diff --git a/modules.json b/modules.json
index 56ce0b4a..dd1ca986 100644
--- a/modules.json
+++ b/modules.json
@@ -3,14 +3,11 @@
     "homePage": "https://github.com/nf-core/blobtoolkit",
     "repos": {
         "nf-core/modules": {
-            "busco": {
-                "git_sha": "9fa6b6c1fc930830c1d819a9273b4ec12ffacb0a"
-            },
             "custom/dumpsoftwareversions": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
-            "mosdepth": {
-                "git_sha": "72a31b76eb1b58879e0d91fb1d992e0118693098"
+            "multiqc": {
+                "git_sha": "5138acca0985ca01c38a1c4fba917d83772b1106"
             }
         }
     }
diff --git a/modules/nf-core/modules/busco/main.nf b/modules/nf-core/modules/busco/main.nf
deleted file mode 100644
index f0713862..00000000
--- a/modules/nf-core/modules/busco/main.nf
+++ /dev/null
@@ -1,84 +0,0 @@
-process BUSCO {
-    tag "$meta.id"
-    label 'process_medium'
-
-    conda (params.enable_conda ? "bioconda::busco=5.3.2" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/busco:5.3.2--pyhdfd78af_0':
-        'quay.io/biocontainers/busco:5.3.2--pyhdfd78af_0' }"
-
-    input:
-    tuple val(meta), path('tmp_input/*')
-    each lineage                          // Required:    lineage to check against, "auto" enables --auto-lineage instead
-    path busco_lineages_path              // Recommended: path to busco lineages - downloads if not set
-    path config_file                      // Optional:    busco configuration file
-
-    output:
-    tuple val(meta), path("*-busco.batch_summary.txt"), emit: batch_summary
-    tuple val(meta), path("short_summary.*.txt")      , emit: short_summaries_txt, optional: true
-    tuple val(meta), path("short_summary.*.json")     , emit: short_summaries_json, optional: true
-    tuple val(meta), path("*-busco")                  , emit: busco_dir
-    path "versions.yml"                               , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}-${lineage}"
-    def busco_config = config_file ? "--config $config_file" : ''
-    def busco_lineage = lineage.equals('auto') ? '--auto-lineage' : "--lineage_dataset ${lineage}"
-    def busco_lineage_dir = busco_lineages_path ? "--offline --download_path ${busco_lineages_path}" : ''
-    """
-    # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
-    # Check for container variable initialisation script and source it.
-    if [ -f "/usr/local/env-activate.sh" ]; then
-        set +u  # Otherwise, errors out because of various unbound variables
-        . "/usr/local/env-activate.sh"
-        set -u
-    fi
-
-    # If the augustus config directory is not writable, then copy to writeable area
-    if [ ! -w "\${AUGUSTUS_CONFIG_PATH}" ]; then
-        # Create writable tmp directory for augustus
-        AUG_CONF_DIR=\$( mktemp -d -p \$PWD )
-        cp -r \$AUGUSTUS_CONFIG_PATH/* \$AUG_CONF_DIR
-        export AUGUSTUS_CONFIG_PATH=\$AUG_CONF_DIR
-        echo "New AUGUSTUS_CONFIG_PATH=\${AUGUSTUS_CONFIG_PATH}"
-    fi
-
-    # Ensure the input is uncompressed
-    INPUT_SEQS=input_seqs
-    mkdir "\$INPUT_SEQS"
-    cd "\$INPUT_SEQS"
-    for FASTA in ../tmp_input/*; do
-        if [ "\${FASTA##*.}" == 'gz' ]; then
-            gzip -cdf "\$FASTA" > \$( basename "\$FASTA" .gz )
-        else
-            ln -s "\$FASTA" .
-        fi
-    done
-    cd ..
-
-    busco \\
-        --cpu $task.cpus \\
-        --in "\$INPUT_SEQS" \\
-        --out ${prefix}-busco \\
-        $busco_lineage \\
-        $busco_lineage_dir \\
-        $busco_config \\
-        $args
-
-    # clean up
-    rm -rf "\$INPUT_SEQS"
-
-    # Move files to avoid staging/publishing issues
-    mv ${prefix}-busco/batch_summary.txt ${prefix}-busco.batch_summary.txt
-    mv ${prefix}-busco/*/short_summary.*.{json,txt} . || echo "Short summaries were not available: No genes were found."
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        busco: \$( busco --version 2>&1 | sed 's/^BUSCO //' )
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/modules/busco/meta.yml b/modules/nf-core/modules/busco/meta.yml
deleted file mode 100644
index ef8c5245..00000000
--- a/modules/nf-core/modules/busco/meta.yml
+++ /dev/null
@@ -1,69 +0,0 @@
-name: busco
-description: Benchmarking Universal Single Copy Orthologs
-keywords:
-  - quality control
-  - genome
-  - transcriptome
-  - proteome
-tools:
-  - busco:
-      description: BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
-      homepage: https://busco.ezlab.org/
-      documentation: https://busco.ezlab.org/busco_userguide.html
-      tool_dev_url: https://gitlab.com/ezlab/busco
-      doi: "10.1007/978-1-4939-9173-0_14"
-      licence: ["MIT"]
-
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - fasta:
-      type: file
-      description: Nucleic or amino acid sequence file in FASTA format.
-      pattern: "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}"
-  - lineage:
-      type: value
-      description: The BUSCO lineage to use, or "auto" to automatically select lineage
-  - busco_lineages_path:
-      type: directory
-      description: Path to local BUSCO lineages directory.
-  - config_file:
-      type: file
-      description: Path to BUSCO config file.
-
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - batch_summary:
-      type: file
-      description: Summary of all sequence files analyzed
-      pattern: "*-busco.batch_summary.txt"
-  - short_summaries_txt:
-      type: file
-      description: Short Busco summary in plain text format
-      pattern: "short_summary.*.txt"
-  - short_summaries_json:
-      type: file
-      description: Short Busco summary in JSON format
-      pattern: "short_summary.*.json"
-  - busco_dir:
-      type: directory
-      description: BUSCO lineage specific output
-      pattern: "*-busco"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-
-authors:
-  - "@priyanka-surana"
-  - "@charles-plessy"
-  - "@mahesh-panchal"
-  - "@muffato"
-  - "@jvhagey"
diff --git a/modules/nf-core/modules/mosdepth/main.nf b/modules/nf-core/modules/mosdepth/main.nf
deleted file mode 100644
index d7e3c929..00000000
--- a/modules/nf-core/modules/mosdepth/main.nf
+++ /dev/null
@@ -1,81 +0,0 @@
-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
deleted file mode 100644
index d1e33447..00000000
--- a/modules/nf-core/modules/mosdepth/meta.yml
+++ /dev/null
@@ -1,99 +0,0 @@
-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/multiqc/main.nf b/modules/nf-core/modules/multiqc/main.nf
new file mode 100644
index 00000000..1e7d6afe
--- /dev/null
+++ b/modules/nf-core/modules/multiqc/main.nf
@@ -0,0 +1,49 @@
+process MULTIQC {
+    label 'process_medium'
+
+    conda (params.enable_conda ? 'bioconda::multiqc=1.13a' : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/multiqc:1.13a--pyhdfd78af_1' :
+        'quay.io/biocontainers/multiqc:1.13a--pyhdfd78af_1' }"
+
+    input:
+    path  multiqc_files, stageAs: "?/*"
+    tuple path(multiqc_config), path(multiqc_logo)
+
+    output:
+    path "*multiqc_report.html", emit: report
+    path "*_data"              , emit: data
+    path "*_plots"             , optional:true, emit: plots
+    path "versions.yml"        , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def config = multiqc_config ? "--config $multiqc_config" : ''
+    """
+    multiqc \\
+        --force \\
+        $config \\
+        $args \\
+        .
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch multiqc_data
+    touch multiqc_plots
+    touch multiqc_report.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/modules/multiqc/meta.yml b/modules/nf-core/modules/multiqc/meta.yml
new file mode 100644
index 00000000..bf3a27fe
--- /dev/null
+++ b/modules/nf-core/modules/multiqc/meta.yml
@@ -0,0 +1,48 @@
+name: MultiQC
+description: Aggregate results from bioinformatics analyses across many samples into a single report
+keywords:
+  - QC
+  - bioinformatics tools
+  - Beautiful stand-alone HTML report
+tools:
+  - multiqc:
+      description: |
+        MultiQC searches a given directory for analysis logs and compiles a HTML report.
+        It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
+      homepage: https://multiqc.info/
+      documentation: https://multiqc.info/docs/
+      licence: ["GPL-3.0-or-later"]
+input:
+  - multiqc_files:
+      type: file
+      description: |
+        List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+  - multiqc_config:
+      type: file
+      description: Config yml for MultiQC
+      pattern: "*.{yml,yaml}"
+  - multiqc_logo:
+      type: file
+      description: Logo file for MultiQC
+      pattern: "*.{png}"
+output:
+  - report:
+      type: file
+      description: MultiQC report file
+      pattern: "multiqc_report.html"
+  - data:
+      type: dir
+      description: MultiQC data dir
+      pattern: "multiqc_data"
+  - plots:
+      type: file
+      description: Plots created by MultiQC
+      pattern: "*_data"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@abhi18av"
+  - "@bunop"
+  - "@drpatelh"