diff --git a/subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf b/subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf
new file mode 100644
index 00000000000..4dd21888b70
--- /dev/null
+++ b/subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf
@@ -0,0 +1,102 @@
+include { UNTAR                     } from '../../../modules/nf-core/untar/main'
+include { GUNZIP                    } from '../../../modules/nf-core/gunzip/main'
+include { BISMARK_GENOMEPREPARATION } from '../../../modules/nf-core/bismark/genomepreparation/main'
+include { BWAMETH_INDEX             } from '../../../modules/nf-core/bwameth/index/main'
+include { SAMTOOLS_FAIDX            } from '../../../modules/nf-core/samtools/faidx/main'
+
+workflow FASTA_INDEX_BISMARK_BWAMETH {
+
+    take:
+    fasta         // channel: [ val(meta), [ fasta ] ]
+    fasta_index   // channel: [ val(meta), [ fasta index ] ]
+    bismark_index // channel: [ val(meta), [ bismark index ] ]
+    bwameth_index // channel: [ val(meta), [ bwameth index ] ]
+
+    main:
+
+    ch_fasta         = Channel.empty()
+    ch_fasta_index   = Channel.empty()
+    ch_bismark_index = Channel.empty()
+    ch_bwameth_index = Channel.empty()
+    ch_versions      = Channel.empty()
+
+    if (fasta.toString().endsWith('.gz')) {
+        GUNZIP (
+            [ [:], file(fasta, checkIfExists: true) ]
+        )
+        ch_fasta    = GUNZIP.out.gunzip
+        ch_versions = ch_versions.mix(GUNZIP.out.versions)
+    } else {
+        ch_fasta    = Channel.value([[:], file(fasta, checkIfExists: true)])
+    }
+
+    // Aligner: bismark or bismark_hisat
+    if( params.aligner =~ /bismark/ ){
+        /*
+         * Generate bismark index if not supplied
+         */
+        if (bismark_index) {
+            if (bismark_index.toString().endsWith('.gz')) {
+                UNTAR (
+                    [ [:], file(bismark_index, checkIfExists: true) ]
+                )
+                ch_bismark_index = UNTAR.out.untar
+                ch_versions      = ch_versions.mix(UNTAR.out.versions)
+            } else {
+                ch_bismark_index = Channel.value([[:], file(bismark_index, checkIfExists: true)])
+            }
+        } else {
+            BISMARK_GENOMEPREPARATION (
+                ch_fasta
+            )
+            ch_bismark_index = BISMARK_GENOMEPREPARATION.out.index
+            ch_versions      = ch_versions.mix(BISMARK_GENOMEPREPARATION.out.versions)
+        }
+    }
+
+    // Aligner: bwameth
+    else if ( params.aligner == 'bwameth' ){
+        /*
+         * Generate bwameth index if not supplied
+         */
+        if (bwameth_index) {
+            if (bwameth_index.toString().endsWith('.gz')) {
+                UNTAR (
+                    [ [:], file(bwameth_index, checkIfExists: true) ]
+                )
+                ch_bwameth_index = UNTAR.out.untar
+                ch_versions      = ch_versions.mix(UNTAR.out.versions)
+            } else {
+                ch_bwameth_index = Channel.value([[:], file(bwameth_index, checkIfExists: true)])
+            }
+        } else {
+            BWAMETH_INDEX (
+                ch_fasta
+            )
+            ch_bwameth_index = BWAMETH_INDEX.out.index
+            ch_versions      = ch_versions.mix(BWAMETH_INDEX.out.versions)
+        }
+
+        /*
+         * Generate fasta index if not supplied
+         */
+        if (fasta_index) {
+            ch_fasta_index = Channel.value(file(fasta_index, checkIfExists: true))
+        } else {
+            SAMTOOLS_FAIDX(
+                ch_fasta,
+                [[:], []]
+            )
+            ch_fasta_index = SAMTOOLS_FAIDX.out.fai
+            ch_versions    = ch_versions.mix(SAMTOOLS_FAIDX.out.versions)
+        }
+    }
+
+    emit:
+    fasta         = ch_fasta         // channel: [ val(meta), [ fasta ] ]
+    fasta_index   = ch_fasta_index   // channel: [ val(meta), [ fasta index ] ]
+    bismark_index = ch_bismark_index // channel: [ val(meta), [ bismark index ] ]
+    bwameth_index = ch_bwameth_index // channel: [ val(meta), [ bwameth index ] ]
+    versions      = ch_versions      // channel: [ versions.yml ]
+}
+
diff --git a/subworkflows/nf-core/fasta_index_bismark_bwameth/meta.yml b/subworkflows/nf-core/fasta_index_bismark_bwameth/meta.yml
new file mode 100644
index 00000000000..558544295e2
--- /dev/null
+++ b/subworkflows/nf-core/fasta_index_bismark_bwameth/meta.yml
@@ -0,0 +1,72 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "fasta_index_bismark_bwameth"
+description: Generate index files from reference fasta for bismark and bwameth
+keywords:
+  - bismark
+  - bwameth
+  - prepare genome
+  - index
+components:
+  - untar
+  - gunzip
+  - bismark/genomepreparation
+  - bwameth/index
+  - samtools/faidx
+input:
+  - fasta:
+      type: file
+      description: |
+        Reference genome
+        Structure: [ val(meta), path(fasta) ]
+      pattern: "*.{fa/fa.gz}"
+  - fasta_index:
+      type: file
+      description: |
+        Reference genome index file
+        Structure: [ val(meta), path(fasta) ]
+      pattern: "*.fai"
+  - bismark_index:
+      type: file
+      description: |
+        Bismark genome index files
+        Structure: [ val(meta), path(bismark_index) ]
+  - bwameth_index:
+      type: file
+      description: |
+        Bwameth genome index files
+        Structure: [ val(meta), path(bwameth_index) ]
+output:
+  - fasta:
+      type: file
+      description: |
+        Reference genome
+        Structure: [ val(meta), path(fasta) ]
+      pattern: "*.fa"
+  - fasta_index:
+      type: file
+      description: |
+        Reference genome index file
+        Structure: [ val(meta), path(fasta) ]
+      pattern: "*.fai"
+  - bismark_index:
+      type: file
+      description: |
+        Bismark genome index files
+        Structure: [ val(meta), path(bismark_index) ]
+        pattern: "BismarkIndex"
+  - bwameth_index:
+      type: file
+      description: |
+        Bwameth genome index files
+        Structure: [ val(meta), path(bwameth_index) ]
+        pattern: "index"
+  - versions:
+      type: file
+      description: |
+        File containing software versions
+        Structure: [ path(versions.yml) ]
+      pattern: "versions.yml"
+authors:
+  - "@sateeshperi"
+maintainers:
+  - "@sateeshperi"
diff --git a/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test b/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test
new file mode 100644
index 00000000000..3219ea6d945
--- /dev/null
+++ b/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test
@@ -0,0 +1,227 @@
+nextflow_workflow {
+
+    name "Test Subworkflow FASTA_INDEX_BISMARK_BWAMETH"
+    script "../main.nf"
+    workflow "FASTA_INDEX_BISMARK_BWAMETH"
+    config "./nextflow.config"
+
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "subworkflows/fasta_index_bismark_bwameth"
+    tag "untar"
+    tag "gunzip"
+    tag "bismark/genomepreparation"
+    tag "bwameth/index"
+    tag "samtools/faidx"
+
+    test("Params: bismark | download bismark index (bowtie2)") {
+
+        when {
+            params {
+                aligner = "bismark"
+            }
+            workflow {
+                """
+                input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
+                input[1] = [] // fasta_index
+                input[2] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bowtie2_Index.tar.gz', checkIfExists: true)
+                input[3] = [] // bwameth_index
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.fasta,
+                    workflow.out.fasta_index,
+                    workflow.out.bismark_index,
+                    workflow.out.bwameth_index,
+                    workflow.out.versions
+                    ).match() }
+            )
+        }
+    }
+
+    test("Params: bismark | generate bismark index (bowtie2)") {
+
+        when {
+            params {
+                aligner = "bismark"
+            }
+            workflow {
+                """
+                input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
+                input[1] = [] // fasta_index
+                input[2] = [] // 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.bwameth_index,
+                    workflow.out.versions
+                    ).match() }
+            )
+        }
+    }
+
+    test("Params: bismark_hisat | download bismark index (hisat2)") {
+
+        when {
+            params {
+                aligner = "bismark_hisat"
+            }
+            workflow {
+                """
+                input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
+                input[1] = [] // fasta_index
+                input[2] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Hisat2_Index.tar.gz', checkIfExists: true)
+                input[3] = [] // bwameth_index
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.fasta,
+                    workflow.out.fasta_index,
+                    workflow.out.bismark_index,
+                    workflow.out.bwameth_index,
+                    workflow.out.versions
+                    ).match() }
+            )
+        }
+    }
+
+    test("Params: bismark_hisat | generate bismark index (hisat2)") {
+
+        when {
+            params {
+                aligner = "bismark_hisat"
+            }
+            workflow {
+                """
+                input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
+                input[1] = [] // fasta_index
+                input[2] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Hisat2_Index.tar.gz', checkIfExists: true)
+                input[3] = [] // bwameth_index
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.fasta,
+                    workflow.out.fasta_index,
+                    workflow.out.bismark_index,
+                    workflow.out.bwameth_index,
+                    workflow.out.versions
+                    ).match() }
+            )
+        }
+    }
+
+    test("Params: bwameth | download fasta index | download bwameth index") {
+
+        when {
+            params {
+                aligner = "bwameth"
+            }
+            workflow {
+                """
+                input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
+                input[1] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai', checkIfExists: true)
+                input[2] = [] // bismark index
+                input[3] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.fasta,
+                    workflow.out.fasta_index,
+                    workflow.out.bismark_index,
+                    workflow.out.bwameth_index,
+                    workflow.out.versions
+                    ).match() }
+            )
+        }
+    }
+
+    test("Params: bwameth | generate fasta index | download bwameth index") {
+
+        when {
+            params {
+                aligner = "bwameth"
+            }
+            workflow {
+                """
+                input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
+                input[1] = [] //fasta index
+                input[2] = [] // bismark index
+                input[3] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    workflow.out.fasta,
+                    workflow.out.fasta_index,
+                    workflow.out.bismark_index,
+                    workflow.out.bwameth_index,
+                    workflow.out.versions
+                    ).match() }
+            )
+        }
+    }
+
+    test("Params: bwameth | generate fasta index | generate bwameth index") {
+
+        when {
+            params {
+                aligner = "bwameth"
+            }
+            workflow {
+                """
+                input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true)
+                input[1] = [] // fasta_index
+                input[2] = [] // 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.bwameth_index,
+                    workflow.out.versions
+                    ).match() }
+            )
+        }
+    }
+
+}
diff --git a/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test.snap b/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test.snap
new file mode 100644
index 00000000000..2bb64c16111
--- /dev/null
+++ b/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test.snap
@@ -0,0 +1,378 @@
+{
+    "Params: bismark | download bismark index (bowtie2)": {
+        "content": [
+            [
+                [
+                    {
+                        
+                    },
+                    "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        
+                    },
+                    [
+                        [
+                            [
+                                "BS_CT.1.bt2:md5,d53bef7d951c7d08e327944581c911eb",
+                                "BS_CT.2.bt2:md5,752a03fc364115fc910e5a28ae154382",
+                                "BS_CT.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee",
+                                "BS_CT.4.bt2:md5,02b3d1855a67fd9cbb4c411406a22fde",
+                                "BS_CT.rev.1.bt2:md5,52ae603fff473b3b25eecd36c533edb9",
+                                "BS_CT.rev.2.bt2:md5,0e290e05f7dae065cae54e29ed97afe5",
+                                "genome_mfa.CT_conversion.fa:md5,4dd181b65f1f3549f4132c9a3759eee8"
+                            ],
+                            [
+                                "BS_GA.1.bt2:md5,9aff51b1712758b891b0c427a988977f",
+                                "BS_GA.2.bt2:md5,579241d95941538b2e75bbdb6cfaa73d",
+                                "BS_GA.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee",
+                                "BS_GA.4.bt2:md5,6b64fa496ffa2af2af235e1c87f06a25",
+                                "BS_GA.rev.1.bt2:md5,dabf2d6f80ba7e8fc96dfdc203f6bbfd",
+                                "BS_GA.rev.2.bt2:md5,fac2f8b39b0e15dec7aa79a0ecf12b49",
+                                "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f"
+                            ]
+                        ],
+                        "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de"
+                    ]
+                ]
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,90950cf3155e6a77273de11ebb93a541",
+                "versions.yml:md5,b0160273bd1b3b049a2748c02496c6d1"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-26T16:24:46.519054694"
+    },
+    "Params: bwameth | generate fasta index | download bwameth index": {
+        "content": [
+            [
+                [
+                    {
+                        
+                    },
+                    "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de"
+                ]
+            ],
+            [
+                [
+                    {
+                        
+                    },
+                    "genome.fa.fai:md5,84f5b44c25877ac58b154706cc8bc451"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        
+                    },
+                    [
+                        "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de",
+                        "genome.fa.bwameth.c2t:md5,e51d48ed28fa0c26e2f9c9f13d09403b",
+                        "genome.fa.bwameth.c2t.amb:md5,010a242c6764efb30141868a45d698b3",
+                        "genome.fa.bwameth.c2t.ann:md5,09b4db3d87a2d4dac9e10e807f377110",
+                        "genome.fa.bwameth.c2t.bwt:md5,4646f8ae6bd523b7f4106bbd32eff95e",
+                        "genome.fa.bwameth.c2t.pac:md5,a662d7add09698e25c8152fd2306ec66",
+                        "genome.fa.bwameth.c2t.sa:md5,4a1e905b828396a1909669bc9c573d8d"
+                    ]
+                ]
+            ],
+            [
+                "versions.yml:md5,90950cf3155e6a77273de11ebb93a541",
+                "versions.yml:md5,b0160273bd1b3b049a2748c02496c6d1",
+                "versions.yml:md5,ee0146f5d2942f9ff466bf275567515e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-26T16:26:40.995024346"
+    },
+    "Params: bwameth | generate fasta index | generate bwameth index": {
+        "content": [
+            [
+                [
+                    {
+                        
+                    },
+                    "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de"
+                ]
+            ],
+            [
+                [
+                    {
+                        
+                    },
+                    "genome.fa.fai:md5,84f5b44c25877ac58b154706cc8bc451"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        
+                    },
+                    [
+                        "genome.fa.bwameth.c2t:md5,e51d48ed28fa0c26e2f9c9f13d09403b",
+                        "genome.fa.bwameth.c2t.amb:md5,010a242c6764efb30141868a45d698b3",
+                        "genome.fa.bwameth.c2t.ann:md5,09b4db3d87a2d4dac9e10e807f377110",
+                        "genome.fa.bwameth.c2t.bwt:md5,4646f8ae6bd523b7f4106bbd32eff95e",
+                        "genome.fa.bwameth.c2t.pac:md5,a662d7add09698e25c8152fd2306ec66",
+                        "genome.fa.bwameth.c2t.sa:md5,4a1e905b828396a1909669bc9c573d8d"
+                    ]
+                ]
+            ],
+            [
+                "versions.yml:md5,3a92f9ed1831ae3a68bc15886e7a95a1",
+                "versions.yml:md5,90950cf3155e6a77273de11ebb93a541",
+                "versions.yml:md5,ee0146f5d2942f9ff466bf275567515e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-26T16:27:06.257485123"
+    },
+    "Params: bismark_hisat | generate bismark index (hisat2)": {
+        "content": [
+            [
+                [
+                    {
+                        
+                    },
+                    "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        
+                    },
+                    [
+                        [
+                            [
+                                "BS_CT.1.ht2:md5,273c7686fc1dc7d93e36433592367f81",
+                                "BS_CT.2.ht2:md5,752a03fc364115fc910e5a28ae154382",
+                                "BS_CT.3.ht2:md5,b41e72eefad74e8ede411c78a5bd5dee",
+                                "BS_CT.4.ht2:md5,02b3d1855a67fd9cbb4c411406a22fde",
+                                "BS_CT.5.ht2:md5,d117de4c2c910a1ae7f0459c11ba6018",
+                                "BS_CT.6.ht2:md5,4097a785a8d1ca92489d83b4c613a50b",
+                                "BS_CT.7.ht2:md5,9013eccd91ad614d7893c739275a394f",
+                                "BS_CT.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb",
+                                "genome_mfa.CT_conversion.fa:md5,4dd181b65f1f3549f4132c9a3759eee8"
+                            ],
+                            [
+                                "BS_GA.1.ht2:md5,c2b02b7987f4ac0578332204678674cd",
+                                "BS_GA.2.ht2:md5,579241d95941538b2e75bbdb6cfaa73d",
+                                "BS_GA.3.ht2:md5,b41e72eefad74e8ede411c78a5bd5dee",
+                                "BS_GA.4.ht2:md5,6b64fa496ffa2af2af235e1c87f06a25",
+                                "BS_GA.5.ht2:md5,43aa1c78c6ec18c4165cf25159578fee",
+                                "BS_GA.6.ht2:md5,2dc0f049d7d0f2a51822df8b195dce41",
+                                "BS_GA.7.ht2:md5,9013eccd91ad614d7893c739275a394f",
+                                "BS_GA.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb",
+                                "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f"
+                            ]
+                        ],
+                        "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de"
+                    ]
+                ]
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,90950cf3155e6a77273de11ebb93a541",
+                "versions.yml:md5,b0160273bd1b3b049a2748c02496c6d1"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-26T16:26:00.163900219"
+    },
+    "Params: bismark_hisat | download bismark index (hisat2)": {
+        "content": [
+            [
+                [
+                    {
+                        
+                    },
+                    "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        
+                    },
+                    [
+                        [
+                            [
+                                "BS_CT.1.ht2:md5,273c7686fc1dc7d93e36433592367f81",
+                                "BS_CT.2.ht2:md5,752a03fc364115fc910e5a28ae154382",
+                                "BS_CT.3.ht2:md5,b41e72eefad74e8ede411c78a5bd5dee",
+                                "BS_CT.4.ht2:md5,02b3d1855a67fd9cbb4c411406a22fde",
+                                "BS_CT.5.ht2:md5,d117de4c2c910a1ae7f0459c11ba6018",
+                                "BS_CT.6.ht2:md5,4097a785a8d1ca92489d83b4c613a50b",
+                                "BS_CT.7.ht2:md5,9013eccd91ad614d7893c739275a394f",
+                                "BS_CT.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb",
+                                "genome_mfa.CT_conversion.fa:md5,4dd181b65f1f3549f4132c9a3759eee8"
+                            ],
+                            [
+                                "BS_GA.1.ht2:md5,c2b02b7987f4ac0578332204678674cd",
+                                "BS_GA.2.ht2:md5,579241d95941538b2e75bbdb6cfaa73d",
+                                "BS_GA.3.ht2:md5,b41e72eefad74e8ede411c78a5bd5dee",
+                                "BS_GA.4.ht2:md5,6b64fa496ffa2af2af235e1c87f06a25",
+                                "BS_GA.5.ht2:md5,43aa1c78c6ec18c4165cf25159578fee",
+                                "BS_GA.6.ht2:md5,2dc0f049d7d0f2a51822df8b195dce41",
+                                "BS_GA.7.ht2:md5,9013eccd91ad614d7893c739275a394f",
+                                "BS_GA.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb",
+                                "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f"
+                            ]
+                        ],
+                        "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de"
+                    ]
+                ]
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,90950cf3155e6a77273de11ebb93a541",
+                "versions.yml:md5,b0160273bd1b3b049a2748c02496c6d1"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-26T16:25:35.90378279"
+    },
+    "Params: bwameth | download fasta index | download bwameth index": {
+        "content": [
+            [
+                [
+                    {
+                        
+                    },
+                    "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de"
+                ]
+            ],
+            [
+                "/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai"
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        
+                    },
+                    [
+                        "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de",
+                        "genome.fa.bwameth.c2t:md5,e51d48ed28fa0c26e2f9c9f13d09403b",
+                        "genome.fa.bwameth.c2t.amb:md5,010a242c6764efb30141868a45d698b3",
+                        "genome.fa.bwameth.c2t.ann:md5,09b4db3d87a2d4dac9e10e807f377110",
+                        "genome.fa.bwameth.c2t.bwt:md5,4646f8ae6bd523b7f4106bbd32eff95e",
+                        "genome.fa.bwameth.c2t.pac:md5,a662d7add09698e25c8152fd2306ec66",
+                        "genome.fa.bwameth.c2t.sa:md5,4a1e905b828396a1909669bc9c573d8d"
+                    ]
+                ]
+            ],
+            [
+                "versions.yml:md5,90950cf3155e6a77273de11ebb93a541",
+                "versions.yml:md5,b0160273bd1b3b049a2748c02496c6d1"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-26T16:26:14.893224201"
+    },
+    "Params: bismark | generate bismark index (bowtie2)": {
+        "content": [
+            [
+                [
+                    {
+                        
+                    },
+                    "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        
+                    },
+                    [
+                        [
+                            [
+                                "BS_CT.1.bt2:md5,d53bef7d951c7d08e327944581c911eb",
+                                "BS_CT.2.bt2:md5,752a03fc364115fc910e5a28ae154382",
+                                "BS_CT.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee",
+                                "BS_CT.4.bt2:md5,02b3d1855a67fd9cbb4c411406a22fde",
+                                "BS_CT.rev.1.bt2:md5,52ae603fff473b3b25eecd36c533edb9",
+                                "BS_CT.rev.2.bt2:md5,0e290e05f7dae065cae54e29ed97afe5",
+                                "genome_mfa.CT_conversion.fa:md5,4dd181b65f1f3549f4132c9a3759eee8"
+                            ],
+                            [
+                                "BS_GA.1.bt2:md5,9aff51b1712758b891b0c427a988977f",
+                                "BS_GA.2.bt2:md5,579241d95941538b2e75bbdb6cfaa73d",
+                                "BS_GA.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee",
+                                "BS_GA.4.bt2:md5,6b64fa496ffa2af2af235e1c87f06a25",
+                                "BS_GA.rev.1.bt2:md5,dabf2d6f80ba7e8fc96dfdc203f6bbfd",
+                                "BS_GA.rev.2.bt2:md5,fac2f8b39b0e15dec7aa79a0ecf12b49",
+                                "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f"
+                            ]
+                        ],
+                        "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de"
+                    ]
+                ]
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,90950cf3155e6a77273de11ebb93a541",
+                "versions.yml:md5,dc24c245324a3b8a8328f1ed6abd3f7c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-26T16:25:20.094964567"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/nextflow.config b/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/nextflow.config
new file mode 100644
index 00000000000..ba4fa6f6b8d
--- /dev/null
+++ b/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: BISMARK_GENOMEPREPARATION {
+        ext.args = { params.aligner == 'bismark_hisat' ? ' --hisat2' : ' --bowtie2' }
+    }
+}