md5,b712fd68ed0322f4bec49ff2a5237fcc"
                 ]
             ],
             [
@@ -1942,9 +1942,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-12T14:24:43.700668074"
+        "timestamp": "2024-12-20T14:51:21.931782328"
     },
     "sarscov2 paired-end [fastq] | with_umi - stub": {
         "content": [