diff --git a/modules.json b/modules.json
index 7311c12b..56ce0b4a 100644
--- a/modules.json
+++ b/modules.json
@@ -3,14 +3,14 @@
     "homePage": "https://github.com/nf-core/blobtoolkit",
     "repos": {
         "nf-core/modules": {
-            "custom/dumpsoftwareversions": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+            "busco": {
+                "git_sha": "9fa6b6c1fc930830c1d819a9273b4ec12ffacb0a"
             },
-            "fastqc": {
+            "custom/dumpsoftwareversions": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
-            "multiqc": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+            "mosdepth": {
+                "git_sha": "72a31b76eb1b58879e0d91fb1d992e0118693098"
             }
         }
     }
diff --git a/modules/nf-core/modules/busco/main.nf b/modules/nf-core/modules/busco/main.nf
new file mode 100644
index 00000000..f0713862
--- /dev/null
+++ b/modules/nf-core/modules/busco/main.nf
@@ -0,0 +1,84 @@
+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
new file mode 100644
index 00000000..ef8c5245
--- /dev/null
+++ b/modules/nf-core/modules/busco/meta.yml
@@ -0,0 +1,69 @@
+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/fastqc/main.nf b/modules/nf-core/modules/fastqc/main.nf
deleted file mode 100644
index ed6b8c50..00000000
--- a/modules/nf-core/modules/fastqc/main.nf
+++ /dev/null
@@ -1,47 +0,0 @@
-process FASTQC {
-    tag "$meta.id"
-    label 'process_medium'
-
-    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
-        'quay.io/biocontainers/fastqc:0.11.9--0' }"
-
-    input:
-    tuple val(meta), path(reads)
-
-    output:
-    tuple val(meta), path("*.html"), emit: html
-    tuple val(meta), path("*.zip") , emit: zip
-    path  "versions.yml"           , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    // Add soft-links to original FastQs for consistent naming in pipeline
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    if (meta.single_end) {
-        """
-        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
-        fastqc $args --threads $task.cpus ${prefix}.fastq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-        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
-        fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-        END_VERSIONS
-        """
-    }
-}
diff --git a/modules/nf-core/modules/fastqc/meta.yml b/modules/nf-core/modules/fastqc/meta.yml
deleted file mode 100644
index 4da5bb5a..00000000
--- a/modules/nf-core/modules/fastqc/meta.yml
+++ /dev/null
@@ -1,52 +0,0 @@
-name: fastqc
-description: Run FastQC on sequenced reads
-keywords:
-  - quality control
-  - qc
-  - adapters
-  - fastq
-tools:
-  - fastqc:
-      description: |
-        FastQC gives general quality metrics about your reads.
-        It provides information about the quality score distribution
-        across your reads, the per base sequence content (%A/C/G/T).
-        You get information about adapter contamination and other
-        overrepresented sequences.
-      homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
-      documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
-      licence: ["GPL-2.0-only"]
-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 ]
-  - html:
-      type: file
-      description: FastQC report
-      pattern: "*_{fastqc.html}"
-  - zip:
-      type: file
-      description: FastQC report archive
-      pattern: "*_{fastqc.zip}"
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
-authors:
-  - "@drpatelh"
-  - "@grst"
-  - "@ewels"
-  - "@FelixKrueger"
diff --git a/modules/nf-core/modules/mosdepth/main.nf b/modules/nf-core/modules/mosdepth/main.nf
new file mode 100644
index 00000000..d7e3c929
--- /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 00000000..d1e33447
--- /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/multiqc/main.nf b/modules/nf-core/modules/multiqc/main.nf
deleted file mode 100644
index 1264aac1..00000000
--- a/modules/nf-core/modules/multiqc/main.nf
+++ /dev/null
@@ -1,31 +0,0 @@
-process MULTIQC {
-    label 'process_medium'
-
-    conda (params.enable_conda ? 'bioconda::multiqc=1.12' : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
-
-    input:
-    path multiqc_files
-
-    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 ?: ''
-    """
-    multiqc -f $args .
-
-    cat <<-END_VERSIONS > versions.yml
-    "${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
deleted file mode 100644
index 6fa891ef..00000000
--- a/modules/nf-core/modules/multiqc/meta.yml
+++ /dev/null
@@ -1,40 +0,0 @@
-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
-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"