diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2437a1a7ef..b0040b3efa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#766](https://github.com/nf-core/sarek/pull/766) - Align box description in subway map
 - [#768](https://github.com/nf-core/sarek/pull/768) - Use double quotes to fix import of singularity images for deepvariant module
 - [#770](https://github.com/nf-core/sarek/pull/770) - Use double quotes to fix import of singularity images for gatk4/cnnscorevariants module
+- [#771](https://github.com/nf-core/sarek/pull/771) - update to new modules syntax
 
 ### Deprecated
 
diff --git a/modules.json b/modules.json
index 492bc65588..d12436c892 100644
--- a/modules.json
+++ b/modules.json
@@ -2,329 +2,334 @@
     "name": "nf-core/sarek",
     "homePage": "https://github.com/nf-core/sarek",
     "repos": {
-        "nf-core/modules": {
-            "git_url": "https://github.com/nf-core/modules.git",
+        "https://github.com/nf-core/modules.git": {
             "modules": {
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+                "nf-core": {
+                    "ascat": {
+                        "branch": "master",
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+                    },
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+                        "patch": "modules/nf-core/bcftools/stats/bcftools-stats.diff"
+                    },
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+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                    "cnvkit/reference": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "controlfreec/freec": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
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+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
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+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                    "custom/dumpsoftwareversions": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                    "ensemblvep": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                    "fgbio/callmolecularconsensusreads": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                    "fgbio/fastqtobam": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                    "fgbio/groupreadsbyumi": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                    "freebayes": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "gatk4/applybqsrspark": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "patch": "modules/nf-core/gatk4/cnnscorevariants/gatk4-cnnscorevariants.diff"
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+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "gatk4/gatherbqsrreports": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "gatk4/gatherpileupsummaries": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "gatk4/genomicsdbimport": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "gatk4/genotypegvcfs": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "gatk4/getpileupsummaries": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "gatk4/haplotypecaller": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "gatk4/intervallisttobed": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "gatk4/learnreadorientationmodel": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "gatk4/markduplicates": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "patch": "modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff"
+                    },
+                    "gatk4/markduplicatesspark": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "gatk4/mergemutectstats": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "gatk4/mergevcfs": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "gatk4/mutect2": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "gatk4/variantrecalibrator": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "manta/germline": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "manta/somatic": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "manta/tumoronly": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "mosdepth": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "msisensorpro/msi_somatic": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "msisensorpro/scan": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "multiqc": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "patch": "modules/nf-core/multiqc/multiqc.diff"
+                    },
+                    "samblaster": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "samtools/bam2fq": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "samtools/collatefastq": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "samtools/convert": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "samtools/faidx": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "samtools/index": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "samtools/merge": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "samtools/mpileup": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "samtools/stats": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "samtools/view": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "patch": "modules/nf-core/samtools/view/samtools-view.diff"
+                    },
+                    "snpeff": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "strelka/germline": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "strelka/somatic": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "svdb/merge": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "tabix/bgziptabix": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "tabix/tabix": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "tiddit/sv": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "untar": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "unzip": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    },
+                    "vcftools": {
+                        "branch": "master",
+                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                    }
                 }
             }
         }
diff --git a/modules/nf-core/modules/ascat/main.nf b/modules/nf-core/ascat/main.nf
similarity index 100%
rename from modules/nf-core/modules/ascat/main.nf
rename to modules/nf-core/ascat/main.nf
diff --git a/modules/nf-core/modules/ascat/meta.yml b/modules/nf-core/ascat/meta.yml
similarity index 100%
rename from modules/nf-core/modules/ascat/meta.yml
rename to modules/nf-core/ascat/meta.yml
diff --git a/modules/nf-core/modules/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf
similarity index 100%
rename from modules/nf-core/modules/bcftools/sort/main.nf
rename to modules/nf-core/bcftools/sort/main.nf
diff --git a/modules/nf-core/modules/bcftools/sort/meta.yml b/modules/nf-core/bcftools/sort/meta.yml
similarity index 100%
rename from modules/nf-core/modules/bcftools/sort/meta.yml
rename to modules/nf-core/bcftools/sort/meta.yml
diff --git a/modules/nf-core/bcftools/stats/bcftools-stats.diff b/modules/nf-core/bcftools/stats/bcftools-stats.diff
new file mode 100644
index 0000000000..471ae8d2ed
--- /dev/null
+++ b/modules/nf-core/bcftools/stats/bcftools-stats.diff
@@ -0,0 +1,36 @@
+Changes in module 'nf-core/bcftools/stats'
+--- modules/nf-core/bcftools/stats/main.nf
++++ modules/nf-core/bcftools/stats/main.nf
+@@ -8,10 +8,8 @@
+         'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
+ 
+     input:
+-    tuple val(meta), path(vcf), path(tbi)
+-    path regions
+-    path targets
+-    path samples
++    tuple val(meta), path(vcf)
++    path(target_bed)
+ 
+     output:
+     tuple val(meta), path("*stats.txt"), emit: stats
+@@ -23,15 +21,11 @@
+     script:
+     def args = task.ext.args ?: ''
+     def prefix = task.ext.prefix ?: "${meta.id}"
+-    def regions_file = regions ? "--regions-file ${regions}" : ""
+-    def targets_file = targets ? "--targets-file ${targets}" : ""
+-    def samples_file =  samples ? "--samples-file ${samples}" : ""
++    def target = target_bed ? "--regions-file ${target_bed}" : ""
+     """
+     bcftools stats \\
+         $args \\
+-        $regions_file \\
+-        $targets_file \\
+-        $samples_file \\
++        $target \\
+         $vcf > ${prefix}.bcftools_stats.txt
+ 
+     cat <<-END_VERSIONS > versions.yml
+
+************************************************************
diff --git a/modules/nf-core/modules/bcftools/stats/main.nf b/modules/nf-core/bcftools/stats/main.nf
similarity index 100%
rename from modules/nf-core/modules/bcftools/stats/main.nf
rename to modules/nf-core/bcftools/stats/main.nf
diff --git a/modules/nf-core/modules/bcftools/stats/meta.yml b/modules/nf-core/bcftools/stats/meta.yml
similarity index 65%
rename from modules/nf-core/modules/bcftools/stats/meta.yml
rename to modules/nf-core/bcftools/stats/meta.yml
index b0aec1ebfb..f7afcd5093 100644
--- a/modules/nf-core/modules/bcftools/stats/meta.yml
+++ b/modules/nf-core/bcftools/stats/meta.yml
@@ -19,14 +19,28 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - target_bed:
-      type: file
-      description: target bed file
-      pattern: "*.{bed}"
   - vcf:
       type: file
       description: VCF input file
       pattern: "*.{vcf}"
+  - tbi:
+      type: file
+      description: |
+        The tab index for the VCF file to be inspected. Optional: only required when parameter regions is chosen.
+      pattern: "*.tbi"
+  - regions:
+      type: file
+      description: |
+        Optionally, restrict the operation to regions listed in this file. (VCF, BED or tab-delimited)
+  - targets:
+      type: file
+      description: |
+        Optionally, restrict the operation to regions listed in this file (doesn't rely upon tbi index files)
+  - samples:
+      type: file
+      description: |
+        Optional, file of sample names to be included or excluded.
+        e.g. 'file.tsv'
 output:
   - meta:
       type: map
diff --git a/modules/nf-core/modules/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf
similarity index 96%
rename from modules/nf-core/modules/bwa/index/main.nf
rename to modules/nf-core/bwa/index/main.nf
index 3affbf16bc..aa75ae5dbb 100644
--- a/modules/nf-core/modules/bwa/index/main.nf
+++ b/modules/nf-core/bwa/index/main.nf
@@ -1,6 +1,6 @@
 process BWA_INDEX {
     tag "$fasta"
-    label 'process_high'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/modules/bwa/index/meta.yml b/modules/nf-core/bwa/index/meta.yml
similarity index 100%
rename from modules/nf-core/modules/bwa/index/meta.yml
rename to modules/nf-core/bwa/index/meta.yml
diff --git a/modules/nf-core/modules/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf
similarity index 100%
rename from modules/nf-core/modules/bwa/mem/main.nf
rename to modules/nf-core/bwa/mem/main.nf
diff --git a/modules/nf-core/modules/bwa/mem/meta.yml b/modules/nf-core/bwa/mem/meta.yml
similarity index 100%
rename from modules/nf-core/modules/bwa/mem/meta.yml
rename to modules/nf-core/bwa/mem/meta.yml
diff --git a/modules/nf-core/modules/bwamem2/index/main.nf b/modules/nf-core/bwamem2/index/main.nf
similarity index 97%
rename from modules/nf-core/modules/bwamem2/index/main.nf
rename to modules/nf-core/bwamem2/index/main.nf
index 6b63ea59a8..0b7ad1991e 100644
--- a/modules/nf-core/modules/bwamem2/index/main.nf
+++ b/modules/nf-core/bwamem2/index/main.nf
@@ -1,6 +1,6 @@
 process BWAMEM2_INDEX {
     tag "$fasta"
-    label 'process_high'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/modules/bwamem2/index/meta.yml b/modules/nf-core/bwamem2/index/meta.yml
similarity index 100%
rename from modules/nf-core/modules/bwamem2/index/meta.yml
rename to modules/nf-core/bwamem2/index/meta.yml
diff --git a/modules/nf-core/modules/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf
similarity index 100%
rename from modules/nf-core/modules/bwamem2/mem/main.nf
rename to modules/nf-core/bwamem2/mem/main.nf
diff --git a/modules/nf-core/modules/bwamem2/mem/meta.yml b/modules/nf-core/bwamem2/mem/meta.yml
similarity index 100%
rename from modules/nf-core/modules/bwamem2/mem/meta.yml
rename to modules/nf-core/bwamem2/mem/meta.yml
diff --git a/modules/nf-core/modules/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf
similarity index 100%
rename from modules/nf-core/modules/cat/cat/main.nf
rename to modules/nf-core/cat/cat/main.nf
diff --git a/modules/nf-core/modules/cat/cat/meta.yml b/modules/nf-core/cat/cat/meta.yml
similarity index 100%
rename from modules/nf-core/modules/cat/cat/meta.yml
rename to modules/nf-core/cat/cat/meta.yml
diff --git a/modules/nf-core/modules/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf
similarity index 88%
rename from modules/nf-core/modules/cat/fastq/main.nf
rename to modules/nf-core/cat/fastq/main.nf
index d275f19c1e..4fa365d33e 100644
--- a/modules/nf-core/modules/cat/fastq/main.nf
+++ b/modules/nf-core/cat/fastq/main.nf
@@ -1,6 +1,6 @@
 process CAT_FASTQ {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -20,9 +20,9 @@ process CAT_FASTQ {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def readList = reads.collect{ it.toString() }
+    def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
     if (meta.single_end) {
-        if (readList.size > 1) {
+        if (readList.size >= 1) {
             """
             cat ${readList.join(' ')} > ${prefix}.merged.fastq.gz
 
@@ -33,7 +33,7 @@ process CAT_FASTQ {
             """
         }
     } else {
-        if (readList.size > 2) {
+        if (readList.size >= 2) {
             def read1 = []
             def read2 = []
             readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
@@ -51,7 +51,7 @@ process CAT_FASTQ {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def readList = reads.collect{ it.toString() }
+    def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
     if (meta.single_end) {
         if (readList.size > 1) {
             """
diff --git a/modules/nf-core/modules/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml
similarity index 100%
rename from modules/nf-core/modules/cat/fastq/meta.yml
rename to modules/nf-core/cat/fastq/meta.yml
diff --git a/modules/nf-core/modules/cnvkit/antitarget/main.nf b/modules/nf-core/cnvkit/antitarget/main.nf
similarity index 100%
rename from modules/nf-core/modules/cnvkit/antitarget/main.nf
rename to modules/nf-core/cnvkit/antitarget/main.nf
diff --git a/modules/nf-core/modules/cnvkit/antitarget/meta.yml b/modules/nf-core/cnvkit/antitarget/meta.yml
similarity index 100%
rename from modules/nf-core/modules/cnvkit/antitarget/meta.yml
rename to modules/nf-core/cnvkit/antitarget/meta.yml
diff --git a/modules/nf-core/modules/cnvkit/batch/main.nf b/modules/nf-core/cnvkit/batch/main.nf
similarity index 100%
rename from modules/nf-core/modules/cnvkit/batch/main.nf
rename to modules/nf-core/cnvkit/batch/main.nf
diff --git a/modules/nf-core/modules/cnvkit/batch/meta.yml b/modules/nf-core/cnvkit/batch/meta.yml
similarity index 100%
rename from modules/nf-core/modules/cnvkit/batch/meta.yml
rename to modules/nf-core/cnvkit/batch/meta.yml
diff --git a/modules/nf-core/modules/cnvkit/reference/main.nf b/modules/nf-core/cnvkit/reference/main.nf
similarity index 100%
rename from modules/nf-core/modules/cnvkit/reference/main.nf
rename to modules/nf-core/cnvkit/reference/main.nf
diff --git a/modules/nf-core/modules/cnvkit/reference/meta.yml b/modules/nf-core/cnvkit/reference/meta.yml
similarity index 100%
rename from modules/nf-core/modules/cnvkit/reference/meta.yml
rename to modules/nf-core/cnvkit/reference/meta.yml
diff --git a/modules/nf-core/modules/controlfreec/assesssignificance/main.nf b/modules/nf-core/controlfreec/assesssignificance/main.nf
similarity index 100%
rename from modules/nf-core/modules/controlfreec/assesssignificance/main.nf
rename to modules/nf-core/controlfreec/assesssignificance/main.nf
diff --git a/modules/nf-core/modules/controlfreec/assesssignificance/meta.yml b/modules/nf-core/controlfreec/assesssignificance/meta.yml
similarity index 100%
rename from modules/nf-core/modules/controlfreec/assesssignificance/meta.yml
rename to modules/nf-core/controlfreec/assesssignificance/meta.yml
diff --git a/modules/nf-core/modules/controlfreec/freec/main.nf b/modules/nf-core/controlfreec/freec/main.nf
similarity index 100%
rename from modules/nf-core/modules/controlfreec/freec/main.nf
rename to modules/nf-core/controlfreec/freec/main.nf
diff --git a/modules/nf-core/modules/controlfreec/freec/meta.yml b/modules/nf-core/controlfreec/freec/meta.yml
similarity index 100%
rename from modules/nf-core/modules/controlfreec/freec/meta.yml
rename to modules/nf-core/controlfreec/freec/meta.yml
diff --git a/modules/nf-core/modules/controlfreec/freec2bed/main.nf b/modules/nf-core/controlfreec/freec2bed/main.nf
similarity index 100%
rename from modules/nf-core/modules/controlfreec/freec2bed/main.nf
rename to modules/nf-core/controlfreec/freec2bed/main.nf
diff --git a/modules/nf-core/modules/controlfreec/freec2bed/meta.yml b/modules/nf-core/controlfreec/freec2bed/meta.yml
similarity index 100%
rename from modules/nf-core/modules/controlfreec/freec2bed/meta.yml
rename to modules/nf-core/controlfreec/freec2bed/meta.yml
diff --git a/modules/nf-core/modules/controlfreec/freec2circos/main.nf b/modules/nf-core/controlfreec/freec2circos/main.nf
similarity index 100%
rename from modules/nf-core/modules/controlfreec/freec2circos/main.nf
rename to modules/nf-core/controlfreec/freec2circos/main.nf
diff --git a/modules/nf-core/modules/controlfreec/freec2circos/meta.yml b/modules/nf-core/controlfreec/freec2circos/meta.yml
similarity index 100%
rename from modules/nf-core/modules/controlfreec/freec2circos/meta.yml
rename to modules/nf-core/controlfreec/freec2circos/meta.yml
diff --git a/modules/nf-core/modules/controlfreec/makegraph/main.nf b/modules/nf-core/controlfreec/makegraph/main.nf
similarity index 100%
rename from modules/nf-core/modules/controlfreec/makegraph/main.nf
rename to modules/nf-core/controlfreec/makegraph/main.nf
diff --git a/modules/nf-core/modules/controlfreec/makegraph/meta.yml b/modules/nf-core/controlfreec/makegraph/meta.yml
similarity index 100%
rename from modules/nf-core/modules/controlfreec/makegraph/meta.yml
rename to modules/nf-core/controlfreec/makegraph/meta.yml
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
similarity index 81%
rename from modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
rename to modules/nf-core/custom/dumpsoftwareversions/main.nf
index 34b50b9f84..cebb6e0589 100644
--- a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda (params.enable_conda ? 'bioconda::multiqc=1.13a' : null)
+    conda (params.enable_conda ? 'bioconda::multiqc=1.13' : 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' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
+        'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
 
     input:
     path versions
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
similarity index 100%
rename from modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml
rename to modules/nf-core/custom/dumpsoftwareversions/meta.yml
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
similarity index 88%
rename from modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
rename to modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
index d139039254..7c2abfa494 100644
--- a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
@@ -58,11 +58,12 @@ def _make_versions_html(versions):
 for process, process_versions in versions_by_process.items():
     module = process.split(":")[-1]
     try:
-        assert versions_by_module[module] == process_versions, (
-            "We assume that software versions are the same between all modules. "
-            "If you see this error-message it means you discovered an edge-case "
-            "and should open an issue in nf-core/tools. "
-        )
+        if versions_by_module[module] != process_versions:
+            raise AssertionError(
+                "We assume that software versions are the same between all modules. "
+                "If you see this error-message it means you discovered an edge-case "
+                "and should open an issue in nf-core/tools. "
+            )
     except KeyError:
         versions_by_module[module] = process_versions
 
diff --git a/modules/nf-core/modules/deepvariant/main.nf b/modules/nf-core/deepvariant/main.nf
similarity index 100%
rename from modules/nf-core/modules/deepvariant/main.nf
rename to modules/nf-core/deepvariant/main.nf
diff --git a/modules/nf-core/modules/deepvariant/meta.yml b/modules/nf-core/deepvariant/meta.yml
similarity index 100%
rename from modules/nf-core/modules/deepvariant/meta.yml
rename to modules/nf-core/deepvariant/meta.yml
diff --git a/modules/nf-core/modules/dragmap/align/main.nf b/modules/nf-core/dragmap/align/main.nf
similarity index 100%
rename from modules/nf-core/modules/dragmap/align/main.nf
rename to modules/nf-core/dragmap/align/main.nf
diff --git a/modules/nf-core/modules/dragmap/align/meta.yml b/modules/nf-core/dragmap/align/meta.yml
similarity index 100%
rename from modules/nf-core/modules/dragmap/align/meta.yml
rename to modules/nf-core/dragmap/align/meta.yml
diff --git a/modules/nf-core/modules/dragmap/hashtable/main.nf b/modules/nf-core/dragmap/hashtable/main.nf
similarity index 100%
rename from modules/nf-core/modules/dragmap/hashtable/main.nf
rename to modules/nf-core/dragmap/hashtable/main.nf
diff --git a/modules/nf-core/modules/dragmap/hashtable/meta.yml b/modules/nf-core/dragmap/hashtable/meta.yml
similarity index 100%
rename from modules/nf-core/modules/dragmap/hashtable/meta.yml
rename to modules/nf-core/dragmap/hashtable/meta.yml
diff --git a/modules/nf-core/modules/ensemblvep/Dockerfile b/modules/nf-core/ensemblvep/Dockerfile
similarity index 100%
rename from modules/nf-core/modules/ensemblvep/Dockerfile
rename to modules/nf-core/ensemblvep/Dockerfile
diff --git a/modules/nf-core/modules/ensemblvep/build.sh b/modules/nf-core/ensemblvep/build.sh
old mode 100644
new mode 100755
similarity index 100%
rename from modules/nf-core/modules/ensemblvep/build.sh
rename to modules/nf-core/ensemblvep/build.sh
diff --git a/modules/nf-core/modules/ensemblvep/environment.yml b/modules/nf-core/ensemblvep/environment.yml
similarity index 100%
rename from modules/nf-core/modules/ensemblvep/environment.yml
rename to modules/nf-core/ensemblvep/environment.yml
diff --git a/modules/nf-core/modules/ensemblvep/main.nf b/modules/nf-core/ensemblvep/main.nf
similarity index 56%
rename from modules/nf-core/modules/ensemblvep/main.nf
rename to modules/nf-core/ensemblvep/main.nf
index 8a2c6363e9..fd2c893aa7 100644
--- a/modules/nf-core/modules/ensemblvep/main.nf
+++ b/modules/nf-core/ensemblvep/main.nf
@@ -17,11 +17,14 @@ process ENSEMBLVEP {
     path  extra_files
 
     output:
-    tuple val(meta), path("*.ann.vcf")  , optional:true, emit: vcf
-    tuple val(meta), path("*.ann.tab")  , optional:true, emit: tab
-    tuple val(meta), path("*.ann.json") , optional:true, emit: json
-    path "*.summary.html"               , emit: report
-    path "versions.yml"                 , emit: versions
+    tuple val(meta), path("*.ann.vcf")     , optional:true, emit: vcf
+    tuple val(meta), path("*.ann.tab")     , optional:true, emit: tab
+    tuple val(meta), path("*.ann.json")    , optional:true, emit: json
+    tuple val(meta), path("*.ann.vcf.gz")  , optional:true, emit: vcf_gz
+    tuple val(meta), path("*.ann.tab.gz")  , optional:true, emit: tab_gz
+    tuple val(meta), path("*.ann.json.gz") , optional:true, emit: json_gz
+    path "*.summary.html"                  , emit: report
+    path "versions.yml"                    , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -29,6 +32,7 @@ process ENSEMBLVEP {
     script:
     def args = task.ext.args ?: ''
     def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json")? 'json' : args.contains("--tab")? 'tab' : 'vcf'
+    def compress_out = args.contains("--compress_output") ? '.gz' : ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def dir_cache = cache ? "\${PWD}/${cache}" : "/.vep"
     def reference = fasta ? "--fasta $fasta" : ""
@@ -36,7 +40,7 @@ process ENSEMBLVEP {
     """
     vep \\
         -i $vcf \\
-        -o ${prefix}.ann.${file_extension} \\
+        -o ${prefix}.ann.${file_extension}${compress_out} \\
         $args \\
         $reference \\
         --assembly $genome \\
@@ -48,6 +52,23 @@ process ENSEMBLVEP {
         --stats_file ${prefix}.summary.html \\
 
 
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.ann.vcf
+    touch ${prefix}.ann.tab
+    touch ${prefix}.ann.json
+    touch ${prefix}.ann.vcf.gz
+    touch ${prefix}.ann.tab.gz
+    touch ${prefix}.ann.json.gz
+    touch ${prefix}.summary.html
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
diff --git a/modules/nf-core/modules/ensemblvep/meta.yml b/modules/nf-core/ensemblvep/meta.yml
similarity index 100%
rename from modules/nf-core/modules/ensemblvep/meta.yml
rename to modules/nf-core/ensemblvep/meta.yml
diff --git a/modules/nf-core/modules/fastp/main.nf b/modules/nf-core/fastp/main.nf
similarity index 74%
rename from modules/nf-core/modules/fastp/main.nf
rename to modules/nf-core/fastp/main.nf
index d9134e143d..11ea4db32a 100644
--- a/modules/nf-core/modules/fastp/main.nf
+++ b/modules/nf-core/fastp/main.nf
@@ -26,16 +26,15 @@ process FASTP {
 
     script:
     def args = task.ext.args ?: ''
-    // Added soft-links to original fastqs for consistent naming in MultiQC
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def fail_fastq = save_trimmed_fail && meta.single_end ? "--failed_out ${prefix}.fail.fastq.gz" : save_trimmed_fail && !meta.single_end ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
+    // Added soft-links to original fastqs for consistent naming in MultiQC
     // Use single ended for interleaved. Add --interleaved_in in config.
-    if (meta.single_end) {
-        def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
+    if ( task.ext.args?.contains('--interleaved_in') ) {
         """
         [ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
-        cat ${prefix}.fastq.gz \\
-        | fastp \\
-            --stdin \\
+
+        fastp \\
             --stdout \\
             --in1 ${prefix}.fastq.gz \\
             --thread $task.cpus \\
@@ -45,13 +44,33 @@ process FASTP {
             $args \\
             2> ${prefix}.fastp.log \\
         | gzip -c > ${prefix}.fastp.fastq.gz
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
+        END_VERSIONS
+        """
+    } else if (meta.single_end) {
+        """
+        [ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
+
+        fastp \\
+            --stdout \\
+            --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
diff --git a/modules/nf-core/modules/fastp/meta.yml b/modules/nf-core/fastp/meta.yml
similarity index 91%
rename from modules/nf-core/modules/fastp/meta.yml
rename to modules/nf-core/fastp/meta.yml
index 598c3368bd..2368fdedde 100644
--- a/modules/nf-core/modules/fastp/meta.yml
+++ b/modules/nf-core/fastp/meta.yml
@@ -21,7 +21,8 @@ input:
       type: file
       description: |
         List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-        respectively.
+        respectively. If you wish to run interleaved paired-end data,  supply as single-end data
+        but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module.
   - save_trimmed_fail:
       type: boolean
       description: Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz`
diff --git a/modules/nf-core/modules/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
similarity index 100%
rename from modules/nf-core/modules/fastqc/main.nf
rename to modules/nf-core/fastqc/main.nf
diff --git a/modules/nf-core/modules/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
similarity index 100%
rename from modules/nf-core/modules/fastqc/meta.yml
rename to modules/nf-core/fastqc/meta.yml
diff --git a/modules/nf-core/modules/fgbio/callmolecularconsensusreads/main.nf b/modules/nf-core/fgbio/callmolecularconsensusreads/main.nf
similarity index 100%
rename from modules/nf-core/modules/fgbio/callmolecularconsensusreads/main.nf
rename to modules/nf-core/fgbio/callmolecularconsensusreads/main.nf
diff --git a/modules/nf-core/modules/fgbio/callmolecularconsensusreads/meta.yml b/modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml
similarity index 100%
rename from modules/nf-core/modules/fgbio/callmolecularconsensusreads/meta.yml
rename to modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml
diff --git a/modules/nf-core/modules/fgbio/fastqtobam/main.nf b/modules/nf-core/fgbio/fastqtobam/main.nf
similarity index 100%
rename from modules/nf-core/modules/fgbio/fastqtobam/main.nf
rename to modules/nf-core/fgbio/fastqtobam/main.nf
diff --git a/modules/nf-core/modules/fgbio/fastqtobam/meta.yml b/modules/nf-core/fgbio/fastqtobam/meta.yml
similarity index 100%
rename from modules/nf-core/modules/fgbio/fastqtobam/meta.yml
rename to modules/nf-core/fgbio/fastqtobam/meta.yml
diff --git a/modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf b/modules/nf-core/fgbio/groupreadsbyumi/main.nf
similarity index 100%
rename from modules/nf-core/modules/fgbio/groupreadsbyumi/main.nf
rename to modules/nf-core/fgbio/groupreadsbyumi/main.nf
diff --git a/modules/nf-core/modules/fgbio/groupreadsbyumi/meta.yml b/modules/nf-core/fgbio/groupreadsbyumi/meta.yml
similarity index 100%
rename from modules/nf-core/modules/fgbio/groupreadsbyumi/meta.yml
rename to modules/nf-core/fgbio/groupreadsbyumi/meta.yml
diff --git a/modules/nf-core/modules/freebayes/main.nf b/modules/nf-core/freebayes/main.nf
similarity index 100%
rename from modules/nf-core/modules/freebayes/main.nf
rename to modules/nf-core/freebayes/main.nf
diff --git a/modules/nf-core/modules/freebayes/meta.yml b/modules/nf-core/freebayes/meta.yml
similarity index 100%
rename from modules/nf-core/modules/freebayes/meta.yml
rename to modules/nf-core/freebayes/meta.yml
diff --git a/modules/nf-core/modules/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/applybqsr/main.nf
rename to modules/nf-core/gatk4/applybqsr/main.nf
diff --git a/modules/nf-core/modules/gatk4/applybqsr/meta.yml b/modules/nf-core/gatk4/applybqsr/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/applybqsr/meta.yml
rename to modules/nf-core/gatk4/applybqsr/meta.yml
diff --git a/modules/nf-core/modules/gatk4/applybqsrspark/main.nf b/modules/nf-core/gatk4/applybqsrspark/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/applybqsrspark/main.nf
rename to modules/nf-core/gatk4/applybqsrspark/main.nf
diff --git a/modules/nf-core/modules/gatk4/applybqsrspark/meta.yml b/modules/nf-core/gatk4/applybqsrspark/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/applybqsrspark/meta.yml
rename to modules/nf-core/gatk4/applybqsrspark/meta.yml
diff --git a/modules/nf-core/modules/gatk4/applyvqsr/main.nf b/modules/nf-core/gatk4/applyvqsr/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/applyvqsr/main.nf
rename to modules/nf-core/gatk4/applyvqsr/main.nf
diff --git a/modules/nf-core/modules/gatk4/applyvqsr/meta.yml b/modules/nf-core/gatk4/applyvqsr/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/applyvqsr/meta.yml
rename to modules/nf-core/gatk4/applyvqsr/meta.yml
diff --git a/modules/nf-core/modules/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/baserecalibrator/main.nf
rename to modules/nf-core/gatk4/baserecalibrator/main.nf
diff --git a/modules/nf-core/modules/gatk4/baserecalibrator/meta.yml b/modules/nf-core/gatk4/baserecalibrator/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/baserecalibrator/meta.yml
rename to modules/nf-core/gatk4/baserecalibrator/meta.yml
diff --git a/modules/nf-core/modules/gatk4/baserecalibratorspark/main.nf b/modules/nf-core/gatk4/baserecalibratorspark/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/baserecalibratorspark/main.nf
rename to modules/nf-core/gatk4/baserecalibratorspark/main.nf
diff --git a/modules/nf-core/modules/gatk4/baserecalibratorspark/meta.yml b/modules/nf-core/gatk4/baserecalibratorspark/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/baserecalibratorspark/meta.yml
rename to modules/nf-core/gatk4/baserecalibratorspark/meta.yml
diff --git a/modules/nf-core/modules/gatk4/calculatecontamination/main.nf b/modules/nf-core/gatk4/calculatecontamination/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/calculatecontamination/main.nf
rename to modules/nf-core/gatk4/calculatecontamination/main.nf
diff --git a/modules/nf-core/modules/gatk4/calculatecontamination/meta.yml b/modules/nf-core/gatk4/calculatecontamination/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/calculatecontamination/meta.yml
rename to modules/nf-core/gatk4/calculatecontamination/meta.yml
diff --git a/modules/nf-core/modules/gatk4/cnnscorevariants/gatk4-cnnscorevariants.diff b/modules/nf-core/gatk4/cnnscorevariants/gatk4-cnnscorevariants.diff
similarity index 74%
rename from modules/nf-core/modules/gatk4/cnnscorevariants/gatk4-cnnscorevariants.diff
rename to modules/nf-core/gatk4/cnnscorevariants/gatk4-cnnscorevariants.diff
index 3630da2ce2..f0448b63b7 100644
--- a/modules/nf-core/modules/gatk4/cnnscorevariants/gatk4-cnnscorevariants.diff
+++ b/modules/nf-core/gatk4/cnnscorevariants/gatk4-cnnscorevariants.diff
@@ -1,6 +1,6 @@
-Changes in module 'nf-core/modules/gatk4/cnnscorevariants'
---- modules/nf-core/modules/gatk4/cnnscorevariants/main.nf
-+++ modules/nf-core/modules/gatk4/cnnscorevariants/main.nf
+Changes in module 'nf-core/gatk4/cnnscorevariants'
+--- modules/nf-core/gatk4/cnnscorevariants/main.nf
++++ modules/nf-core/gatk4/cnnscorevariants/main.nf
 @@ -6,7 +6,7 @@
      if (params.enable_conda) {
          exit 1, "Conda environments cannot be used for GATK4/CNNScoreVariants at the moment. Please use docker or singularity containers."
diff --git a/modules/nf-core/modules/gatk4/cnnscorevariants/main.nf b/modules/nf-core/gatk4/cnnscorevariants/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/cnnscorevariants/main.nf
rename to modules/nf-core/gatk4/cnnscorevariants/main.nf
diff --git a/modules/nf-core/modules/gatk4/cnnscorevariants/meta.yml b/modules/nf-core/gatk4/cnnscorevariants/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/cnnscorevariants/meta.yml
rename to modules/nf-core/gatk4/cnnscorevariants/meta.yml
diff --git a/modules/nf-core/modules/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/createsequencedictionary/main.nf
rename to modules/nf-core/gatk4/createsequencedictionary/main.nf
diff --git a/modules/nf-core/modules/gatk4/createsequencedictionary/meta.yml b/modules/nf-core/gatk4/createsequencedictionary/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/createsequencedictionary/meta.yml
rename to modules/nf-core/gatk4/createsequencedictionary/meta.yml
diff --git a/modules/nf-core/modules/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/estimatelibrarycomplexity/main.nf
rename to modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf
diff --git a/modules/nf-core/modules/gatk4/estimatelibrarycomplexity/meta.yml b/modules/nf-core/gatk4/estimatelibrarycomplexity/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/estimatelibrarycomplexity/meta.yml
rename to modules/nf-core/gatk4/estimatelibrarycomplexity/meta.yml
diff --git a/modules/nf-core/modules/gatk4/filtermutectcalls/main.nf b/modules/nf-core/gatk4/filtermutectcalls/main.nf
similarity index 86%
rename from modules/nf-core/modules/gatk4/filtermutectcalls/main.nf
rename to modules/nf-core/gatk4/filtermutectcalls/main.nf
index 91f6defa9a..71de16f6d4 100644
--- a/modules/nf-core/modules/gatk4/filtermutectcalls/main.nf
+++ b/modules/nf-core/gatk4/filtermutectcalls/main.nf
@@ -54,4 +54,17 @@ process GATK4_FILTERMUTECTCALLS {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.vcf.gz
+    touch ${prefix}.vcf.gz.tbi
+    touch ${prefix}.vcf.gz.filteringStats.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/modules/gatk4/filtermutectcalls/meta.yml b/modules/nf-core/gatk4/filtermutectcalls/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/filtermutectcalls/meta.yml
rename to modules/nf-core/gatk4/filtermutectcalls/meta.yml
diff --git a/modules/nf-core/modules/gatk4/filtervarianttranches/main.nf b/modules/nf-core/gatk4/filtervarianttranches/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/filtervarianttranches/main.nf
rename to modules/nf-core/gatk4/filtervarianttranches/main.nf
diff --git a/modules/nf-core/modules/gatk4/filtervarianttranches/meta.yml b/modules/nf-core/gatk4/filtervarianttranches/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/filtervarianttranches/meta.yml
rename to modules/nf-core/gatk4/filtervarianttranches/meta.yml
diff --git a/modules/nf-core/modules/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/gatk4/gatherbqsrreports/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/gatherbqsrreports/main.nf
rename to modules/nf-core/gatk4/gatherbqsrreports/main.nf
diff --git a/modules/nf-core/modules/gatk4/gatherbqsrreports/meta.yml b/modules/nf-core/gatk4/gatherbqsrreports/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/gatherbqsrreports/meta.yml
rename to modules/nf-core/gatk4/gatherbqsrreports/meta.yml
diff --git a/modules/nf-core/modules/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/gatherpileupsummaries/main.nf
rename to modules/nf-core/gatk4/gatherpileupsummaries/main.nf
diff --git a/modules/nf-core/modules/gatk4/gatherpileupsummaries/meta.yml b/modules/nf-core/gatk4/gatherpileupsummaries/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/gatherpileupsummaries/meta.yml
rename to modules/nf-core/gatk4/gatherpileupsummaries/meta.yml
diff --git a/modules/nf-core/modules/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/genomicsdbimport/main.nf
rename to modules/nf-core/gatk4/genomicsdbimport/main.nf
diff --git a/modules/nf-core/modules/gatk4/genomicsdbimport/meta.yml b/modules/nf-core/gatk4/genomicsdbimport/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/genomicsdbimport/meta.yml
rename to modules/nf-core/gatk4/genomicsdbimport/meta.yml
diff --git a/modules/nf-core/modules/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/genotypegvcfs/main.nf
rename to modules/nf-core/gatk4/genotypegvcfs/main.nf
diff --git a/modules/nf-core/modules/gatk4/genotypegvcfs/meta.yml b/modules/nf-core/gatk4/genotypegvcfs/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/genotypegvcfs/meta.yml
rename to modules/nf-core/gatk4/genotypegvcfs/meta.yml
diff --git a/modules/nf-core/modules/gatk4/getpileupsummaries/main.nf b/modules/nf-core/gatk4/getpileupsummaries/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/getpileupsummaries/main.nf
rename to modules/nf-core/gatk4/getpileupsummaries/main.nf
diff --git a/modules/nf-core/modules/gatk4/getpileupsummaries/meta.yml b/modules/nf-core/gatk4/getpileupsummaries/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/getpileupsummaries/meta.yml
rename to modules/nf-core/gatk4/getpileupsummaries/meta.yml
diff --git a/modules/nf-core/modules/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/haplotypecaller/main.nf
rename to modules/nf-core/gatk4/haplotypecaller/main.nf
diff --git a/modules/nf-core/modules/gatk4/haplotypecaller/meta.yml b/modules/nf-core/gatk4/haplotypecaller/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/haplotypecaller/meta.yml
rename to modules/nf-core/gatk4/haplotypecaller/meta.yml
diff --git a/modules/nf-core/modules/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/intervallisttobed/main.nf
rename to modules/nf-core/gatk4/intervallisttobed/main.nf
diff --git a/modules/nf-core/modules/gatk4/intervallisttobed/meta.yml b/modules/nf-core/gatk4/intervallisttobed/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/intervallisttobed/meta.yml
rename to modules/nf-core/gatk4/intervallisttobed/meta.yml
diff --git a/modules/nf-core/modules/gatk4/learnreadorientationmodel/main.nf b/modules/nf-core/gatk4/learnreadorientationmodel/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/learnreadorientationmodel/main.nf
rename to modules/nf-core/gatk4/learnreadorientationmodel/main.nf
diff --git a/modules/nf-core/modules/gatk4/learnreadorientationmodel/meta.yml b/modules/nf-core/gatk4/learnreadorientationmodel/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/learnreadorientationmodel/meta.yml
rename to modules/nf-core/gatk4/learnreadorientationmodel/meta.yml
diff --git a/modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff b/modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff
new file mode 100644
index 0000000000..14cac1cecc
--- /dev/null
+++ b/modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff
@@ -0,0 +1,53 @@
+Changes in module 'nf-core/gatk4/markduplicates'
+--- modules/nf-core/gatk4/markduplicates/main.nf
++++ modules/nf-core/gatk4/markduplicates/main.nf
+@@ -9,25 +9,20 @@
+ 
+     input:
+     tuple val(meta), path(bam)
+-    path  fasta
+-    path  fasta_fai
+ 
+     output:
+-    tuple val(meta), path("*cram"),     emit: cram,  optional: true
+-    tuple val(meta), path("*bam"),      emit: bam,   optional: true
+-    tuple val(meta), path("*.crai"),    emit: crai,  optional: true
+-    tuple val(meta), path("*.bai"),     emit: bai,   optional: true
++    tuple val(meta), path("*.bam")    , emit: bam
++    tuple val(meta), path("*.bai")    , optional:true, emit: bai
+     tuple val(meta), path("*.metrics"), emit: metrics
+-    path "versions.yml",                emit: versions
++    path "versions.yml"               , emit: versions
+ 
+     when:
+     task.ext.when == null || task.ext.when
+ 
+     script:
+     def args = task.ext.args ?: ''
+-    prefix = task.ext.prefix ?: "${meta.id}"
++    def prefix = task.ext.prefix ?: "${meta.id}"
+     def input_list = bam.collect{"--INPUT $it"}.join(' ')
+-    def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
+ 
+     def avail_mem = 3
+     if (!task.memory) {
+@@ -38,16 +33,10 @@
+     """
+     gatk --java-options "-Xmx${avail_mem}g" MarkDuplicates \\
+         $input_list \\
+-        --OUTPUT ${prefix} \\
++        --OUTPUT ${prefix}.bam \\
+         --METRICS_FILE ${prefix}.metrics \\
+         --TMP_DIR . \\
+-        ${reference} \\
+         $args
+-
+-
+-    if  [[ ${prefix} == *.cram ]]; then
+-        mv ${prefix}.bai ${prefix}.crai
+-    fi
+ 
+     cat <<-END_VERSIONS > versions.yml
+     "${task.process}":
+
+************************************************************
diff --git a/modules/nf-core/modules/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/markduplicates/main.nf
rename to modules/nf-core/gatk4/markduplicates/main.nf
diff --git a/modules/nf-core/modules/gatk4/markduplicates/meta.yml b/modules/nf-core/gatk4/markduplicates/meta.yml
similarity index 78%
rename from modules/nf-core/modules/gatk4/markduplicates/meta.yml
rename to modules/nf-core/gatk4/markduplicates/meta.yml
index 93877f479b..ddf98d2f5a 100644
--- a/modules/nf-core/modules/gatk4/markduplicates/meta.yml
+++ b/modules/nf-core/gatk4/markduplicates/meta.yml
@@ -26,6 +26,14 @@ input:
       type: file
       description: Sorted BAM file
       pattern: "*.{bam}"
+  - fasta:
+      type: file
+      description: Fasta file
+      pattern: "*.{fasta}"
+  - fasta_fai:
+      type: file
+      description: Fasta index file
+      pattern: "*.{fai}"
 
 output:
   - meta:
@@ -41,6 +49,18 @@ output:
       type: file
       description: Marked duplicates BAM file
       pattern: "*.{bam}"
+  - cram:
+      type: file
+      description: Marked duplicates CRAM file
+      pattern: "*.{cram}"
+  - bai:
+      type: file
+      description: BAM index file
+      pattern: "*.{bam.bai}"
+  - crai:
+      type: file
+      description: CRAM index file
+      pattern: "*.{cram.crai}"
   - metrics:
       type: file
       description: Duplicate metrics file generated by GATK
diff --git a/modules/nf-core/modules/gatk4/markduplicatesspark/main.nf b/modules/nf-core/gatk4/markduplicatesspark/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/markduplicatesspark/main.nf
rename to modules/nf-core/gatk4/markduplicatesspark/main.nf
diff --git a/modules/nf-core/modules/gatk4/markduplicatesspark/meta.yml b/modules/nf-core/gatk4/markduplicatesspark/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/markduplicatesspark/meta.yml
rename to modules/nf-core/gatk4/markduplicatesspark/meta.yml
diff --git a/modules/nf-core/modules/gatk4/mergemutectstats/main.nf b/modules/nf-core/gatk4/mergemutectstats/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/mergemutectstats/main.nf
rename to modules/nf-core/gatk4/mergemutectstats/main.nf
diff --git a/modules/nf-core/modules/gatk4/mergemutectstats/meta.yml b/modules/nf-core/gatk4/mergemutectstats/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/mergemutectstats/meta.yml
rename to modules/nf-core/gatk4/mergemutectstats/meta.yml
diff --git a/modules/nf-core/modules/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf
similarity index 83%
rename from modules/nf-core/modules/gatk4/mergevcfs/main.nf
rename to modules/nf-core/gatk4/mergevcfs/main.nf
index 35930a6e51..c1ec942ec2 100644
--- a/modules/nf-core/modules/gatk4/mergevcfs/main.nf
+++ b/modules/nf-core/gatk4/mergevcfs/main.nf
@@ -44,4 +44,16 @@ process GATK4_MERGEVCFS {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.vcf.gz
+    touch ${prefix}.vcf.gz.tbi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/modules/gatk4/mergevcfs/meta.yml b/modules/nf-core/gatk4/mergevcfs/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/mergevcfs/meta.yml
rename to modules/nf-core/gatk4/mergevcfs/meta.yml
diff --git a/modules/nf-core/modules/gatk4/mutect2/main.nf b/modules/nf-core/gatk4/mutect2/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/mutect2/main.nf
rename to modules/nf-core/gatk4/mutect2/main.nf
diff --git a/modules/nf-core/modules/gatk4/mutect2/meta.yml b/modules/nf-core/gatk4/mutect2/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/mutect2/meta.yml
rename to modules/nf-core/gatk4/mutect2/meta.yml
diff --git a/modules/nf-core/modules/gatk4/variantrecalibrator/main.nf b/modules/nf-core/gatk4/variantrecalibrator/main.nf
similarity index 100%
rename from modules/nf-core/modules/gatk4/variantrecalibrator/main.nf
rename to modules/nf-core/gatk4/variantrecalibrator/main.nf
diff --git a/modules/nf-core/modules/gatk4/variantrecalibrator/meta.yml b/modules/nf-core/gatk4/variantrecalibrator/meta.yml
similarity index 100%
rename from modules/nf-core/modules/gatk4/variantrecalibrator/meta.yml
rename to modules/nf-core/gatk4/variantrecalibrator/meta.yml
diff --git a/modules/nf-core/modules/manta/germline/main.nf b/modules/nf-core/manta/germline/main.nf
similarity index 100%
rename from modules/nf-core/modules/manta/germline/main.nf
rename to modules/nf-core/manta/germline/main.nf
diff --git a/modules/nf-core/modules/manta/germline/meta.yml b/modules/nf-core/manta/germline/meta.yml
similarity index 100%
rename from modules/nf-core/modules/manta/germline/meta.yml
rename to modules/nf-core/manta/germline/meta.yml
diff --git a/modules/nf-core/modules/manta/somatic/main.nf b/modules/nf-core/manta/somatic/main.nf
similarity index 100%
rename from modules/nf-core/modules/manta/somatic/main.nf
rename to modules/nf-core/manta/somatic/main.nf
diff --git a/modules/nf-core/modules/manta/somatic/meta.yml b/modules/nf-core/manta/somatic/meta.yml
similarity index 100%
rename from modules/nf-core/modules/manta/somatic/meta.yml
rename to modules/nf-core/manta/somatic/meta.yml
diff --git a/modules/nf-core/modules/manta/tumoronly/main.nf b/modules/nf-core/manta/tumoronly/main.nf
similarity index 100%
rename from modules/nf-core/modules/manta/tumoronly/main.nf
rename to modules/nf-core/manta/tumoronly/main.nf
diff --git a/modules/nf-core/modules/manta/tumoronly/meta.yml b/modules/nf-core/manta/tumoronly/meta.yml
similarity index 100%
rename from modules/nf-core/modules/manta/tumoronly/meta.yml
rename to modules/nf-core/manta/tumoronly/meta.yml
diff --git a/modules/nf-core/modules/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf
similarity index 100%
rename from modules/nf-core/modules/mosdepth/main.nf
rename to modules/nf-core/mosdepth/main.nf
diff --git a/modules/nf-core/modules/mosdepth/meta.yml b/modules/nf-core/mosdepth/meta.yml
similarity index 100%
rename from modules/nf-core/modules/mosdepth/meta.yml
rename to modules/nf-core/mosdepth/meta.yml
diff --git a/modules/nf-core/modules/msisensorpro/msi_somatic/main.nf b/modules/nf-core/msisensorpro/msi_somatic/main.nf
similarity index 100%
rename from modules/nf-core/modules/msisensorpro/msi_somatic/main.nf
rename to modules/nf-core/msisensorpro/msi_somatic/main.nf
diff --git a/modules/nf-core/modules/msisensorpro/msi_somatic/meta.yml b/modules/nf-core/msisensorpro/msi_somatic/meta.yml
similarity index 100%
rename from modules/nf-core/modules/msisensorpro/msi_somatic/meta.yml
rename to modules/nf-core/msisensorpro/msi_somatic/meta.yml
diff --git a/modules/nf-core/modules/msisensorpro/scan/main.nf b/modules/nf-core/msisensorpro/scan/main.nf
similarity index 100%
rename from modules/nf-core/modules/msisensorpro/scan/main.nf
rename to modules/nf-core/msisensorpro/scan/main.nf
diff --git a/modules/nf-core/modules/msisensorpro/scan/meta.yml b/modules/nf-core/msisensorpro/scan/meta.yml
similarity index 100%
rename from modules/nf-core/modules/msisensorpro/scan/meta.yml
rename to modules/nf-core/msisensorpro/scan/meta.yml
diff --git a/modules/nf-core/modules/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
similarity index 100%
rename from modules/nf-core/modules/multiqc/main.nf
rename to modules/nf-core/multiqc/main.nf
diff --git a/modules/nf-core/modules/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
similarity index 81%
rename from modules/nf-core/modules/multiqc/meta.yml
rename to modules/nf-core/multiqc/meta.yml
index bf3a27fe73..ebc29b279d 100644
--- a/modules/nf-core/modules/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -12,6 +12,7 @@ tools:
       homepage: https://multiqc.info/
       documentation: https://multiqc.info/docs/
       licence: ["GPL-3.0-or-later"]
+
 input:
   - multiqc_files:
       type: file
@@ -19,12 +20,17 @@ input:
         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
+      description: Optional config yml for MultiQC
+      pattern: "*.{yml,yaml}"
+  - extra_multiqc_config:
+      type: file
+      description: Second optional config yml for MultiQC. Will override common sections in multiqc_config.
       pattern: "*.{yml,yaml}"
   - multiqc_logo:
       type: file
-      description: Logo file for MultiQC
+      description: Optional logo file for MultiQC
       pattern: "*.{png}"
+
 output:
   - report:
       type: file
@@ -46,3 +52,4 @@ authors:
   - "@abhi18av"
   - "@bunop"
   - "@drpatelh"
+  - "@jfy133"
diff --git a/modules/nf-core/multiqc/multiqc.diff b/modules/nf-core/multiqc/multiqc.diff
new file mode 100644
index 0000000000..f6c829984a
--- /dev/null
+++ b/modules/nf-core/multiqc/multiqc.diff
@@ -0,0 +1,42 @@
+Changes in module 'nf-core/multiqc'
+--- modules/nf-core/multiqc/main.nf
++++ modules/nf-core/multiqc/main.nf
+@@ -1,16 +1,14 @@
+ process MULTIQC {
+-    label 'process_single'
++    label 'process_medium'
+ 
+-    conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
++    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:1.13--pyhdfd78af_0' :
+-        'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
++        'https://depot.galaxyproject.org/singularity/multiqc:1.13a--pyhdfd78af_1' :
++        'quay.io/biocontainers/multiqc:1.13a--pyhdfd78af_1' }"
+ 
+     input:
+     path  multiqc_files, stageAs: "?/*"
+-    path(multiqc_config)
+-    path(extra_multiqc_config)
+-    path(multiqc_logo)
++    tuple path(multiqc_config), path(multiqc_logo)
+ 
+     output:
+     path "*multiqc_report.html", emit: report
+@@ -24,13 +22,11 @@
+     script:
+     def args = task.ext.args ?: ''
+     def config = multiqc_config ? "--config $multiqc_config" : ''
+-    def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
+     """
+     multiqc \\
+         --force \\
++        $config \\
+         $args \\
+-        $config \\
+-        $extra_config \\
+         .
+ 
+     cat <<-END_VERSIONS > versions.yml
+
+************************************************************
diff --git a/modules/nf-core/modules/samblaster/main.nf b/modules/nf-core/samblaster/main.nf
similarity index 100%
rename from modules/nf-core/modules/samblaster/main.nf
rename to modules/nf-core/samblaster/main.nf
diff --git a/modules/nf-core/modules/samblaster/meta.yml b/modules/nf-core/samblaster/meta.yml
similarity index 100%
rename from modules/nf-core/modules/samblaster/meta.yml
rename to modules/nf-core/samblaster/meta.yml
diff --git a/modules/nf-core/modules/samtools/bam2fq/main.nf b/modules/nf-core/samtools/bam2fq/main.nf
similarity index 100%
rename from modules/nf-core/modules/samtools/bam2fq/main.nf
rename to modules/nf-core/samtools/bam2fq/main.nf
diff --git a/modules/nf-core/modules/samtools/bam2fq/meta.yml b/modules/nf-core/samtools/bam2fq/meta.yml
similarity index 100%
rename from modules/nf-core/modules/samtools/bam2fq/meta.yml
rename to modules/nf-core/samtools/bam2fq/meta.yml
diff --git a/modules/nf-core/modules/samtools/collatefastq/main.nf b/modules/nf-core/samtools/collatefastq/main.nf
similarity index 100%
rename from modules/nf-core/modules/samtools/collatefastq/main.nf
rename to modules/nf-core/samtools/collatefastq/main.nf
diff --git a/modules/nf-core/modules/samtools/collatefastq/meta.yml b/modules/nf-core/samtools/collatefastq/meta.yml
similarity index 100%
rename from modules/nf-core/modules/samtools/collatefastq/meta.yml
rename to modules/nf-core/samtools/collatefastq/meta.yml
diff --git a/modules/nf-core/modules/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf
similarity index 100%
rename from modules/nf-core/modules/samtools/convert/main.nf
rename to modules/nf-core/samtools/convert/main.nf
diff --git a/modules/nf-core/modules/samtools/convert/meta.yml b/modules/nf-core/samtools/convert/meta.yml
similarity index 100%
rename from modules/nf-core/modules/samtools/convert/meta.yml
rename to modules/nf-core/samtools/convert/meta.yml
diff --git a/modules/nf-core/modules/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf
similarity index 94%
rename from modules/nf-core/modules/samtools/faidx/main.nf
rename to modules/nf-core/samtools/faidx/main.nf
index 36b3538e55..ef940db279 100644
--- a/modules/nf-core/modules/samtools/faidx/main.nf
+++ b/modules/nf-core/samtools/faidx/main.nf
@@ -12,6 +12,7 @@ process SAMTOOLS_FAIDX {
 
     output:
     tuple val(meta), path ("*.fai"), emit: fai
+    tuple val(meta), path ("*.gzi"), emit: gzi, optional: true
     path "versions.yml"            , emit: versions
 
     when:
diff --git a/modules/nf-core/modules/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml
similarity index 91%
rename from modules/nf-core/modules/samtools/faidx/meta.yml
rename to modules/nf-core/samtools/faidx/meta.yml
index e976776436..fe2fe9a174 100644
--- a/modules/nf-core/modules/samtools/faidx/meta.yml
+++ b/modules/nf-core/samtools/faidx/meta.yml
@@ -33,6 +33,10 @@ output:
       type: file
       description: FASTA index file
       pattern: "*.{fai}"
+  - gzi:
+      type: file
+      description: Optional gzip index file for compressed inputs
+      pattern: "*.gzi"
   - versions:
       type: file
       description: File containing software versions
diff --git a/modules/nf-core/modules/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf
similarity index 100%
rename from modules/nf-core/modules/samtools/index/main.nf
rename to modules/nf-core/samtools/index/main.nf
diff --git a/modules/nf-core/modules/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml
similarity index 100%
rename from modules/nf-core/modules/samtools/index/meta.yml
rename to modules/nf-core/samtools/index/meta.yml
diff --git a/modules/nf-core/modules/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf
similarity index 84%
rename from modules/nf-core/modules/samtools/merge/main.nf
rename to modules/nf-core/samtools/merge/main.nf
index d01bbed8bd..91f141166c 100644
--- a/modules/nf-core/modules/samtools/merge/main.nf
+++ b/modules/nf-core/samtools/merge/main.nf
@@ -15,15 +15,17 @@ process SAMTOOLS_MERGE {
     output:
     tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam
     tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram
+    tuple val(meta), path("*.csi")         , optional:true, emit: csi
     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 file_type = input_files[0].getExtension()
+    def file_type = input_files instanceof List ? input_files[0].getExtension() : input_files.getExtension()
     def reference = fasta ? "--reference ${fasta}" : ""
     """
     samtools \\
@@ -42,7 +44,7 @@ process SAMTOOLS_MERGE {
 
     stub:
     prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
-    def file_type = input_files[0].getExtension()
+    def file_type = input_files instanceof List ? input_files[0].getExtension() : input_files.getExtension()
     """
     touch ${prefix}.${file_type}
 
diff --git a/modules/nf-core/modules/samtools/merge/meta.yml b/modules/nf-core/samtools/merge/meta.yml
similarity index 94%
rename from modules/nf-core/modules/samtools/merge/meta.yml
rename to modules/nf-core/samtools/merge/meta.yml
index f6833d0c7e..5bd84bc5fc 100644
--- a/modules/nf-core/modules/samtools/merge/meta.yml
+++ b/modules/nf-core/samtools/merge/meta.yml
@@ -51,6 +51,10 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
+  - csi:
+      type: file
+      description: BAM index file (optional)
+      pattern: "*.csi"
 authors:
   - "@drpatelh"
   - "@yuukiiwa "
diff --git a/modules/nf-core/modules/samtools/mpileup/main.nf b/modules/nf-core/samtools/mpileup/main.nf
similarity index 100%
rename from modules/nf-core/modules/samtools/mpileup/main.nf
rename to modules/nf-core/samtools/mpileup/main.nf
diff --git a/modules/nf-core/modules/samtools/mpileup/meta.yml b/modules/nf-core/samtools/mpileup/meta.yml
similarity index 100%
rename from modules/nf-core/modules/samtools/mpileup/meta.yml
rename to modules/nf-core/samtools/mpileup/meta.yml
diff --git a/modules/nf-core/modules/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf
similarity index 100%
rename from modules/nf-core/modules/samtools/stats/main.nf
rename to modules/nf-core/samtools/stats/main.nf
diff --git a/modules/nf-core/modules/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml
similarity index 100%
rename from modules/nf-core/modules/samtools/stats/meta.yml
rename to modules/nf-core/samtools/stats/meta.yml
diff --git a/modules/nf-core/modules/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf
similarity index 100%
rename from modules/nf-core/modules/samtools/view/main.nf
rename to modules/nf-core/samtools/view/main.nf
diff --git a/modules/nf-core/modules/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml
similarity index 64%
rename from modules/nf-core/modules/samtools/view/meta.yml
rename to modules/nf-core/samtools/view/meta.yml
index a8b43ecce6..a52e4f8d8b 100644
--- a/modules/nf-core/modules/samtools/view/meta.yml
+++ b/modules/nf-core/samtools/view/meta.yml
@@ -33,6 +33,10 @@ input:
       type: optional file
       description: Reference file the CRAM was created with
       pattern: "*.{fasta,fa}"
+  - qname:
+      type: file
+      description: Optional file with read names to output only select alignments
+      pattern: "*.{txt,list}"
 output:
   - meta:
       type: map
@@ -41,12 +45,29 @@ output:
         e.g. [ id:'test', single_end:false ]
   - bam:
       type: file
-      description: filtered/converted BAM/SAM file
-      pattern: "*.{bam,sam}"
+      description: optional filtered/converted BAM file
+      pattern: "*.{bam}"
   - cram:
       type: file
-      description: filtered/converted CRAM file
-      pattern: "*.cram"
+      description: optional filtered/converted CRAM file
+      pattern: "*.{cram}"
+  - sam:
+      type: file
+      description: optional filtered/converted SAM file
+      pattern: "*.{sam}"
+  # bai, csi, and crai are created with `--write-index`
+  - bai:
+      type: file
+      description: optional BAM file index
+      pattern: "*.{bai}"
+  - csi:
+      type: file
+      description: optional tabix BAM file index
+      pattern: "*.{csi}"
+  - crai:
+      type: file
+      description: optional CRAM file index
+      pattern: "*.{crai}"
   - versions:
       type: file
       description: File containing software versions
@@ -55,3 +76,4 @@ authors:
   - "@drpatelh"
   - "@joseespinosa"
   - "@FriederikeHanssen"
+  - "@priyanka-surana"
diff --git a/modules/nf-core/samtools/view/samtools-view.diff b/modules/nf-core/samtools/view/samtools-view.diff
new file mode 100644
index 0000000000..1ee7b0c1ae
--- /dev/null
+++ b/modules/nf-core/samtools/view/samtools-view.diff
@@ -0,0 +1,54 @@
+Changes in module 'nf-core/samtools/view'
+--- modules/nf-core/samtools/view/main.nf
++++ modules/nf-core/samtools/view/main.nf
+@@ -10,39 +10,31 @@
+     input:
+     tuple val(meta), path(input), path(index)
+     path fasta
+-    path qname
+ 
+     output:
+-    tuple val(meta), path("*.bam"),  emit: bam,     optional: true
+-    tuple val(meta), path("*.cram"), emit: cram,    optional: true
+-    tuple val(meta), path("*.sam"),  emit: sam,     optional: true
+-    tuple val(meta), path("*.bai"),  emit: bai,     optional: true
+-    tuple val(meta), path("*.csi"),  emit: csi,     optional: true
+-    tuple val(meta), path("*.crai"), emit: crai,    optional: true
+-    path  "versions.yml",            emit: versions
++    tuple val(meta), path("*.bam") , emit: bam , optional: true
++    tuple val(meta), path("*.cram"), emit: cram, optional: true
++    path  "versions.yml"           , emit: versions
+ 
+     when:
+     task.ext.when == null || task.ext.when
+ 
+     script:
+     def args = task.ext.args ?: ''
++    def args2 = task.ext.args2 ?: ''
+     def prefix = task.ext.prefix ?: "${meta.id}"
+-    def reference = fasta ? "--reference ${fasta}" : ""
+-    def readnames = qname ? "--qname-file ${qname}": ""
+-    def file_type = args.contains("--output-fmt sam") ? "sam" :
+-                    args.contains("--output-fmt bam") ? "bam" :
+-                    args.contains("--output-fmt cram") ? "cram" :
+-                    input.getExtension()
++    def reference = fasta ? "--reference ${fasta} -C" : ""
++    def file_type = input.getExtension()
+     if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+     """
+     samtools \\
+         view \\
+         --threads ${task.cpus-1} \\
+         ${reference} \\
+-        ${readnames} \\
+         $args \\
+-        -o ${prefix}.${file_type} \\
+-        $input
++        $input \\
++        $args2 \\
++        > ${prefix}.${file_type}
+ 
+     cat <<-END_VERSIONS > versions.yml
+     "${task.process}":
+
+************************************************************
diff --git a/modules/nf-core/modules/snpeff/Dockerfile b/modules/nf-core/snpeff/Dockerfile
similarity index 100%
rename from modules/nf-core/modules/snpeff/Dockerfile
rename to modules/nf-core/snpeff/Dockerfile
diff --git a/modules/nf-core/modules/snpeff/build.sh b/modules/nf-core/snpeff/build.sh
old mode 100644
new mode 100755
similarity index 100%
rename from modules/nf-core/modules/snpeff/build.sh
rename to modules/nf-core/snpeff/build.sh
diff --git a/modules/nf-core/modules/snpeff/environment.yml b/modules/nf-core/snpeff/environment.yml
similarity index 100%
rename from modules/nf-core/modules/snpeff/environment.yml
rename to modules/nf-core/snpeff/environment.yml
diff --git a/modules/nf-core/modules/snpeff/main.nf b/modules/nf-core/snpeff/main.nf
similarity index 100%
rename from modules/nf-core/modules/snpeff/main.nf
rename to modules/nf-core/snpeff/main.nf
diff --git a/modules/nf-core/modules/snpeff/meta.yml b/modules/nf-core/snpeff/meta.yml
similarity index 100%
rename from modules/nf-core/modules/snpeff/meta.yml
rename to modules/nf-core/snpeff/meta.yml
diff --git a/modules/nf-core/modules/strelka/germline/main.nf b/modules/nf-core/strelka/germline/main.nf
similarity index 100%
rename from modules/nf-core/modules/strelka/germline/main.nf
rename to modules/nf-core/strelka/germline/main.nf
diff --git a/modules/nf-core/modules/strelka/germline/meta.yml b/modules/nf-core/strelka/germline/meta.yml
similarity index 100%
rename from modules/nf-core/modules/strelka/germline/meta.yml
rename to modules/nf-core/strelka/germline/meta.yml
diff --git a/modules/nf-core/modules/strelka/somatic/main.nf b/modules/nf-core/strelka/somatic/main.nf
similarity index 100%
rename from modules/nf-core/modules/strelka/somatic/main.nf
rename to modules/nf-core/strelka/somatic/main.nf
diff --git a/modules/nf-core/modules/strelka/somatic/meta.yml b/modules/nf-core/strelka/somatic/meta.yml
similarity index 100%
rename from modules/nf-core/modules/strelka/somatic/meta.yml
rename to modules/nf-core/strelka/somatic/meta.yml
diff --git a/modules/nf-core/modules/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf
similarity index 98%
rename from modules/nf-core/modules/svdb/merge/main.nf
rename to modules/nf-core/svdb/merge/main.nf
index 05fb2b1754..477dbb0d31 100644
--- a/modules/nf-core/modules/svdb/merge/main.nf
+++ b/modules/nf-core/svdb/merge/main.nf
@@ -48,7 +48,7 @@ process SVDB_MERGE {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}_sv_merge.vcf
+    touch ${prefix}_sv_merge.vcf.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/modules/svdb/merge/meta.yml b/modules/nf-core/svdb/merge/meta.yml
similarity index 100%
rename from modules/nf-core/modules/svdb/merge/meta.yml
rename to modules/nf-core/svdb/merge/meta.yml
diff --git a/modules/nf-core/modules/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf
similarity index 100%
rename from modules/nf-core/modules/tabix/bgziptabix/main.nf
rename to modules/nf-core/tabix/bgziptabix/main.nf
diff --git a/modules/nf-core/modules/tabix/bgziptabix/meta.yml b/modules/nf-core/tabix/bgziptabix/meta.yml
similarity index 100%
rename from modules/nf-core/modules/tabix/bgziptabix/meta.yml
rename to modules/nf-core/tabix/bgziptabix/meta.yml
diff --git a/modules/nf-core/modules/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf
similarity index 100%
rename from modules/nf-core/modules/tabix/tabix/main.nf
rename to modules/nf-core/tabix/tabix/main.nf
diff --git a/modules/nf-core/modules/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml
similarity index 100%
rename from modules/nf-core/modules/tabix/tabix/meta.yml
rename to modules/nf-core/tabix/tabix/meta.yml
diff --git a/modules/nf-core/modules/tiddit/sv/main.nf b/modules/nf-core/tiddit/sv/main.nf
similarity index 100%
rename from modules/nf-core/modules/tiddit/sv/main.nf
rename to modules/nf-core/tiddit/sv/main.nf
diff --git a/modules/nf-core/modules/tiddit/sv/meta.yml b/modules/nf-core/tiddit/sv/meta.yml
similarity index 100%
rename from modules/nf-core/modules/tiddit/sv/meta.yml
rename to modules/nf-core/tiddit/sv/meta.yml
diff --git a/modules/nf-core/modules/untar/main.nf b/modules/nf-core/untar/main.nf
similarity index 68%
rename from modules/nf-core/modules/untar/main.nf
rename to modules/nf-core/untar/main.nf
index 4128652008..71eea7b2c6 100644
--- a/modules/nf-core/modules/untar/main.nf
+++ b/modules/nf-core/untar/main.nf
@@ -25,12 +25,23 @@ process UNTAR {
     """
     mkdir output
 
-    tar \\
-        -C output --strip-components 1 \\
-        -xzvf \\
-        $args \\
-        $archive \\
-        $args2
+    ## Ensures --strip-components only applied when top level of tar contents is a directory
+    ## If just files or multiple directories, place all in output
+    if [[ \$(tar -tzf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
+        tar \\
+            -C output --strip-components 1 \\
+            -xzvf \\
+            $args \\
+            $archive \\
+            $args2
+    else
+        tar \\
+            -C output \\
+            -xzvf \\
+            $args \\
+            $archive \\
+            $args2
+    fi
 
     mv output ${untar}
 
diff --git a/modules/nf-core/modules/untar/meta.yml b/modules/nf-core/untar/meta.yml
similarity index 85%
rename from modules/nf-core/modules/untar/meta.yml
rename to modules/nf-core/untar/meta.yml
index d426919bd3..ea7a3f382a 100644
--- a/modules/nf-core/modules/untar/meta.yml
+++ b/modules/nf-core/untar/meta.yml
@@ -26,9 +26,9 @@ output:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   - untar:
-      type: file
-      description:
-      pattern: "*.*"
+      type: directory
+      description: Directory containing contents of archive
+      pattern: "*/"
   - versions:
       type: file
       description: File containing software versions
@@ -36,3 +36,5 @@ output:
 authors:
   - "@joseespinosa"
   - "@drpatelh"
+  - "@matthdsm"
+  - "@jfy133"
diff --git a/modules/nf-core/modules/unzip/main.nf b/modules/nf-core/unzip/main.nf
similarity index 100%
rename from modules/nf-core/modules/unzip/main.nf
rename to modules/nf-core/unzip/main.nf
diff --git a/modules/nf-core/modules/unzip/meta.yml b/modules/nf-core/unzip/meta.yml
similarity index 100%
rename from modules/nf-core/modules/unzip/meta.yml
rename to modules/nf-core/unzip/meta.yml
diff --git a/modules/nf-core/modules/vcftools/main.nf b/modules/nf-core/vcftools/main.nf
similarity index 100%
rename from modules/nf-core/modules/vcftools/main.nf
rename to modules/nf-core/vcftools/main.nf
diff --git a/modules/nf-core/modules/vcftools/meta.yml b/modules/nf-core/vcftools/meta.yml
similarity index 100%
rename from modules/nf-core/modules/vcftools/meta.yml
rename to modules/nf-core/vcftools/meta.yml
diff --git a/subworkflows/local/pair_variant_calling.nf b/subworkflows/local/pair_variant_calling.nf
index 7ad59f35eb..8ca97496d0 100644
--- a/subworkflows/local/pair_variant_calling.nf
+++ b/subworkflows/local/pair_variant_calling.nf
@@ -2,7 +2,7 @@
 // PAIRED VARIANT CALLING
 //
 include { GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING } from '../../subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main'
-include { MSISENSORPRO_MSI_SOMATIC                  } from '../../modules/nf-core/modules/msisensorpro/msi_somatic/main'
+include { MSISENSORPRO_MSI_SOMATIC                  } from '../../modules/nf-core/msisensorpro/msi_somatic/main'
 include { RUN_CONTROLFREEC_SOMATIC                  } from '../nf-core/variantcalling/controlfreec/somatic/main.nf'
 include { RUN_FREEBAYES as RUN_FREEBAYES_SOMATIC    } from '../nf-core/variantcalling/freebayes/main.nf'
 include { RUN_MANTA_SOMATIC                         } from '../nf-core/variantcalling/manta/somatic/main.nf'
diff --git a/subworkflows/local/prepare_cnvkit_reference.nf b/subworkflows/local/prepare_cnvkit_reference.nf
index 67042c23ea..6dde092d6a 100644
--- a/subworkflows/local/prepare_cnvkit_reference.nf
+++ b/subworkflows/local/prepare_cnvkit_reference.nf
@@ -6,8 +6,8 @@
 // For all modules here:
 // A when clause condition is defined in the conf/modules.config to determine if the module should be run
 
-include { CNVKIT_ANTITARGET } from '../../modules/nf-core/modules/cnvkit/antitarget/main'
-include { CNVKIT_REFERENCE  } from '../../modules/nf-core/modules/cnvkit/reference/main'
+include { CNVKIT_ANTITARGET } from '../../modules/nf-core/cnvkit/antitarget/main'
+include { CNVKIT_REFERENCE  } from '../../modules/nf-core/cnvkit/reference/main'
 
 workflow PREPARE_CNVKIT_REFERENCE {
     take:
diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf
index f2652b6f5c..a69893b61b 100644
--- a/subworkflows/local/prepare_genome.nf
+++ b/subworkflows/local/prepare_genome.nf
@@ -8,22 +8,22 @@
 // Condition is based on params.step and params.tools
 // If and extra condition exists, it's specified in comments
 
-include { BWA_INDEX as BWAMEM1_INDEX             } from '../../modules/nf-core/modules/bwa/index/main'
-include { BWAMEM2_INDEX                          } from '../../modules/nf-core/modules/bwamem2/index/main'
-include { DRAGMAP_HASHTABLE                      } from '../../modules/nf-core/modules/dragmap/hashtable/main'
-include { GATK4_CREATESEQUENCEDICTIONARY         } from '../../modules/nf-core/modules/gatk4/createsequencedictionary/main'
-include { MSISENSORPRO_SCAN                      } from '../../modules/nf-core/modules/msisensorpro/scan/main'
-include { SAMTOOLS_FAIDX                         } from '../../modules/nf-core/modules/samtools/faidx/main'
-include { TABIX_TABIX as TABIX_DBSNP             } from '../../modules/nf-core/modules/tabix/tabix/main'
-include { TABIX_TABIX as TABIX_GERMLINE_RESOURCE } from '../../modules/nf-core/modules/tabix/tabix/main'
-include { TABIX_TABIX as TABIX_KNOWN_INDELS      } from '../../modules/nf-core/modules/tabix/tabix/main'
-include { TABIX_TABIX as TABIX_KNOWN_SNPS        } from '../../modules/nf-core/modules/tabix/tabix/main'
-include { TABIX_TABIX as TABIX_PON               } from '../../modules/nf-core/modules/tabix/tabix/main'
-include { UNTAR as UNTAR_CHR_DIR                 } from '../../modules/nf-core/modules/untar/main'
-include { UNZIP as UNZIP_ALLELES                 } from '../../modules/nf-core/modules/unzip/main'
-include { UNZIP as UNZIP_LOCI                    } from '../../modules/nf-core/modules/unzip/main'
-include { UNZIP as UNZIP_GC                      } from '../../modules/nf-core/modules/unzip/main'
-include { UNZIP as UNZIP_RT                      } from '../../modules/nf-core/modules/unzip/main'
+include { BWA_INDEX as BWAMEM1_INDEX             } from '../../modules/nf-core/bwa/index/main'
+include { BWAMEM2_INDEX                          } from '../../modules/nf-core/bwamem2/index/main'
+include { DRAGMAP_HASHTABLE                      } from '../../modules/nf-core/dragmap/hashtable/main'
+include { GATK4_CREATESEQUENCEDICTIONARY         } from '../../modules/nf-core/gatk4/createsequencedictionary/main'
+include { MSISENSORPRO_SCAN                      } from '../../modules/nf-core/msisensorpro/scan/main'
+include { SAMTOOLS_FAIDX                         } from '../../modules/nf-core/samtools/faidx/main'
+include { TABIX_TABIX as TABIX_DBSNP             } from '../../modules/nf-core/tabix/tabix/main'
+include { TABIX_TABIX as TABIX_GERMLINE_RESOURCE } from '../../modules/nf-core/tabix/tabix/main'
+include { TABIX_TABIX as TABIX_KNOWN_INDELS      } from '../../modules/nf-core/tabix/tabix/main'
+include { TABIX_TABIX as TABIX_KNOWN_SNPS        } from '../../modules/nf-core/tabix/tabix/main'
+include { TABIX_TABIX as TABIX_PON               } from '../../modules/nf-core/tabix/tabix/main'
+include { UNTAR as UNTAR_CHR_DIR                 } from '../../modules/nf-core/untar/main'
+include { UNZIP as UNZIP_ALLELES                 } from '../../modules/nf-core/unzip/main'
+include { UNZIP as UNZIP_LOCI                    } from '../../modules/nf-core/unzip/main'
+include { UNZIP as UNZIP_GC                      } from '../../modules/nf-core/unzip/main'
+include { UNZIP as UNZIP_RT                      } from '../../modules/nf-core/unzip/main'
 
 workflow PREPARE_GENOME {
     take:
diff --git a/subworkflows/local/prepare_intervals.nf b/subworkflows/local/prepare_intervals.nf
index 3d20481802..3b294c9ad9 100644
--- a/subworkflows/local/prepare_intervals.nf
+++ b/subworkflows/local/prepare_intervals.nf
@@ -7,11 +7,11 @@
 // A when clause condition is defined in the conf/modules.config to determine if the module should be run
 
 include { BUILD_INTERVALS                                     } from '../../modules/local/build_intervals/main'
-include { CNVKIT_ANTITARGET                                   } from '../../modules/nf-core/modules/cnvkit/antitarget/main'
-include { CNVKIT_REFERENCE                                    } from '../../modules/nf-core/modules/cnvkit/reference/main'
+include { CNVKIT_ANTITARGET                                   } from '../../modules/nf-core/cnvkit/antitarget/main'
+include { CNVKIT_REFERENCE                                    } from '../../modules/nf-core/cnvkit/reference/main'
 include { CREATE_INTERVALS_BED                                } from '../../modules/local/create_intervals_bed/main'
-include { GATK4_INTERVALLISTTOBED                             } from '../../modules/nf-core/modules/gatk4/intervallisttobed/main'
-include { TABIX_BGZIPTABIX as TABIX_BGZIPTABIX_INTERVAL_SPLIT } from '../../modules/nf-core/modules/tabix/bgziptabix/main'
+include { GATK4_INTERVALLISTTOBED                             } from '../../modules/nf-core/gatk4/intervallisttobed/main'
+include { TABIX_BGZIPTABIX as TABIX_BGZIPTABIX_INTERVAL_SPLIT } from '../../modules/nf-core/tabix/bgziptabix/main'
 
 workflow PREPARE_INTERVALS {
     take:
diff --git a/subworkflows/nf-core/alignment_to_fastq.nf b/subworkflows/nf-core/alignment_to_fastq.nf
index a5806f8733..a0b8b81993 100644
--- a/subworkflows/nf-core/alignment_to_fastq.nf
+++ b/subworkflows/nf-core/alignment_to_fastq.nf
@@ -2,14 +2,14 @@
 // BAM/CRAM to FASTQ conversion, paired end only
 //
 
-include { SAMTOOLS_VIEW  as SAMTOOLS_VIEW_MAP_MAP      } from '../../modules/nf-core/modules/samtools/view/main'
-include { SAMTOOLS_VIEW  as SAMTOOLS_VIEW_UNMAP_UNMAP  } from '../../modules/nf-core/modules/samtools/view/main'
-include { SAMTOOLS_VIEW  as SAMTOOLS_VIEW_UNMAP_MAP    } from '../../modules/nf-core/modules/samtools/view/main'
-include { SAMTOOLS_VIEW  as SAMTOOLS_VIEW_MAP_UNMAP    } from '../../modules/nf-core/modules/samtools/view/main'
-include { SAMTOOLS_MERGE as SAMTOOLS_MERGE_UNMAP       } from '../../modules/nf-core/modules/samtools/merge/main'
-include { SAMTOOLS_COLLATEFASTQ as COLLATE_FASTQ_UNMAP } from '../../modules/nf-core/modules/samtools/collatefastq/main'
-include { SAMTOOLS_COLLATEFASTQ as COLLATE_FASTQ_MAP   } from '../../modules/nf-core/modules/samtools/collatefastq/main'
-include { CAT_FASTQ                                    } from '../../modules/nf-core/modules/cat/fastq/main'
+include { SAMTOOLS_VIEW  as SAMTOOLS_VIEW_MAP_MAP      } from '../../modules/nf-core/samtools/view/main'
+include { SAMTOOLS_VIEW  as SAMTOOLS_VIEW_UNMAP_UNMAP  } from '../../modules/nf-core/samtools/view/main'
+include { SAMTOOLS_VIEW  as SAMTOOLS_VIEW_UNMAP_MAP    } from '../../modules/nf-core/samtools/view/main'
+include { SAMTOOLS_VIEW  as SAMTOOLS_VIEW_MAP_UNMAP    } from '../../modules/nf-core/samtools/view/main'
+include { SAMTOOLS_MERGE as SAMTOOLS_MERGE_UNMAP       } from '../../modules/nf-core/samtools/merge/main'
+include { SAMTOOLS_COLLATEFASTQ as COLLATE_FASTQ_UNMAP } from '../../modules/nf-core/samtools/collatefastq/main'
+include { SAMTOOLS_COLLATEFASTQ as COLLATE_FASTQ_MAP   } from '../../modules/nf-core/samtools/collatefastq/main'
+include { CAT_FASTQ                                    } from '../../modules/nf-core/cat/fastq/main'
 
 workflow ALIGNMENT_TO_FASTQ {
     take:
diff --git a/subworkflows/nf-core/annotation/ensemblvep/main.nf b/subworkflows/nf-core/annotation/ensemblvep/main.nf
index f62553e39e..c5b1eff6b1 100644
--- a/subworkflows/nf-core/annotation/ensemblvep/main.nf
+++ b/subworkflows/nf-core/annotation/ensemblvep/main.nf
@@ -2,8 +2,8 @@
 // Run VEP to annotate VCF files
 //
 
-include { ENSEMBLVEP       } from '../../../../modules/nf-core/modules/ensemblvep/main'
-include { TABIX_BGZIPTABIX } from '../../../../modules/nf-core/modules/tabix/bgziptabix/main'
+include { ENSEMBLVEP       } from '../../../../modules/nf-core/ensemblvep/main'
+include { TABIX_BGZIPTABIX } from '../../../../modules/nf-core/tabix/bgziptabix/main'
 
 workflow ANNOTATION_ENSEMBLVEP {
     take:
diff --git a/subworkflows/nf-core/annotation/snpeff/main.nf b/subworkflows/nf-core/annotation/snpeff/main.nf
index 54bfb9caa2..30d1c2df92 100644
--- a/subworkflows/nf-core/annotation/snpeff/main.nf
+++ b/subworkflows/nf-core/annotation/snpeff/main.nf
@@ -2,8 +2,8 @@
 // Run SNPEFF to annotate VCF files
 //
 
-include { SNPEFF           } from '../../../../modules/nf-core/modules/snpeff/main'
-include { TABIX_BGZIPTABIX } from '../../../../modules/nf-core/modules/tabix/bgziptabix/main'
+include { SNPEFF           } from '../../../../modules/nf-core/snpeff/main'
+include { TABIX_BGZIPTABIX } from '../../../../modules/nf-core/tabix/bgziptabix/main'
 
 workflow ANNOTATION_SNPEFF {
     take:
diff --git a/subworkflows/nf-core/bam_to_cram.nf b/subworkflows/nf-core/bam_to_cram.nf
index e1c0ffff56..22654e72b5 100644
--- a/subworkflows/nf-core/bam_to_cram.nf
+++ b/subworkflows/nf-core/bam_to_cram.nf
@@ -4,9 +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 { 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'
+include { SAMTOOLS_CONVERT as SAMTOOLS_BAMTOCRAM } from '../../modules/nf-core/samtools/convert/main'
+include { SAMTOOLS_STATS as SAMTOOLS_STATS_CRAM  } from '../../modules/nf-core/samtools/stats/main'
+include { MOSDEPTH                               } from '../../modules/nf-core/mosdepth/main'
 
 workflow BAM_TO_CRAM {
     take:
diff --git a/subworkflows/nf-core/cram_qc.nf b/subworkflows/nf-core/cram_qc.nf
index eb74fab07c..6595ae097a 100644
--- a/subworkflows/nf-core/cram_qc.nf
+++ b/subworkflows/nf-core/cram_qc.nf
@@ -4,8 +4,8 @@
 // For all modules here:
 // 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 { MOSDEPTH           } from '../../modules/nf-core/modules/mosdepth/main'
+include { SAMTOOLS_STATS     } from '../../modules/nf-core/samtools/stats/main'
+include { MOSDEPTH           } from '../../modules/nf-core/mosdepth/main'
 
 workflow CRAM_QC {
     take:
diff --git a/subworkflows/nf-core/fgbio_create_umi_consensus/main.nf b/subworkflows/nf-core/fgbio_create_umi_consensus/main.nf
index df5302619e..3a29775834 100644
--- a/subworkflows/nf-core/fgbio_create_umi_consensus/main.nf
+++ b/subworkflows/nf-core/fgbio_create_umi_consensus/main.nf
@@ -6,12 +6,12 @@
 // For all modules here:
 // A when clause condition is defined in the conf/modules.config to determine if the module should be run
 
-include { FGBIO_CALLMOLECULARCONSENSUSREADS as CALLUMICONSENSUS } from '../../../modules/nf-core/modules/fgbio/callmolecularconsensusreads/main.nf'
-include { FGBIO_FASTQTOBAM                  as FASTQTOBAM       } from '../../../modules/nf-core/modules/fgbio/fastqtobam/main'
-include { FGBIO_GROUPREADSBYUMI             as GROUPREADSBYUMI  } from '../../../modules/nf-core/modules/fgbio/groupreadsbyumi/main'
+include { FGBIO_CALLMOLECULARCONSENSUSREADS as CALLUMICONSENSUS } from '../../../modules/nf-core/fgbio/callmolecularconsensusreads/main.nf'
+include { FGBIO_FASTQTOBAM                  as FASTQTOBAM       } from '../../../modules/nf-core/fgbio/fastqtobam/main'
+include { FGBIO_GROUPREADSBYUMI             as GROUPREADSBYUMI  } from '../../../modules/nf-core/fgbio/groupreadsbyumi/main'
 include { GATK4_MAPPING                     as MAPPING_UMI      } from '../gatk4/mapping/main'
-include { SAMBLASTER                                            } from '../../../modules/nf-core/modules/samblaster/main'
-include { SAMTOOLS_BAM2FQ                   as BAM2FASTQ        } from '../../../modules/nf-core/modules/samtools/bam2fq/main.nf'
+include { SAMBLASTER                                            } from '../../../modules/nf-core/samblaster/main'
+include { SAMTOOLS_BAM2FQ                   as BAM2FASTQ        } from '../../../modules/nf-core/samtools/bam2fq/main.nf'
 
 workflow CREATE_UMI_CONSENSUS {
     take:
diff --git a/subworkflows/nf-core/gatk4/joint_germline_variant_calling/main.nf b/subworkflows/nf-core/gatk4/joint_germline_variant_calling/main.nf
index c2427c05b4..8bdb9cffdf 100644
--- a/subworkflows/nf-core/gatk4/joint_germline_variant_calling/main.nf
+++ b/subworkflows/nf-core/gatk4/joint_germline_variant_calling/main.nf
@@ -1,15 +1,15 @@
 //
 // merge samples with genomicsdbimport, perform joint genotyping with genotypeGVCFS
-include { BCFTOOLS_SORT                                         } from '../../../../modules/nf-core/modules/bcftools/sort/main'
-include { TABIX_TABIX as TABIX                                  } from '../../../../modules/nf-core/modules/tabix/tabix/main'
-include { GATK4_GENOMICSDBIMPORT                                } from '../../../../modules/nf-core/modules/gatk4/genomicsdbimport/main'
-include { GATK4_GENOTYPEGVCFS                                   } from '../../../../modules/nf-core/modules/gatk4/genotypegvcfs/main'
-include { GATK4_MERGEVCFS as MERGE_GENOTYPEGVCFS                } from '../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { GATK4_MERGEVCFS as MERGE_VQSR                         } from '../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { GATK4_VARIANTRECALIBRATOR as VARIANTRECALIBRATOR_SNP  } from '../../../../modules/nf-core/modules/gatk4/variantrecalibrator/main'
-include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_SNP                } from '../../../../modules/nf-core/modules/gatk4/applyvqsr/main'
-include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_INDEL              } from '../../../../modules/nf-core/modules/gatk4/applyvqsr/main'
-include { GATK4_VARIANTRECALIBRATOR as VARIANTRECALIBRATOR_INDEL} from '../../../../modules/nf-core/modules/gatk4/variantrecalibrator/main'
+include { BCFTOOLS_SORT                                         } from '../../../../modules/nf-core/bcftools/sort/main'
+include { TABIX_TABIX as TABIX                                  } from '../../../../modules/nf-core/tabix/tabix/main'
+include { GATK4_GENOMICSDBIMPORT                                } from '../../../../modules/nf-core/gatk4/genomicsdbimport/main'
+include { GATK4_GENOTYPEGVCFS                                   } from '../../../../modules/nf-core/gatk4/genotypegvcfs/main'
+include { GATK4_MERGEVCFS as MERGE_GENOTYPEGVCFS                } from '../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { GATK4_MERGEVCFS as MERGE_VQSR                         } from '../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { GATK4_VARIANTRECALIBRATOR as VARIANTRECALIBRATOR_SNP  } from '../../../../modules/nf-core/gatk4/variantrecalibrator/main'
+include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_SNP                } from '../../../../modules/nf-core/gatk4/applyvqsr/main'
+include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_INDEL              } from '../../../../modules/nf-core/gatk4/applyvqsr/main'
+include { GATK4_VARIANTRECALIBRATOR as VARIANTRECALIBRATOR_INDEL} from '../../../../modules/nf-core/gatk4/variantrecalibrator/main'
 
 workflow GATK_JOINT_GERMLINE_VARIANT_CALLING {
     take:
diff --git a/subworkflows/nf-core/gatk4/mapping/main.nf b/subworkflows/nf-core/gatk4/mapping/main.nf
index bc89fdb394..5db6bb451b 100644
--- a/subworkflows/nf-core/gatk4/mapping/main.nf
+++ b/subworkflows/nf-core/gatk4/mapping/main.nf
@@ -4,9 +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 { BWAMEM2_MEM            } from '../../../../modules/nf-core/modules/bwamem2/mem/main'
-include { BWA_MEM as BWAMEM1_MEM } from '../../../../modules/nf-core/modules/bwa/mem/main'
-include { DRAGMAP_ALIGN          } from '../../../../modules/nf-core/modules/dragmap/align/main'
+include { BWAMEM2_MEM            } from '../../../../modules/nf-core/bwamem2/mem/main'
+include { BWA_MEM as BWAMEM1_MEM } from '../../../../modules/nf-core/bwa/mem/main'
+include { DRAGMAP_ALIGN          } from '../../../../modules/nf-core/dragmap/align/main'
 
 workflow GATK4_MAPPING {
     take:
diff --git a/subworkflows/nf-core/gatk4/markduplicates/main.nf b/subworkflows/nf-core/gatk4/markduplicates/main.nf
index ce5ab91012..8d52a9eb13 100644
--- a/subworkflows/nf-core/gatk4/markduplicates/main.nf
+++ b/subworkflows/nf-core/gatk4/markduplicates/main.nf
@@ -4,7 +4,7 @@
 // For all modules here:
 // A when clause condition is defined in the conf/modules.config to determine if the module should be run
 
-include { GATK4_MARKDUPLICATES } from '../../../../modules/nf-core/modules/gatk4/markduplicates/main'
+include { GATK4_MARKDUPLICATES } from '../../../../modules/nf-core/gatk4/markduplicates/main'
 include { BAM_TO_CRAM          } from '../../bam_to_cram'
 
 workflow MARKDUPLICATES {
diff --git a/subworkflows/nf-core/gatk4/markduplicates_spark/main.nf b/subworkflows/nf-core/gatk4/markduplicates_spark/main.nf
index 0e5b46c4e4..00856301f9 100644
--- a/subworkflows/nf-core/gatk4/markduplicates_spark/main.nf
+++ b/subworkflows/nf-core/gatk4/markduplicates_spark/main.nf
@@ -5,10 +5,10 @@
 // A when clause condition is defined in the conf/modules.config to determine if the module should be run
 
 include { BAM_TO_CRAM                            } from '../../bam_to_cram'
-include { GATK4_ESTIMATELIBRARYCOMPLEXITY        } from '../../../../modules/nf-core/modules/gatk4/estimatelibrarycomplexity/main'
-include { GATK4_MARKDUPLICATES_SPARK             } from '../../../../modules/nf-core/modules/gatk4/markduplicatesspark/main'
-include { SAMTOOLS_INDEX as INDEX_MARKDUPLICATES } from '../../../../modules/nf-core/modules/samtools/index/main'
-include { SAMTOOLS_CONVERT as SAMTOOLS_CRAMTOBAM } from '../../../../modules/nf-core/modules/samtools/convert/main'
+include { GATK4_ESTIMATELIBRARYCOMPLEXITY        } from '../../../../modules/nf-core/gatk4/estimatelibrarycomplexity/main'
+include { GATK4_MARKDUPLICATES_SPARK             } from '../../../../modules/nf-core/gatk4/markduplicatesspark/main'
+include { SAMTOOLS_INDEX as INDEX_MARKDUPLICATES } from '../../../../modules/nf-core/samtools/index/main'
+include { SAMTOOLS_CONVERT as SAMTOOLS_CRAMTOBAM } from '../../../../modules/nf-core/samtools/convert/main'
 
 workflow MARKDUPLICATES_SPARK {
     take:
diff --git a/subworkflows/nf-core/gatk4/prepare_recalibration/main.nf b/subworkflows/nf-core/gatk4/prepare_recalibration/main.nf
index 8253a29b1d..15a740f2c5 100644
--- a/subworkflows/nf-core/gatk4/prepare_recalibration/main.nf
+++ b/subworkflows/nf-core/gatk4/prepare_recalibration/main.nf
@@ -4,8 +4,8 @@
 // For all modules here:
 // A when clause condition is defined in the conf/modules.config to determine if the module should be run
 
-include { GATK4_BASERECALIBRATOR  as BASERECALIBRATOR  } from '../../../../modules/nf-core/modules/gatk4/baserecalibrator/main'
-include { GATK4_GATHERBQSRREPORTS as GATHERBQSRREPORTS } from '../../../../modules/nf-core/modules/gatk4/gatherbqsrreports/main'
+include { GATK4_BASERECALIBRATOR  as BASERECALIBRATOR  } from '../../../../modules/nf-core/gatk4/baserecalibrator/main'
+include { GATK4_GATHERBQSRREPORTS as GATHERBQSRREPORTS } from '../../../../modules/nf-core/gatk4/gatherbqsrreports/main'
 
 workflow PREPARE_RECALIBRATION {
     take:
diff --git a/subworkflows/nf-core/gatk4/prepare_recalibration_spark/main.nf b/subworkflows/nf-core/gatk4/prepare_recalibration_spark/main.nf
index ba8a7f3992..2ebf9325d1 100644
--- a/subworkflows/nf-core/gatk4/prepare_recalibration_spark/main.nf
+++ b/subworkflows/nf-core/gatk4/prepare_recalibration_spark/main.nf
@@ -4,8 +4,8 @@
 // For all modules here:
 // A when clause condition is defined in the conf/modules.config to determine if the module should be run
 
-include { GATK4_BASERECALIBRATOR_SPARK as BASERECALIBRATOR_SPARK } from '../../../../modules/nf-core/modules/gatk4/baserecalibratorspark/main'
-include { GATK4_GATHERBQSRREPORTS      as GATHERBQSRREPORTS      } from '../../../../modules/nf-core/modules/gatk4/gatherbqsrreports/main'
+include { GATK4_BASERECALIBRATOR_SPARK as BASERECALIBRATOR_SPARK } from '../../../../modules/nf-core/gatk4/baserecalibratorspark/main'
+include { GATK4_GATHERBQSRREPORTS      as GATHERBQSRREPORTS      } from '../../../../modules/nf-core/gatk4/gatherbqsrreports/main'
 
 workflow PREPARE_RECALIBRATION_SPARK {
     take:
diff --git a/subworkflows/nf-core/gatk4/recalibrate/main.nf b/subworkflows/nf-core/gatk4/recalibrate/main.nf
index 6e9fb289b5..54dd698f4f 100644
--- a/subworkflows/nf-core/gatk4/recalibrate/main.nf
+++ b/subworkflows/nf-core/gatk4/recalibrate/main.nf
@@ -4,7 +4,7 @@
 // For all modules here:
 // A when clause condition is defined in the conf/modules.config to determine if the module should be run
 
-include { GATK4_APPLYBQSR as APPLYBQSR } from '../../../../modules/nf-core/modules/gatk4/applybqsr/main'
+include { GATK4_APPLYBQSR as APPLYBQSR } from '../../../../modules/nf-core/gatk4/applybqsr/main'
 include { MERGE_INDEX_CRAM             } from '../../merge_index_cram'
 
 workflow RECALIBRATE {
diff --git a/subworkflows/nf-core/gatk4/recalibrate_spark/main.nf b/subworkflows/nf-core/gatk4/recalibrate_spark/main.nf
index 538b791a02..75d9ed815e 100644
--- a/subworkflows/nf-core/gatk4/recalibrate_spark/main.nf
+++ b/subworkflows/nf-core/gatk4/recalibrate_spark/main.nf
@@ -4,7 +4,7 @@
 // For all modules here:
 // A when clause condition is defined in the conf/modules.config to determine if the module should be run
 
-include { GATK4_APPLYBQSR_SPARK as APPLYBQSR_SPARK } from '../../../../modules/nf-core/modules/gatk4/applybqsrspark/main'
+include { GATK4_APPLYBQSR_SPARK as APPLYBQSR_SPARK } from '../../../../modules/nf-core/gatk4/applybqsrspark/main'
 include { MERGE_INDEX_CRAM                         } from '../../merge_index_cram'
 
 workflow RECALIBRATE_SPARK {
diff --git a/subworkflows/nf-core/gatk4/single_sample_germline_variant_calling/main.nf b/subworkflows/nf-core/gatk4/single_sample_germline_variant_calling/main.nf
index 9ea75b1a51..86e1223782 100644
--- a/subworkflows/nf-core/gatk4/single_sample_germline_variant_calling/main.nf
+++ b/subworkflows/nf-core/gatk4/single_sample_germline_variant_calling/main.nf
@@ -1,5 +1,5 @@
-include { GATK4_CNNSCOREVARIANTS      as CNNSCOREVARIANTS               } from '../../../../modules/nf-core/modules/gatk4/cnnscorevariants/main'
-include { GATK4_FILTERVARIANTTRANCHES as FILTERVARIANTTRANCHES          } from '../../../../modules/nf-core/modules/gatk4/filtervarianttranches/main'
+include { GATK4_CNNSCOREVARIANTS      as CNNSCOREVARIANTS               } from '../../../../modules/nf-core/gatk4/cnnscorevariants/main'
+include { GATK4_FILTERVARIANTTRANCHES as FILTERVARIANTTRANCHES          } from '../../../../modules/nf-core/gatk4/filtervarianttranches/main'
 
 workflow GATK_SINGLE_SAMPLE_GERMLINE_VARIANT_CALLING{
 
diff --git a/subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main.nf b/subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main.nf
index 26c3b2f839..21fd4590fd 100644
--- a/subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main.nf
+++ b/subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main.nf
@@ -2,16 +2,16 @@
 // Run GATK mutect2 in tumor normal mode, getepileupsummaries, calculatecontamination, learnreadorientationmodel and filtermutectcalls
 //
 
-include { GATK4_MERGEVCFS                 as MERGE_MUTECT2               } from '../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { GATK4_CALCULATECONTAMINATION    as CALCULATECONTAMINATION      } from '../../../../modules/nf-core/modules/gatk4/calculatecontamination/main'
-include { GATK4_FILTERMUTECTCALLS         as FILTERMUTECTCALLS           } from '../../../../modules/nf-core/modules/gatk4/filtermutectcalls/main'
-include { GATK4_GATHERPILEUPSUMMARIES     as GATHERPILEUPSUMMARIES_NORMAL} from '../../../../modules/nf-core/modules/gatk4/gatherpileupsummaries/main'
-include { GATK4_GATHERPILEUPSUMMARIES     as GATHERPILEUPSUMMARIES_TUMOR } from '../../../../modules/nf-core/modules/gatk4/gatherpileupsummaries/main'
-include { GATK4_GETPILEUPSUMMARIES        as GETPILEUPSUMMARIES_NORMAL   } from '../../../../modules/nf-core/modules/gatk4/getpileupsummaries/main'
-include { GATK4_GETPILEUPSUMMARIES        as GETPILEUPSUMMARIES_TUMOR    } from '../../../../modules/nf-core/modules/gatk4/getpileupsummaries/main'
-include { GATK4_LEARNREADORIENTATIONMODEL as LEARNREADORIENTATIONMODEL   } from '../../../../modules/nf-core/modules/gatk4/learnreadorientationmodel/main'
-include { GATK4_MERGEMUTECTSTATS          as MERGEMUTECTSTATS            } from '../../../../modules/nf-core/modules/gatk4/mergemutectstats/main'
-include { GATK4_MUTECT2                   as MUTECT2                     } from '../../../../modules/nf-core/modules/gatk4/mutect2/main'
+include { GATK4_MERGEVCFS                 as MERGE_MUTECT2               } from '../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { GATK4_CALCULATECONTAMINATION    as CALCULATECONTAMINATION      } from '../../../../modules/nf-core/gatk4/calculatecontamination/main'
+include { GATK4_FILTERMUTECTCALLS         as FILTERMUTECTCALLS           } from '../../../../modules/nf-core/gatk4/filtermutectcalls/main'
+include { GATK4_GATHERPILEUPSUMMARIES     as GATHERPILEUPSUMMARIES_NORMAL} from '../../../../modules/nf-core/gatk4/gatherpileupsummaries/main'
+include { GATK4_GATHERPILEUPSUMMARIES     as GATHERPILEUPSUMMARIES_TUMOR } from '../../../../modules/nf-core/gatk4/gatherpileupsummaries/main'
+include { GATK4_GETPILEUPSUMMARIES        as GETPILEUPSUMMARIES_NORMAL   } from '../../../../modules/nf-core/gatk4/getpileupsummaries/main'
+include { GATK4_GETPILEUPSUMMARIES        as GETPILEUPSUMMARIES_TUMOR    } from '../../../../modules/nf-core/gatk4/getpileupsummaries/main'
+include { GATK4_LEARNREADORIENTATIONMODEL as LEARNREADORIENTATIONMODEL   } from '../../../../modules/nf-core/gatk4/learnreadorientationmodel/main'
+include { GATK4_MERGEMUTECTSTATS          as MERGEMUTECTSTATS            } from '../../../../modules/nf-core/gatk4/mergemutectstats/main'
+include { GATK4_MUTECT2                   as MUTECT2                     } from '../../../../modules/nf-core/gatk4/mutect2/main'
 
 workflow GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING {
     take:
diff --git a/subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf b/subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf
index 187bdaf9bc..1641da08a7 100644
--- a/subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf
+++ b/subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf
@@ -2,14 +2,14 @@
 // Run GATK mutect2 in tumor only mode, getepileupsummaries, calculatecontamination and filtermutectcalls
 //
 
-include { GATK4_MERGEVCFS                 as MERGE_MUTECT2             } from '../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { GATK4_CALCULATECONTAMINATION    as CALCULATECONTAMINATION    } from '../../../../modules/nf-core/modules/gatk4/calculatecontamination/main'
-include { GATK4_FILTERMUTECTCALLS         as FILTERMUTECTCALLS         } from '../../../../modules/nf-core/modules/gatk4/filtermutectcalls/main'
-include { GATK4_GETPILEUPSUMMARIES        as GETPILEUPSUMMARIES        } from '../../../../modules/nf-core/modules/gatk4/getpileupsummaries/main'
-include { GATK4_GATHERPILEUPSUMMARIES     as GATHERPILEUPSUMMARIES     } from '../../../../modules/nf-core/modules/gatk4/gatherpileupsummaries/main'
-include { GATK4_LEARNREADORIENTATIONMODEL as LEARNREADORIENTATIONMODEL } from '../../../../modules/nf-core/modules/gatk4/learnreadorientationmodel/main'
-include { GATK4_MERGEMUTECTSTATS          as MERGEMUTECTSTATS          } from '../../../../modules/nf-core/modules/gatk4/mergemutectstats/main'
-include { GATK4_MUTECT2                   as MUTECT2                   } from '../../../../modules/nf-core/modules/gatk4/mutect2/main'
+include { GATK4_MERGEVCFS                 as MERGE_MUTECT2             } from '../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { GATK4_CALCULATECONTAMINATION    as CALCULATECONTAMINATION    } from '../../../../modules/nf-core/gatk4/calculatecontamination/main'
+include { GATK4_FILTERMUTECTCALLS         as FILTERMUTECTCALLS         } from '../../../../modules/nf-core/gatk4/filtermutectcalls/main'
+include { GATK4_GETPILEUPSUMMARIES        as GETPILEUPSUMMARIES        } from '../../../../modules/nf-core/gatk4/getpileupsummaries/main'
+include { GATK4_GATHERPILEUPSUMMARIES     as GATHERPILEUPSUMMARIES     } from '../../../../modules/nf-core/gatk4/gatherpileupsummaries/main'
+include { GATK4_LEARNREADORIENTATIONMODEL as LEARNREADORIENTATIONMODEL } from '../../../../modules/nf-core/gatk4/learnreadorientationmodel/main'
+include { GATK4_MERGEMUTECTSTATS          as MERGEMUTECTSTATS          } from '../../../../modules/nf-core/gatk4/mergemutectstats/main'
+include { GATK4_MUTECT2                   as MUTECT2                   } from '../../../../modules/nf-core/gatk4/mutect2/main'
 
 workflow GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING {
     take:
diff --git a/subworkflows/nf-core/merge_index_bam.nf b/subworkflows/nf-core/merge_index_bam.nf
index 6bee133ce6..060073d550 100644
--- a/subworkflows/nf-core/merge_index_bam.nf
+++ b/subworkflows/nf-core/merge_index_bam.nf
@@ -4,8 +4,8 @@
 // For all modules here:
 // A when clause condition is defined in the conf/modules.config to determine if the module should be run
 
-include { SAMTOOLS_INDEX as INDEX_MERGE_BAM } from '../../modules/nf-core/modules/samtools/index/main'
-include { SAMTOOLS_MERGE as MERGE_BAM       } from '../../modules/nf-core/modules/samtools/merge/main'
+include { SAMTOOLS_INDEX as INDEX_MERGE_BAM } from '../../modules/nf-core/samtools/index/main'
+include { SAMTOOLS_MERGE as MERGE_BAM       } from '../../modules/nf-core/samtools/merge/main'
 
 workflow MERGE_INDEX_BAM {
     take:
diff --git a/subworkflows/nf-core/merge_index_cram.nf b/subworkflows/nf-core/merge_index_cram.nf
index eb7dea55f3..b791efc189 100644
--- a/subworkflows/nf-core/merge_index_cram.nf
+++ b/subworkflows/nf-core/merge_index_cram.nf
@@ -4,8 +4,8 @@
 // For all modules here:
 // A when clause condition is defined in the conf/modules.config to determine if the module should be run
 
-include { SAMTOOLS_INDEX as INDEX_CRAM } from '../../modules/nf-core/modules/samtools/index/main'
-include { SAMTOOLS_MERGE as MERGE_CRAM } from '../../modules/nf-core/modules/samtools/merge/main'
+include { SAMTOOLS_INDEX as INDEX_CRAM } from '../../modules/nf-core/samtools/index/main'
+include { SAMTOOLS_MERGE as MERGE_CRAM } from '../../modules/nf-core/samtools/merge/main'
 
 workflow MERGE_INDEX_CRAM {
     take:
diff --git a/subworkflows/nf-core/run_fastqc.nf b/subworkflows/nf-core/run_fastqc.nf
index 3fff9ac70d..24b186d291 100644
--- a/subworkflows/nf-core/run_fastqc.nf
+++ b/subworkflows/nf-core/run_fastqc.nf
@@ -2,7 +2,7 @@
 // Read QC
 //
 
-include { FASTQC     } from '../../modules/nf-core/modules/fastqc/main'
+include { FASTQC     } from '../../modules/nf-core/fastqc/main'
 
 workflow RUN_FASTQC {
     take:
diff --git a/subworkflows/nf-core/variantcalling/ascat/main.nf b/subworkflows/nf-core/variantcalling/ascat/main.nf
index 5577c465c5..33ff1f60be 100644
--- a/subworkflows/nf-core/variantcalling/ascat/main.nf
+++ b/subworkflows/nf-core/variantcalling/ascat/main.nf
@@ -1,4 +1,4 @@
-include { ASCAT } from '../../../../modules/nf-core/modules/ascat/main'
+include { ASCAT } from '../../../../modules/nf-core/ascat/main'
 
 workflow RUN_ASCAT_SOMATIC {
 
diff --git a/subworkflows/nf-core/variantcalling/cnvkit/main.nf b/subworkflows/nf-core/variantcalling/cnvkit/main.nf
index 4b96470994..6625245e42 100644
--- a/subworkflows/nf-core/variantcalling/cnvkit/main.nf
+++ b/subworkflows/nf-core/variantcalling/cnvkit/main.nf
@@ -4,7 +4,7 @@
 // For all modules here:
 // A when clause condition is defined in the conf/modules.config to determine if the module should be run
 
-include { CNVKIT_BATCH } from '../../../../modules/nf-core/modules/cnvkit/batch/main'
+include { CNVKIT_BATCH } from '../../../../modules/nf-core/cnvkit/batch/main'
 
 workflow RUN_CNVKIT {
     take:
diff --git a/subworkflows/nf-core/variantcalling/controlfreec/somatic/main.nf b/subworkflows/nf-core/variantcalling/controlfreec/somatic/main.nf
index 2af46aed54..ba2e78403f 100644
--- a/subworkflows/nf-core/variantcalling/controlfreec/somatic/main.nf
+++ b/subworkflows/nf-core/variantcalling/controlfreec/somatic/main.nf
@@ -1,8 +1,8 @@
-include { CONTROLFREEC_FREEC as FREEC_SOMATIC                    } from '../../../../../modules/nf-core/modules/controlfreec/freec/main'
-include { CONTROLFREEC_ASSESSSIGNIFICANCE as ASSESS_SIGNIFICANCE } from '../../../../../modules/nf-core/modules/controlfreec/assesssignificance/main'
-include { CONTROLFREEC_FREEC2BED as FREEC2BED                    } from '../../../../../modules/nf-core/modules/controlfreec/freec2bed/main'
-include { CONTROLFREEC_FREEC2CIRCOS as FREEC2CIRCOS              } from '../../../../../modules/nf-core/modules/controlfreec/freec2circos/main'
-include { CONTROLFREEC_MAKEGRAPH as MAKEGRAPH                    } from '../../../../../modules/nf-core/modules/controlfreec/makegraph/main'
+include { CONTROLFREEC_FREEC as FREEC_SOMATIC                    } from '../../../../../modules/nf-core/controlfreec/freec/main'
+include { CONTROLFREEC_ASSESSSIGNIFICANCE as ASSESS_SIGNIFICANCE } from '../../../../../modules/nf-core/controlfreec/assesssignificance/main'
+include { CONTROLFREEC_FREEC2BED as FREEC2BED                    } from '../../../../../modules/nf-core/controlfreec/freec2bed/main'
+include { CONTROLFREEC_FREEC2CIRCOS as FREEC2CIRCOS              } from '../../../../../modules/nf-core/controlfreec/freec2circos/main'
+include { CONTROLFREEC_MAKEGRAPH as MAKEGRAPH                    } from '../../../../../modules/nf-core/controlfreec/makegraph/main'
 
 workflow RUN_CONTROLFREEC_SOMATIC {
     take:
diff --git a/subworkflows/nf-core/variantcalling/controlfreec/tumoronly/main.nf b/subworkflows/nf-core/variantcalling/controlfreec/tumoronly/main.nf
index 2f1713429e..555b374175 100644
--- a/subworkflows/nf-core/variantcalling/controlfreec/tumoronly/main.nf
+++ b/subworkflows/nf-core/variantcalling/controlfreec/tumoronly/main.nf
@@ -1,8 +1,8 @@
-include { CONTROLFREEC_FREEC as FREEC_TUMORONLY                  } from '../../../../../modules/nf-core/modules/controlfreec/freec/main'
-include { CONTROLFREEC_ASSESSSIGNIFICANCE as ASSESS_SIGNIFICANCE } from '../../../../../modules/nf-core/modules/controlfreec/assesssignificance/main'
-include { CONTROLFREEC_FREEC2BED as FREEC2BED                    } from '../../../../../modules/nf-core/modules/controlfreec/freec2bed/main'
-include { CONTROLFREEC_FREEC2CIRCOS as FREEC2CIRCOS              } from '../../../../../modules/nf-core/modules/controlfreec/freec2circos/main'
-include { CONTROLFREEC_MAKEGRAPH as MAKEGRAPH                    } from '../../../../../modules/nf-core/modules/controlfreec/makegraph/main'
+include { CONTROLFREEC_FREEC as FREEC_TUMORONLY                  } from '../../../../../modules/nf-core/controlfreec/freec/main'
+include { CONTROLFREEC_ASSESSSIGNIFICANCE as ASSESS_SIGNIFICANCE } from '../../../../../modules/nf-core/controlfreec/assesssignificance/main'
+include { CONTROLFREEC_FREEC2BED as FREEC2BED                    } from '../../../../../modules/nf-core/controlfreec/freec2bed/main'
+include { CONTROLFREEC_FREEC2CIRCOS as FREEC2CIRCOS              } from '../../../../../modules/nf-core/controlfreec/freec2circos/main'
+include { CONTROLFREEC_MAKEGRAPH as MAKEGRAPH                    } from '../../../../../modules/nf-core/controlfreec/makegraph/main'
 
 workflow RUN_CONTROLFREEC_TUMORONLY {
     take:
diff --git a/subworkflows/nf-core/variantcalling/deepvariant/main.nf b/subworkflows/nf-core/variantcalling/deepvariant/main.nf
index 8812cfa329..c64f60bee5 100644
--- a/subworkflows/nf-core/variantcalling/deepvariant/main.nf
+++ b/subworkflows/nf-core/variantcalling/deepvariant/main.nf
@@ -1,8 +1,8 @@
-include { GATK4_MERGEVCFS as MERGE_DEEPVARIANT_GVCF } from '../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { GATK4_MERGEVCFS as MERGE_DEEPVARIANT_VCF  } from '../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { DEEPVARIANT                               } from '../../../../modules/nf-core/modules/deepvariant/main'
-include { TABIX_TABIX as TABIX_VC_DEEPVARIANT_GVCF  } from '../../../../modules/nf-core/modules/tabix/tabix/main'
-include { TABIX_TABIX as TABIX_VC_DEEPVARIANT_VCF   } from '../../../../modules/nf-core/modules/tabix/tabix/main'
+include { GATK4_MERGEVCFS as MERGE_DEEPVARIANT_GVCF } from '../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { GATK4_MERGEVCFS as MERGE_DEEPVARIANT_VCF  } from '../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { DEEPVARIANT                               } from '../../../../modules/nf-core/deepvariant/main'
+include { TABIX_TABIX as TABIX_VC_DEEPVARIANT_GVCF  } from '../../../../modules/nf-core/tabix/tabix/main'
+include { TABIX_TABIX as TABIX_VC_DEEPVARIANT_VCF   } from '../../../../modules/nf-core/tabix/tabix/main'
 
 // Deepvariant: https://github.com/google/deepvariant/issues/510
 workflow RUN_DEEPVARIANT {
diff --git a/subworkflows/nf-core/variantcalling/freebayes/main.nf b/subworkflows/nf-core/variantcalling/freebayes/main.nf
index 8e784af91c..189ab280c4 100644
--- a/subworkflows/nf-core/variantcalling/freebayes/main.nf
+++ b/subworkflows/nf-core/variantcalling/freebayes/main.nf
@@ -1,7 +1,7 @@
-include { BCFTOOLS_SORT                                } from '../../../../modules/nf-core/modules/bcftools/sort/main'
-include { GATK4_MERGEVCFS as MERGE_FREEBAYES           } from '../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { FREEBAYES                                    } from '../../../../modules/nf-core/modules/freebayes/main'
-include { TABIX_TABIX as TABIX_VC_FREEBAYES            } from '../../../../modules/nf-core/modules/tabix/tabix/main'
+include { BCFTOOLS_SORT                                } from '../../../../modules/nf-core/bcftools/sort/main'
+include { GATK4_MERGEVCFS as MERGE_FREEBAYES           } from '../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { FREEBAYES                                    } from '../../../../modules/nf-core/freebayes/main'
+include { TABIX_TABIX as TABIX_VC_FREEBAYES            } from '../../../../modules/nf-core/tabix/tabix/main'
 
 workflow RUN_FREEBAYES {
     take:
diff --git a/subworkflows/nf-core/variantcalling/haplotypecaller/main.nf b/subworkflows/nf-core/variantcalling/haplotypecaller/main.nf
index f2d948fc67..e1540cd085 100644
--- a/subworkflows/nf-core/variantcalling/haplotypecaller/main.nf
+++ b/subworkflows/nf-core/variantcalling/haplotypecaller/main.nf
@@ -1,5 +1,5 @@
-include { GATK4_MERGEVCFS                             as MERGE_HAPLOTYPECALLER } from '../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { GATK4_HAPLOTYPECALLER                       as HAPLOTYPECALLER       } from '../../../../modules/nf-core/modules/gatk4/haplotypecaller/main'
+include { GATK4_MERGEVCFS                             as MERGE_HAPLOTYPECALLER } from '../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { GATK4_HAPLOTYPECALLER                       as HAPLOTYPECALLER       } from '../../../../modules/nf-core/gatk4/haplotypecaller/main'
 include { GATK_JOINT_GERMLINE_VARIANT_CALLING         as JOINT_GERMLINE        } from '../../../../subworkflows/nf-core/gatk4/joint_germline_variant_calling/main'
 include { GATK_SINGLE_SAMPLE_GERMLINE_VARIANT_CALLING as SINGLE_SAMPLE         } from '../../../../subworkflows/nf-core/gatk4/single_sample_germline_variant_calling/main'
 
diff --git a/subworkflows/nf-core/variantcalling/manta/germline/main.nf b/subworkflows/nf-core/variantcalling/manta/germline/main.nf
index 128299f4d6..3a3ff8f174 100644
--- a/subworkflows/nf-core/variantcalling/manta/germline/main.nf
+++ b/subworkflows/nf-core/variantcalling/manta/germline/main.nf
@@ -1,7 +1,7 @@
-include { GATK4_MERGEVCFS as MERGE_MANTA_DIPLOID      } from '../../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { GATK4_MERGEVCFS as MERGE_MANTA_SMALL_INDELS } from '../../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { GATK4_MERGEVCFS as MERGE_MANTA_SV           } from '../../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { MANTA_GERMLINE                              } from '../../../../../modules/nf-core/modules/manta/germline/main'
+include { GATK4_MERGEVCFS as MERGE_MANTA_DIPLOID      } from '../../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { GATK4_MERGEVCFS as MERGE_MANTA_SMALL_INDELS } from '../../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { GATK4_MERGEVCFS as MERGE_MANTA_SV           } from '../../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { MANTA_GERMLINE                              } from '../../../../../modules/nf-core/manta/germline/main'
 
 // Seems to be the consensus on upstream modules implementation too
 workflow RUN_MANTA_GERMLINE {
diff --git a/subworkflows/nf-core/variantcalling/manta/somatic/main.nf b/subworkflows/nf-core/variantcalling/manta/somatic/main.nf
index a1eb740832..3895deeebe 100644
--- a/subworkflows/nf-core/variantcalling/manta/somatic/main.nf
+++ b/subworkflows/nf-core/variantcalling/manta/somatic/main.nf
@@ -1,8 +1,8 @@
-include { GATK4_MERGEVCFS as MERGE_MANTA_DIPLOID           } from '../../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { GATK4_MERGEVCFS as MERGE_MANTA_SMALL_INDELS      } from '../../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { GATK4_MERGEVCFS as MERGE_MANTA_SOMATIC           } from '../../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { GATK4_MERGEVCFS as MERGE_MANTA_SV                } from '../../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { MANTA_SOMATIC                                    } from '../../../../../modules/nf-core/modules/manta/somatic/main'
+include { GATK4_MERGEVCFS as MERGE_MANTA_DIPLOID           } from '../../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { GATK4_MERGEVCFS as MERGE_MANTA_SMALL_INDELS      } from '../../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { GATK4_MERGEVCFS as MERGE_MANTA_SOMATIC           } from '../../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { GATK4_MERGEVCFS as MERGE_MANTA_SV                } from '../../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { MANTA_SOMATIC                                    } from '../../../../../modules/nf-core/manta/somatic/main'
 
 workflow RUN_MANTA_SOMATIC {
     take:
diff --git a/subworkflows/nf-core/variantcalling/manta/tumoronly/main.nf b/subworkflows/nf-core/variantcalling/manta/tumoronly/main.nf
index 4202352588..0f5a2f97e6 100644
--- a/subworkflows/nf-core/variantcalling/manta/tumoronly/main.nf
+++ b/subworkflows/nf-core/variantcalling/manta/tumoronly/main.nf
@@ -1,7 +1,7 @@
-include { GATK4_MERGEVCFS as MERGE_MANTA_SMALL_INDELS      } from '../../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { GATK4_MERGEVCFS as MERGE_MANTA_SV                } from '../../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { GATK4_MERGEVCFS as MERGE_MANTA_TUMOR             } from '../../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { MANTA_TUMORONLY                                  } from '../../../../../modules/nf-core/modules/manta/tumoronly/main'
+include { GATK4_MERGEVCFS as MERGE_MANTA_SMALL_INDELS      } from '../../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { GATK4_MERGEVCFS as MERGE_MANTA_SV                } from '../../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { GATK4_MERGEVCFS as MERGE_MANTA_TUMOR             } from '../../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { MANTA_TUMORONLY                                  } from '../../../../../modules/nf-core/manta/tumoronly/main'
 
 // Seems to be the consensus on upstream modules implementation too
 workflow RUN_MANTA_TUMORONLY {
diff --git a/subworkflows/nf-core/variantcalling/mpileup/main.nf b/subworkflows/nf-core/variantcalling/mpileup/main.nf
index c4868d964e..17c0f170ba 100644
--- a/subworkflows/nf-core/variantcalling/mpileup/main.nf
+++ b/subworkflows/nf-core/variantcalling/mpileup/main.nf
@@ -1,5 +1,5 @@
-include { CAT_CAT as CAT_MPILEUP         } from '../../../../modules/nf-core/modules/cat/cat/main'
-include { SAMTOOLS_MPILEUP               } from '../../../../modules/nf-core/modules/samtools/mpileup/main'
+include { CAT_CAT as CAT_MPILEUP         } from '../../../../modules/nf-core/cat/cat/main'
+include { SAMTOOLS_MPILEUP               } from '../../../../modules/nf-core/samtools/mpileup/main'
 
 workflow RUN_MPILEUP {
     take:
diff --git a/subworkflows/nf-core/variantcalling/strelka/single/main.nf b/subworkflows/nf-core/variantcalling/strelka/single/main.nf
index bc6b0b70f9..da721fb5cd 100644
--- a/subworkflows/nf-core/variantcalling/strelka/single/main.nf
+++ b/subworkflows/nf-core/variantcalling/strelka/single/main.nf
@@ -1,6 +1,6 @@
-include { GATK4_MERGEVCFS as MERGE_STRELKA        } from '../../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { GATK4_MERGEVCFS as MERGE_STRELKA_GENOME } from '../../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { STRELKA_GERMLINE as STRELKA_SINGLE      } from '../../../../../modules/nf-core/modules/strelka/germline/main'
+include { GATK4_MERGEVCFS as MERGE_STRELKA        } from '../../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { GATK4_MERGEVCFS as MERGE_STRELKA_GENOME } from '../../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { STRELKA_GERMLINE as STRELKA_SINGLE      } from '../../../../../modules/nf-core/strelka/germline/main'
 
 workflow RUN_STRELKA_SINGLE {
     take:
diff --git a/subworkflows/nf-core/variantcalling/strelka/somatic/main.nf b/subworkflows/nf-core/variantcalling/strelka/somatic/main.nf
index 8686d3dcb5..f05e3e163a 100644
--- a/subworkflows/nf-core/variantcalling/strelka/somatic/main.nf
+++ b/subworkflows/nf-core/variantcalling/strelka/somatic/main.nf
@@ -1,6 +1,6 @@
-include { GATK4_MERGEVCFS as MERGE_STRELKA_INDELS } from '../../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { GATK4_MERGEVCFS as MERGE_STRELKA_SNVS   } from '../../../../../modules/nf-core/modules/gatk4/mergevcfs/main'
-include { STRELKA_SOMATIC                         } from '../../../../../modules/nf-core/modules/strelka/somatic/main'
+include { GATK4_MERGEVCFS as MERGE_STRELKA_INDELS } from '../../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { GATK4_MERGEVCFS as MERGE_STRELKA_SNVS   } from '../../../../../modules/nf-core/gatk4/mergevcfs/main'
+include { STRELKA_SOMATIC                         } from '../../../../../modules/nf-core/strelka/somatic/main'
 
 workflow RUN_STRELKA_SOMATIC {
     take:
diff --git a/subworkflows/nf-core/variantcalling/tiddit/single/main.nf b/subworkflows/nf-core/variantcalling/tiddit/single/main.nf
index 1615a874e2..fe915287a3 100644
--- a/subworkflows/nf-core/variantcalling/tiddit/single/main.nf
+++ b/subworkflows/nf-core/variantcalling/tiddit/single/main.nf
@@ -1,5 +1,5 @@
-include { TABIX_BGZIPTABIX as TABIX_BGZIP_TIDDIT_SV } from '../../../../../modules/nf-core/modules/tabix/bgziptabix/main'
-include { TIDDIT_SV                                 } from '../../../../../modules/nf-core/modules/tiddit/sv/main'
+include { TABIX_BGZIPTABIX as TABIX_BGZIP_TIDDIT_SV } from '../../../../../modules/nf-core/tabix/bgziptabix/main'
+include { TIDDIT_SV                                 } from '../../../../../modules/nf-core/tiddit/sv/main'
 
 workflow RUN_TIDDIT {
     take:
diff --git a/subworkflows/nf-core/variantcalling/tiddit/somatic/main.nf b/subworkflows/nf-core/variantcalling/tiddit/somatic/main.nf
index 89531819ad..bbff784217 100644
--- a/subworkflows/nf-core/variantcalling/tiddit/somatic/main.nf
+++ b/subworkflows/nf-core/variantcalling/tiddit/somatic/main.nf
@@ -1,6 +1,6 @@
 include { RUN_TIDDIT as RUN_TIDDIT_NORMAL           } from '../single/main.nf'
 include { RUN_TIDDIT as RUN_TIDDIT_TUMOR            } from '../single/main.nf'
-include { SVDB_MERGE                                } from '../../../../../modules/nf-core/modules/svdb/merge/main.nf'
+include { SVDB_MERGE                                } from '../../../../../modules/nf-core/svdb/merge/main.nf'
 
 workflow RUN_TIDDIT_SOMATIC {
     take:
diff --git a/subworkflows/nf-core/vcf_qc.nf b/subworkflows/nf-core/vcf_qc.nf
index 598c906218..333f51b259 100644
--- a/subworkflows/nf-core/vcf_qc.nf
+++ b/subworkflows/nf-core/vcf_qc.nf
@@ -1,7 +1,7 @@
-include { BCFTOOLS_STATS                  } from '../../modules/nf-core/modules/bcftools/stats/main'
-include { VCFTOOLS as VCFTOOLS_SUMMARY    } from '../../modules/nf-core/modules/vcftools/main'
-include { VCFTOOLS as VCFTOOLS_TSTV_COUNT } from '../../modules/nf-core/modules/vcftools/main'
-include { VCFTOOLS as VCFTOOLS_TSTV_QUAL  } from '../../modules/nf-core/modules/vcftools/main'
+include { BCFTOOLS_STATS                  } from '../../modules/nf-core/bcftools/stats/main'
+include { VCFTOOLS as VCFTOOLS_SUMMARY    } from '../../modules/nf-core/vcftools/main'
+include { VCFTOOLS as VCFTOOLS_TSTV_COUNT } from '../../modules/nf-core/vcftools/main'
+include { VCFTOOLS as VCFTOOLS_TSTV_QUAL  } from '../../modules/nf-core/vcftools/main'
 
 workflow VCF_QC {
     take:
diff --git a/workflows/sarek.nf b/workflows/sarek.nf
index 23782bbdda..35a49f67c6 100644
--- a/workflows/sarek.nf
+++ b/workflows/sarek.nf
@@ -223,7 +223,7 @@ include { ALIGNMENT_TO_FASTQ as ALIGNMENT_TO_FASTQ_UMI         } from '../subwor
 include { RUN_FASTQC                                           } from '../subworkflows/nf-core/run_fastqc'
 
 // TRIM/SPLIT FASTQ Files
-include { FASTP                                                } from '../modules/nf-core/modules/fastp/main'
+include { FASTP                                                } from '../modules/nf-core/fastp/main'
 
 // Create umi consensus bams from fastq
 include { CREATE_UMI_CONSENSUS                                 } from '../subworkflows/nf-core/fgbio_create_umi_consensus/main'
@@ -234,11 +234,11 @@ include { GATK4_MAPPING                                        } from '../subwor
 // Merge and index BAM files (optional)
 include { MERGE_INDEX_BAM                                      } from '../subworkflows/nf-core/merge_index_bam'
 
-include { SAMTOOLS_CONVERT as SAMTOOLS_CRAMTOBAM               } from '../modules/nf-core/modules/samtools/convert/main'
-include { SAMTOOLS_CONVERT as SAMTOOLS_CRAMTOBAM_RECAL         } from '../modules/nf-core/modules/samtools/convert/main'
+include { SAMTOOLS_CONVERT as SAMTOOLS_CRAMTOBAM               } from '../modules/nf-core/samtools/convert/main'
+include { SAMTOOLS_CONVERT as SAMTOOLS_CRAMTOBAM_RECAL         } from '../modules/nf-core/samtools/convert/main'
 
-include { SAMTOOLS_CONVERT as SAMTOOLS_BAMTOCRAM               } from '../modules/nf-core/modules/samtools/convert/main'
-include { SAMTOOLS_CONVERT as SAMTOOLS_BAMTOCRAM_VARIANTCALLING} from '../modules/nf-core/modules/samtools/convert/main'
+include { SAMTOOLS_CONVERT as SAMTOOLS_BAMTOCRAM               } from '../modules/nf-core/samtools/convert/main'
+include { SAMTOOLS_CONVERT as SAMTOOLS_BAMTOCRAM_VARIANTCALLING} from '../modules/nf-core/samtools/convert/main'
 
 // Mark Duplicates (+QC)
 include { MARKDUPLICATES                                       } from '../subworkflows/nf-core/gatk4/markduplicates/main'
@@ -279,10 +279,10 @@ include { VCF_QC                                               } from '../subwor
 include { ANNOTATE                                             } from '../subworkflows/local/annotate'
 
 // REPORTING VERSIONS OF SOFTWARE USED
-include { CUSTOM_DUMPSOFTWAREVERSIONS                          } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
+include { CUSTOM_DUMPSOFTWAREVERSIONS                          } from '../modules/nf-core/custom/dumpsoftwareversions/main'
 
 // MULTIQC
-include { MULTIQC                                              } from '../modules/nf-core/modules/multiqc/main'
+include { MULTIQC                                              } from '../modules/nf-core/multiqc/main'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~