diff --git a/bin/generate_cram_csv.sh b/bin/generate_cram_csv.sh
index 89920fd..9e56831 100755
--- a/bin/generate_cram_csv.sh
+++ b/bin/generate_cram_csv.sh
@@ -7,36 +7,42 @@
 # Author = yy5
 # ><((((°>    Y    ><((((°>    U     ><((((°>    M     ><((((°>     I     ><((((°>
 
+# NOTE: chunk_size is the number of containers per chunk (not records/reads)
+
 # Function to process chunking of a CRAM file
+
 chunk_cram() {
     local cram=$1
     local chunkn=$2
     local outcsv=$3
     local crai=$4
-    realcram=$(readlink -f ${cram})
-    # realcrai=$(readlink -f ${cram}.crai)
-    realcrai=$(readlink -f ${crai})
+    local chunk_size=$5
+
     local rgline=$(samtools view -H "${realcram}" | grep "@RG" | sed 's/\t/\\t/g' | sed "s/'//g")
     local ncontainers=$(zcat "${realcrai}" | wc -l)
-    # local ncontainers=$(cat "${realcram}" | wc -l)
     local base=$(basename "${realcram}" .cram)
-    local from=0
-    local to=10000
 
+    if [ $chunk_size -gt $ncontainers ]; then
+        chunk_size=$((ncontainers - 1))
+    fi
+    local from=0
+    local to=$((chunk_size - 1))
 
     while [ $to -lt $ncontainers ]; do
+        #echo "chunk $chunkn: $from - $to"
         echo "${realcram},${realcrai},${from},${to},${base},${chunkn},${rgline}" >> $outcsv
         from=$((to + 1))
-        ((to += 10000))
+        to=$((to + chunk_size))
         ((chunkn++))
     done
 
-    if [ $from -le $ncontainers ]; then
-        echo "${realcram},${realcrai},${from},${ncontainers},${base},${chunkn},${rgline}" >> $outcsv
+    # Catch any remainder
+    if [ $from -lt $ncontainers ]; then
+        to=$((ncontainers - 1))
+        #echo "chunk $chunkn: $from - $to"
+        echo "${realcram},${realcrai},${from},${to},${base},${chunkn},${rgline}" >> $outcsv
         ((chunkn++))
     fi
-
-    echo $chunkn
 }
 
 # Function to process a CRAM file
@@ -45,24 +51,23 @@ process_cram_file() {
     local chunkn=$2
     local outcsv=$3
     local crai=$4
+    local chunk_size=$5
 
     local read_groups=$(samtools view -H "$cram" | grep '@RG' | awk '{for(i=1;i<=NF;i++){if($i ~ /^ID:/){print substr($i,4)}}}')
     local num_read_groups=$(echo "$read_groups" | wc -w)
-
     if [ "$num_read_groups" -gt 1 ]; then
         # Multiple read groups: process each separately
         for rg in $read_groups; do
             local output_cram="$(basename "${cram%.cram}")_output_${rg}.cram"
             samtools view -h -r "$rg" -o "$output_cram" "$cram"
-            samtools index "$output_cram"
-            chunkn=$(chunk_cram "$output_cram" "$chunkn" "$outcsv" "$crai")
+            #chunkn=$(chunk_cram "$output_cram" "$chunkn" "$outcsv" "$crai" "$chunk_size")
+            chunk_cram "$output_cram" "$chunkn" "$outcsv" "$crai" "$chunk_size"
         done
     else
         # Single read group or no read groups
-        chunkn=$(chunk_cram "$cram" "$chunkn" "$outcsv" "$crai")
+        #chunkn=$(chunk_cram "$cram" "$chunkn" "$outcsv" "$crai" "$chunk_size")
+        chunk_cram "$cram" "$chunkn" "$outcsv" "$crai" "$chunk_size"
     fi
-
-    echo $chunkn
 }
 
 #  /\_/\        /\_/\
@@ -70,22 +75,25 @@ process_cram_file() {
 #  > ^ <        > ^ <
 
 # Check if cram_path is provided
-if [ -z "$1" ]; then
-    echo "Usage: $0 <cram_path>"
+if [ $# -lt 3 ]; then
+    echo "Usage: $0 <cram_path> <output_csv> <crai_file> <chunk_size>"
     exit 1
 fi
 
-# cram_path=$1
 cram=$1
-chunkn=0
 outcsv=$2
 crai=$3
+if [ -z "$4" ]; then
+    chunk_size=10000
+else
+    chunk_size=$4
+fi
+chunkn=0
 
-# # Loop through each CRAM file in the specified directory. cram cannot be the synlinked cram
-# for cram in ${cram_path}/*.cram; do
-#     realcram=$(readlink -f $cram)
-#     chunkn=$(process_cram_file $realcram $chunkn $outcsv)
-# done
+# Operates on a single CRAM file
 realcram=$(readlink -f $cram)
 realcrai=$(readlink -f $crai)
-chunkn=$(process_cram_file $realcram $chunkn $outcsv $realcrai)
+if [ -f "$outcsv" ]; then
+    rm "$outcsv"
+fi
+process_cram_file $realcram $chunkn $outcsv $realcrai $chunk_size
diff --git a/conf/modules.config b/conf/modules.config
index a7a59cb..ebf3fb0 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -15,14 +15,6 @@ process {
         ext.args = '-F 0x200 -nt'
     }
 
-    withName: '.*:.*:ALIGN_HIC:BWAMEM2_MEM' {
-        ext.args = { "-5SPCp -R ${meta.read_group}" }
-    }
-
-    withName: '.*:.*:ALIGN_ILLUMINA:BWAMEM2_MEM' {
-        ext.args = { "-R ${meta.read_group}" }
-    }
-
     withName: SAMTOOLS_MERGE {
         ext.args = { "-c -p" }
         ext.prefix = { "${meta.id}.merge" }
@@ -50,23 +42,47 @@ process {
         ext.args = "--output-fmt cram"
     }
 
-    withName: ".*:.*:HIC_BWAMEM2:CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT" {
+    withName: '.*:.*:ALIGN_HIC:BWAMEM2_MEM' {
+        ext.args = { "-5SPCp -R ${meta.read_group}" }
+    }
+
+    withName: '.*:.*:ALIGN_ILLUMINA:BWAMEM2_MEM' {
+        ext.args = { "-p -R ${meta.read_group}" }
+    }
+
+    withName: ".*:ALIGN_ILLUMINA:.*:CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT" {
         ext.args        = ""
-        ext.args1       = { "-F 0x200 -nt -1 '${base}_${chunkid}_1.fastq.gz'" }
+        ext.args1       = { "-F 0x200 -nt" }
+        ext.args2       = { "-p -R '${rglines}'" }
+        ext.args3       = "-mpu"
+        ext.args4       = { "--write-index -l1" }
+    }
+
+    withName: ".*:ALIGN_ILLUMINA:.*:CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT" {
+        ext.args        = ""
+        ext.args1       = { "-F 0x200 -nt" }
+        ext.args2       = { "-ax sr" }
+        ext.args3       = "-mpu"
+        ext.args4       = { "--write-index -l1" }
+    }
+
+    withName: ".*:ALIGN_HIC:.*:CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT" {
+        ext.args        = ""
+        ext.args1       = { "-F 0x200 -nt" }
         ext.args2       = { "-5SPCp -R '${rglines}'" }
         ext.args3       = "-mpu"
         ext.args4       = { "--write-index -l1" }
     }
 
-    withName: ".*:.*:HIC_MINIMAP2:CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT" {
+    withName: ".*:ALIGN_HIC:.*:CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT" {
         ext.args        = ""
-        ext.args1       = { "-F 0x200 -nt -1 '${base}_${chunkid}_1.fastq.gz'" }
+        ext.args1       = { "" }
         ext.args2       = { "-ax sr" }
         ext.args3       = "-mpu"
         ext.args4       = { "--write-index -l1" }
     }
 
-    withName: ".*:.*:HIC_MINIMAP2:MINIMAP2_INDEX" {
+    withName: "MINIMAP2_INDEX" {
         ext.args        = { "${fasta.size() > 2.5e9 ? (" -I " + Math.ceil(fasta.size()/1e9)+"G") : ""} "}
     }
 
@@ -105,6 +121,11 @@ process {
         ext.prefix = { "${bam.baseName}" }
     }
 
+    withName: SAMTOOLS_ADDREPLACERG {
+        ext.prefix = { "${input.baseName}_addRG" }
+        ext.args = { "-r ${meta.read_group} --no-PG" }
+    }
+
     withName: SAMTOOLS_STATS {
         ext.prefix = { "${input.baseName}" }
     }
diff --git a/conf/test.config b/conf/test.config
index e59b389..add9178 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -26,7 +26,7 @@ params {
     outdir = "${projectDir}/results"
 
     // Aligner
-    hic_aligner = "minimap2"
+    short_aligner = "minimap2"
 
     // Fasta references
     fasta = "https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/assembly/release/mMelMel3.1_paternal_haplotype/GCA_922984935.2.subset.fasta.gz"
diff --git a/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf b/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf
index 9b5ca29..667e49b 100644
--- a/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf
+++ b/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf
@@ -1,5 +1,5 @@
 process CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT {
-    tag "$meta.id"
+    tag "$meta.chunk_id"
     label "process_high"
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/local/cram_filter_minimap2_filter5end_fixmate_sort.nf b/modules/local/cram_filter_minimap2_filter5end_fixmate_sort.nf
index 8d8d69e..ceafb86 100644
--- a/modules/local/cram_filter_minimap2_filter5end_fixmate_sort.nf
+++ b/modules/local/cram_filter_minimap2_filter5end_fixmate_sort.nf
@@ -1,5 +1,5 @@
 process CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT {
-    tag "$meta.id"
+    tag "$meta.chunk_id"
     label "process_high"
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/local/generate_cram_csv.nf b/modules/local/generate_cram_csv.nf
index 6a3b120..f3cfe96 100644
--- a/modules/local/generate_cram_csv.nf
+++ b/modules/local/generate_cram_csv.nf
@@ -1,8 +1,10 @@
 process GENERATE_CRAM_CSV {
     tag "${meta.id}"
-    // label 'process_tiny'
+    label 'process_single'
 
-    container 'quay.io/sanger-tol/cramfilter_bwamem2_minimap2_samtools_perl:0.001-c1'
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://quay.io/sanger-tol/cramfilter_bwamem2_minimap2_samtools_perl:0.001-c1' :
+        'sanger-tol/cramfilter_bwamem2_minimap2_samtools_perl:0.001-c1' }"
 
     input:
     tuple val(meta), path(crampath), path(crai)
@@ -15,7 +17,7 @@ process GENERATE_CRAM_CSV {
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    generate_cram_csv.sh $crampath ${prefix}_cram.csv $crai
+    generate_cram_csv.sh $crampath ${prefix}_cram.csv $crai ${params.chunk_size}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/samtools_addreplacerg.nf b/modules/local/samtools_addreplacerg.nf
new file mode 100644
index 0000000..6515c3e
--- /dev/null
+++ b/modules/local/samtools_addreplacerg.nf
@@ -0,0 +1,56 @@
+process SAMTOOLS_ADDREPLACERG {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "bioconda::samtools=1.20"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
+
+    input:
+    tuple val(meta), path(input)
+
+    output:
+    tuple val(meta), path("${prefix}.bam"),                                    emit: bam,              optional: true
+    tuple val(meta), path("${prefix}.cram"),                                   emit: cram,             optional: true
+    tuple val(meta), path("${prefix}.sam"),                                    emit: sam,              optional: true
+    path  "versions.yml",                                                      emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    file_type = input.getExtension()
+    if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    """
+    samtools \\
+        addreplacerg \\
+        --threads $task.cpus \\
+        $args \\
+        -o ${prefix}.${file_type} \\
+        $input
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    file_type = input.getExtension()
+    if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+
+    """
+    touch ${prefix}.${file_type}
+    ${index}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/nextflow.config b/nextflow.config
index 8c3c4d0..d143247 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -15,8 +15,11 @@ params {
     bwamem2_index              = null
     fasta                      = null
     header                     = null
+
     // Aligner option
-    hic_aligner                = "minimap2" // Can choose minimap2 and bwamem2
+    short_aligner              = "minimap2" // Can choose minimap2 and bwamem2
+    chunk_size                 = 10000
+
     // Output format options
     outfmt                     = "cram"
     compression                = "crumble"
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 63a6999..91eb9f6 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -54,13 +54,6 @@
                     "fa_icon": "fas fa-envelope",
                     "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                     "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
-                },
-                "hic_aligner": {
-                    "type": "string",
-                    "description": "The aligner to be used for HiC reads.",
-                    "enum": ["bwamem2", "minimap2"],
-                    "default": "minimap2",
-                    "fa_icon": "fas fa-code"
                 }
             }
         },
@@ -93,6 +86,26 @@
                 }
             }
         },
+        "aligner_options": {
+            "title": "Aligner options",
+            "type": "object",
+            "description": "",
+            "default": "",
+            "properties": {
+                "short_aligner": {
+                    "type": "string",
+                    "default": "minimap2",
+                    "description": "Alignment method to use for short-reads (options are: \"minimap2\" or \"bwamem2\"",
+                    "enum": ["minimap2", "bwamem2"]
+                },
+                "chunk_size": {
+                    "type": "integer",
+                    "default": 10000,
+                    "description": "Chunk size for parallel processing of CRAM files, in number of containers",
+                    "minimum": 1
+                }
+            }
+        },
         "execution": {
             "title": "Execution",
             "type": "object",
@@ -292,6 +305,9 @@
         {
             "$ref": "#/definitions/reference_genome_options"
         },
+        {
+            "$ref": "#/definitions/aligner_options"
+        },
         {
             "$ref": "#/definitions/execution"
         },
diff --git a/subworkflows/local/align_short.nf b/subworkflows/local/align_short.nf
index cebc194..4f49cdc 100644
--- a/subworkflows/local/align_short.nf
+++ b/subworkflows/local/align_short.nf
@@ -2,21 +2,26 @@
 // Align short read (HiC and Illumina) data against the genome
 //
 
-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_SORMADUP } from '../../modules/local/samtools_sormadup'
-
+include { SAMTOOLS_FASTQ                        } from '../../modules/nf-core/samtools/fastq/main'
+include { SAMTOOLS_MERGE                        } from '../../modules/nf-core/samtools/merge/main'
+include { SAMTOOLS_SORMADUP                     } from '../../modules/local/samtools_sormadup'
+include { SAMTOOLS_INDEX                        } from '../../modules/nf-core/samtools/index/main'
+include { GENERATE_CRAM_CSV                     } from '../../modules/local/generate_cram_csv'
+include { SAMTOOLS_SORMADUP as CONVERT_CRAM     } from '../../modules/local/samtools_sormadup'
+include { SAMTOOLS_ADDREPLACERG                 } from '../../modules/local/samtools_addreplacerg'
+include { MINIMAP2_MAPREDUCE                    } from '../../subworkflows/local/minimap2_mapreduce'
+include { BWAMEM2_MAPREDUCE                     } from '../../subworkflows/local/bwamem2_mapreduce'
 
 workflow ALIGN_SHORT {
     take:
-    fasta    // channel: [ val(meta), /path/to/fasta ]
+    fasta    // channel: [ val(meta), /path/to/fasta ] reference_tuple
     index    // channel: [ val(meta), /path/to/bwamem2/ ]
-    reads    // channel: [ val(meta), /path/to/datafile ]
+    reads    // channel: [ val(meta), /path/to/datafile ] hic_reads_path
 
 
     main:
     ch_versions = Channel.empty()
+    ch_merged_bam   = Channel.empty()
 
     // Check file types and branch
     reads
@@ -28,23 +33,60 @@ workflow ALIGN_SHORT {
     | set { ch_reads }
 
 
-    // Convert from CRAM to FASTQ only if CRAM files were provided as input
-    SAMTOOLS_FASTQ ( ch_reads.cram, false )
-    ch_versions = ch_versions.mix ( SAMTOOLS_FASTQ.out.versions.first() )
-
-
-    SAMTOOLS_FASTQ.out.fastq
-    | mix ( ch_reads.fastq )
-    | set { ch_reads_fastq }
-
+    // Convert FASTQ to CRAM only if FASTQ were provided as input
+    CONVERT_CRAM ( ch_reads.fastq, fasta )
+    ch_versions = ch_versions.mix ( CONVERT_CRAM.out.versions )
+
+    SAMTOOLS_ADDREPLACERG ( CONVERT_CRAM.out.bam )
+    ch_versions = ch_versions.mix ( SAMTOOLS_ADDREPLACERG.out.versions )
+
+    SAMTOOLS_ADDREPLACERG.out.cram
+    | mix ( ch_reads.cram )
+    | set { ch_reads_cram }
+
+    // Index the CRAM file
+    SAMTOOLS_INDEX ( ch_reads_cram )
+    ch_versions = ch_versions.mix( SAMTOOLS_INDEX.out.versions )
+
+    ch_reads_cram
+    | join ( SAMTOOLS_INDEX.out.crai )
+    | set { ch_reads_cram_crai }
+
+
+    //
+    // MODULE: generate a CRAM CSV file containing the required parametres for CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT
+    //
+    GENERATE_CRAM_CSV( ch_reads_cram_crai )
+    ch_versions = ch_versions.mix( GENERATE_CRAM_CSV.out.versions )
+
+    //
+    // SUBWORKFLOW: mapping hic reads using minimap2 or bwamem2
+    //
+    if (params.short_aligner.startsWith("minimap")) {
+        MINIMAP2_MAPREDUCE (
+            fasta,
+            GENERATE_CRAM_CSV.out.csv
+        )
+        ch_versions         = ch_versions.mix( MINIMAP2_MAPREDUCE.out.versions )
+        ch_merged_bam           = ch_merged_bam.mix(MINIMAP2_MAPREDUCE.out.mergedbam)
+    } else {
+        BWAMEM2_MAPREDUCE (
+            fasta,
+            GENERATE_CRAM_CSV.out.csv,
+            index
+        )
+        ch_versions         = ch_versions.mix( BWAMEM2_MAPREDUCE.out.versions )
+        ch_merged_bam           = ch_merged_bam.mix(BWAMEM2_MAPREDUCE.out.mergedbam)
+    }
 
-    // Align Fastq to Genome and output sorted BAM
-    BWAMEM2_MEM ( ch_reads_fastq, index, fasta, true )
-    ch_versions = ch_versions.mix ( BWAMEM2_MEM.out.versions.first() )
+    ch_merged_bam
+    | combine( ch_reads_cram_crai )
+    | map { meta_bam, bam, meta_cram, cram, crai -> [ meta_cram, bam ] }
+    | set { ch_merged_bam }
 
 
-    // Collect all BWAMEM2 output by sample name
-    BWAMEM2_MEM.out.bam
+    // Collect all BAM output by sample name
+    ch_merged_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] }
@@ -58,7 +100,7 @@ workflow ALIGN_SHORT {
 
     // Merge, but only if there is more than 1 file
     SAMTOOLS_MERGE ( ch_bams.multi_bams, [ [], [] ], [ [], [] ] )
-    ch_versions = ch_versions.mix ( SAMTOOLS_MERGE.out.versions.first() )
+    ch_versions = ch_versions.mix ( SAMTOOLS_MERGE.out.versions )
 
 
     SAMTOOLS_MERGE.out.bam
diff --git a/subworkflows/local/align_short_hic.nf b/subworkflows/local/align_short_hic.nf
deleted file mode 100644
index 39e0cab..0000000
--- a/subworkflows/local/align_short_hic.nf
+++ /dev/null
@@ -1,116 +0,0 @@
-//
-// Align short read (HiC and Illumina) data against the genome
-//
-
-include { SAMTOOLS_FASTQ                        } from '../../modules/nf-core/samtools/fastq/main'
-include { SAMTOOLS_MERGE                        } from '../../modules/nf-core/samtools/merge/main'
-include { SAMTOOLS_SORMADUP                     } from '../../modules/local/samtools_sormadup'
-include { SAMTOOLS_INDEX                        } from '../../modules/nf-core/samtools/index/main'
-include { GENERATE_CRAM_CSV                     } from '../../modules/local/generate_cram_csv'
-include { SAMTOOLS_SORMADUP as CONVERT_CRAM     } from '../../modules/local/samtools_sormadup'
-include { HIC_MINIMAP2                          } from '../../subworkflows/local/hic_minimap2'
-include { HIC_BWAMEM2                           } from '../../subworkflows/local/hic_bwamem2'
-
-workflow ALIGN_SHORT_HIC {
-    take:
-    fasta    // channel: [ val(meta), /path/to/fasta ] reference_tuple
-    index    // channel: [ val(meta), /path/to/bwamem2/ ]
-    reads    // channel: [ val(meta), /path/to/datafile ] hic_reads_path
-
-
-    main:
-    ch_versions = Channel.empty()
-    ch_merged_bam   = Channel.empty()
-
-    // Check file types and branch
-    reads
-    | branch {
-        meta, reads ->
-            fastq : reads.findAll { it.getName().toLowerCase() =~ /.*f.*\.gz/ }
-            cram : true
-    }
-    | set { ch_reads }
-
-
-    // Convert FASTQ to CRAM only if FASTQ were provided as input
-    CONVERT_CRAM ( ch_reads.fastq, fasta )
-    ch_versions = ch_versions.mix (    CONVERT_CRAM.out.versions )
-
-    CONVERT_CRAM.out.bam
-    | mix ( ch_reads.cram )
-    | set { ch_reads_cram }
-
-
-    // Index the CRAM file
-    SAMTOOLS_INDEX ( ch_reads_cram )
-    ch_versions = ch_versions.mix( SAMTOOLS_INDEX.out.versions )
-
-    ch_reads_cram
-    | join ( SAMTOOLS_INDEX.out.crai )
-    | set { ch_reads_cram_crai }
-
-
-    //
-    // MODULE: generate a CRAM CSV file containing the required parametres for CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT
-    //
-    GENERATE_CRAM_CSV( ch_reads_cram_crai )
-    ch_versions = ch_versions.mix( GENERATE_CRAM_CSV.out.versions )
-
-
-    //
-    // SUBWORKFLOW: mapping hic reads using minimap2 or bwamem2
-    //
-    if (params.hic_aligner == 'minimap2') {
-        HIC_MINIMAP2 (
-            fasta,
-            GENERATE_CRAM_CSV.out.csv
-        )
-        ch_versions         = ch_versions.mix( HIC_MINIMAP2.out.versions )
-        ch_merged_bam           = ch_merged_bam.mix(HIC_MINIMAP2.out.mergedbam)
-    } else {
-        HIC_BWAMEM2 (
-            fasta,
-            GENERATE_CRAM_CSV.out.csv,
-            index
-        )
-        ch_versions         = ch_versions.mix( HIC_BWAMEM2.out.versions )
-        ch_merged_bam           = ch_merged_bam.mix(HIC_BWAMEM2.out.mergedbam)
-    }
-
-    ch_merged_bam
-    | combine( ch_reads_cram_crai )
-    | map { meta_bam, bam, meta_cram, cram, crai -> [ meta_cram, bam ] }
-    | set { ch_merged_bam }
-
-
-    // Collect all BAM output by sample name
-    ch_merged_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] }
-    | branch {
-        meta, bams ->
-            single_bam: bams.size() == 1
-            multi_bams: true
-    }
-    | set { ch_bams }
-
-
-    // Merge, but only if there is more than 1 file
-    SAMTOOLS_MERGE ( ch_bams.multi_bams, [ [], [] ], [ [], [] ] )
-    ch_versions = ch_versions.mix ( SAMTOOLS_MERGE.out.versions.first() )
-
-
-    SAMTOOLS_MERGE.out.bam
-    | mix ( ch_bams.single_bam )
-    | set { ch_bam }
-
-
-    // Mark duplicates
-    SAMTOOLS_SORMADUP ( ch_bam, fasta )
-    ch_versions = ch_versions.mix ( SAMTOOLS_SORMADUP.out.versions )
-
-    emit:
-    bam      = SAMTOOLS_SORMADUP.out.bam     // channel: [ val(meta), /path/to/bam ]
-    versions = ch_versions                   // channel: [ versions.yml ]
-}
diff --git a/subworkflows/local/hic_bwamem2.nf b/subworkflows/local/bwamem2_mapreduce.nf
similarity index 91%
rename from subworkflows/local/hic_bwamem2.nf
rename to subworkflows/local/bwamem2_mapreduce.nf
index edf4691..13711fb 100644
--- a/subworkflows/local/hic_bwamem2.nf
+++ b/subworkflows/local/bwamem2_mapreduce.nf
@@ -6,7 +6,7 @@
 include { CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT          } from '../../modules/local/cram_filter_align_bwamem2_fixmate_sort'
 include { SAMTOOLS_MERGE                                  } from '../../modules/nf-core/samtools/merge/main'
 
-workflow HIC_BWAMEM2 {
+workflow BWAMEM2_MAPREDUCE {
     take:
     fasta     // Channel: tuple [ val(meta), path( file )      ]
     csv_ch
@@ -22,7 +22,8 @@ workflow HIC_BWAMEM2 {
         .splitCsv()
         .map{ cram_id, cram_info ->
             tuple([
-                    id: cram_id.id
+                    id: cram_id.id,
+                    chunk_id: cram_id.id + "_" + cram_info[5]
                     ],
                 file(cram_info[0]),
                 cram_info[1],
@@ -35,8 +36,9 @@ workflow HIC_BWAMEM2 {
     }
     .set { ch_filtering_input }
 
+
     //
-    // MODULE: map hic reads by 10,000 container per time using bwamem2
+    // MODULE: map hic reads in each chunk using bwamem2
     //
     CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT (
         ch_filtering_input,
diff --git a/subworkflows/local/hic_minimap2.nf b/subworkflows/local/minimap2_mapreduce.nf
similarity index 95%
rename from subworkflows/local/hic_minimap2.nf
rename to subworkflows/local/minimap2_mapreduce.nf
index 23ab866..35b5aae 100644
--- a/subworkflows/local/hic_minimap2.nf
+++ b/subworkflows/local/minimap2_mapreduce.nf
@@ -8,7 +8,7 @@ include { SAMTOOLS_MERGE                                  } from '../../modules/
 include { MINIMAP2_INDEX                                  } from '../../modules/nf-core/minimap2/index/main'
 
 
-workflow HIC_MINIMAP2 {
+workflow MINIMAP2_MAPREDUCE {
     take:
     fasta    // Channel: tuple [ val(meta), path( file )      ]
     csv_ch
@@ -37,7 +37,8 @@ workflow HIC_MINIMAP2 {
         .combine ( MINIMAP2_INDEX.out.index )
         .map{ cram_id, cram_info, ref_id, ref_dir, mmi_id, mmi_path->
             tuple([
-                    id: cram_id.id
+                    id: cram_id.id,
+                    chunk_id: cram_id.id + "_" + cram_info[5]
                     ],
                 file(cram_info[0]),
                 cram_info[1],
diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf
index aa951b6..f7a4754 100644
--- a/subworkflows/local/prepare_genome.nf
+++ b/subworkflows/local/prepare_genome.nf
@@ -30,7 +30,7 @@ workflow PREPARE_GENOME {
 
     // Unmask genome fasta
     UNMASK ( ch_fasta )
-    ch_versions = ch_versions.mix ( UNMASK.out.versions.first() )
+    ch_versions = ch_versions.mix ( UNMASK.out.versions )
 
     // Generate BWA index
     if ( checkShortReads( params.input ) ) {
@@ -42,14 +42,14 @@ workflow PREPARE_GENOME {
 
             if ( params.bwamem2_index.endsWith('.tar.gz') ) {
                 ch_bwamem2_index = UNTAR ( ch_bwamem ).untar
-                ch_versions      = ch_versions.mix ( UNTAR.out.versions.first() )
+                ch_versions      = ch_versions.mix ( UNTAR.out.versions )
             } else {
                 ch_bwamem2_index = ch_bwamem
             }
 
         } else {
             ch_bwamem2_index = BWAMEM2_INDEX ( UNMASK.out.fasta ).index
-            ch_versions      = ch_versions.mix ( BWAMEM2_INDEX.out.versions.first() )
+            ch_versions      = ch_versions.mix ( BWAMEM2_INDEX.out.versions )
         }
     } else {
         ch_bwamem2_index = Channel.empty()
diff --git a/workflows/readmapping.nf b/workflows/readmapping.nf
index a5e9575..a71c77e 100644
--- a/workflows/readmapping.nf
+++ b/workflows/readmapping.nf
@@ -18,7 +18,7 @@ include { SAMTOOLS_REHEADER           } from '../modules/local/samtools_replaceh
 
 include { INPUT_CHECK                   } from '../subworkflows/local/input_check'
 include { PREPARE_GENOME                } from '../subworkflows/local/prepare_genome'
-include { ALIGN_SHORT_HIC as ALIGN_HIC  } from '../subworkflows/local/align_short_hic'
+include { ALIGN_SHORT as ALIGN_HIC      } from '../subworkflows/local/align_short'
 include { ALIGN_SHORT as ALIGN_ILLUMINA } from '../subworkflows/local/align_short'
 include { ALIGN_PACBIO as ALIGN_HIFI    } from '../subworkflows/local/align_pacbio'
 include { ALIGN_PACBIO as ALIGN_CLR     } from '../subworkflows/local/align_pacbio'