diff --git a/conf/base.config b/conf/base.config
index ca753f3..386bbb4 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -100,4 +100,16 @@ process {
     withName:CUSTOM_DUMPSOFTWAREVERSIONS {
         cache = false
     }
+
+    withName: SEQKIT_SPLIT2 {
+        cpus   = { log_increase_cpus(2, 1*task.attempt, meta.read_count/1000000, 2) }
+        memory = { check_max( 2.GB + 500.MB * log_increase_cpus(2, 1*task.attempt, meta.read_count/1000000, 2), 'memory' ) }
+        time   = { check_max( 1.h * Math.ceil( meta.read_count / 1000000 ) * task.attempt, 'time' ) }
+    }
+
+    withName: SAMTOOLS_SPLIT {
+        cpus   = { log_increase_cpus(2, 2*task.attempt, 1, 2) }
+        memory = { check_max( 1.GB * task.attempt, 'memory' ) }
+        time   = { check_max( 2.hour * task.attempt, 'time' ) }
+    }
 }
diff --git a/conf/modules.config b/conf/modules.config
index 089592e..d14e0ef 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -28,6 +28,11 @@ process {
         ext.prefix = { "${meta.id}.merge" }
     }
 
+    withName: SAMTOOLS_MERGE_CHUNKS {
+        ext.args = { "-c -p" }
+        ext.prefix = { "${meta.id}.merge" }
+    }
+
     // If custom header provided, this is inserted in place of existing
     // @HD and @SQ lines, while preserving any other header entries
     withName: SAMTOOLS_REHEADER {
@@ -100,5 +105,13 @@ process {
             pattern: '*_versions.yml'
         ]
     }
+   
+    withName: SEQKIT_SPLIT2 {
+        ext.args = "--by-part 10"
+    }
 
+    withName: SAMTOOLS_SPLIT {
+        ext.args = "-h"
+        ext.chunk_size = 10000
+    }
 }
diff --git a/modules.json b/modules.json
index 113030b..74e9748 100644
--- a/modules.json
+++ b/modules.json
@@ -84,7 +84,17 @@
                     "samtools/view": {
                         "branch": "master",
                         "git_sha": "6c2309aaec566c0d44a6cf14d4b2d0c51afe2e91",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
+                    },
+                    "seqkit/split2": {
+                        "branch": "master",
+                        "git_sha": "2be41ca2cc780eca4293d1b0dd3850b0b7ac40a3",
+                        "installed_by": [
+                            "modules"
+                        ],
+                        "patch": "modules/nf-core/seqkit/split2/seqkit-split2.diff"
                     },
                     "untar": {
                         "branch": "master",
diff --git a/modules/local/samtools_split.nf b/modules/local/samtools_split.nf
new file mode 100644
index 0000000..b5ac080
--- /dev/null
+++ b/modules/local/samtools_split.nf
@@ -0,0 +1,62 @@
+process SAMTOOLS_SPLIT {
+    tag "$meta.id"
+    label "process_high"
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
+
+    input:
+    tuple val(meta), path(reads)
+    tuple val(meta2), path(fasta)
+
+    output:
+    tuple val(meta), path("*.bam"), optional: true, emit: chunked_bam
+    tuple val(meta), path("*.cram"), optional: true, emit: chunked_cram
+    
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def chunk_size = task.ext.chunk_size ?: 10000
+    def reference = fasta ? "--reference ${fasta}" : ""
+    def file_extension = reads.name.split('\\.')[-1]
+    def cpus = task.ext.cpus ?: 1
+
+    """
+    # Convert BAM or CRAM to SAM
+    if [ "${file_extension}" == "bam" ]; then
+        samtools view -@ ${cpus} ${args} ${reads} > ${prefix}.sam
+
+        # Split SAM file into chunks
+        split -l ${chunk_size} ${prefix}.sam ${prefix}_part_
+
+        # Convert each chunk back to BAM
+        for chunk in ${prefix}_part_*; do
+            samtools view -@ ${cpus} -b -h \$chunk > \${chunk}.bam
+        done
+    elif [ "${file_extension}" == "cram" ]; then
+        samtools view -@ ${cpus} ${args} ${reference} ${reads} > ${prefix}.sam
+        # Split SAM file into chunks
+        split -l ${chunk_size} ${prefix}.sam ${prefix}_part_
+
+        # Convert each chunk back to BAM
+        for chunk in ${prefix}_part_*; do
+            samtools view -@ ${cpus} -b -h \$chunk > \${chunk}.cram
+        done
+    else
+        echo "Unsupported file type: ${file_extension}"
+        exit 1
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/seqkit/split2/environment.yml b/modules/nf-core/seqkit/split2/environment.yml
new file mode 100644
index 0000000..85716aa
--- /dev/null
+++ b/modules/nf-core/seqkit/split2/environment.yml
@@ -0,0 +1,7 @@
+name: seqkit_split2
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::seqkit=2.8.1
diff --git a/modules/nf-core/seqkit/split2/main.nf b/modules/nf-core/seqkit/split2/main.nf
new file mode 100644
index 0000000..b4543b8
--- /dev/null
+++ b/modules/nf-core/seqkit/split2/main.nf
@@ -0,0 +1,51 @@
+process SEQKIT_SPLIT2 {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0' :
+        'biocontainers/seqkit:2.8.1--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("**/*.gz"), emit: reads
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args   = task.ext.args   ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if(reads instanceof List && reads.size() == 2){
+        """
+        seqkit \\
+            split2 \\
+            $args \\
+            --threads $task.cpus \\
+            --read1 ${reads[0]} \\
+            --read2 ${reads[1]}
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            seqkit: \$(echo \$(seqkit 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+        END_VERSIONS
+        """
+    } else {
+        """
+        seqkit \\
+            split2 \\
+            $args \\
+            --threads $task.cpus \\
+            $reads
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            seqkit: \$(echo \$(seqkit 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+        END_VERSIONS
+        """
+    }
+}
diff --git a/modules/nf-core/seqkit/split2/meta.yml b/modules/nf-core/seqkit/split2/meta.yml
new file mode 100644
index 0000000..14babd4
--- /dev/null
+++ b/modules/nf-core/seqkit/split2/meta.yml
@@ -0,0 +1,42 @@
+name: seqkit_split2
+description: Split single or paired-end fastq.gz files
+keywords:
+  - split
+  - fastq
+  - seqkit
+tools:
+  - seqkit:
+      description: |
+        Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
+      homepage: https://github.com/shenwei356/seqkit
+      documentation: https://bioinf.shenwei.me/seqkit/
+      doi: 10.1371/journal.pone.0163962
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: FastQ files
+      pattern: "*.{fq.gz/fastq.gz}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: Split fastq files
+      pattern: "*.{fq.gz/fastq.gz}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@FriederikeHanssen"
+maintainers:
+  - "@FriederikeHanssen"
diff --git a/modules/nf-core/seqkit/split2/seqkit-split2.diff b/modules/nf-core/seqkit/split2/seqkit-split2.diff
new file mode 100644
index 0000000..f6d5ce7
--- /dev/null
+++ b/modules/nf-core/seqkit/split2/seqkit-split2.diff
@@ -0,0 +1,34 @@
+Changes in module 'nf-core/seqkit/split2'
+--- modules/nf-core/seqkit/split2/main.nf
++++ modules/nf-core/seqkit/split2/main.nf
+@@ -20,14 +20,14 @@
+     script:
+     def args   = task.ext.args   ?: ''
+     def prefix = task.ext.prefix ?: "${meta.id}"
+-    if(meta.single_end){
++    if(reads instanceof List && reads.size() == 2){
+         """
+         seqkit \\
+             split2 \\
+             $args \\
+             --threads $task.cpus \\
+-            $reads \\
+-            --out-dir ${prefix}
++            --read1 ${reads[0]} \\
++            --read2 ${reads[1]}
+ 
+         cat <<-END_VERSIONS > versions.yml
+         "${task.process}":
+@@ -40,9 +40,7 @@
+             split2 \\
+             $args \\
+             --threads $task.cpus \\
+-            --read1 ${reads[0]} \\
+-            --read2 ${reads[1]} \\
+-            --out-dir ${prefix}
++            $reads
+ 
+         cat <<-END_VERSIONS > versions.yml
+         "${task.process}":
+
+************************************************************
diff --git a/modules/nf-core/seqkit/split2/tests/length.config b/modules/nf-core/seqkit/split2/tests/length.config
new file mode 100644
index 0000000..64d8a9a
--- /dev/null
+++ b/modules/nf-core/seqkit/split2/tests/length.config
@@ -0,0 +1,5 @@
+process {
+    withName: SEQKIT_SPLIT2 {
+        ext.args = '--by-length 8K'
+    }
+}
diff --git a/modules/nf-core/seqkit/split2/tests/main.nf.test b/modules/nf-core/seqkit/split2/tests/main.nf.test
new file mode 100644
index 0000000..abf8d06
--- /dev/null
+++ b/modules/nf-core/seqkit/split2/tests/main.nf.test
@@ -0,0 +1,222 @@
+nextflow_process {
+
+    name "Test Process SEQKIT_SPLIT2"
+    script "../main.nf"
+    process "SEQKIT_SPLIT2"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "seqkit"
+    tag "seqkit/split2"
+
+    test("single_end - length") {
+
+        config "./length.config"
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:true ], // meta map
+                             [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+                     ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("paired_end - length") {
+
+        config "./length.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                             [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                               file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+                     ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("single_end - length - stub") {
+
+        options "-stub"
+        config "./length.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:true ], // meta map
+                             [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+                     ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("single_end - part") {
+
+        config "./part.config"
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:true ], // meta map
+                             [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+                     ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("paired_end - part") {
+
+        config "./part.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                             [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                               file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+                     ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("single_end - part - stub") {
+
+        options "-stub"
+        config "./part.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:true ], // meta map
+                             [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+                     ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("single_end - size") {
+
+        config "./size.config"
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:true ], // meta map
+                             [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+                     ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("paired_end - size") {
+
+        config "./size.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:false ], // meta map
+                             [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                               file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+                     ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("single_end - size - stub") {
+
+        options "-stub"
+        config "./size.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test', single_end:true ], // meta map
+                             [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+                     ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/seqkit/split2/tests/main.nf.test.snap b/modules/nf-core/seqkit/split2/tests/main.nf.test.snap
new file mode 100644
index 0000000..071e358
--- /dev/null
+++ b/modules/nf-core/seqkit/split2/tests/main.nf.test.snap
@@ -0,0 +1,414 @@
+{
+    "paired_end - size": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.part_001.fastq.gz:md5,ecc4b1841cd94704bba742ea4dcd48b0",
+                            "test_1.part_002.fastq.gz:md5,b3de467f2b6ab0d14e1f6ce14932a411",
+                            "test_2.part_001.fastq.gz:md5,201ee95b559240e27830970b78a547c8",
+                            "test_2.part_002.fastq.gz:md5,35ff29a76f34b2507a37287352324650"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.part_001.fastq.gz:md5,ecc4b1841cd94704bba742ea4dcd48b0",
+                            "test_1.part_002.fastq.gz:md5,b3de467f2b6ab0d14e1f6ce14932a411",
+                            "test_2.part_001.fastq.gz:md5,201ee95b559240e27830970b78a547c8",
+                            "test_2.part_002.fastq.gz:md5,35ff29a76f34b2507a37287352324650"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-08T05:49:27.111190403"
+    },
+    "single_end - size": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_1.part_001.fastq.gz:md5,ecc4b1841cd94704bba742ea4dcd48b0",
+                            "test_1.part_002.fastq.gz:md5,b3de467f2b6ab0d14e1f6ce14932a411"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_1.part_001.fastq.gz:md5,ecc4b1841cd94704bba742ea4dcd48b0",
+                            "test_1.part_002.fastq.gz:md5,b3de467f2b6ab0d14e1f6ce14932a411"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-08T05:43:42.879258276"
+    },
+    "single_end - part": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_1.part_001.fastq.gz:md5,b3c4d28be7ea9b960fbf1cb452adb53c",
+                            "test_1.part_002.fastq.gz:md5,c134c70c5b70c6b3c65979448b38917e",
+                            "test_1.part_003.fastq.gz:md5,822a40283637e2715e77d1ed0ed5bd52"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_1.part_001.fastq.gz:md5,b3c4d28be7ea9b960fbf1cb452adb53c",
+                            "test_1.part_002.fastq.gz:md5,c134c70c5b70c6b3c65979448b38917e",
+                            "test_1.part_003.fastq.gz:md5,822a40283637e2715e77d1ed0ed5bd52"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-08T05:43:16.85414188"
+    },
+    "single_end - length": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_1.part_001.fastq.gz:md5,ffc87eb34d91d23ec9095bd8609a6a70",
+                            "test_1.part_002.fastq.gz:md5,8d71a0abe239e05e5c57c4d27c799a1d"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_1.part_001.fastq.gz:md5,ffc87eb34d91d23ec9095bd8609a6a70",
+                            "test_1.part_002.fastq.gz:md5,8d71a0abe239e05e5c57c4d27c799a1d"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-08T05:42:47.553659985"
+    },
+    "single_end - size - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_1.part_001.fastq.gz:md5,ecc4b1841cd94704bba742ea4dcd48b0",
+                            "test_1.part_002.fastq.gz:md5,b3de467f2b6ab0d14e1f6ce14932a411"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_1.part_001.fastq.gz:md5,ecc4b1841cd94704bba742ea4dcd48b0",
+                            "test_1.part_002.fastq.gz:md5,b3de467f2b6ab0d14e1f6ce14932a411"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-08T05:44:01.29740288"
+    },
+    "single_end - part - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_1.part_001.fastq.gz:md5,b3c4d28be7ea9b960fbf1cb452adb53c",
+                            "test_1.part_002.fastq.gz:md5,c134c70c5b70c6b3c65979448b38917e",
+                            "test_1.part_003.fastq.gz:md5,822a40283637e2715e77d1ed0ed5bd52"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_1.part_001.fastq.gz:md5,b3c4d28be7ea9b960fbf1cb452adb53c",
+                            "test_1.part_002.fastq.gz:md5,c134c70c5b70c6b3c65979448b38917e",
+                            "test_1.part_003.fastq.gz:md5,822a40283637e2715e77d1ed0ed5bd52"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-08T05:43:33.964460368"
+    },
+    "paired_end - length - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "reads": [
+                    
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-08T05:42:57.687195505"
+    },
+    "single_end - length - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_1.part_001.fastq.gz:md5,ffc87eb34d91d23ec9095bd8609a6a70",
+                            "test_1.part_002.fastq.gz:md5,8d71a0abe239e05e5c57c4d27c799a1d"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        [
+                            "test_1.part_001.fastq.gz:md5,ffc87eb34d91d23ec9095bd8609a6a70",
+                            "test_1.part_002.fastq.gz:md5,8d71a0abe239e05e5c57c4d27c799a1d"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-08T05:43:07.15316163"
+    },
+    "paired_end - part": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.part_001.fastq.gz:md5,b3c4d28be7ea9b960fbf1cb452adb53c",
+                            "test_1.part_002.fastq.gz:md5,c134c70c5b70c6b3c65979448b38917e",
+                            "test_1.part_003.fastq.gz:md5,822a40283637e2715e77d1ed0ed5bd52",
+                            "test_2.part_001.fastq.gz:md5,13d14d69744bd93c8c51873b529bf714",
+                            "test_2.part_002.fastq.gz:md5,5f5a78d78f312164a1159c62d65c15f1",
+                            "test_2.part_003.fastq.gz:md5,48bcbceb485b73bcf1f198e252b016d8"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.part_001.fastq.gz:md5,b3c4d28be7ea9b960fbf1cb452adb53c",
+                            "test_1.part_002.fastq.gz:md5,c134c70c5b70c6b3c65979448b38917e",
+                            "test_1.part_003.fastq.gz:md5,822a40283637e2715e77d1ed0ed5bd52",
+                            "test_2.part_001.fastq.gz:md5,13d14d69744bd93c8c51873b529bf714",
+                            "test_2.part_002.fastq.gz:md5,5f5a78d78f312164a1159c62d65c15f1",
+                            "test_2.part_003.fastq.gz:md5,48bcbceb485b73bcf1f198e252b016d8"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-08T05:48:43.715062381"
+    },
+    "paired_end - length": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.part_001.fastq.gz:md5,ffc87eb34d91d23ec9095bd8609a6a70",
+                            "test_1.part_002.fastq.gz:md5,8d71a0abe239e05e5c57c4d27c799a1d",
+                            "test_2.part_001.fastq.gz:md5,77b9076f82a762711582584342bde5a1",
+                            "test_2.part_002.fastq.gz:md5,33bb6e3edc759baa7ba6580da36def48"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "test_1.part_001.fastq.gz:md5,ffc87eb34d91d23ec9095bd8609a6a70",
+                            "test_1.part_002.fastq.gz:md5,8d71a0abe239e05e5c57c4d27c799a1d",
+                            "test_2.part_001.fastq.gz:md5,77b9076f82a762711582584342bde5a1",
+                            "test_2.part_002.fastq.gz:md5,33bb6e3edc759baa7ba6580da36def48"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,7725bee2f34895f4c1678afacf87ed4f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-08T05:46:21.786837526"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/seqkit/split2/tests/part.config b/modules/nf-core/seqkit/split2/tests/part.config
new file mode 100644
index 0000000..2436bfb
--- /dev/null
+++ b/modules/nf-core/seqkit/split2/tests/part.config
@@ -0,0 +1,5 @@
+process {
+    withName: SEQKIT_SPLIT2 {
+        ext.args = '--by-part 3'
+    }
+}
diff --git a/modules/nf-core/seqkit/split2/tests/size.config b/modules/nf-core/seqkit/split2/tests/size.config
new file mode 100644
index 0000000..42a153d
--- /dev/null
+++ b/modules/nf-core/seqkit/split2/tests/size.config
@@ -0,0 +1,5 @@
+process {
+    withName: SEQKIT_SPLIT2 {
+        ext.args = '--by-size 50'
+    }
+}
diff --git a/modules/nf-core/seqkit/split2/tests/tags.yml b/modules/nf-core/seqkit/split2/tests/tags.yml
new file mode 100644
index 0000000..cd4f5c4
--- /dev/null
+++ b/modules/nf-core/seqkit/split2/tests/tags.yml
@@ -0,0 +1,2 @@
+seqkit/split2:
+  - "modules/nf-core/seqkit/split2/**"
diff --git a/subworkflows/local/align_ont.nf b/subworkflows/local/align_ont.nf
index ef1a021..b1681df 100644
--- a/subworkflows/local/align_ont.nf
+++ b/subworkflows/local/align_ont.nf
@@ -4,6 +4,8 @@
 
 include { MINIMAP2_ALIGN } from '../../modules/nf-core/minimap2/align/main'
 include { SAMTOOLS_MERGE } from '../../modules/nf-core/samtools/merge/main'
+include { SAMTOOLS_MERGE as SAMTOOLS_MERGE_CHUNKS } from '../../modules/nf-core/samtools/merge/main'
+include { SEQKIT_SPLIT2 } from '../../modules/nf-core/seqkit/split2/main'
 
 
 workflow ALIGN_ONT {
@@ -16,13 +18,43 @@ workflow ALIGN_ONT {
     ch_versions = Channel.empty()
 
 
+    // Split FASTQ files into chunks
+    SEQKIT_SPLIT2 ( reads )
+    ch_versions = ch_versions.mix ( SEQKIT_SPLIT2.out.versions.first() )
+
+
+    // Rename reads to include the chunk number, then align individually
+    SEQKIT_SPLIT2.out.reads
+    | flatMap { meta, reads -> 
+        reads.collect { 
+            def chunk_number = it.getName().toString().split('\\.')[-3]
+            def new_meta = meta.clone()
+            new_meta.id = "${meta.id}_${chunk_number}"
+            [new_meta, it]
+        }
+    }
+    | set { ch_reads_rg }
+
+
     // Align Fastq to Genome with minimap2. bam_format is set to true, making the output a *sorted* BAM
-    MINIMAP2_ALIGN ( reads, fasta, true, "bai", false, false )
+    MINIMAP2_ALIGN ( ch_reads_rg, fasta, true, "bai", false, false )
     ch_versions = ch_versions.mix ( MINIMAP2_ALIGN.out.versions.first() )
 
 
-    // Collect all alignment output by sample name
+    // Assign chunked BAM files to new identifiers
     MINIMAP2_ALIGN.out.bam
+    | map { meta, bam -> [['id': meta.id.split('_')[0..1].join('_'), 'datatype': meta.datatype, 'read_group':meta.read_group, 'read_count': meta.read_count ], bam] }
+    | groupTuple( by: [0] )
+    | set { ch_bams_merge }
+
+
+    // Merge chunks
+    SAMTOOLS_MERGE_CHUNKS ( ch_bams_merge, [ [], [] ], [ [], [] ] )
+    ch_versions = ch_versions.mix ( SAMTOOLS_MERGE_CHUNKS.out.versions.first() )
+
+
+    // Collect all alignment output by sample name
+    SAMTOOLS_MERGE_CHUNKS.out.bam
     | map { meta, bam -> [['id': meta.id.split('_')[0..-2].join('_'), 'datatype': meta.datatype], meta.read_count, bam] }
     | groupTuple ( by: [0] )
     | map { meta, read_counts, bams -> [meta + [read_count: read_counts.sum()], bams] }
diff --git a/subworkflows/local/align_pacbio.nf b/subworkflows/local/align_pacbio.nf
index f472a6c..e18a292 100644
--- a/subworkflows/local/align_pacbio.nf
+++ b/subworkflows/local/align_pacbio.nf
@@ -5,6 +5,8 @@
 include { FILTER_PACBIO  } from '../../subworkflows/local/filter_pacbio'
 include { MINIMAP2_ALIGN } from '../../modules/nf-core/minimap2/align/main'
 include { SAMTOOLS_MERGE } from '../../modules/nf-core/samtools/merge/main'
+include { SEQKIT_SPLIT2  } from '../../modules/nf-core/seqkit/split2/main'
+include { SAMTOOLS_MERGE as SAMTOOLS_MERGE_CHUNKS } from '../../modules/nf-core/samtools/merge/main'
 
 
 workflow ALIGN_PACBIO {
@@ -23,12 +25,43 @@ workflow ALIGN_PACBIO {
     ch_versions = ch_versions.mix ( FILTER_PACBIO.out.versions )
 
 
+    // Split FASTQ files into chunks
+    SEQKIT_SPLIT2 ( FILTER_PACBIO.out.fastq )
+    ch_versions = ch_versions.mix ( SEQKIT_SPLIT2.out.versions.first() )
+
+
+    // Rename reads to include the chunk number, then align individually
+    SEQKIT_SPLIT2.out.reads
+    | flatMap { meta, reads -> 
+        reads.collect { 
+            def chunk_number = it.getName().toString().split('\\.')[-3]
+            def new_meta = meta.clone()
+            new_meta.id = "${meta.id}_${chunk_number}"
+            [new_meta, it]
+        }
+    }
+    | set { ch_reads_rg }
+
+
     // Align Fastq to Genome with minimap2. bam_format is set to true, making the output a *sorted* BAM
-    MINIMAP2_ALIGN ( FILTER_PACBIO.out.fastq, fasta, true, "bai", false, false )
+    MINIMAP2_ALIGN ( ch_reads_rg, fasta, true, "bai", false, false )
     ch_versions = ch_versions.mix ( MINIMAP2_ALIGN.out.versions.first() )
 
-    // Collect all alignment output by sample name
+
+    // Assign chunked BAM files to new identifiers
     MINIMAP2_ALIGN.out.bam
+    | map { meta, bam -> [['id': meta.id.split('_')[0..1].join('_'), 'datatype': meta.datatype, 'read_group':meta.read_group, 'read_count': meta.read_count ], bam] }
+    | groupTuple( by: [0] )
+    | set { ch_bams_merge }
+
+
+    // Merge chunks
+    SAMTOOLS_MERGE_CHUNKS ( ch_bams_merge, [ [], [] ], [ [], [] ] )
+    ch_versions = ch_versions.mix ( SAMTOOLS_MERGE_CHUNKS.out.versions.first() )
+
+
+    // Collect all alignment output by sample name
+    SAMTOOLS_MERGE_CHUNKS.out.bam
     | map { meta, bam -> [['id': meta.id.split('_')[0..-2].join('_'), 'datatype': meta.datatype], meta.read_count, bam] }
     | groupTuple ( by: [0] )
     | map { meta, read_counts, bams -> [meta + [read_count: read_counts.sum()], bams] }
diff --git a/subworkflows/local/align_short.nf b/subworkflows/local/align_short.nf
index e74b480..df97d12 100644
--- a/subworkflows/local/align_short.nf
+++ b/subworkflows/local/align_short.nf
@@ -1,11 +1,15 @@
 //
 // Align short read (HiC and Illumina) data against the genome
 //
+params.num_chunks = 4
 
 include { SAMTOOLS_FASTQ    } from '../../modules/nf-core/samtools/fastq/main'
 include { BWAMEM2_MEM       } from '../../modules/nf-core/bwamem2/mem/main'
 include { SAMTOOLS_MERGE    } from '../../modules/nf-core/samtools/merge/main'
+include { SAMTOOLS_MERGE as SAMTOOLS_MERGE_CHUNKS } from '../../modules/nf-core/samtools/merge/main' 
 include { SAMTOOLS_SORMADUP } from '../../modules/local/samtools_sormadup'
+include { SEQKIT_SPLIT2     } from '../../modules/nf-core/seqkit/split2/main'
+include { SAMTOOLS_SPLIT    } from '../../modules/local/samtools_split'
 
 
 workflow ALIGN_SHORT {
@@ -28,13 +32,50 @@ workflow ALIGN_SHORT {
     | set { ch_reads }
 
 
+    // Split CRAM files into chunks
+    SAMTOOLS_SPLIT ( ch_reads.cram, fasta )
+    ch_versions = ch_versions.mix ( SAMTOOLS_SPLIT.out.versions.first() )
+
+
+    // Assign chunked files to new identifiers
+    SAMTOOLS_SPLIT.out.chunked_cram
+    | flatMap { meta, chunked_cram -> 
+        chunked_cram.collect { 
+            def chunk_number = it.getName().toString().split('\\.')[0].split('_')[2..3].join('_')
+            def new_meta = meta.clone()
+            new_meta.id = "${meta.id}_${chunk_number}"
+            [new_meta, it]
+        }
+    }
+    | set { ch_chunks_from_cram }
+
+
     // Convert from CRAM to FASTQ only if CRAM files were provided as input
-    SAMTOOLS_FASTQ ( ch_reads.cram, false )
+    SAMTOOLS_FASTQ ( ch_chunks_from_cram, false )
     ch_versions = ch_versions.mix ( SAMTOOLS_FASTQ.out.versions.first() )
-    
-    
-    SAMTOOLS_FASTQ.out.fastq
-    | mix ( ch_reads.fastq )
+
+
+    // Split FASTQ files into chunks
+    SEQKIT_SPLIT2 ( ch_reads.fastq )
+    ch_versions = ch_versions.mix ( SEQKIT_SPLIT2.out.versions.first() )
+
+
+    // Rename reads to include the chunk number, then align individually
+    SEQKIT_SPLIT2.out.reads
+    | flatMap { meta, reads -> 
+        reads.collect { 
+            def chunk_number = it.getName().toString().split('\\.')[-3]
+            def new_meta = meta.clone()
+            new_meta.id = "${meta.id}_${chunk_number}"
+            [new_meta, it]
+        }
+    }
+    | set { ch_chunks_from_fastq }
+
+
+    // Mix FASTQ files
+    ch_chunks_from_fastq
+    | mix ( SAMTOOLS_FASTQ.out.fastq )
     | set { ch_reads_fastq }
 
 
@@ -43,8 +84,18 @@ workflow ALIGN_SHORT {
     ch_versions = ch_versions.mix ( BWAMEM2_MEM.out.versions.first() )
 
 
-    // Collect all BWAMEM2 output by sample name
     BWAMEM2_MEM.out.bam
+    | map { meta, bam -> [['id': meta.id.split('_')[0..1].join('_'), 'datatype': meta.datatype, 'read_group':meta.read_group, 'read_count': meta.read_count ], bam] }
+    | groupTuple( by: [0] )
+    | set { ch_bams_merge }
+
+
+    SAMTOOLS_MERGE_CHUNKS ( ch_bams_merge, [ [], [] ], [ [], [] ] )
+    ch_versions = ch_versions.mix ( SAMTOOLS_MERGE_CHUNKS.out.versions.first() )
+
+
+    // Collect all SAMTOOLS_SORT output by sample name
+    SAMTOOLS_MERGE_CHUNKS.out.bam
     | map { meta, bam -> [['id': meta.id.split('_')[0..-2].join('_'), 'datatype': meta.datatype], meta.read_count, bam] }
     | groupTuple( by: [0] )
     | map { meta, read_counts, bams -> [meta + [read_count: read_counts.sum()], bams] }