diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 0b753a453d..f4ac5b3605 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -55,6 +55,7 @@ jobs:
           - "strelkabp"
           - "targeted"
           - "tiddit"
+          - "trimming"
           - "tumor_normal_pair"
           - "variantcalling_channel"
 
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 9c69efef1f..6b6fdb1c7f 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -18,10 +18,10 @@ export_plots: true
 run_modules:
   - custom_content
   - fastqc
-  - cutadapt
+  - fastp
   - picard
   - samtools
-  - qualimap
+  - mosdepth
   - gatk
   - bcftools
   - vcftools
@@ -33,19 +33,15 @@ module_order:
       name: "FastQC (raw)"
       path_filters_exclude:
         - "*_val_*.zip"
-  - cutadapt:
-      name: "Cutadapt"
-  - fastqc:
-      name: "FastQC (trimmed)"
-      path_filters:
-        - "*_val_*.zip"
+  - fastp:
+      name: "FastP (Read preprocessing)"
   - picard:
       name: "GATK4 MarkDuplicates"
       info: " metrics generated either by GATK4 MarkDuplicates or EstimateLibraryComplexity (with --use_gatk_spark)."
   - samtools:
       name: "Samtools Flagstat"
-  - qualimap:
-      name: "Qualimap"
+  - mosdepth:
+      name: "Mosdepth"
   - gatk:
       name: "GATK4 BQSR"
   - bcftools:
diff --git a/conf/modules.config b/conf/modules.config
index c767a03ee3..939f271688 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -193,23 +193,29 @@ process {
     }
 
 // TRIMMING
-    withName: 'TRIMGALORE' {
-        ext.args         = '--fastqc'
-        publishDir       = [
-            [
-                path: { "${params.outdir}/reports/trimgalore/${meta.id}/fastqc" },
-                mode: params.publish_dir_mode,
-                pattern: "*{html,zip}"
-            ],
+
+    withName: FASTP {
+        ext.args = [ "",
+            params.trim_fastq              ?: "--disable_adapter_trimming",
+            params.clip_r1 > 0             ? "--trim_front1 ${params.clip_r1}" : "", // Remove bp from the 5' end of read 1.
+            params.three_prime_clip_r1 > 0 ? "--trim_tail1 ${params.three_prime_clip_r1}" : "", // Remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.
+            params.clip_r2   > 0           ? "--trim_front2 ${params.clip_r2}" : "", //Remove bp from the 5' end of read 2.
+            params.three_prime_clip_r2 > 0 ? "--trim_tail2 ${params.three_prime_clip_r2}" : "", // Remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed.
+            params.trim_nextseq            ? "--trim_poly_g" : "", // Apply the --nextseq=X option, to trim based on quality after removing poly-G tails.
+            params.split_fastq > 0         ? "--split_by_lines ${params.split_fastq * 4}" : "",
+
+        ].join(" ").trim()
+        publishDir = [
             [
-                path: { "${params.outdir}/trimgalore/${meta.id}" },
+                path: { "${params.outdir}/reports/fastp/${meta.sample}" },
                 mode: params.publish_dir_mode,
-                pattern: "*fq.gz"
+                pattern: "*.{html,json,log}"
             ],
             [
-                path: { "${params.outdir}/reports/trimgalore/${meta.id}" },
+                enabled: params.save_trimmed || params.save_split_fastqs,
+                path: { "${params.outdir}/preprocessing/${meta.sample}/fastp" },
                 mode: params.publish_dir_mode,
-                pattern: "*txt"
+                pattern: "*.fastp.fastq.gz"
             ]
         ]
     }
@@ -239,19 +245,6 @@ process {
         ext.prefix       = {"${meta.id}_unsorted_tagged"}
     }
 
-// SPLIT FASTQ
-
-    withName: 'SEQKIT_SPLIT2' {
-        ext.args         = { "--by-size ${params.split_fastq}" }
-        ext.when         = { params.split_fastq > 1 }
-        publishDir       = [
-            enabled: params.save_split_fastqs,
-            mode: params.publish_dir_mode,
-            path: { "${params.outdir}/preprocessing/${meta.sample}/seqkit" },
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
 // MAPPING
     if (params.step == 'mapping') {
         withName: ".*GATK4_MAPPING:BWAMEM1_MEM" {
@@ -272,12 +265,12 @@ process {
             // However if it's skipped, reads need to be coordinate-sorted
             // Only name sort if Spark for Markduplicates + duplicate marking is not skipped
             ext.args2        = { params.use_gatk_spark && params.use_gatk_spark.contains('markduplicates') && (!params.skip_tools || (params.skip_tools && !params.skip_tools.contains('markduplicates'))) ? '-n' : '' }
-            ext.prefix       = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.findAll(/part_([0-9]+)?/).last()) : "" }
+            ext.prefix       = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.tokenize('.')[0]) : "" }
             publishDir       = [
                 mode: params.publish_dir_mode,
-                path: { "${params.outdir}/preprocessing/${meta.id}/" },
+                path: { "${params.outdir}/preprocessing/" },
                 pattern: "*bam",
-                saveAs: { (params.save_bam_mapped || (params.skip_tools && params.skip_tools.contains('markduplicates'))) && (meta.size * meta.numLanes == 1) ? "mapped/${it}" : null }
+                saveAs: { (params.save_bam_mapped || (params.skip_tools && params.skip_tools.contains('markduplicates'))) && (meta.size * meta.numLanes == 1) ? "${meta.id}/mapped/${it}" : null }
             ]
         }
 
@@ -479,28 +472,18 @@ process {
         ]
     }
 
-    withName: 'DEEPTOOLS_BAMCOVERAGE' {
-        ext.when         = { !(params.skip_tools && params.skip_tools.contains('deeptools')) }
-        publishDir       = [
-            mode: params.publish_dir_mode,
-            path: { "${params.outdir}/reports/deeptools/${meta.id}" },
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: 'QUALIMAP_BAMQCCRAM' {
-        ext.args         = '--paint-chromosome-limits --genome-gc-distr HUMAN -skip-duplicated --skip-dup-mode 0 -outformat HTML'
+    withName: 'MOSDEPTH' {
+        ext.args = { !params.wes ? "-n --fast-mode --by 500" : ""}
         ext.prefix       = { "${meta.id}.mapped" }
-        ext.when         = { !(params.skip_tools && params.skip_tools.contains('bamqc')) }
-        publishDir       = [
+        publishDir = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/reports/qualimap/${meta.id}" },
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            path: { "${params.outdir}/reports/mosdepth/${meta.id}" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
     if (params.step == 'mapping' || params.step == 'markduplicates'|| params.step == 'prepare_recalibration'|| params.step == 'recalibrate') {
-        withName: 'NFCORE_SAREK:SAREK:CRAM_QC:QUALIMAP_BAMQCCRAM' {
+        withName: 'NFCORE_SAREK:SAREK:CRAM_QC:MOSDEPTH' {
             ext.prefix       = { "${meta.id}.recal" }
         }
 
@@ -1146,6 +1129,7 @@ process{
     // VEP
     if (params.tools && (params.tools.contains('vep') || params.tools.contains('merge'))) {
         withName: 'ENSEMBLVEP' {
+            // If just VEP: <vcf prefix>_VEP.ann.vcf
             ext.prefix       = { "${vcf.baseName.minus(".vcf")}_VEP" }
             ext.args          = [
                 '--everything --filter_common --per_gene --total_length --offline --format vcf',
@@ -1171,16 +1155,10 @@ process{
         }
     }
 
-    if (params.tools && params.tools.contains('vep')) {
-        withName: 'NFCORE_SAREK:SAREK:ANNOTATE:ANNOTATION_ENSEMBLVEP:ENSEMBLVEP' {
-            ext.prefix      = {"${meta.id}_VEP"}
-        }
-    }
-
     // SNPEFF THEN VEP
     if (params.tools && params.tools.contains('merge')) {
         withName: ".*:ANNOTATION_MERGE:ENSEMBLVEP" {
-            // Output file will have format *_snpEff_VEP.ann.vcf, *_snpEff_VEP.ann.json or *_snpEff_VEP.ann.tab
+            // If megre: Output file will have format *_snpEff_VEP.ann.vcf, *_snpEff_VEP.ann.json or *_snpEff_VEP.ann.tab
             ext.prefix       = { "${vcf.baseName.minus(".ann.vcf")}_VEP" }
         }
     }
diff --git a/docs/images/sarek_subway.png b/docs/images/sarek_subway.png
index edd0a166a2..af1d6f11fc 100644
Binary files a/docs/images/sarek_subway.png and b/docs/images/sarek_subway.png differ
diff --git a/docs/images/sarek_subway.svg b/docs/images/sarek_subway.svg
index 802e7fcbdf..372dea2590 100644
--- a/docs/images/sarek_subway.svg
+++ b/docs/images/sarek_subway.svg
@@ -7,7 +7,7 @@
    viewBox="0 0 297 210"
    version="1.1"
    id="svg5"
-   inkscape:version="1.2 (dc2aeda, 2022-05-15)"
+   inkscape:version="1.1 (c4e8f9e, 2021-05-24)"
    sodipodi:docname="sarek_subway.svg"
    inkscape:export-filename="sarek_subway.png"
    inkscape:export-xdpi="90"
@@ -27,13 +27,13 @@
      inkscape:document-units="mm"
      showgrid="true"
      inkscape:zoom="1.4127647"
-     inkscape:cx="577.23696"
-     inkscape:cy="353.56206"
+     inkscape:cx="552.10893"
+     inkscape:cy="134.13416"
      inkscape:window-width="1600"
-     inkscape:window-height="947"
-     inkscape:window-x="1024"
-     inkscape:window-y="25"
-     inkscape:window-maximized="1"
+     inkscape:window-height="587"
+     inkscape:window-x="60"
+     inkscape:window-y="41"
+     inkscape:window-maximized="0"
      inkscape:current-layer="layer4"
      width="211mm"
      fit-margin-top="0"
@@ -846,25 +846,25 @@
       <path
          sodipodi:nodetypes="cscc"
          id="path6719"
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+         d="m 391.8947,-539.69042 c -3.49369,-0.0379 -7.47317,0.84402 -9.94369,3.31454 l -5.80048,5.80048 c -2.47057,2.47052 -6.45005,3.3524 -9.94374,3.31454"
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+         d="m 402.16469,-539.69042 c 3.49369,-0.0379 7.47317,0.84402 9.94369,3.31454 l 5.80048,5.80048 c 2.47057,2.47052 6.45005,3.3524 9.94374,3.31454"
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+         d="m 391.8947,-514.83128 c -3.49369,0.0379 -7.47317,-0.84402 -9.94369,-3.31454 l -5.80048,-5.80048 c -2.47057,-2.47052 -6.45005,-3.3524 -9.94374,-3.31454"
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          id="path6741"
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+         d="m 402.16469,-514.83128 c 3.49369,0.0379 7.47317,-0.84402 9.94369,-3.31454 l 5.80048,-5.80048 c 2.47057,-2.47052 6.45005,-3.3524 9.94374,-3.31454"
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@@ -873,34 +873,19 @@
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          inkscape:export-ydpi="90"
          inkscape:export-xdpi="90"
          inkscape:export-filename="./polygon4618.png"
          id="text6799"
-         y="-164.05272"
-         x="540.05475"
+         y="-199.84988"
+         x="504.25781"
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-           y="-164.05272"
-           x="540.05475"
+           y="-199.84988"
+           x="504.25781"
            sodipodi:role="line"
            id="tspan1907">UMI</tspan></text>
       <text
@@ -909,14 +894,14 @@
          inkscape:export-xdpi="90"
          inkscape:export-filename="./polygon4618.png"
          id="text6807"
-         y="-115.43808"
-         x="576.64441"
+         y="-136.65131"
+         x="555.43152"
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-           y="-115.43808"
-           x="576.64441"
+           y="-136.65131"
+           x="555.43152"
            sodipodi:role="line">mapping</tspan></text>
       <g
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@@ -1241,35 +1226,20 @@
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+         y="-232.09396"
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+           y="-232.09396"
+           x="466.81354"
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@@ -1279,7 +1249,7 @@
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+         d="M 127.33708,-527.26085 H 371.3683"
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@@ -1287,62 +1257,21 @@
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diff --git a/modules.json b/modules.json
index 4d27a00113..95ad7850e9 100644
--- a/modules.json
+++ b/modules.json
@@ -54,9 +54,6 @@
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@@ -69,6 +66,9 @@
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@@ -168,6 +168,9 @@
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@@ -177,12 +180,6 @@
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-            },
             "snpeff": {
                 "git_sha": "40dd662fd26c3eb3160b7c8cbbe9bff80bbe2c30"
             },
@@ -234,9 +228,6 @@
             "tiddit/sv": {
                 "git_sha": "b689b8ed88a9f89eb2f7c75d3eb0bace77ade109"
             },
-            "trimgalore": {
-                "git_sha": "85ec13ff1fc2196c5a507ea497de468101baabed"
-            },
             "untar": {
                 "git_sha": "51be617b1ca9bff973655eb899d591ed6ab253b5"
             },
diff --git a/modules/nf-core/modules/deeptools/bamcoverage/main.nf b/modules/nf-core/modules/deeptools/bamcoverage/main.nf
deleted file mode 100644
index 04073ed948..0000000000
--- a/modules/nf-core/modules/deeptools/bamcoverage/main.nf
+++ /dev/null
@@ -1,67 +0,0 @@
-process DEEPTOOLS_BAMCOVERAGE {
-    tag "$meta.id"
-    label 'process_low'
-
-    conda (params.enable_conda ? "bioconda::deeptools=3.5.1 bioconda::samtools=1.15.1" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0':
-        'quay.io/biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:2c687053c0252667cca265c9f4118f2c205a604c-0' }"
-
-    input:
-    tuple val(meta), path(input), path(input_index)
-    path(fasta)
-    path(fasta_fai)
-
-    output:
-    tuple val(meta), path("*.bigWig")   , emit: bigwig, optional: true
-    tuple val(meta), path("*.bedgraph") , emit: bedgraph, optional: true
-    path "versions.yml"                 , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}.bigWig"
-
-    // cram_input is currently not working with deeptools
-    // therefore it's required to convert cram to bam first
-    def is_cram = input.Extension == "cram" ? true : false
-    def input_out = is_cram ? input.BaseName + ".bam" : "${input}"
-    def fai_reference = fasta_fai ? "--fai-reference ${fasta_fai}" : ""
-
-    if (is_cram){
-        """
-        samtools view -T $fasta $input $fai_reference -@ $task.cpus -o $input_out
-        samtools index -b $input_out -@ $task.cpus
-
-        bamCoverage \\
-            --bam $input_out \\
-            $args \\
-            --numberOfProcessors ${task.cpus} \\
-            --outFileName ${prefix}
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-            deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
-        END_VERSIONS
-        """
-
-    }
-    else {
-        """
-        bamCoverage \\
-            --bam $input_out \\
-            $args \\
-            --numberOfProcessors ${task.cpus} \\
-            --outFileName ${prefix}
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
-        END_VERSIONS
-        """
-    }
-
-}
diff --git a/modules/nf-core/modules/deeptools/bamcoverage/meta.yml b/modules/nf-core/modules/deeptools/bamcoverage/meta.yml
deleted file mode 100644
index c656691064..0000000000
--- a/modules/nf-core/modules/deeptools/bamcoverage/meta.yml
+++ /dev/null
@@ -1,58 +0,0 @@
-name: deeptools_bamcoverage
-description: This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output.
-keywords:
-  - sort
-tools:
-  - deeptools:
-      description: A set of user-friendly tools for normalization and visualzation of deep-sequencing data
-      homepage: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
-      documentation: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
-      tool_dev_url: https://github.com/deeptools/deepTools/
-      doi: "https://doi.org/10.1093/nar/gkw257"
-      licence: ["GPL v3"]
-
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - input:
-      type: file
-      description: BAM/CRAM file
-      pattern: "*.{bam,cram}"
-  - input_index:
-      type: file
-      description: BAM/CRAM index file
-      pattern: "*.{bai,crai}"
-  - fasta:
-      type: file
-      description: Reference file the CRAM file was created with (required with CRAM input)
-      pattern: "*.{fasta,fa}"
-  - fasta_fai:
-      type: file
-      description: Index of the reference file (optional, but recommended)
-      pattern: "*.{fai}"
-
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-  - bigWig:
-      type: file
-      description: BigWig file
-      pattern: "*.bigWig"
-  - bedgraph:
-      type: file
-      description: Bedgraph file
-      pattern: "*.bedgraph"
-
-authors:
-  - "@FriederikeHanssen"
-  - "@SusiJo"
diff --git a/modules/nf-core/modules/fastp/main.nf b/modules/nf-core/modules/fastp/main.nf
new file mode 100644
index 0000000000..120392c561
--- /dev/null
+++ b/modules/nf-core/modules/fastp/main.nf
@@ -0,0 +1,75 @@
+process FASTP {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' :
+        'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }"
+
+    input:
+    tuple val(meta), path(reads)
+    val   save_trimmed_fail
+    val   save_merged
+
+    output:
+    tuple val(meta), path('*.fastp.fastq.gz') , optional:true, emit: reads
+    tuple val(meta), path('*.json')           , emit: json
+    tuple val(meta), path('*.html')           , emit: html
+    tuple val(meta), path('*.log')            , emit: log
+    path "versions.yml"                       , emit: versions
+    tuple val(meta), path('*.fail.fastq.gz')  , optional:true, emit: reads_fail
+    tuple val(meta), path('*.merged.fastq.gz'), optional:true, emit: reads_merged
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    // Added soft-links to original fastqs for consistent naming in MultiQC
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if (meta.single_end) {
+        def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
+        """
+        [ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
+        fastp \\
+            --in1 ${prefix}.fastq.gz \\
+            --out1 ${prefix}.fastp.fastq.gz \\
+            --thread $task.cpus \\
+            --json ${prefix}.fastp.json \\
+            --html ${prefix}.fastp.html \\
+            $fail_fastq \\
+            $args \\
+            2> ${prefix}.fastp.log
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
+        END_VERSIONS
+        """
+    } else {
+        def fail_fastq  = save_trimmed_fail ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
+        def merge_fastq = save_merged ? "-m --merged_out ${prefix}.merged.fastq.gz" : ''
+        """
+        [ ! -f  ${prefix}_1.fastq.gz ] && ln -sf ${reads[0]} ${prefix}_1.fastq.gz
+        [ ! -f  ${prefix}_2.fastq.gz ] && ln -sf ${reads[1]} ${prefix}_2.fastq.gz
+        fastp \\
+            --in1 ${prefix}_1.fastq.gz \\
+            --in2 ${prefix}_2.fastq.gz \\
+            --out1 ${prefix}_1.fastp.fastq.gz \\
+            --out2 ${prefix}_2.fastp.fastq.gz \\
+            --json ${prefix}.fastp.json \\
+            --html ${prefix}.fastp.html \\
+            $fail_fastq \\
+            $merge_fastq \\
+            --thread $task.cpus \\
+            --detect_adapter_for_pe \\
+            $args \\
+            2> ${prefix}.fastp.log
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
+        END_VERSIONS
+        """
+    }
+}
diff --git a/modules/nf-core/modules/fastp/meta.yml b/modules/nf-core/modules/fastp/meta.yml
new file mode 100644
index 0000000000..2bd2b1a91f
--- /dev/null
+++ b/modules/nf-core/modules/fastp/meta.yml
@@ -0,0 +1,68 @@
+name: fastp
+description: Perform adapter/quality trimming on sequencing reads
+keywords:
+  - trimming
+  - quality control
+  - fastq
+tools:
+  - fastp:
+      description: |
+        A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
+      documentation: https://github.com/OpenGene/fastp
+      doi: https://doi.org/10.1093/bioinformatics/bty560
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+  - save_trimmed_fail:
+      type: boolean
+      description: Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz`
+  - save_merged:
+      type: boolean
+      description: Specify true to save all merged reads to the a file ending in `*.merged.fastq.gz`
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: The trimmed/modified/unmerged fastq reads
+      pattern: "*fastp.fastq.gz"
+  - json:
+      type: file
+      description: Results in JSON format
+      pattern: "*.json"
+  - html:
+      type: file
+      description: Results in HTML format
+      pattern: "*.html"
+  - log:
+      type: file
+      description: fastq log file
+      pattern: "*.log"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - reads_fail:
+      type: file
+      description: Reads the failed the preprocessing
+      pattern: "*fail.fastq.gz"
+  - reads_merged:
+      type: file
+      description: Reads that were successfully merged
+      pattern: "*.{merged.fastq.gz}"
+authors:
+  - "@drpatelh"
+  - "@kevinmenden"
diff --git a/modules/nf-core/modules/mosdepth/main.nf b/modules/nf-core/modules/mosdepth/main.nf
new file mode 100644
index 0000000000..d7e3c92904
--- /dev/null
+++ b/modules/nf-core/modules/mosdepth/main.nf
@@ -0,0 +1,81 @@
+process MOSDEPTH {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? 'bioconda::mosdepth=0.3.3' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mosdepth:0.3.3--hdfd78af_1' :
+        'quay.io/biocontainers/mosdepth:0.3.3--hdfd78af_1'}"
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    path  bed
+    path  fasta
+
+    output:
+    tuple val(meta), path('*.global.dist.txt')      , emit: global_txt
+    tuple val(meta), path('*.summary.txt')          , emit: summary_txt
+    tuple val(meta), path('*.region.dist.txt')      , optional:true, emit: regions_txt
+    tuple val(meta), path('*.per-base.d4')          , optional:true, emit: per_base_d4
+    tuple val(meta), path('*.per-base.bed.gz')      , optional:true, emit: per_base_bed
+    tuple val(meta), path('*.per-base.bed.gz.csi')  , optional:true, emit: per_base_csi
+    tuple val(meta), path('*.regions.bed.gz')       , optional:true, emit: regions_bed
+    tuple val(meta), path('*.regions.bed.gz.csi')   , optional:true, emit: regions_csi
+    tuple val(meta), path('*.quantized.bed.gz')     , optional:true, emit: quantized_bed
+    tuple val(meta), path('*.quantized.bed.gz.csi') , optional:true, emit: quantized_csi
+    tuple val(meta), path('*.thresholds.bed.gz')    , optional:true, emit: thresholds_bed
+    tuple val(meta), path('*.thresholds.bed.gz.csi'), optional:true, emit: thresholds_csi
+    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 reference = fasta ? "--fasta ${fasta}" : ""
+    def interval = bed ? "--by ${bed}" : ""
+    if (bed && args.contains("--by")) {
+        exit 1, "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition"
+    }
+    if (!bed && args.contains("--thresholds")) {
+        exit 1, "'--thresholds' can only be specified in conjunction with '--by'"
+    }
+
+    """
+    mosdepth \\
+        --threads $task.cpus \\
+        $interval \\
+        $reference \\
+        $args \\
+        $prefix \\
+        $bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.global.dist.txt
+    touch ${prefix}.region.dist.txt
+    touch ${prefix}.summary.txt
+    touch ${prefix}.per-base.d4
+    touch ${prefix}.per-base.bed.gz
+    touch ${prefix}.per-base.bed.gz.csi
+    touch ${prefix}.regions.bed.gz
+    touch ${prefix}.regions.bed.gz.csi
+    touch ${prefix}.quantized.bed.gz
+    touch ${prefix}.quantized.bed.gz.csi
+    touch ${prefix}.thresholds.bed.gz
+    touch ${prefix}.thresholds.bed.gz.csi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/modules/mosdepth/meta.yml b/modules/nf-core/modules/mosdepth/meta.yml
new file mode 100644
index 0000000000..d1e3344719
--- /dev/null
+++ b/modules/nf-core/modules/mosdepth/meta.yml
@@ -0,0 +1,99 @@
+name: mosdepth
+description: Calculates genome-wide sequencing coverage.
+keywords:
+  - mosdepth
+  - bam
+  - cram
+  - coverage
+tools:
+  - mosdepth:
+      description: |
+        Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.
+      documentation: https://github.com/brentp/mosdepth
+      doi: 10.1093/bioinformatics/btx699
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: Input BAM/CRAM file
+      pattern: "*.{bam,cram}"
+  - bai:
+      type: file
+      description: Index for BAM/CRAM file
+      pattern: "*.{bai,crai}"
+  - bed:
+      type: file
+      description: BED file with intersected intervals
+      pattern: "*.{bed}"
+  - fasta:
+      type: file
+      description: Reference genome FASTA file
+      pattern: "*.{fa,fasta}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - global_txt:
+      type: file
+      description: Text file with global cumulative coverage distribution
+      pattern: "*.{global.dist.txt}"
+  - regions_txt:
+      type: file
+      description: Text file with region cumulative coverage distribution
+      pattern: "*.{region.dist.txt}"
+  - summary_txt:
+      type: file
+      description: Text file with summary mean depths per chromosome and regions
+      pattern: "*.{summary.txt}"
+  - per_base_bed:
+      type: file
+      description: BED file with per-base coverage
+      pattern: "*.{per-base.bed.gz}"
+  - per_base_csi:
+      type: file
+      description: Index file for BED file with per-base coverage
+      pattern: "*.{per-base.bed.gz.csi}"
+  - per_base_d4:
+      type: file
+      description: D4 file with per-base coverage
+      pattern: "*.{per-base.d4}"
+  - regions_bed:
+      type: file
+      description: BED file with per-region coverage
+      pattern: "*.{regions.bed.gz}"
+  - regions_csi:
+      type: file
+      description: Index file for BED file with per-region coverage
+      pattern: "*.{regions.bed.gz.csi}"
+  - quantized_bed:
+      type: file
+      description: BED file with binned coverage
+      pattern: "*.{quantized.bed.gz}"
+  - quantized_csi:
+      type: file
+      description: Index file for BED file with binned coverage
+      pattern: "*.{quantized.bed.gz.csi}"
+  - thresholds_bed:
+      type: file
+      description: BED file with the number of bases in each region that are covered at or above each threshold
+      pattern: "*.{thresholds.bed.gz}"
+  - thresholds_csi:
+      type: file
+      description: Index file for BED file with threshold coverage
+      pattern: "*.{thresholds.bed.gz.csi}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"
+  - "@ramprasadn"
+  - "@matthdsm"
diff --git a/modules/nf-core/modules/qualimap/bamqc/main.nf b/modules/nf-core/modules/qualimap/bamqc/main.nf
deleted file mode 100644
index 3bfcb4c1f5..0000000000
--- a/modules/nf-core/modules/qualimap/bamqc/main.nf
+++ /dev/null
@@ -1,123 +0,0 @@
-process QUALIMAP_BAMQC {
-    tag "$meta.id"
-    label 'process_medium'
-
-    conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1' :
-        'quay.io/biocontainers/qualimap:2.2.2d--1' }"
-
-    input:
-    tuple val(meta), path(bam)
-    path gff
-
-    output:
-    tuple val(meta), path("${prefix}"), emit: results
-    path  "versions.yml"              , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args   ?: ''
-    prefix   = task.ext.prefix ?: "${meta.id}"
-
-    def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs'
-    def memory     = task.memory.toGiga() + "G"
-    def regions = gff ? "--gff $gff" : ''
-
-    def strandedness = 'non-strand-specific'
-    if (meta.strandedness == 'forward') {
-        strandedness = 'strand-specific-forward'
-    } else if (meta.strandedness == 'reverse') {
-        strandedness = 'strand-specific-reverse'
-    }
-    """
-    unset DISPLAY
-    mkdir tmp
-    export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp
-    qualimap \\
-        --java-mem-size=$memory \\
-        bamqc \\
-        $args \\
-        -bam $bam \\
-        $regions \\
-        -p $strandedness \\
-        $collect_pairs \\
-        -outdir $prefix \\
-        -nt $task.cpus
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
-    END_VERSIONS
-    """
-
-    stub:
-    prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
-    """
-    mkdir -p $prefix/css
-    mkdir $prefix/images_qualimapReport
-    mkdir $prefix/raw_data_qualimapReport
-    cd $prefix/css
-    touch agogo.css
-    touch basic.css
-    touch bgtop.png
-    touch comment-close.png
-    touch doctools.js
-    touch down-pressed.png
-    touch jquery.js
-    touch plus.png
-    touch qualimap_logo_small.png
-    touch searchtools.js
-    touch up.png
-    touch websupport.js
-    touch ajax-loader.gif
-    touch bgfooter.png
-    touch comment-bright.png
-    touch comment.png
-    touch down.png
-    touch file.png
-    touch minus.png
-    touch pygments.css
-    touch report.css
-    touch underscore.js
-    touch up-pressed.png
-    cd ../images_qualimapReport/
-    touch genome_coverage_0to50_histogram.png
-    touch genome_coverage_quotes.png
-    touch genome_insert_size_across_reference.png
-    touch genome_mapping_quality_histogram.png
-    touch genome_uniq_read_starts_histogram.png
-    touch genome_coverage_across_reference.png
-    touch genome_gc_content_per_window.png
-    touch genome_insert_size_histogram.png
-    touch genome_reads_clipping_profile.png
-    touch genome_coverage_histogram.png
-    touch genome_homopolymer_indels.png
-    touch genome_mapping_quality_across_reference.png
-    touch genome_reads_content_per_read_position.png
-    cd ../raw_data_qualimapReport
-    touch coverage_across_reference.txt
-    touch genome_fraction_coverage.txt
-    touch insert_size_histogram.txt
-    touch mapped_reads_nucleotide_content.txt
-    touch coverage_histogram.txt
-    touch homopolymer_indels.txt
-    touch mapped_reads_clipping_profile.txt
-    touch mapping_quality_across_reference.txt
-    touch duplication_rate_histogram.txt
-    touch insert_size_across_reference.txt
-    touch mapped_reads_gc-content_distribution.txt
-    touch mapping_quality_histogram.txt
-    cd ../
-    touch genome_results.txt
-    touch qualimapReport.html
-    cd ../
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/modules/qualimap/bamqc/meta.yml b/modules/nf-core/modules/qualimap/bamqc/meta.yml
deleted file mode 100644
index 303532eb7c..0000000000
--- a/modules/nf-core/modules/qualimap/bamqc/meta.yml
+++ /dev/null
@@ -1,47 +0,0 @@
-name: qualimap_bamqc
-description: Evaluate alignment data
-keywords:
-  - quality control
-  - qc
-  - bam
-tools:
-  - qualimap:
-      description: |
-        Qualimap 2 is a platform-independent application written in
-        Java and R that provides both a Graphical User Interface and
-        a command-line interface to facilitate the quality control of
-        alignment sequencing data and its derivatives like feature counts.
-      homepage: http://qualimap.bioinfo.cipf.es/
-      documentation: http://qualimap.conesalab.org/doc_html/index.html
-      doi: 10.1093/bioinformatics/bts503
-      licence: ["GPL-2.0-only"]
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - bam:
-      type: file
-      description: BAM file
-      pattern: "*.{bam}"
-  - gff:
-      type: file
-      description: Feature file with regions of interest
-      pattern: "*.{gff,gtf,bed}"
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - results:
-      type: dir
-      description: Qualimap results dir
-      pattern: "*/*"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-authors:
-  - "@phue"
diff --git a/modules/nf-core/modules/qualimap/bamqccram/main.nf b/modules/nf-core/modules/qualimap/bamqccram/main.nf
deleted file mode 100644
index e136b8e24f..0000000000
--- a/modules/nf-core/modules/qualimap/bamqccram/main.nf
+++ /dev/null
@@ -1,60 +0,0 @@
-process QUALIMAP_BAMQCCRAM {
-    tag "$meta.id"
-    label 'process_medium'
-
-    conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.15.1" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0' :
-        'quay.io/biocontainers/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:61f6d4658ac88635fc37623af50bba77561988ab-0' }"
-
-    input:
-    tuple val(meta), path(cram), path(crai)
-    path  gff
-    path  fasta
-    path  fasta_fai
-
-    output:
-    tuple val(meta), path("${prefix}"), emit: results
-    path  "versions.yml"              , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args   ?: ''
-    prefix   = task.ext.prefix ?: "${meta.id}"
-
-    def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs'
-    def memory     = task.memory.toGiga() + "G"
-    def regions = gff ? "--gff $gff" : ''
-
-    def strandedness = 'non-strand-specific'
-    if (meta.strandedness == 'forward') {
-        strandedness = 'strand-specific-forward'
-    } else if (meta.strandedness == 'reverse') {
-        strandedness = 'strand-specific-reverse'
-    }
-    """
-    unset DISPLAY
-    mkdir tmp
-    export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp
-
-    samtools view -hb -T ${fasta} ${cram} |
-    qualimap \\
-        --java-mem-size=$memory \\
-        bamqc \\
-        $args \\
-        -bam /dev/stdin \\
-        $regions \\
-        -p $strandedness \\
-        $collect_pairs \\
-        -outdir $prefix \\
-        -nt $task.cpus
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/modules/qualimap/bamqccram/meta.yml b/modules/nf-core/modules/qualimap/bamqccram/meta.yml
deleted file mode 100644
index d72f203df6..0000000000
--- a/modules/nf-core/modules/qualimap/bamqccram/meta.yml
+++ /dev/null
@@ -1,51 +0,0 @@
-name: qualimap_bamqccram
-description: Evaluate alignment data
-keywords:
-  - quality control
-  - qc
-  - bam
-tools:
-  - qualimap:
-      description: |
-        Qualimap 2 is a platform-independent application written in
-        Java and R that provides both a Graphical User Interface and
-        a command-line interface to facilitate the quality control of
-        alignment sequencing data and its derivatives like feature counts.
-      homepage: http://qualimap.bioinfo.cipf.es/
-      documentation: http://qualimap.conesalab.org/doc_html/index.html
-      doi: 10.1093/bioinformatics/bts503
-      licence: ["GPL-2.0-only"]
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - bacramm:
-      type: file
-      description: BAM file
-      pattern: "*.{bam}"
-  - gff:
-      type: file
-      description: Feature file with regions of interest
-      pattern: "*.{gff,gtf,bed}"
-  - fasta:
-      type: file
-      description: Reference file of cram file
-      pattern: "*.{fasta,fa,fna}"
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - results:
-      type: dir
-      description: Qualimap results dir
-      pattern: "*/*"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-authors:
-  - "@FriederikeHanssen"
diff --git a/modules/nf-core/modules/seqkit/split2/main.nf b/modules/nf-core/modules/seqkit/split2/main.nf
deleted file mode 100644
index ff91d86bd9..0000000000
--- a/modules/nf-core/modules/seqkit/split2/main.nf
+++ /dev/null
@@ -1,53 +0,0 @@
-process SEQKIT_SPLIT2 {
-    tag "$meta.id"
-    label 'process_medium'
-
-    conda (params.enable_conda ? 'bioconda::seqkit=2.1.0' : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0' :
-        'quay.io/biocontainers/seqkit:2.1.0--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(meta.single_end){
-        """
-        seqkit \\
-            split2 \\
-            $args \\
-            --threads $task.cpus \\
-            $reads \\
-            --out-dir ${prefix}
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            seqkit: \$(echo \$(seqkit 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
-        END_VERSIONS
-        """
-    } else {
-        """
-        seqkit \\
-            split2 \\
-            $args \\
-            --threads $task.cpus \\
-            --read1 ${reads[0]} \\
-            --read2 ${reads[1]} \\
-            --out-dir ${prefix}
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            seqkit: \$(echo \$(seqkit 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
-        END_VERSIONS
-        """
-    }
-}
diff --git a/modules/nf-core/modules/seqkit/split2/meta.yml b/modules/nf-core/modules/seqkit/split2/meta.yml
deleted file mode 100644
index 91c74b0c3e..0000000000
--- a/modules/nf-core/modules/seqkit/split2/meta.yml
+++ /dev/null
@@ -1,39 +0,0 @@
-name: seqkit_split2
-description: Split single or paired-end fastq.gz files
-keywords:
-  - split
-  - fastq
-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"
diff --git a/modules/nf-core/modules/trimgalore/main.nf b/modules/nf-core/modules/trimgalore/main.nf
deleted file mode 100644
index 3a3fca9044..0000000000
--- a/modules/nf-core/modules/trimgalore/main.nf
+++ /dev/null
@@ -1,86 +0,0 @@
-process TRIMGALORE {
-    tag "$meta.id"
-    label 'process_high'
-
-    conda (params.enable_conda ? 'bioconda::trim-galore=0.6.7' : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0' :
-        'quay.io/biocontainers/trim-galore:0.6.7--hdfd78af_0' }"
-
-    input:
-    tuple val(meta), path(reads)
-
-    output:
-    tuple val(meta), path("*{trimmed,val}*.fq.gz"), emit: reads
-    tuple val(meta), path("*report.txt")          , emit: log
-    path "versions.yml"                           , emit: versions
-
-    tuple val(meta), path("*unpaired*.fq.gz")     , emit: unpaired, optional: true
-    tuple val(meta), path("*.html")               , emit: html    , optional: true
-    tuple val(meta), path("*.zip")                , emit: zip     , optional: true
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    // Calculate number of --cores for TrimGalore based on value of task.cpus
-    // See: https://github.com/FelixKrueger/TrimGalore/blob/master/Changelog.md#version-060-release-on-1-mar-2019
-    // See: https://github.com/nf-core/atacseq/pull/65
-    def cores = 1
-    if (task.cpus) {
-        cores = (task.cpus as int) - 4
-        if (meta.single_end) cores = (task.cpus as int) - 3
-        if (cores < 1) cores = 1
-        if (cores > 4) cores = 4
-    }
-
-    // Clipping presets have to be evaluated in the context of SE/PE
-    def c_r1   = params.clip_r1 > 0             ? "--clip_r1 ${params.clip_r1}"                         : ''
-    def c_r2   = params.clip_r2 > 0             ? "--clip_r2 ${params.clip_r2}"                         : ''
-    def tpc_r1 = params.three_prime_clip_r1 > 0 ? "--three_prime_clip_r1 ${params.three_prime_clip_r1}" : ''
-    def tpc_r2 = params.three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${params.three_prime_clip_r2}" : ''
-
-    // Added soft-links to original fastqs for consistent naming in MultiQC
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    if (meta.single_end) {
-        """
-        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
-        trim_galore \\
-            $args \\
-            --cores $cores \\
-            --gzip \\
-            $c_r1 \\
-            $tpc_r1 \\
-            ${prefix}.fastq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
-            cutadapt: \$(cutadapt --version)
-        END_VERSIONS
-        """
-    } else {
-        """
-        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
-        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
-        trim_galore \\
-            $args \\
-            --cores $cores \\
-            --paired \\
-            --gzip \\
-            $c_r1 \\
-            $c_r2 \\
-            $tpc_r1 \\
-            $tpc_r2 \\
-            ${prefix}_1.fastq.gz \\
-            ${prefix}_2.fastq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
-            cutadapt: \$(cutadapt --version)
-        END_VERSIONS
-        """
-    }
-}
diff --git a/modules/nf-core/modules/trimgalore/meta.yml b/modules/nf-core/modules/trimgalore/meta.yml
deleted file mode 100644
index 439f566dff..0000000000
--- a/modules/nf-core/modules/trimgalore/meta.yml
+++ /dev/null
@@ -1,64 +0,0 @@
-name: trimgalore
-description: Trim FastQ files using Trim Galore!
-keywords:
-  - trimming
-  - adapters
-  - sequencing adapters
-  - fastq
-tools:
-  - trimgalore:
-      description: |
-        A wrapper tool around Cutadapt and FastQC to consistently apply quality
-        and adapter trimming to FastQ files, with some extra functionality for
-        MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
-      homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
-      documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md
-      licence: ["GPL-3.0-or-later"]
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input adapter trimmed FastQ files of size 1 and 2 for
-        single-end and paired-end data, respectively.
-      pattern: "*.{fq.gz}"
-  - unpaired:
-      type: file
-      description: |
-        FastQ files containing unpaired reads from read 1 or read 2
-      pattern: "*unpaired*.fq.gz"
-  - html:
-      type: file
-      description: FastQC report (optional)
-      pattern: "*_{fastqc.html}"
-  - zip:
-      type: file
-      description: FastQC report archive (optional)
-      pattern: "*_{fastqc.zip}"
-  - log:
-      type: file
-      description: Trim Galore! trimming report
-      pattern: "*_{report.txt}"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-authors:
-  - "@drpatelh"
-  - "@ewels"
-  - "@FelixKrueger"
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 7826b83cd1..8b89da2bab 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -84,7 +84,7 @@
                     "fa_icon": "fas fa-forward",
                     "description": "Disable specified tools.",
                     "help_text": "Multiple tools can be specified, separated by commas.\n\n> **NB** `--skip_tools baserecalibrator_report` is actually just not saving the reports.\n> **NB** `--skip_tools markduplicates_report` does not skip `MarkDuplicates` but prevent the collection of duplicate metrics that slows down performance.\n> **NB** tools can be specified with no concern for case.",
-                    "pattern": "^((bamqc|baserecalibrator|baserecalibrator_report|bcftools|documentation|fastqc|markduplicates|markduplicates_report|multiqc|samtools|vcftools|versions|deeptools)*(,)*)*$"
+                    "pattern": "^((baserecalibrator|baserecalibrator_report|bcftools|documentation|fastqc|markduplicates|markduplicates_report|mosdepth|multiqc|samtools|vcftools|versions)*(,)*)*$"
                 },
                 "wes": {
                     "type": "boolean",
diff --git a/subworkflows/local/split_fastq.nf b/subworkflows/local/split_fastq.nf
deleted file mode 100644
index f58d967407..0000000000
--- a/subworkflows/local/split_fastq.nf
+++ /dev/null
@@ -1,37 +0,0 @@
-//
-// SPLIT_FASTQ
-//
-// For all modules here:
-// A when clause condition is defined in the conf/modules.config to determine if the module should be run
-
-include { SEQKIT_SPLIT2 } from '../../modules/nf-core/modules/seqkit/split2/main'
-
-workflow SPLIT_FASTQ {
-    take:
-        reads_input // channel: [mandatory] meta, reads_input
-
-    main:
-
-    ch_versions = Channel.empty()
-
-    // Only if we want to split fastq files
-    SEQKIT_SPLIT2(reads_input)
-
-    // Remapping the channel
-    reads = SEQKIT_SPLIT2.out.reads.map{ key, reads ->
-        //TODO maybe this can be replaced by a regex to include part_001 etc.
-        //sorts list of split fq files by :
-        //[R1.part_001, R2.part_001, R1.part_002, R2.part_002,R1.part_003, R2.part_003,...]
-        //TODO: determine whether it is possible to have an uneven number of parts, so remainder: true woud need to be used, I guess this could be possible for unfiltered reads, reads that don't have pairs etc.
-        read_files = reads.sort{ a,b -> a.getName().tokenize('.')[ a.getName().tokenize('.').size() - 3] <=> b.getName().tokenize('.')[ b.getName().tokenize('.').size() - 3]}.collate(2)
-        [[patient: key.patient, sample:key.sample, gender:key.gender, status:key.status, id:key.id, numLanes:key.numLanes, read_group:key.read_group, data_type:key.data_type, size:read_files.size()],
-        read_files]
-    }.transpose()
-
-    ch_versions = ch_versions.mix(SEQKIT_SPLIT2.out.versions)
-
-    emit:
-        reads    = reads
-        versions = ch_versions
-}
-
diff --git a/subworkflows/nf-core/bam_to_cram.nf b/subworkflows/nf-core/bam_to_cram.nf
index 70ab9deb6a..e1c0ffff56 100644
--- a/subworkflows/nf-core/bam_to_cram.nf
+++ b/subworkflows/nf-core/bam_to_cram.nf
@@ -4,10 +4,9 @@
 // For all modules here:
 // A when clause condition is defined in the conf/modules.config to determine if the module should be run
 
-include { DEEPTOOLS_BAMCOVERAGE                  } from '../../modules/nf-core/modules/deeptools/bamcoverage/main'
-include { QUALIMAP_BAMQCCRAM                     } from '../../modules/nf-core/modules/qualimap/bamqccram/main'
 include { SAMTOOLS_CONVERT as SAMTOOLS_BAMTOCRAM } from '../../modules/nf-core/modules/samtools/convert/main'
 include { SAMTOOLS_STATS as SAMTOOLS_STATS_CRAM  } from '../../modules/nf-core/modules/samtools/stats/main'
+include { MOSDEPTH                               } from '../../modules/nf-core/modules/mosdepth/main'
 
 workflow BAM_TO_CRAM {
     take:
@@ -15,7 +14,8 @@ workflow BAM_TO_CRAM {
         cram_indexed
         fasta                         // channel: [mandatory] fasta
         fasta_fai                     // channel: [mandatory] fai
-        intervals_combined_bed_gz_tbi // channel: [optional]  intervals_bed.gz, intervals_bed.gz.tbi
+        intervals_bed_combined        // channel: [optional]  intervals_bed
+
 
     main:
     ch_versions = Channel.empty()
@@ -30,19 +30,17 @@ workflow BAM_TO_CRAM {
     cram_indexed = Channel.empty().mix(cram_indexed,SAMTOOLS_BAMTOCRAM.out.alignment_index)
 
     // Reports on cram
-    DEEPTOOLS_BAMCOVERAGE(cram_indexed, fasta, fasta_fai)
-    QUALIMAP_BAMQCCRAM(cram_indexed, intervals_combined_bed_gz_tbi, fasta, fasta_fai)
     SAMTOOLS_STATS_CRAM(cram_indexed, fasta)
+    MOSDEPTH(cram_indexed, intervals_bed_combined, fasta)
 
     // Gather all reports generated
-    qc_reports = qc_reports.mix(DEEPTOOLS_BAMCOVERAGE.out.bigwig)
-    qc_reports = qc_reports.mix(QUALIMAP_BAMQCCRAM.out.results)
     qc_reports = qc_reports.mix(SAMTOOLS_STATS_CRAM.out.stats)
+    qc_reports = qc_reports.mix(MOSDEPTH.out.global_txt,
+                                MOSDEPTH.out.regions_txt)
 
     // Gather versions of all tools used
-    ch_versions = ch_versions.mix(DEEPTOOLS_BAMCOVERAGE.out.versions.first())
-    ch_versions = ch_versions.mix(QUALIMAP_BAMQCCRAM.out.versions.first())
-    ch_versions = ch_versions.mix(SAMTOOLS_BAMTOCRAM.out.versions.first())
+    ch_versions = ch_versions.mix(MOSDEPTH.out.versions)
+    ch_versions = ch_versions.mix(SAMTOOLS_BAMTOCRAM.out.versions)
     ch_versions = ch_versions.mix(SAMTOOLS_STATS_CRAM.out.versions)
 
     emit:
diff --git a/subworkflows/nf-core/cram_qc.nf b/subworkflows/nf-core/cram_qc.nf
index 8acd2d65c1..eb74fab07c 100644
--- a/subworkflows/nf-core/cram_qc.nf
+++ b/subworkflows/nf-core/cram_qc.nf
@@ -5,14 +5,14 @@
 // A when clause condition is defined in the conf/modules.config to determine if the module should be run
 
 include { SAMTOOLS_STATS     } from '../../modules/nf-core/modules/samtools/stats/main'
-include { QUALIMAP_BAMQCCRAM } from '../../modules/nf-core/modules/qualimap/bamqccram/main'
+include { MOSDEPTH           } from '../../modules/nf-core/modules/mosdepth/main'
 
 workflow CRAM_QC {
     take:
         cram                          // channel: [mandatory] meta, cram, crai
         fasta                         // channel: [mandatory] fasta
         fasta_fai                     // channel: [mandatory] fasta_fai
-        intervals_combined_bed_gz_tbi
+        intervals_bed_combined
 
     main:
     ch_versions = Channel.empty()
@@ -20,14 +20,15 @@ workflow CRAM_QC {
 
     // Reports run on cram
     SAMTOOLS_STATS(cram, fasta)
-    QUALIMAP_BAMQCCRAM(cram, intervals_combined_bed_gz_tbi, fasta, fasta_fai)
+    MOSDEPTH(cram, intervals_bed_combined, fasta)
 
     // Gather all reports generated
     qc_reports = qc_reports.mix(SAMTOOLS_STATS.out.stats)
-    qc_reports = qc_reports.mix(QUALIMAP_BAMQCCRAM.out.results)
+    qc_reports = qc_reports.mix(MOSDEPTH.out.global_txt,
+                                MOSDEPTH.out.regions_txt)
 
     // Gather versions of all tools used
-    ch_versions = ch_versions.mix(QUALIMAP_BAMQCCRAM.out.versions.first())
+    ch_versions = ch_versions.mix(MOSDEPTH.out.versions)
     ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first())
 
     emit:
diff --git a/subworkflows/nf-core/gatk4/markduplicates/main.nf b/subworkflows/nf-core/gatk4/markduplicates/main.nf
index f211a8b54c..fdc7d248da 100644
--- a/subworkflows/nf-core/gatk4/markduplicates/main.nf
+++ b/subworkflows/nf-core/gatk4/markduplicates/main.nf
@@ -12,7 +12,7 @@ workflow MARKDUPLICATES {
         bam                           // channel: [mandatory] meta, bam
         fasta                         // channel: [mandatory] fasta
         fasta_fai                     // channel: [mandatory] fasta_fai
-        intervals_combined_bed_gz_tbi // channel: [optional]  intervals_bed.gz, intervals_bed.gz.tbi
+        intervals_bed_combined        // channel: [optional]  intervals_bed
 
     main:
     ch_versions = Channel.empty()
@@ -22,7 +22,7 @@ workflow MARKDUPLICATES {
     GATK4_MARKDUPLICATES(bam)
 
     // Convert output to cram
-    BAM_TO_CRAM(GATK4_MARKDUPLICATES.out.bam.join(GATK4_MARKDUPLICATES.out.bai), Channel.empty(), fasta, fasta_fai, intervals_combined_bed_gz_tbi)
+    BAM_TO_CRAM(GATK4_MARKDUPLICATES.out.bam.join(GATK4_MARKDUPLICATES.out.bai), Channel.empty(), fasta, fasta_fai, intervals_bed_combined)
 
     // Gather all reports generated
     qc_reports = qc_reports.mix(GATK4_MARKDUPLICATES.out.metrics)
diff --git a/subworkflows/nf-core/gatk4/markduplicates_spark/main.nf b/subworkflows/nf-core/gatk4/markduplicates_spark/main.nf
index 6e07f2c823..bffb2500d5 100644
--- a/subworkflows/nf-core/gatk4/markduplicates_spark/main.nf
+++ b/subworkflows/nf-core/gatk4/markduplicates_spark/main.nf
@@ -16,7 +16,7 @@ workflow MARKDUPLICATES_SPARK {
         dict                          // channel: [mandatory] dict
         fasta                         // channel: [mandatory] fasta
         fasta_fai                     // channel: [mandatory] fasta_fai
-        intervals_combined_bed_gz_tbi // channel: [optional]  intervals_bed.gz, intervals_bed.gz.tbi
+        intervals_bed_combined        // channel: [optional]  intervals_bed
 
     main:
     ch_versions = Channel.empty()
@@ -33,7 +33,7 @@ workflow MARKDUPLICATES_SPARK {
     SAMTOOLS_CRAMTOBAM(cram_markduplicates, fasta, fasta_fai)
 
     // Convert Markupduplicates spark bam output to cram when running bamqc and/or deeptools
-    BAM_TO_CRAM(Channel.empty(), cram_markduplicates, fasta, fasta_fai, intervals_combined_bed_gz_tbi)
+    BAM_TO_CRAM(Channel.empty(), cram_markduplicates, fasta, fasta_fai, intervals_bed_combined)
 
     // When running Marduplicates spark, and saving reports
     GATK4_ESTIMATELIBRARYCOMPLEXITY(bam, fasta, fasta_fai, dict)
diff --git a/tests/test_aligner.yml b/tests/test_aligner.yml
index f84125d652..07db7a9767 100644
--- a/tests/test_aligner.yml
+++ b/tests/test_aligner.yml
@@ -20,8 +20,14 @@
     - path: results/reference/bwamem2/genome.fasta.bwt.2bit.64
     - path: results/reference/bwamem2/genome.fasta.pac
     - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/qualimap/test/test.mapped
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools_stats/test/test.md.cram.stats
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
 - name: Run dragmap
@@ -49,7 +55,13 @@
     - path: results/reference/dragmap/repeat_mask.bin
     - path: results/reference/dragmap/str_table.bin
     - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/qualimap/test/test.mapped
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools_stats/test/test.md.cram.stats
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
diff --git a/tests/test_default.yml b/tests/test_default.yml
index 92bcae62eb..03eda15635 100644
--- a/tests/test_default.yml
+++ b/tests/test_default.yml
@@ -15,11 +15,16 @@
     - path: results/csv/recalibrated.csv
     - path: results/reports/fastqc/test-test_L1
     - path: results/reports/markduplicates/test/test.md.metrics
-    - path: results/reports/qualimap/test/test.mapped
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools_stats/test/test.md.cram.stats
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
-    - path: results/reports/deeptools/test/test.bigWig
 
 - name: Run default pipeline without intervals
   command: nextflow run main.nf -profile test,no_intervals,docker
@@ -39,11 +44,16 @@
     - path: results/csv/recalibrated.csv
     - path: results/reports/fastqc/test-test_L1
     - path: results/reports/markduplicates/test/test.md.metrics
-    - path: results/reports/qualimap/test/test.mapped
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools_stats/test/test.md.cram.stats
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
-    - path: results/reports/deeptools/test/test.bigWig
 
 - name: Run default pipeline with VC
   command: nextflow run main.nf -profile test,docker --tools strelka
@@ -62,11 +72,16 @@
     - path: results/csv/recalibrated.csv
     - path: results/reports/fastqc/test-test_L1
     - path: results/reports/markduplicates/test/test.md.metrics
-    - path: results/reports/qualimap/test/test.mapped
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools_stats/test/test.md.cram.stats
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
-    - path: results/reports/deeptools/test/test.bigWig
     - path: results/variant_calling/test/strelka/test.genome.vcf.gz
     - path: results/variant_calling/test/strelka/test.genome.vcf.gz.tbi
     - path: results/variant_calling/test/strelka/test.variants.vcf.gz
diff --git a/tests/test_gatk_spark.yml b/tests/test_gatk_spark.yml
index 609d7fbed7..588335e66e 100644
--- a/tests/test_gatk_spark.yml
+++ b/tests/test_gatk_spark.yml
@@ -16,8 +16,13 @@
     - path: results/csv/recalibrated.csv
     - path: results/reports/fastqc/test-test_L1
     - path: results/reports/markduplicates/test/test.md.metrics
-    - path: results/reports/qualimap/test/test.mapped
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools_stats/test/test.md.cram.stats
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
-    - path: results/reports/deeptools/test/test.bigWig
diff --git a/tests/test_markduplicates.yml b/tests/test_markduplicates.yml
index 4b69f5a332..7c9c459c85 100644
--- a/tests/test_markduplicates.yml
+++ b/tests/test_markduplicates.yml
@@ -14,8 +14,14 @@
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
-    - path: results/reports/qualimap/test/test.mapped
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools_stats/test/test.md.cram.stats
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
     - path: results/variant_calling/test/strelka/test.genome.vcf.gz
@@ -39,8 +45,14 @@
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
-    - path: results/reports/qualimap/test/test.mapped
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools_stats/test/test.md.cram.stats
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
     - path: results/variant_calling/test/strelka/test.genome.vcf.gz
diff --git a/tests/test_pair.yml b/tests/test_pair.yml
index 1df6c387e6..a6306bfc0f 100644
--- a/tests/test_pair.yml
+++ b/tests/test_pair.yml
@@ -22,13 +22,23 @@
     - path: results/reports/fastqc/test2-test_L1
     - path: results/reports/markduplicates/test/test.md.metrics
     - path: results/reports/markduplicates/test2/test2.md.metrics
-    - path: results/reports/qualimap/test/test.mapped
-    - path: results/reports/qualimap/test/test.recal
-    - path: results/reports/qualimap/test2/test2.mapped
-    - path: results/reports/qualimap/test2/test2.recal
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+    - path: results/reports/mosdepth/test2/test2.mapped.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test2/test2.mapped.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test2/test2.mapped.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test2/test2.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz
     - path: results/reports/samtools_stats/test/test.md.cram.stats
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
     - path: results/reports/samtools_stats/test2/test2.md.cram.stats
     - path: results/reports/samtools_stats/test2/test2.recal.cram.stats
-    - path: results/reports/deeptools/test/test.bigWig
-    - path: results/reports/deeptools/test2/test2.bigWig
diff --git a/tests/test_prepare_recalibration.yml b/tests/test_prepare_recalibration.yml
index 136cfa18eb..d6e0b4a752 100644
--- a/tests/test_prepare_recalibration.yml
+++ b/tests/test_prepare_recalibration.yml
@@ -10,7 +10,10 @@
     - path: results/preprocessing/test/recalibrated/test.recal.cram
     - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
     - path: results/csv/recalibrated.csv
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
     - path: results/variant_calling/test/strelka/test.genome.vcf.gz
     - path: results/variant_calling/test/strelka/test.genome.vcf.gz.tbi
@@ -29,7 +32,10 @@
     - path: results/preprocessing/test/recalibrated/test.recal.cram
     - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
     - path: results/csv/recalibrated.csv
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
     - path: results/variant_calling/test/strelka/test.genome.vcf.gz
     - path: results/variant_calling/test/strelka/test.genome.vcf.gz.tbi
@@ -54,7 +60,13 @@
       should_exist: false
     - path: results/csv/recalibrated.csv
       should_exist: false
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
       should_exist: false
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
       should_exist: false
@@ -83,7 +95,13 @@
       should_exist: false
     - path: results/csv/recalibrated.csv
       should_exist: false
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
       should_exist: false
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
       should_exist: false
diff --git a/tests/test_recalibrate.yml b/tests/test_recalibrate.yml
index e8846781f3..47b470a00f 100644
--- a/tests/test_recalibrate.yml
+++ b/tests/test_recalibrate.yml
@@ -8,7 +8,10 @@
     - path: results/multiqc
     - path: results/preprocessing/test/recalibrated/test.recal.cram
     - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
     - path: results/csv/recalibrated.csv
     - path: results/variant_calling/test/strelka/test.genome.vcf.gz
@@ -26,7 +29,10 @@
     - path: results/multiqc
     - path: results/preprocessing/test/recalibrated/test.recal.cram
     - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
     - path: results/csv/recalibrated.csv
     - path: results/variant_calling/test/strelka/test.genome.vcf.gz
@@ -52,7 +58,13 @@
       should_exist: false
     - path: results/csv/recalibrated.csv
       should_exist: false
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
       should_exist: false
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
       should_exist: false
@@ -81,7 +93,13 @@
       should_exist: false
     - path: results/csv/recalibrated.csv
       should_exist: false
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
       should_exist: false
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
       should_exist: false
diff --git a/tests/test_save_bam_mapped.yml b/tests/test_save_bam_mapped.yml
index f4e1787535..11368db0d0 100644
--- a/tests/test_save_bam_mapped.yml
+++ b/tests/test_save_bam_mapped.yml
@@ -17,7 +17,13 @@
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
     - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/qualimap/test/test.mapped
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools_stats/test/test.md.cram.stats
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
diff --git a/tests/test_save_output_bam.yml b/tests/test_save_output_bam.yml
index 2cc9a27fac..4ae277002c 100644
--- a/tests/test_save_output_bam.yml
+++ b/tests/test_save_output_bam.yml
@@ -14,8 +14,14 @@
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
     - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/qualimap/test/test.mapped
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools_stats/test/test.md.cram.stats
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
 
@@ -35,7 +41,13 @@
     - path: results/csv/markduplicates_no_table.csv
     - path: results/csv/recalibrated.csv
     - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/qualimap/test/test.mapped
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools_stats/test/test.md.cram.stats
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
diff --git a/tests/test_skip_markduplicates.yml b/tests/test_skip_markduplicates.yml
index 3b8802cfb8..ef5ef221f7 100644
--- a/tests/test_skip_markduplicates.yml
+++ b/tests/test_skip_markduplicates.yml
@@ -16,11 +16,16 @@
     - path: results/csv/markduplicates_no_table.csv # TODO These are no actually duplicate marked crams, but just mapped converted crams TODO renaming
     - path: results/csv/recalibrated.csv
     - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/qualimap/test/test.mapped
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools_stats/test/test.md.cram.stats
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
-    - path: results/reports/deeptools/test/test.bigWig
     - path: results/variant_calling/test/strelka/test.genome.vcf.gz
     - path: results/variant_calling/test/strelka/test.genome.vcf.gz.tbi
     - path: results/variant_calling/test/strelka/test.variants.vcf.gz
@@ -42,11 +47,16 @@
     - path: results/csv/recalibrated.csv
     - path: results/csv/markduplicates.csv
     - path: results/csv/markduplicates_no_table.csv # TODO These are no actually duplicate marked crams, but just mapped converted crams TODO renaming
-    - path: results/reports/qualimap/test/test.mapped
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools_stats/test/test.md.cram.stats
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
-    - path: results/reports/deeptools/test/test.bigWig
     - path: results/variant_calling/test/strelka/test.genome.vcf.gz
     - path: results/variant_calling/test/strelka/test.genome.vcf.gz.tbi
     - path: results/variant_calling/test/strelka/test.variants.vcf.gz
@@ -72,11 +82,16 @@
       should_exist: false
     - path: results/csv/markduplicates_no_table.csv
       should_exist: false
-    - path: results/reports/qualimap/test/test.mapped
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools_stats/test/test.paired_end.sorted.cram.stats
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
-    - path: results/reports/deeptools/test/test.bigWig
     - path: results/variant_calling/test/strelka/test.genome.vcf.gz
     - path: results/variant_calling/test/strelka/test.genome.vcf.gz.tbi
     - path: results/variant_calling/test/strelka/test.variants.vcf.gz
diff --git a/tests/test_split_fastq.yml b/tests/test_split_fastq.yml
index 96bec90012..c00b9cb470 100644
--- a/tests/test_split_fastq.yml
+++ b/tests/test_split_fastq.yml
@@ -3,7 +3,7 @@
   tags:
     - split_fastq
   files:
-    - path: results/preprocessing/test/seqkit/test-test_L1/test_1.part_001.fastq.gz
-    - path: results/preprocessing/test/seqkit/test-test_L1/test_1.part_002.fastq.gz
-    - path: results/preprocessing/test/seqkit/test-test_L1/test_2.part_001.fastq.gz
-    - path: results/preprocessing/test/seqkit/test-test_L1/test_2.part_002.fastq.gz
+    - path: results/preprocessing/test/fastp/0001.test-test_L1_1.fastp.fastq.gz
+    - path: results/preprocessing/test/fastp/0001.test-test_L1_2.fastp.fastq.gz
+    - path: results/preprocessing/test/fastp/0002.test-test_L1_1.fastp.fastq.gz
+    - path: results/preprocessing/test/fastp/0002.test-test_L1_2.fastp.fastq.gz
diff --git a/tests/test_targeted.yml b/tests/test_targeted.yml
index 0797b67680..da32e43673 100644
--- a/tests/test_targeted.yml
+++ b/tests/test_targeted.yml
@@ -15,8 +15,13 @@
     - path: results/csv/recalibrated.csv
     - path: results/reports/fastqc/test-test_L1
     - path: results/reports/markduplicates/test/test.md.metrics
-    - path: results/reports/qualimap/test/test.mapped
-    - path: results/reports/qualimap/test/test.recal
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
     - path: results/reports/samtools_stats/test/test.md.cram.stats
     - path: results/reports/samtools_stats/test/test.recal.cram.stats
-    - path: results/reports/deeptools/test/test.bigWig
diff --git a/tests/test_trimming.yml b/tests/test_trimming.yml
new file mode 100644
index 0000000000..b00e19f81f
--- /dev/null
+++ b/tests/test_trimming.yml
@@ -0,0 +1,29 @@
+- name: Run trimming pipeline
+  command: nextflow run main.nf -profile test,trimming,docker --save_trimmed
+  tags:
+    - trimming
+    - preprocessing
+  files:
+    - path: results/multiqc
+    - path: results/preprocessing/test/fastp/test-test_L1_1.fastp.fastq.gz
+    - path: results/preprocessing/test/fastp/test-test_L1_2.fastp.fastq.gz
+    - path: results/preprocessing/test/markduplicates/test.md.cram
+    - path: results/preprocessing/test/markduplicates/test.md.cram.crai
+    - path: results/preprocessing/test/recal_table/test.recal.table
+    - path: results/preprocessing/test/recalibrated/test.recal.cram
+    - path: results/preprocessing/test/recalibrated/test.recal.cram.crai
+    - path: results/csv/markduplicates.csv
+    - path: results/csv/markduplicates_no_table.csv
+    - path: results/csv/recalibrated.csv
+    - path: results/reports/fastqc/test-test_L1
+    - path: results/reports/markduplicates/test/test.md.metrics
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.mapped.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.mapped.regions.bed.gz
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+    - path: results/reports/samtools_stats/test/test.md.cram.stats
+    - path: results/reports/samtools_stats/test/test.recal.cram.stats
diff --git a/workflows/sarek.nf b/workflows/sarek.nf
index f265f8eae5..184a0f99e6 100644
--- a/workflows/sarek.nf
+++ b/workflows/sarek.nf
@@ -53,7 +53,7 @@ for (param in checkPathParamList) if (param) file(param, checkIfExists: true)
 ch_input_sample = extract_csv(file(params.input, checkIfExists: true))
 
 if (params.wes) {
-    if (params.intervals && !params.intervals.endsWith("bed")) exit 1, "Target file must be in BED format"
+    if (params.intervals && !params.intervals.endsWith("bed")) exit 1, "Target file specified with `--intervals` must be in BED format"
 } else {
     if (params.intervals && !params.intervals.endsWith("bed") && !params.intervals.endsWith("interval_list")) exit 1, "Interval file must end with .bed or .interval_list"
 }
@@ -165,14 +165,11 @@ include { PREPARE_INTERVALS                                    } from '../subwor
 include { ALIGNMENT_TO_FASTQ as ALIGNMENT_TO_FASTQ_INPUT       } from '../subworkflows/nf-core/alignment_to_fastq'
 include { ALIGNMENT_TO_FASTQ as ALIGNMENT_TO_FASTQ_UMI         } from '../subworkflows/nf-core/alignment_to_fastq'
 
-// Split FASTQ files
-include { SPLIT_FASTQ                                          } from '../subworkflows/local/split_fastq'
-
 // Run FASTQC
 include { RUN_FASTQC                                           } from '../subworkflows/nf-core/run_fastqc'
 
-// Run TRIMGALORE
-include { RUN_TRIMGALORE                                       } from '../subworkflows/nf-core/run_trimgalore'
+// TRIM/SPLIT FASTQ Files
+include { FASTP                                                } from '../modules/nf-core/modules/fastp/main'
 
 // Create umi consensus bams from fastq
 include { CREATE_UMI_CONSENSUS                                 } from '../subworkflows/nf-core/fgbio_create_umi_consensus/main'
@@ -294,13 +291,17 @@ workflow SAREK {
     PREPARE_INTERVALS(fasta_fai)
 
     // Intervals for speed up preprocessing/variant calling by spread/gather
-    intervals_bed_combined        = (params.intervals && params.wes) ? Channel.fromPath(params.intervals).collect() : []
+    // this is not good, we need the combined bed for some tools that don't support scatter/gather. Why would we not use the same intervals for WGS?
+    // intervals_bed_combined        = (params.intervals && params.wes) ? Channel.fromPath(params.intervals).collect() : []
+    // check if this actually still works if interval_list format
+    intervals_bed_combined        = params.intervals ? Channel.fromPath(params.intervals).collect() : []
+    //TODO: intervals also with WGS data? Probably need a parameter if WGS for deepvariant tool, that would allow to check here too
+    intervals_for_preprocessing              = (params.wes && params.intervals) ? intervals_bed_combined : []
 
     intervals                     = PREPARE_INTERVALS.out.intervals_bed        // [interval, num_intervals] multiple interval.bed files, divided by useful intervals for scatter/gather
     intervals_bed_gz_tbi          = PREPARE_INTERVALS.out.intervals_bed_gz_tbi // [interval_bed, tbi, num_intervals] multiple interval.bed.gz/.tbi files, divided by useful intervals for scatter/gather
 
-    //TODO: intervals also with WGS data? Probably need a parameter if WGS for deepvariant tool, that would allow to check here too
-    intervals_for_preprocessing   = (params.wes && !params.no_intervals) ? intervals_bed_combined : []
+
 
     // Gather used softwares versions
     ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)
@@ -338,24 +339,9 @@ workflow SAREK {
             ch_versions = ch_versions.mix(RUN_FASTQC.out.versions)
         }
 
-        // Trimming
-        if (params.trim_fastq) {
-            RUN_TRIMGALORE(ch_input_fastq)
-
-            ch_reads = RUN_TRIMGALORE.out.reads
-
-            ch_reports  = ch_reports.mix(RUN_TRIMGALORE.out.trim_html.collect{it[1]}.ifEmpty([]))
-            ch_reports  = ch_reports.mix(RUN_TRIMGALORE.out.trim_log.collect{it[1]}.ifEmpty([]))
-            ch_reports  = ch_reports.mix(RUN_TRIMGALORE.out.trim_zip.collect{it[1]}.ifEmpty([]))
-
-            ch_versions = ch_versions.mix(RUN_TRIMGALORE.out.versions)
-        } else {
-            ch_reads = ch_input_fastq
-        }
-
         // UMI consensus calling
         if (params.umi_read_structure) {
-            CREATE_UMI_CONSENSUS(ch_reads,
+            CREATE_UMI_CONSENSUS(ch_input_fastq,
                 fasta,
                 ch_map_index,
                 umi_read_structure,
@@ -364,25 +350,35 @@ workflow SAREK {
             // convert back to fastq for further preprocessing
             ALIGNMENT_TO_FASTQ_UMI(CREATE_UMI_CONSENSUS.out.consensusbam, [])
 
-            ch_input_sample_to_split = ALIGNMENT_TO_FASTQ_UMI.out.reads
+            ch_reads_fastp = ALIGNMENT_TO_FASTQ_UMI.out.reads
 
             // Gather used softwares versions
             ch_versions = ch_versions.mix(ALIGNMENT_TO_FASTQ_UMI.out.versions)
             ch_versions = ch_versions.mix(CREATE_UMI_CONSENSUS.out.versions)
         } else {
-            ch_input_sample_to_split = ch_reads
+            ch_reads_fastp = ch_input_fastq
         }
 
-        // SPLIT OF FASTQ FILES WITH SEQKIT_SPLIT2
-        if (params.split_fastq > 1) {
-            SPLIT_FASTQ(ch_input_sample_to_split)
+        // Trimming and/or splitting
+        if (params.trim_fastq || params.split_fastq > 0) {
+            FASTP(ch_reads_fastp, false, false)
 
-            ch_reads_to_map = SPLIT_FASTQ.out.reads
+            ch_reports = ch_reports.mix(FASTP.out.json.collect{it[1]}.ifEmpty([]),FASTP.out.html.collect{it[1]}.ifEmpty([]))
 
-            // Gather used softwares versions
-            ch_versions = ch_versions.mix(SPLIT_FASTQ.out.versions)
+            if(params.split_fastq){
+                ch_reads_to_map = FASTP.out.reads.map{ key, reads ->
+
+                        read_files = reads.sort{ a,b -> a.getName().tokenize('.')[0] <=> b.getName().tokenize('.')[0] }.collate(2)
+                        [[patient: key.patient, sample:key.sample, gender:key.gender, status:key.status, id:key.id, numLanes:key.numLanes, read_group:key.read_group, data_type:key.data_type, size:read_files.size()],
+                        read_files]
+                    }.transpose()
+            }else{
+                ch_reads_to_map = FASTP.out.reads
+            }
+
+            ch_versions = ch_versions.mix(FASTP.out.versions)
         } else {
-            ch_reads_to_map = ch_input_sample_to_split
+            ch_reads_to_map = ch_reads_fastp
         }
 
         // STEP 1: MAPPING READS TO REFERENCE GENOME