diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index 9ed83f89..4834d2aa 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -68,7 +68,6 @@ workflow PREPARE_GENOME {
             ch_bwameth_index = BWAMETH_INDEX.out.index
             ch_versions      = ch_versions.mix(BWAMETH_INDEX.out.versions)
         }
-    }
 
         /*
          * Generate fasta index if not supplied
@@ -83,6 +82,7 @@ workflow PREPARE_GENOME {
             ch_fasta_index = SAMTOOLS_FAIDX.out.fai.map{ return(it[1])}
             ch_versions    = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
         }
+    }
 
     emit:
     fasta         = ch_fasta                  // channel: path(genome.fasta)
diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test
index 147e6ca2..93066a75 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test
@@ -4,67 +4,7 @@ nextflow_workflow {
     script "../main.nf"
     workflow "PREPARE_GENOME"
 
-    test("BISMARK - All Indexes supplied") {
-
-        when {
-            params {
-                aligner = "bismark"
-            }
-            workflow {
-                """
-                input[0] = file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) // fasta
-                input[1] = file(params.pipelines_testdata_base_path + 'reference/genome.fa.fai', checkIfExists: true) // fasta_index
-                input[2] = file(params.pipelines_testdata_base_path + 'reference/Bowtie2_Index.tar.gz',  checkIfExists: true) // bismark_index
-                input[3] = [] // bwameth_index
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(
-                    workflow.out.fasta,
-                    workflow.out.fasta_index,
-                    workflow.out.bismark_index,
-                    workflow.out.versions
-                    ).match() }
-            )
-        }
-
-    }
-
-    test("BISMARK - Generate Fasta Index") {
-
-        when {
-            params {
-                aligner = "bismark"
-            }
-            workflow {
-                """
-                input[0] = file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) // fasta
-                input[1] = []  // fasta_index
-                input[2] = file(params.pipelines_testdata_base_path + 'reference/Bowtie2_Index.tar.gz',  checkIfExists: true) // bismark_index
-                input[3] = [] // bwameth_index
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(
-                    workflow.out.fasta,
-                    workflow.out.fasta_index,
-                    workflow.out.bismark_index,
-                    workflow.out.versions
-                    ).match() }
-            )
-        }
-
-    }
-
-    test("BISMARK - Generate Fasta Index & Bowtie Index") {
+    test("BISMARK - Generate Index") {
 
         when {
             params {
@@ -85,7 +25,6 @@ nextflow_workflow {
                 { assert workflow.success },
                 { assert snapshot(
                     workflow.out.fasta,
-                    workflow.out.fasta_index,
                     workflow.out.bismark_index,
                     workflow.out.versions
                     ).match() }
@@ -94,67 +33,7 @@ nextflow_workflow {
 
     }
 
-    test("BWAMETH - All Indexes supplied") {
-
-        when {
-            params {
-                aligner = "bwameth"
-            }
-            workflow {
-                """
-                input[0] = file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) // fasta
-                input[1] = file(params.pipelines_testdata_base_path + 'reference/genome.fa.fai', checkIfExists: true) // fasta_index
-                input[2] = [] // bismark_index
-                input[3] = file(params.pipelines_testdata_base_path + 'reference/Bwameth_Index.tar.gz',  checkIfExists: true) // bwameth_index
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(
-                    workflow.out.fasta,
-                    workflow.out.fasta_index,
-                    workflow.out.bwameth_index,
-                    workflow.out.versions
-                    ).match() }
-            )
-        }
-
-    }
-
-    test("BWAMETH - Generate Fasta Index") {
-
-        when {
-            params {
-                aligner = "bwameth"
-            }
-            workflow {
-                """
-                input[0] = file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) // fasta
-                input[1] = []  // fasta_index
-                input[2] = [] // bismark_index
-                input[3] = file(params.pipelines_testdata_base_path + 'reference/Bwameth_Index.tar.gz',  checkIfExists: true) // bwameth_index
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(
-                    workflow.out.fasta,
-                    workflow.out.fasta_index,
-                    workflow.out.bwameth_index,
-                    workflow.out.versions
-                    ).match() }
-            )
-        }
-
-    }
-
-    test("BWAMETH - Generate Fasta Index & bwameth Index") {
+    test("BWAMETH - Generate Index") {
 
         when {
             params {
diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
index 9f58495c..71af1f7e 100644
--- a/subworkflows/local/prepare_genome/tests/main.nf.test.snap
+++ b/subworkflows/local/prepare_genome/tests/main.nf.test.snap
@@ -1,47 +1,5 @@
 {
-    "BWAMETH - All Indexes supplied": {
-        "content": [
-            [
-                "/nf-core/test-datasets/raw/methylseq/reference/genome.fa"
-            ],
-            [
-                "/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai"
-            ],
-            [
-                "/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz"
-            ],
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-09-08T07:11:39.601007949"
-    },
-    "BISMARK - Generate Fasta Index": {
-        "content": [
-            [
-                "/nf-core/test-datasets/raw/methylseq/reference/genome.fa"
-            ],
-            [
-                "genome.fa.fai:md5,84f5b44c25877ac58b154706cc8bc451"
-            ],
-            [
-                "/nf-core/test-datasets/raw/methylseq/reference/Bowtie2_Index.tar.gz"
-            ],
-            [
-                "versions.yml:md5,67124f8c3356bccd688e07c65a52e48a"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-09-08T07:13:17.406358667"
-    },
-    "BWAMETH - Generate Fasta Index & bwameth Index": {
+    "BWAMETH - Generate Index": {
         "content": [
             [
                 "/nf-core/test-datasets/raw/methylseq/reference/genome.fa"
@@ -69,58 +27,13 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-08T07:12:28.477635099"
+        "timestamp": "2024-09-08T12:38:36.730702552"
     },
-    "BWAMETH - Generate Fasta Index": {
+    "BISMARK - Generate Index": {
         "content": [
             [
                 "/nf-core/test-datasets/raw/methylseq/reference/genome.fa"
             ],
-            [
-                "genome.fa.fai:md5,84f5b44c25877ac58b154706cc8bc451"
-            ],
-            [
-                "/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz"
-            ],
-            [
-                "versions.yml:md5,67124f8c3356bccd688e07c65a52e48a"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-09-08T07:11:57.30233052"
-    },
-    "BISMARK - All Indexes supplied": {
-        "content": [
-            [
-                "/nf-core/test-datasets/raw/methylseq/reference/genome.fa"
-            ],
-            [
-                "/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai"
-            ],
-            [
-                "/nf-core/test-datasets/raw/methylseq/reference/Bowtie2_Index.tar.gz"
-            ],
-            [
-                
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-09-08T07:12:48.994204422"
-    },
-    "BISMARK - Generate Fasta Index & Bowtie Index": {
-        "content": [
-            [
-                "/nf-core/test-datasets/raw/methylseq/reference/genome.fa"
-            ],
-            [
-                "genome.fa.fai:md5,84f5b44c25877ac58b154706cc8bc451"
-            ],
             [
                 [
                     [
@@ -147,14 +60,13 @@
                 ]
             ],
             [
-                "versions.yml:md5,48a4baa99421c3dd839946dd1af8d7aa",
-                "versions.yml:md5,67124f8c3356bccd688e07c65a52e48a"
+                "versions.yml:md5,48a4baa99421c3dd839946dd1af8d7aa"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-08T07:13:52.673839987"
+        "timestamp": "2024-09-08T12:38:22.021170374"
     }
-}
\ No newline at end of file
+}