diff --git a/modules/nf-core/bismark/genomepreparation/main.nf b/modules/nf-core/bismark/genomepreparation/main.nf
index e8b9fedae20..c94e9fec64d 100644
--- a/modules/nf-core/bismark/genomepreparation/main.nf
+++ b/modules/nf-core/bismark/genomepreparation/main.nf
@@ -8,7 +8,7 @@ process BISMARK_GENOMEPREPARATION {
         'biocontainers/bismark:0.24.2--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(fasta)
+    tuple val(meta), path(fasta, name:"BismarkIndex/")
 
     output:
     tuple val(meta), path("BismarkIndex"), emit: index
@@ -20,14 +20,11 @@ process BISMARK_GENOMEPREPARATION {
     script:
     def args = task.ext.args ?: ''
     """
-    mkdir BismarkIndex
-    mv $fasta BismarkIndex/
-
     bismark_genome_preparation \\
         $args \\
         BismarkIndex
 
-    rm BismarkIndex/$fasta
+    rm $fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -38,8 +35,25 @@ process BISMARK_GENOMEPREPARATION {
     stub:
     def args = task.ext.args ?: ''
     """
-    mkdir BismarkIndex
-    touch BismarkIndex/$fasta
+    rm $fasta
+
+    mkdir -p BismarkIndex/Bisulfite_Genome/CT_conversion
+    touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.1.bt2
+    touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.2.bt2
+    touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.3.bt2
+    touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.4.bt2
+    touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.rev.1.bt2
+    touch BismarkIndex/Bisulfite_Genome/CT_conversion/BS_CT.rev.2.bt2
+    touch BismarkIndex/Bisulfite_Genome/CT_conversion/genome_mfa.CT_conversion.fa
+
+    mkdir -p BismarkIndex/Bisulfite_Genome/GA_conversion
+    touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.1.bt2
+    touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.2.bt2
+    touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.3.bt2
+    touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.4.bt2
+    touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.rev.1.bt2
+    touch BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.rev.2.bt2
+    touch BismarkIndex/Bisulfite_Genome/GA_conversion/genome_mfa.GA_conversion.fa
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap b/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap
index caf8afc8891..d56b414d37c 100644
--- a/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap
+++ b/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap
@@ -8,7 +8,26 @@
                             "id": "test"
                         },
                         [
-                            "genome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                            [
+                                [
+                                    "BS_CT.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "BS_CT.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "BS_CT.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "BS_CT.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "BS_CT.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "BS_CT.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "genome_mfa.CT_conversion.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                                ],
+                                [
+                                    "BS_GA.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "BS_GA.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "BS_GA.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "BS_GA.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "BS_GA.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "BS_GA.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "genome_mfa.GA_conversion.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                                ]
+                            ]
                         ]
                     ]
                 ],
@@ -21,7 +40,26 @@
                             "id": "test"
                         },
                         [
-                            "genome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                            [
+                                [
+                                    "BS_CT.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "BS_CT.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "BS_CT.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "BS_CT.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "BS_CT.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "BS_CT.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "genome_mfa.CT_conversion.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                                ],
+                                [
+                                    "BS_GA.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "BS_GA.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "BS_GA.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "BS_GA.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "BS_GA.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "BS_GA.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                                    "genome_mfa.GA_conversion.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                                ]
+                            ]
                         ]
                     ]
                 ],
@@ -34,7 +72,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-13T08:26:30.051110425"
+        "timestamp": "2024-10-18T15:50:44.009733"
     },
     "sarscov2 genome [fasta]": {
         "content": [