diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf
index 9e718431d5c8..f148f56bb4f8 100644
--- a/modules/nf-core/samtools/flagstat/main.nf
+++ b/modules/nf-core/samtools/flagstat/main.nf
@@ -35,7 +35,19 @@ process SAMTOOLS_FLAGSTAT {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.flagstat
+    cat <<-END_FLAGSTAT > ${prefix}.flagstat
+    1000000 + 0 in total (QC-passed reads + QC-failed reads)
+    0 + 0 secondary
+    0 + 0 supplementary
+    0 + 0 duplicates
+    900000 + 0 mapped (90.00% : N/A)
+    1000000 + 0 paired in sequencing
+    500000 + 0 read1
+    500000 + 0 read2
+    800000 + 0 properly paired (80.00% : N/A)
+    850000 + 0 with mate mapped to a different chr
+    50000 + 0 with mate mapped to a different chr (mapQ>=5)
+    END_FLAGSTAT
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap
index 79960bcbad5f..0a0a9b15cde5 100644
--- a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "1": [
@@ -20,7 +20,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "versions": [
@@ -32,7 +32,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T13:31:17.098789"
+        "timestamp": "2025-09-15T15:02:00.813612"
     },
     "BAM": {
         "content": [
@@ -67,6 +67,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T13:31:12.661288"
+        "timestamp": "2025-09-15T15:01:55.232954"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap
index fa4a194cb4e4..dadc71a7100f 100644
--- a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap
@@ -17,7 +17,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "2": [
@@ -40,7 +40,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "idxstats": [
@@ -72,7 +72,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T13:37:48.492968"
+        "timestamp": "2025-09-15T15:20:35.417926"
     },
     "test_bam_stats_samtools_single_end - stub": {
         "content": [
@@ -92,7 +92,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "2": [
@@ -115,7 +115,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "idxstats": [
@@ -147,7 +147,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T13:37:43.4053"
+        "timestamp": "2025-09-15T15:20:25.439222"
     },
     "test_bam_stats_samtools_paired_end_cram - stub": {
         "content": [
@@ -167,7 +167,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "2": [
@@ -190,7 +190,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "idxstats": [
@@ -222,7 +222,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T13:37:53.52248"
+        "timestamp": "2025-09-15T15:20:46.02738"
     },
     "test_bam_stats_samtools_single_end": {
         "content": [
@@ -263,7 +263,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T13:37:27.672053"
+        "timestamp": "2025-09-15T15:20:00.064679"
     },
     "test_bam_stats_samtools_paired_end": {
         "content": [
@@ -304,7 +304,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T13:37:32.985079"
+        "timestamp": "2025-09-15T15:20:08.141202"
     },
     "test_bam_stats_samtools_paired_end_cram": {
         "content": [
@@ -345,6 +345,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-10T13:37:38.347584"
+        "timestamp": "2025-09-15T15:20:16.06318"
     }
 }
\ No newline at end of file