diff --git a/modules/nf-core/bamtofastq10x/main.nf b/modules/nf-core/bamtofastq10x/main.nf
index be1b14415be..bff379c19ee 100644
--- a/modules/nf-core/bamtofastq10x/main.nf
+++ b/modules/nf-core/bamtofastq10x/main.nf
@@ -11,8 +11,8 @@ process BAMTOFASTQ10X {
     tuple val(meta), path(bam)
 
     output:
-    tuple val(meta), path("*.fastq.gz"), emit: fastq
-    path "versions.yml"                , emit: versions
+    tuple val(meta), path("**/*.fastq.gz"), emit: fastq
+    path "versions.yml"                   , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -24,7 +24,7 @@ process BAMTOFASTQ10X {
     bamtofastq \\
         $args \\
         $bam \\
-        ${prefix}.fastq.gz
+        $prefix
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -35,7 +35,8 @@ process BAMTOFASTQ10X {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.fastq.gz
+    mkdir -p ${prefix}/bamtofastq10x
+    touch ${prefix}/bamtofastq10x/bamtofastq.fastq.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/bamtofastq10x/meta.yml b/modules/nf-core/bamtofastq10x/meta.yml
index ace49c25182..f3e5dfcaa24 100644
--- a/modules/nf-core/bamtofastq10x/meta.yml
+++ b/modules/nf-core/bamtofastq10x/meta.yml
@@ -37,10 +37,10 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1', single_end:false ]`
-      - "*.fastq.gz":
+      - "**/*.fastq.gz":
           type: file
           description: fastq compressed file
-          pattern: "*.fastq.gz"
+          pattern: "**/*.fastq.gz"
   - versions:
       - versions.yml:
           type: file
diff --git a/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap b/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap
index d534674592d..fd531091017 100644
--- a/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap
+++ b/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap
@@ -8,11 +8,9 @@
                             "id": "test"
                         },
                         [
-                            [
-                                "bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0",
-                                "bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f",
-                                "bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002"
-                            ]
+                            "bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0",
+                            "bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f",
+                            "bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002"
                         ]
                     ]
                 ],
@@ -25,11 +23,9 @@
                             "id": "test"
                         },
                         [
-                            [
-                                "bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0",
-                                "bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f",
-                                "bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002"
-                            ]
+                            "bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0",
+                            "bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f",
+                            "bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002"
                         ]
                     ]
                 ],
@@ -39,9 +35,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.0"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-22T16:43:24.999397"
+        "timestamp": "2024-10-02T12:56:21.808042"
     }
 }
\ No newline at end of file