diff --git a/bin/awk_filter_reads.sh b/bin/awk_filter_reads.sh
new file mode 100755
index 0000000..d50aa9e
--- /dev/null
+++ b/bin/awk_filter_reads.sh
@@ -0,0 +1 @@
+awk 'BEGIN{OFS="\t"}{if($1 ~ /^\@/) {print($0)} else {$2=and($2,compl(2048)); print(substr($0,2))}}'
diff --git a/bin/filter_five_end.pl b/bin/filter_five_end.pl
new file mode 100644
index 0000000..6f9b4d5
--- /dev/null
+++ b/bin/filter_five_end.pl
@@ -0,0 +1,109 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+
+my $prev_id = "";
+my @five;
+my @three;
+my @unmap;
+my @mid;
+my @all;
+my $counter = 0;
+
+while (<STDIN>){
+    chomp;
+    if (/^@/){
+        print $_."\n";
+        next;
+    }
+    my ($id, $flag, $chr_from, $loc_from, $mapq, $cigar, $d1, $d2, $d3, $read, $read_qual, @rest) = split /\t/;
+    my $bin = reverse(dec2bin($flag));
+    my @binary = split(//,$bin);
+    if ($prev_id ne $id && $prev_id ne ""){
+        if ($counter == 1){
+            if (@five == 1){
+                print $five[0]."\n";
+            }
+            else{
+                my ($id_1, $flag_1, $chr_from_1, $loc_from_1, $mapq_1, $cigar_1, $d1_1, $d2_1, $d3_1, $read_1, $read_qual_1, @rest_1) = split /\t/, $all[0];
+                my $bin_1 = reverse(dec2bin($flag_1));
+                my @binary_1 = split(//,$bin_1);
+                $binary_1[2] = 1;
+                my $bin_1_new = reverse(join("",@binary_1));
+                my $flag_1_new =  bin2dec($bin_1_new);
+                print(join("\t",$id_1, $flag_1_new, $chr_from_1, $loc_from_1, $mapq_1, $cigar_1, $d1_1, $d2_1, $d3_1, $read_1, $read_qual_1, @rest_1)."\n");
+            }
+        }
+        elsif ($counter == 2 && @five == 1){
+            print $five[0]."\n";
+        }
+        else{
+            my ($id_1, $flag_1, $chr_from_1, $loc_from_1, $mapq_1, $cigar_1, $d1_1, $d2_1, $d3_1, $read_1, $read_qual_1, @rest_1) = split /\t/, $all[0];
+            my $bin_1 = reverse(dec2bin($flag_1));
+            my @binary_1 = split(//,$bin_1);
+            $binary_1[2] = 1;
+            my $bin_1_new = reverse(join("",@binary_1));
+            my $flag_1_new =  bin2dec($bin_1_new);
+            print(join("\t",$id_1, $flag_1_new, $chr_from_1, $loc_from_1, $mapq_1, $cigar_1, $d1_1, $d2_1, $d3_1, $read_1, $read_qual_1, @rest_1)."\n");
+        }
+
+        $counter = 0;
+        undef @unmap;
+        undef @five;
+        undef @three;
+        undef @mid;
+        undef @all;
+    }
+
+    $counter++;
+    $prev_id = $id;
+    push @all,$_;
+    if ($binary[2]==1){
+        push @unmap,$_;
+    }
+    elsif ($binary[4]==0 && $cigar =~ m/^[0-9]*M/ || $binary[4]==1 && $cigar =~ m/.*M$/){
+        push @five, $_;
+    }
+    elsif ($binary[4]==1 && $cigar =~ m/^[0-9]*M/ || $binary[4]==0 && $cigar =~ m/.*M$/){
+        push @three, $_;
+    }
+    elsif ($cigar =~ m/^[0-9]*[HS].*M.*[HS]$/){
+        push @mid, $_;
+    }
+}
+
+if ($counter == 1){
+    if (@five == 1){
+        print $five[0]."\n";
+    }
+    else{
+        my ($id_1, $flag_1, $chr_from_1, $loc_from_1, $mapq_1, $cigar_1, $d1_1, $d2_1, $d3_1, $read_1, $read_qual_1, @rest_1) = split /\t/, $all[0];
+        my $bin_1 = reverse(dec2bin($flag_1));
+        my @binary_1 = split(//,$bin_1);
+        $binary_1[2] = 1;
+        my $bin_1_new = reverse(join("",@binary_1));
+        my $flag_1_new =  bin2dec($bin_1_new);
+        print(join("\t",$id_1, $flag_1_new, $chr_from_1, $loc_from_1, $mapq_1, $cigar_1, $d1_1, $d2_1, $d3_1, $read_1, $read_qual_1, @rest_1)."\n");
+    }
+}
+elsif ($counter == 2 && @five == 1){
+    print $five[0]."\n";
+}
+else{
+    my ($id_1, $flag_1, $chr_from_1, $loc_from_1, $mapq_1, $cigar_1, $d1_1, $d2_1, $d3_1, $read_1, $read_qual_1, @rest_1) = split /\t/, $all[0];
+    my $bin_1 = reverse(dec2bin($flag_1));
+    my @binary_1 = split(//,$bin_1);
+    $binary_1[2] = 1;
+    my $bin_1_new = reverse(join("",@binary_1));
+    my $flag_1_new =  bin2dec($bin_1_new);
+    print(join("\t",$id_1, $flag_1_new, $chr_from_1, $loc_from_1, $mapq_1, $cigar_1, $d1_1, $d2_1, $d3_1, $read_1, $read_qual_1, @rest_1)."\n");
+}
+
+sub dec2bin {
+    my $str = unpack("B32", pack("N", shift));
+    return $str;
+}
+
+sub bin2dec {
+    return unpack("N", pack("B32", substr("0" x 32 . shift, -32)));
+}
diff --git a/bin/generate_cram_csv.sh b/bin/generate_cram_csv.sh
new file mode 100755
index 0000000..9e56831
--- /dev/null
+++ b/bin/generate_cram_csv.sh
@@ -0,0 +1,99 @@
+#!/bin/bash
+
+# generate_cram_csv.sh
+# -------------------
+# Generate a csv file describing the CRAM folder
+# ><((((°>    Y    ><((((°>    U     ><((((°>    M     ><((((°>     I     ><((((°>
+# 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
+    local chunk_size=$5
+
+    local rgline=$(samtools view -H "${realcram}" | grep "@RG" | sed 's/\t/\\t/g' | sed "s/'//g")
+    local ncontainers=$(zcat "${realcrai}" | wc -l)
+    local base=$(basename "${realcram}" .cram)
+
+    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=$((to + chunk_size))
+        ((chunkn++))
+    done
+
+    # 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
+}
+
+# Function to process a CRAM file
+process_cram_file() {
+    local cram=$1
+    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" "$cram"
+            #chunkn=$(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" "$crai" "$chunk_size")
+        chunk_cram "$cram" "$chunkn" "$outcsv" "$crai" "$chunk_size"
+    fi
+}
+
+#  /\_/\        /\_/\
+# ( o.o ) main ( o.o )
+#  > ^ <        > ^ <
+
+# Check if cram_path is provided
+if [ $# -lt 3 ]; then
+    echo "Usage: $0 <cram_path> <output_csv> <crai_file> <chunk_size>"
+    exit 1
+fi
+
+cram=$1
+outcsv=$2
+crai=$3
+if [ -z "$4" ]; then
+    chunk_size=10000
+else
+    chunk_size=$4
+fi
+chunkn=0
+
+# Operates on a single CRAM file
+realcram=$(readlink -f $cram)
+realcrai=$(readlink -f $crai)
+if [ -f "$outcsv" ]; then
+    rm "$outcsv"
+fi
+process_cram_file $realcram $chunkn $outcsv $realcrai $chunk_size
diff --git a/bin/grep_pg.sh b/bin/grep_pg.sh
new file mode 100755
index 0000000..680b5ec
--- /dev/null
+++ b/bin/grep_pg.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+# grep_pg.sh
+# -------------------
+# A shell script to exclude pg lines and label read 1 and read 2 from cram containers
+#
+# -------------------
+# Author = yy5
+
+grep -v "^\@PG" | awk '{if($1 ~ /^\@/) {print($0)} else {if(and($2,64)>0) {print(1$0)} else {print(2$0)}}}'
diff --git a/conf/base.config b/conf/base.config
index 10ab224..6f3dab3 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -57,6 +57,12 @@ process {
         time   = { check_max( 2.h * Math.ceil( meta.read_count / 100000000 ) * task.attempt / log_increase_cpus(2, 6*task.attempt, 1, 2), 'time' ) }
     }
 
+    withName: SAMTOOLS_INDEX {
+        cpus   = { log_increase_cpus(2, 6*task.attempt, 1, 2) }
+        memory = { check_max( 4.GB + 850.MB * log_increase_cpus(2, 6*task.attempt, 1, 2) * task.attempt + 0.6.GB * Math.ceil( meta.read_count / 100000000 ), 'memory' ) }
+        time   = { check_max( 2.h * Math.ceil( meta.read_count / 100000000 ) * task.attempt / log_increase_cpus(2, 6*task.attempt, 1, 2), 'time' ) }
+    }
+
     withName: BLAST_BLASTN {
         time   = { check_max(          2.hour  * Math.ceil( meta.read_count / 1000000 ) * task.attempt, 'time'   ) }
         memory = { check_max( 100.MB + 20.MB   * Math.ceil( meta.read_count / 1000000 ) * task.attempt, 'memory' ) }
@@ -93,6 +99,21 @@ process {
         time   = { check_max(        1.h  * Math.ceil( meta.read_count   / 1000000   ) * task.attempt, 'time'   ) }
     }
 
+    withName: CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT {
+        cpus    = { check_max( 16       * 1                                                            , 'cpus'   ) }
+        memory  = { check_max( 1.GB     * ( reference.size() < 2e9 ? 50 : Math.ceil( ( reference.size() / 1e+9 ) * 20 ) * Math.ceil( task.attempt * 1 ) ) , 'memory') }
+    }
+
+    withName: CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT {
+        cpus    = { check_max( 16       * 1                                                 , 'cpus'   ) }
+        memory  = { check_max( 1.GB     * ( reference.size() < 2e9 ? 50 : Math.ceil( ( reference.size() / 1e+9 ) * 20 ) * Math.ceil( task.attempt * 1 ) ) , 'memory') }
+    }
+
+    withName: MINIMAP2_INDEX {
+        cpus    = { check_max( 2    * task.attempt, 'cpus'    ) }
+        memory  = { check_max( 1.GB * Math.ceil( 30 * fasta.size() / 1e+9 ) * task.attempt, 'memory' ) }
+    }
+
     withName: CRUMBLE {
         // No correlation between memory usage and the number of reads or the genome size.
         // Most genomes seem happy with 1 GB, then some with 2 GB, then some with 5 GB.
diff --git a/conf/modules.config b/conf/modules.config
index d05fe4b..28116bd 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -12,6 +12,7 @@
 
 process {
     withName: SAMTOOLS_FASTQ {
+        beforeScript = { "export REF_PATH=spoof"}
         ext.args = '-F 0x200 -nt'
     }
 
@@ -28,6 +29,7 @@ process {
     }
 
     withName: SAMTOOLS_MERGE {
+        beforeScript = { "export REF_PATH=spoof"}
         ext.args = { "-c -p" }
         ext.prefix = { "${meta.id}.merge" }
     }
@@ -39,6 +41,7 @@ process {
     }
 
     withName: SAMTOOLS_COLLATETOFASTA {
+        beforeScript = { "export REF_PATH=spoof"}
         ext.args   = { (params.use_work_dir_as_temp ? "-T." : "") }
     }
 
@@ -47,9 +50,58 @@ process {
     }
 
     withName: SAMTOOLS_CONVERT {
+        beforeScript = { "export REF_PATH=spoof"}
         ext.args = "-be '[rq]>=0.99' -x fi -x fp -x ri -x rp --write-index"
     }
 
+    withName: CONVERT_CRAM {
+        ext.args = "--output-fmt cram"
+    }
+
+    withName: '.*:.*:ALIGN_HIC:BWAMEM2_MEM' {
+        ext.args = { "-5SPCp -R ${meta.read_group}" }
+    }
+
+    withName: '.*:.*:ALIGN_ILLUMINA:BWAMEM2_MEM' {
+        ext.args = { "-p -R ${meta.read_group}" }
+    }
+
+    withName: ".*:ALIGN_ILLUMINA:.*:CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT" {
+        ext.args        = ""
+        ext.args1       = { "-F 0x200 -nt" }
+        ext.args2       = { "-p -R '${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 '${rglines}'" }
+        ext.args3       = "-mpu"
+        ext.args4       = { "--write-index -l1" }
+    }
+
+    withName: ".*:ALIGN_HIC:.*:CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT" {
+        ext.args        = ""
+        ext.args1       = { "" }
+        ext.args2       = { "-ax sr" }
+        ext.args3       = "-mpu"
+        ext.args4       = { "--write-index -l1" }
+    }
+
+    withName: "MINIMAP2_INDEX" {
+        ext.args        = { "${fasta.size() > 2.5e9 ? (" -I " + Math.ceil(fasta.size()/1e9)+"G") : ""} "}
+    }
+
         // minimap2 2.24 can only work with genomes up to 4 Gbp. For larger genomes, add the -I option with the genome size in Gbp.
         // In fact, we can also use -I to *decrease* the memory requirements for smaller genomes
         // NOTE: minimap2 uses the decimal system ! 1G = 1,000,000,000 bp
@@ -68,6 +120,7 @@ process {
     }
 
     withName: '.*:CONVERT_STATS:SAMTOOLS_CRAM' {
+        beforeScript = { "export REF_PATH=spoof"}
         ext.prefix = { "${fasta.baseName}.${meta.datatype}.${meta.id}" }
         ext.args   = '--output-fmt cram --write-index'
     }
@@ -85,7 +138,13 @@ process {
         ext.prefix = { "${bam.baseName}" }
     }
 
+    withName: SAMTOOLS_ADDREPLACERG {
+        ext.prefix = { "${input.baseName}_addRG" }
+        ext.args = { "-r ${meta.read_group} --no-PG" }
+    }
+
     withName: SAMTOOLS_STATS {
+        beforeScript = { "export REF_PATH=spoof"}
         ext.prefix = { "${input.baseName}" }
     }
 
@@ -95,6 +154,7 @@ process {
     }
 
     withName: '.*:CONVERT_STATS:SAMTOOLS_.*' {
+        beforeScript = { "export REF_PATH=spoof"}
         publishDir = [
             path: { "${params.outdir}/read_mapping/${meta.datatype}" },
             mode: params.publish_dir_mode,
diff --git a/conf/test.config b/conf/test.config
index d78e008..add9178 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -25,6 +25,9 @@ params {
     // Output directory
     outdir = "${projectDir}/results"
 
+    // Aligner
+    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"
     header = "https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/assembly/release/mMelMel3.1_paternal_haplotype/GCA_922984935.2.subset.header.sam"
diff --git a/modules.json b/modules.json
index 522bb30..ea8b364 100644
--- a/modules.json
+++ b/modules.json
@@ -45,6 +45,11 @@
                         "git_sha": "a33ef9475558c6b8da08c5f522ddaca1ec810306",
                         "installed_by": ["modules"]
                     },
+                    "minimap2/index": {
+                        "branch": "master",
+                        "git_sha": "72e277acfd9e61a9f1368eafb4a9e83f5bcaa9f5",
+                        "installed_by": ["modules"]
+                    },
                     "samtools/faidx": {
                         "branch": "master",
                         "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
@@ -65,6 +70,11 @@
                         "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["modules"]
                     },
+                    "samtools/index": {
+                        "branch": "master",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "installed_by": ["modules"]
+                    },
                     "samtools/merge": {
                         "branch": "master",
                         "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
diff --git a/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf b/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf
new file mode 100644
index 0000000..667e49b
--- /dev/null
+++ b/modules/local/cram_filter_align_bwamem2_fixmate_sort.nf
@@ -0,0 +1,60 @@
+process CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT {
+    tag "$meta.chunk_id"
+    label "process_high"
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-1a6fe65bd6674daba65066aa796ed8f5e8b4687b:688e175eb0db54de17822ba7810cc9e20fa06dd5-0' :
+        'biocontainers/mulled-v2-1a6fe65bd6674daba65066aa796ed8f5e8b4687b:688e175eb0db54de17822ba7810cc9e20fa06dd5-0' }"
+
+    input:
+    tuple val(meta), path(cramfile), path(cramindex), val(from), val(to), val(base), val(chunkid), val(rglines)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(index)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: mappedbam
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args1 = task.ext.args1 ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def args3 = task.ext.args3 ?: ''
+    def args4 = task.ext.args4 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    // Please be aware one of the tools here required mem = 28 * reference size!!!
+
+    """
+    INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'`
+
+    cram_filter -n ${from}-${to} ${cramfile} - | \\
+        samtools fastq ${args1} | \\
+        bwa-mem2 mem \$INDEX -t ${task.cpus} ${args2} - | \\
+        samtools fixmate ${args3} - - | \\
+        samtools sort ${args4} -@${task.cpus} -T ${base}_${chunkid}_sort_tmp -o ${prefix}_${base}_${chunkid}_mem.bam -
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' )
+        bwa-mem2: \$(bwa-mem2 --version | sed 's/bwa-mem2 //g')
+    END_VERSIONS
+    """
+    // temp removal staden_io_lib: \$(echo \$(staden_io_lib --version 2>&1) | sed 's/^.*staden_io_lib //; s/Using.*\$//') CAUSES ERROR
+
+    stub:
+    def prefix  = task.ext.prefix ?: "${meta.id}"
+    def base    = "45022_3#2"
+    def chunkid = "1"
+    """
+    touch ${prefix}_${base}_${chunkid}_mem.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' )
+        bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/cram_filter_minimap2_filter5end_fixmate_sort.nf b/modules/local/cram_filter_minimap2_filter5end_fixmate_sort.nf
new file mode 100644
index 0000000..ceafb86
--- /dev/null
+++ b/modules/local/cram_filter_minimap2_filter5end_fixmate_sort.nf
@@ -0,0 +1,59 @@
+process CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT {
+    tag "$meta.chunk_id"
+    label "process_high"
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-1a6fe65bd6674daba65066aa796ed8f5e8b4687b:688e175eb0db54de17822ba7810cc9e20fa06dd5-0' :
+        'biocontainers/mulled-v2-1a6fe65bd6674daba65066aa796ed8f5e8b4687b:688e175eb0db54de17822ba7810cc9e20fa06dd5-0' }"
+
+    input:
+    tuple val(meta), path(cramfile), path(cramindex), val(from), val(to), val(base), val(chunkid), val(rglines), val(ref), path(reference)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: mappedbam
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args1 = task.ext.args1 ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def args3 = task.ext.args3 ?: ''
+    def args4 = task.ext.args4 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = "1.15" // Staden_io versions break the pipeline
+    """
+    cram_filter -n ${from}-${to} ${cramfile} - | \\
+        samtools fastq ${args1} - |  \\
+        minimap2 -t${task.cpus} -R '${rglines}' ${args2} ${ref} - |  \\
+        ${projectDir}/bin/grep_pg.sh |  \\
+        perl ${projectDir}/bin/filter_five_end.pl |  \\
+        ${projectDir}/bin/awk_filter_reads.sh |  \\
+        samtools fixmate ${args3} - - | \\
+        samtools sort ${args4} -@${task.cpus} -T ${base}_${chunkid}_sort_tmp -o ${prefix}_${base}_${chunkid}_mm.bam -
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' )
+        minimap2: \$(minimap2 --version | sed 's/minimap2 //g')
+        staden_io: $VERSION
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix  = task.ext.prefix ?: "${meta.id}"
+    def base    = "45022_3#2"
+    def chunkid = "1"
+    """
+    touch ${prefix}_${base}_${chunkid}_mm.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' )
+        minimap2: \$(echo \$(minimap2 version 2>&1) | sed 's/.* //')
+        staden_io: $VERSION
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/generate_cram_csv.nf b/modules/local/generate_cram_csv.nf
new file mode 100644
index 0000000..f3cfe96
--- /dev/null
+++ b/modules/local/generate_cram_csv.nf
@@ -0,0 +1,37 @@
+process GENERATE_CRAM_CSV {
+    tag "${meta.id}"
+    label 'process_single'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://quay.io/sanger-tol/cramfilter_bwamem2_minimap2_samtools_perl:0.001-c1' :
+        'sanger-tol/cramfilter_bwamem2_minimap2_samtools_perl:0.001-c1' }"
+
+    input:
+    tuple val(meta), path(crampath), path(crai)
+
+
+    output:
+    tuple val(meta), path('*.csv'), emit: csv
+    path "versions.yml",            emit: versions
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    generate_cram_csv.sh $crampath ${prefix}_cram.csv $crai ${params.chunk_size}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' )
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch ${meta.id}.csv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' )
+    END_VERSIONS
+    """
+}
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/modules/nf-core/minimap2/index/environment.yml b/modules/nf-core/minimap2/index/environment.yml
new file mode 100644
index 0000000..8a912a1
--- /dev/null
+++ b/modules/nf-core/minimap2/index/environment.yml
@@ -0,0 +1,7 @@
+name: minimap2_index
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::minimap2=2.28
diff --git a/modules/nf-core/minimap2/index/main.nf b/modules/nf-core/minimap2/index/main.nf
new file mode 100644
index 0000000..3832021
--- /dev/null
+++ b/modules/nf-core/minimap2/index/main.nf
@@ -0,0 +1,44 @@
+process MINIMAP2_INDEX {
+    label 'process_low'
+
+    // Note: the versions here need to match the versions used in minimap2/align
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/minimap2:2.28--he4a0461_0' :
+        'biocontainers/minimap2:2.28--he4a0461_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.mmi"), emit: index
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    minimap2 \\
+        -t $task.cpus \\
+        -d ${fasta.baseName}.mmi \\
+        $args \\
+        $fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        minimap2: \$(minimap2 --version 2>&1)
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch ${fasta.baseName}.mmi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        minimap2: \$(minimap2 --version 2>&1)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/minimap2/index/meta.yml b/modules/nf-core/minimap2/index/meta.yml
new file mode 100644
index 0000000..1d29e3f
--- /dev/null
+++ b/modules/nf-core/minimap2/index/meta.yml
@@ -0,0 +1,43 @@
+name: minimap2_index
+description: Provides fasta index required by minimap2 alignment.
+keywords:
+  - index
+  - fasta
+  - reference
+tools:
+  - minimap2:
+      description: |
+        A versatile pairwise aligner for genomic and spliced nucleotide sequences.
+      homepage: https://github.com/lh3/minimap2
+      documentation: https://github.com/lh3/minimap2#uguide
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: |
+        Reference database in FASTA format.
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - index:
+      type: file
+      description: Minimap2 fasta index.
+      pattern: "*.mmi"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@yuukiiwa"
+  - "@drpatelh"
+maintainers:
+  - "@yuukiiwa"
+  - "@drpatelh"
diff --git a/modules/nf-core/minimap2/index/tests/main.nf.test b/modules/nf-core/minimap2/index/tests/main.nf.test
new file mode 100644
index 0000000..97840ff
--- /dev/null
+++ b/modules/nf-core/minimap2/index/tests/main.nf.test
@@ -0,0 +1,32 @@
+nextflow_process {
+
+    name "Test Process MINIMAP2_INDEX"
+    script "../main.nf"
+    process "MINIMAP2_INDEX"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "minimap2"
+    tag "minimap2/index"
+
+    test("minimap2 index") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+}
\ No newline at end of file
diff --git a/modules/nf-core/minimap2/index/tests/main.nf.test.snap b/modules/nf-core/minimap2/index/tests/main.nf.test.snap
new file mode 100644
index 0000000..0b09882
--- /dev/null
+++ b/modules/nf-core/minimap2/index/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_ref"
+                        },
+                        "genome.mmi:md5,72e450f12dc691e763c697463bdb1571"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,0fced0ee8015e7f50b82566e3db8f7b0"
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "test_ref"
+                        },
+                        "genome.mmi:md5,72e450f12dc691e763c697463bdb1571"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0fced0ee8015e7f50b82566e3db8f7b0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-18T11:46:30.000058092"
+    },
+    "minimap2 index": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.mmi:md5,72e450f12dc691e763c697463bdb1571"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,2f8340380c6741e9261a284262a90bde"
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "genome.mmi:md5,72e450f12dc691e763c697463bdb1571"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,2f8340380c6741e9261a284262a90bde"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-04-05T10:58:29.828187662"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/minimap2/index/tests/tags.yml b/modules/nf-core/minimap2/index/tests/tags.yml
new file mode 100644
index 0000000..e5ef8e1
--- /dev/null
+++ b/modules/nf-core/minimap2/index/tests/tags.yml
@@ -0,0 +1,2 @@
+minimap2/index:
+  - modules/nf-core/minimap2/index/**
diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml
new file mode 100644
index 0000000..260d516
--- /dev/null
+++ b/modules/nf-core/samtools/index/environment.yml
@@ -0,0 +1,8 @@
+name: samtools_index
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::samtools=1.20
+  - bioconda::htslib=1.20
diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf
new file mode 100644
index 0000000..e002585
--- /dev/null
+++ b/modules/nf-core/samtools/index/main.nf
@@ -0,0 +1,49 @@
+process SAMTOOLS_INDEX {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${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(input)
+
+    output:
+    tuple val(meta), path("*.bai") , optional:true, emit: bai
+    tuple val(meta), path("*.csi") , optional:true, emit: csi
+    tuple val(meta), path("*.crai"), optional:true, emit: crai
+    path  "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    samtools \\
+        index \\
+        -@ ${task.cpus-1} \\
+        $args \\
+        $input
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def extension = file(input).getExtension() == 'cram' ?
+                    "crai" : args.contains("-c") ?  "csi" : "bai"
+    """
+    touch ${input}.${extension}
+
+    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/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml
new file mode 100644
index 0000000..01a4ee0
--- /dev/null
+++ b/modules/nf-core/samtools/index/meta.yml
@@ -0,0 +1,57 @@
+name: samtools_index
+description: Index SAM/BAM/CRAM file
+keywords:
+  - index
+  - bam
+  - sam
+  - cram
+tools:
+  - samtools:
+      description: |
+        SAMtools is a set of utilities for interacting with and post-processing
+        short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+        These files are generated as output by short read aligners like BWA.
+      homepage: http://www.htslib.org/
+      documentation: http://www.htslib.org/doc/samtools.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bai:
+      type: file
+      description: BAM/CRAM/SAM index file
+      pattern: "*.{bai,crai,sai}"
+  - crai:
+      type: file
+      description: BAM/CRAM/SAM index file
+      pattern: "*.{bai,crai,sai}"
+  - csi:
+      type: file
+      description: CSI index file
+      pattern: "*.{csi}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@drpatelh"
+  - "@ewels"
+  - "@maxulysse"
+maintainers:
+  - "@drpatelh"
+  - "@ewels"
+  - "@maxulysse"
diff --git a/modules/nf-core/samtools/index/tests/csi.nextflow.config b/modules/nf-core/samtools/index/tests/csi.nextflow.config
new file mode 100644
index 0000000..0ed260e
--- /dev/null
+++ b/modules/nf-core/samtools/index/tests/csi.nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: SAMTOOLS_INDEX {
+        ext.args = '-c'
+    }
+
+}
diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test
new file mode 100644
index 0000000..ca34fb5
--- /dev/null
+++ b/modules/nf-core/samtools/index/tests/main.nf.test
@@ -0,0 +1,140 @@
+nextflow_process {
+
+    name "Test Process SAMTOOLS_INDEX"
+    script "../main.nf"
+    process "SAMTOOLS_INDEX"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "samtools"
+    tag "samtools/index"
+
+    test("bai") {
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("crai") {
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("csi") {
+        config "./csi.nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.csi[0][1]).name,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("bai - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("crai - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("csi - stub") {
+        options "-stub"
+        config "./csi.nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap
new file mode 100644
index 0000000..799d199
--- /dev/null
+++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap
@@ -0,0 +1,250 @@
+{
+    "csi - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                ],
+                "bai": [
+                    
+                ],
+                "crai": [
+                    
+                ],
+                "csi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T16:51:53.9057"
+    },
+    "crai - stub": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                ],
+                "bai": [
+                    
+                ],
+                "crai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "csi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T16:51:45.931558"
+    },
+    "bai - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "csi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T16:51:34.807525"
+    },
+    "csi": {
+        "content": [
+            "test.paired_end.sorted.bam.csi",
+            [
+                "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T16:52:55.688799"
+    },
+    "crai": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                ],
+                "bai": [
+                    
+                ],
+                "crai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029"
+                    ]
+                ],
+                "csi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T16:51:17.609533"
+    },
+    "bai": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4"
+                    ]
+                ],
+                "crai": [
+                    
+                ],
+                "csi": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T16:51:04.16585"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/samtools/index/tests/tags.yml b/modules/nf-core/samtools/index/tests/tags.yml
new file mode 100644
index 0000000..e0f58a7
--- /dev/null
+++ b/modules/nf-core/samtools/index/tests/tags.yml
@@ -0,0 +1,2 @@
+samtools/index:
+  - modules/nf-core/samtools/index/**
diff --git a/nextflow.config b/nextflow.config
index 35f7911..536987e 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -16,6 +16,10 @@ params {
     fasta                      = null
     header                     = null
 
+    // Aligner option
+    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 2209d6b..91eb9f6 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -86,6 +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",
@@ -285,6 +305,9 @@
         {
             "$ref": "#/definitions/reference_genome_options"
         },
+        {
+            "$ref": "#/definitions/aligner_options"
+        },
         {
             "$ref": "#/definitions/execution"
         },
diff --git a/seq_cache_populate.pl b/seq_cache_populate.pl
new file mode 100644
index 0000000..e69de29
diff --git a/subworkflows/local/align_short.nf b/subworkflows/local/align_short.nf
index 6b58e4e..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, true )
-    ch_versions = ch_versions.mix ( SAMTOOLS_FASTQ.out.versions.first() )
-
-
-    SAMTOOLS_FASTQ.out.interleaved
-    | 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/bwamem2_mapreduce.nf b/subworkflows/local/bwamem2_mapreduce.nf
new file mode 100644
index 0000000..13711fb
--- /dev/null
+++ b/subworkflows/local/bwamem2_mapreduce.nf
@@ -0,0 +1,85 @@
+#!/usr/bin/env nextflow
+
+//
+// MODULE IMPORT BLOCK
+//
+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 BWAMEM2_MAPREDUCE {
+    take:
+    fasta     // Channel: tuple [ val(meta), path( file )      ]
+    csv_ch
+    index
+
+
+    main:
+    ch_versions         = Channel.empty()
+    mappedbam_ch        = Channel.empty()
+
+
+    csv_ch
+        .splitCsv()
+        .map{ cram_id, cram_info ->
+            tuple([
+                    id: cram_id.id,
+                    chunk_id: cram_id.id + "_" + cram_info[5]
+                    ],
+                file(cram_info[0]),
+                cram_info[1],
+                cram_info[2],
+                cram_info[3],
+                cram_info[4],
+                cram_info[5],
+                cram_info[6]
+            )
+    }
+    .set { ch_filtering_input }
+
+
+    //
+    // MODULE: map hic reads in each chunk using bwamem2
+    //
+    CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT (
+        ch_filtering_input,
+        fasta,
+        index
+
+    )
+    ch_versions         = ch_versions.mix( CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT.out.versions )
+    mappedbam_ch        = CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT.out.mappedbam
+
+    //
+    // LOGIC: PREPARING BAMS FOR MERGE
+    //
+    mappedbam_ch
+        .map{ meta, file ->
+            tuple( file )
+        }
+        .collect()
+        .map { file ->
+            tuple (
+                [
+                id: file[0].toString().split('/')[-1].split('_')[0] + '_' + file[0].toString().split('/')[-1].split('_')[1]
+                ],
+                file
+            )
+        }
+        .set { collected_files_for_merge }
+
+
+    //
+    // MODULE: MERGE POSITION SORTED BAM FILES AND MARK DUPLICATES
+    //
+    SAMTOOLS_MERGE (
+        collected_files_for_merge,
+        fasta,
+        [ [], [] ]
+    )
+    ch_versions         = ch_versions.mix ( SAMTOOLS_MERGE.out.versions.first() )
+
+
+    emit:
+    mergedbam           = SAMTOOLS_MERGE.out.bam
+    versions            = ch_versions.ifEmpty(null)
+}
diff --git a/subworkflows/local/minimap2_mapreduce.nf b/subworkflows/local/minimap2_mapreduce.nf
new file mode 100644
index 0000000..35b5aae
--- /dev/null
+++ b/subworkflows/local/minimap2_mapreduce.nf
@@ -0,0 +1,101 @@
+#!/usr/bin/env nextflow
+
+//
+// MODULE IMPORT BLOCK
+//
+include { CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT    } from '../../modules/local/cram_filter_minimap2_filter5end_fixmate_sort'
+include { SAMTOOLS_MERGE                                  } from '../../modules/nf-core/samtools/merge/main'
+include { MINIMAP2_INDEX                                  } from '../../modules/nf-core/minimap2/index/main'
+
+
+workflow MINIMAP2_MAPREDUCE {
+    take:
+    fasta    // Channel: tuple [ val(meta), path( file )      ]
+    csv_ch
+
+
+    main:
+    ch_versions         = Channel.empty()
+    mappedbam_ch        = Channel.empty()
+
+
+    //
+    // MODULE: generate minimap2 mmi file
+    //
+    MINIMAP2_INDEX (
+        fasta
+        )
+    ch_versions         = ch_versions.mix( MINIMAP2_INDEX.out.versions )
+
+
+    //
+    // LOGIC: generate input channel for mapping
+    //
+    csv_ch
+        .splitCsv()
+        .combine ( fasta )
+        .combine ( MINIMAP2_INDEX.out.index )
+        .map{ cram_id, cram_info, ref_id, ref_dir, mmi_id, mmi_path->
+            tuple([
+                    id: cram_id.id,
+                    chunk_id: cram_id.id + "_" + cram_info[5]
+                    ],
+                file(cram_info[0]),
+                cram_info[1],
+                cram_info[2],
+                cram_info[3],
+                cram_info[4],
+                cram_info[5],
+                cram_info[6],
+                mmi_path.toString(),
+                ref_dir
+            )
+    }
+    .set { ch_filtering_input }
+
+
+    //
+    // MODULE: map hic reads by 10,000 container per time
+    //
+    CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT (
+        ch_filtering_input
+
+    )
+    ch_versions         = ch_versions.mix( CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT.out.versions )
+    mappedbam_ch        = CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT.out.mappedbam
+
+
+    //
+    // LOGIC: PREPARING BAMS FOR MERGE
+    //
+    mappedbam_ch
+        .map{ meta, file ->
+            tuple( file )
+        }
+        .collect()
+        .map { file ->
+            tuple (
+                [
+                id: file[0].toString().split('/')[-1].split('_')[0] + '_' + file[0].toString().split('/')[-1].split('_')[1]
+                ],
+                file
+            )
+        }
+        .set { collected_files_for_merge }
+
+
+    //
+    // MODULE: MERGE POSITION SORTED BAM FILES AND MARK DUPLICATES
+    //
+    SAMTOOLS_MERGE (
+        collected_files_for_merge,
+        fasta,
+        [ [], [] ]
+    )
+    ch_versions         = ch_versions.mix ( SAMTOOLS_MERGE.out.versions.first() )
+
+
+    emit:
+    mergedbam           = SAMTOOLS_MERGE.out.bam
+    versions            = ch_versions.ifEmpty(null)
+}
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 c70a406..a71c77e 100644
--- a/workflows/readmapping.nf
+++ b/workflows/readmapping.nf
@@ -104,7 +104,7 @@ workflow READMAPPING {
     //
     ALIGN_HIC ( PREPARE_GENOME.out.fasta, PREPARE_GENOME.out.bwaidx, ch_reads.hic )
     ch_versions = ch_versions.mix ( ALIGN_HIC.out.versions )
-    
+
     ALIGN_ILLUMINA ( PREPARE_GENOME.out.fasta, PREPARE_GENOME.out.bwaidx, ch_reads.illumina )
     ch_versions = ch_versions.mix ( ALIGN_ILLUMINA.out.versions )