diff --git a/modules/artic/minion/main.nf b/modules/artic/minion/main.nf
index ce04fcc8..c25ec0db 100644
--- a/modules/artic/minion/main.nf
+++ b/modules/artic/minion/main.nf
@@ -43,7 +43,10 @@ process ARTIC_MINION {
         summary = ""
         model = file(medaka_model).exists() ? "--medaka-model ./$medaka_model" : "--medaka-model $medaka_model"
     }
+    def hd5_plugin_path = task.ext.hd5_plugin_path ? "export HDF5_PLUGIN_PATH=" + task.ext.hd5_plugin_path : "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin"
     """
+    $hd5_plugin_path
+
     artic \\
         minion \\
         $args \\
diff --git a/modules/ataqv/ataqv/main.nf b/modules/ataqv/ataqv/main.nf
index 20525e85..fbd623f4 100644
--- a/modules/ataqv/ataqv/main.nf
+++ b/modules/ataqv/ataqv/main.nf
@@ -5,7 +5,7 @@ process ATAQV_ATAQV {
     conda (params.enable_conda ? "bioconda::ataqv=1.2.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ataqv:1.2.1--py39ha23c084_2' :
-        'quay.io/biocontainers/ataqv:1.2.1--py36hfdecbe1_2' }"
+        'quay.io/biocontainers/ataqv:1.2.1--py39ha23c084_2' }"
 
     input:
     tuple val(meta), path(bam), path(bai), path(peak_file)
diff --git a/modules/bcftools/concat/main.nf b/modules/bcftools/concat/main.nf
index cebd2443..d02e7605 100644
--- a/modules/bcftools/concat/main.nf
+++ b/modules/bcftools/concat/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_CONCAT {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::bcftools=1.11" : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0' :
-        'quay.io/biocontainers/bcftools:1.11--h7c999a4_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(vcfs)
diff --git a/modules/bcftools/consensus/main.nf b/modules/bcftools/consensus/main.nf
index 4633790e..040e6534 100644
--- a/modules/bcftools/consensus/main.nf
+++ b/modules/bcftools/consensus/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_CONSENSUS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi), path(fasta)
@@ -18,9 +18,12 @@ process BCFTOOLS_CONSENSUS {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    cat $fasta | bcftools consensus $vcf $args > ${prefix}.fa
-    header=\$(head -n 1 ${prefix}.fa | sed 's/>//g')
-    sed -i 's/\${header}/${meta.id}/g' ${prefix}.fa
+    cat $fasta \\
+        | bcftools \\
+            consensus \\
+            $vcf \\
+            $args \\
+            > ${prefix}.fa
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/bcftools/filter/main.nf b/modules/bcftools/filter/main.nf
index 95e0249a..98b422b1 100644
--- a/modules/bcftools/filter/main.nf
+++ b/modules/bcftools/filter/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_FILTER {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(vcf)
diff --git a/modules/bcftools/index/main.nf b/modules/bcftools/index/main.nf
index 0cdebf31..e5275003 100644
--- a/modules/bcftools/index/main.nf
+++ b/modules/bcftools/index/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_INDEX {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(vcf)
@@ -13,7 +13,7 @@ process BCFTOOLS_INDEX {
     output:
     tuple val(meta), path("*.csi"), optional:true, emit: csi
     tuple val(meta), path("*.tbi"), optional:true, emit: tbi
-    path "versions.yml"          , emit: version
+    path "versions.yml"           , emit: versions
 
     script:
     def args = task.ext.args ?: ''
diff --git a/modules/bcftools/isec/main.nf b/modules/bcftools/isec/main.nf
index 08323f28..fdde3022 100644
--- a/modules/bcftools/isec/main.nf
+++ b/modules/bcftools/isec/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_ISEC {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(vcfs), path(tbis)
diff --git a/modules/bcftools/merge/main.nf b/modules/bcftools/merge/main.nf
index bfb0f162..f1c02e8d 100644
--- a/modules/bcftools/merge/main.nf
+++ b/modules/bcftools/merge/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_MERGE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(vcfs), path(tbis)
diff --git a/modules/bcftools/mpileup/main.nf b/modules/bcftools/mpileup/main.nf
index 8a209a66..cdd38eec 100644
--- a/modules/bcftools/mpileup/main.nf
+++ b/modules/bcftools/mpileup/main.nf
@@ -2,19 +2,21 @@ process BCFTOOLS_MPILEUP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(bam)
-    path  fasta
+    path fasta
+    val save_mpileup
 
     output:
     tuple val(meta), path("*.gz")      , emit: vcf
     tuple val(meta), path("*.tbi")     , emit: tbi
     tuple val(meta), path("*stats.txt"), emit: stats
+    tuple val(meta), path("*.mpileup") , emit: mpileup, optional: true
     path  "versions.yml"               , emit: versions
 
     script:
@@ -22,13 +24,16 @@ process BCFTOOLS_MPILEUP {
     def args2 = task.ext.args2 ?: ''
     def args3 = task.ext.args3 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def mpileup = save_mpileup ? "| tee ${prefix}.mpileup" : ""
     """
     echo "${meta.id}" > sample_name.list
 
-    bcftools mpileup \\
+    bcftools \\
+        mpileup \\
         --fasta-ref $fasta \\
         $args \\
         $bam \\
+        $mpileup \\
         | bcftools call --output-type v $args2 \\
         | bcftools reheader --samples sample_name.list \\
         | bcftools view --output-file ${prefix}.vcf.gz --output-type z $args3
diff --git a/modules/bcftools/mpileup/meta.yml b/modules/bcftools/mpileup/meta.yml
index c31180ee..483d0e71 100644
--- a/modules/bcftools/mpileup/meta.yml
+++ b/modules/bcftools/mpileup/meta.yml
@@ -26,6 +26,10 @@ input:
         type: file
         description: FASTA reference file
         pattern: "*.{fasta,fa}"
+    - save_mpileup:
+        type: boolean
+        description: Save mpileup file generated by bcftools mpileup
+        patter: "*.mpileup"
 output:
     - meta:
         type: map
diff --git a/modules/bcftools/norm/main.nf b/modules/bcftools/norm/main.nf
index 95da56db..e8bf6324 100644
--- a/modules/bcftools/norm/main.nf
+++ b/modules/bcftools/norm/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_NORM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(vcf)
diff --git a/modules/bcftools/query/main.nf b/modules/bcftools/query/main.nf
index d1098f99..5f4135f4 100644
--- a/modules/bcftools/query/main.nf
+++ b/modules/bcftools/query/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_QUERY {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(vcf), path(index)
diff --git a/modules/bcftools/reheader/main.nf b/modules/bcftools/reheader/main.nf
index 018431a9..e6d9025d 100644
--- a/modules/bcftools/reheader/main.nf
+++ b/modules/bcftools/reheader/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_REHEADER {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(vcf)
diff --git a/modules/bcftools/sort/main.nf b/modules/bcftools/sort/main.nf
new file mode 100644
index 00000000..2fcadc98
--- /dev/null
+++ b/modules/bcftools/sort/main.nf
@@ -0,0 +1,32 @@
+process BCFTOOLS_SORT {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::bcftools=1.14" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0':
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
+
+    input:
+    tuple val(meta), path(vcf)
+
+    output:
+    tuple val(meta), path("*.gz"), emit: vcf
+    path "versions.yml"           , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    bcftools \\
+        sort \\
+        --output ${prefix}.vcf.gz \\
+        $args \\
+        $vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/bcftools/sort/meta.yml b/modules/bcftools/sort/meta.yml
new file mode 100644
index 00000000..af894e82
--- /dev/null
+++ b/modules/bcftools/sort/meta.yml
@@ -0,0 +1,43 @@
+name: bcftools_sort
+description: Sorts VCF files
+keywords:
+  - sorting
+  - VCF
+  - variant calling
+tools:
+  - sort:
+      description: Sort VCF files by coordinates.
+      homepage: http://samtools.github.io/bcftools/bcftools.html
+      documentation: http://www.htslib.org/doc/bcftools.html
+      tool_dev_url: https://github.com/samtools/bcftools
+      doi: "10.1093/bioinformatics/btp352"
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: The VCF/BCF file to be sorted
+      pattern: "*.{vcf.gz,vcf,bcf}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - vcf:
+      type: file
+      description: Sorted VCF file
+      pattern: "*.{vcf.gz}"
+
+authors:
+  - "@Gwennid"
diff --git a/modules/bcftools/stats/main.nf b/modules/bcftools/stats/main.nf
index 67e8dca7..54a28bce 100644
--- a/modules/bcftools/stats/main.nf
+++ b/modules/bcftools/stats/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_STATS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::bcftools=1.13' : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(vcf)
diff --git a/modules/bcftools/view/main.nf b/modules/bcftools/view/main.nf
index f37c1ab9..7056ecdb 100644
--- a/modules/bcftools/view/main.nf
+++ b/modules/bcftools/view/main.nf
@@ -2,10 +2,10 @@ process BCFTOOLS_VIEW {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
+    conda (params.enable_conda ? 'bioconda::bcftools=1.14' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(vcf), path(index)
diff --git a/modules/bowtie2/align/main.nf b/modules/bowtie2/align/main.nf
index 41c8a6bf..20b08f72 100644
--- a/modules/bowtie2/align/main.nf
+++ b/modules/bowtie2/align/main.nf
@@ -2,27 +2,28 @@ process BOWTIE2_ALIGN {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? 'bioconda::bowtie2=2.4.2 bioconda::samtools=1.11 conda-forge::pigz=2.3.4' : null)
+    conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.14 conda-forge::pigz=2.6' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0' :
-        'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' :
+        'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' }"
 
     input:
     tuple val(meta), path(reads)
     path  index
+    val   save_unaligned
 
     output:
-    tuple val(meta), path('*.bam'), emit: bam
-    tuple val(meta), path('*.log'), emit: log
-    path  "versions.yml"          , emit: versions
-    tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq
+    tuple val(meta), path('*.bam')    , emit: bam
+    tuple val(meta), path('*.log')    , emit: log
+    tuple val(meta), path('*fastq.gz'), emit: fastq, optional:true
+    path  "versions.yml"              , emit: versions
 
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     if (meta.single_end) {
-        def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
+        def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
         """
         INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
         bowtie2 \\
@@ -42,7 +43,7 @@ process BOWTIE2_ALIGN {
         END_VERSIONS
         """
     } else {
-        def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
+        def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
         """
         INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
         bowtie2 \\
diff --git a/modules/bowtie2/build/main.nf b/modules/bowtie2/build/main.nf
index c0cbcd79..da2e9ed5 100644
--- a/modules/bowtie2/build/main.nf
+++ b/modules/bowtie2/build/main.nf
@@ -5,7 +5,7 @@ process BOWTIE2_BUILD {
     conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bowtie2:2.4.4--py39hbb4e92a_0' :
-        'quay.io/biocontainers/bowtie2:2.4.4--py36hd4290be_0' }"
+        'quay.io/biocontainers/bowtie2:2.4.4--py39hbb4e92a_0' }"
 
     input:
     path fasta
diff --git a/modules/cat/cat/main.nf b/modules/cat/cat/main.nf
index 0c087270..2efe20a5 100644
--- a/modules/cat/cat/main.nf
+++ b/modules/cat/cat/main.nf
@@ -18,30 +18,28 @@ process CAT_CAT {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def file_list = files_in.collect { it.toString() }
-    if (file_list.size > 1) {
 
-        // | input     | output     | command1 | command2 |
-        // |-----------|------------|----------|----------|
-        // | gzipped   | gzipped    | cat      |          |
-        // | ungzipped | ungzipped  | cat      |          |
-        // | gzipped   | ungzipped  | zcat     |          |
-        // | ungzipped | gzipped    | cat      | pigz     |
+    // | input     | output     | command1 | command2 |
+    // |-----------|------------|----------|----------|
+    // | gzipped   | gzipped    | cat      |          |
+    // | ungzipped | ungzipped  | cat      |          |
+    // | gzipped   | ungzipped  | zcat     |          |
+    // | ungzipped | gzipped    | cat      | pigz     |
 
-        def in_zip   = file_list[0].endsWith('.gz')
-        def out_zip  = file_out.endsWith('.gz')
-        def command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
-        def command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
-        """
-        $command1 \\
-            $args \\
-            ${file_list.join(' ')} \\
-            $command2 \\
-            > $file_out
+    def in_zip   = file_list[0].endsWith('.gz')
+    def out_zip  = file_out.endsWith('.gz')
+    def command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
+    def command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
+    """
+    $command1 \\
+        $args \\
+        ${file_list.join(' ')} \\
+        $command2 \\
+        > $file_out
 
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
-        END_VERSIONS
-        """
-    }
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+    END_VERSIONS
+    """
 }
diff --git a/modules/chromap/index/main.nf b/modules/chromap/index/main.nf
index cafeca2f..61bcee10 100644
--- a/modules/chromap/index/main.nf
+++ b/modules/chromap/index/main.nf
@@ -1,13 +1,12 @@
-def VERSION = '0.1' // Version information not provided by tool on CLI
-
 process CHROMAP_INDEX {
     tag '$fasta'
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::chromap=0.1 bioconda::samtools=1.13" : null)
+    conda (params.enable_conda ? "bioconda::chromap=0.1.5" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0' :
-        'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0' }"
+        'https://depot.galaxyproject.org/singularity/chromap:0.1.5--h9a82719_0' :
+        'quay.io/biocontainers/chromap:0.1.5--h9a82719_0' }"
+
 
     input:
     path fasta
@@ -29,8 +28,7 @@ process CHROMAP_INDEX {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        chromap: $VERSION
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        chromap: \$(echo \$(chromap --version 2>&1))
     END_VERSIONS
     """
 }
diff --git a/modules/cutadapt/main.nf b/modules/cutadapt/main.nf
index 89105715..74c42768 100644
--- a/modules/cutadapt/main.nf
+++ b/modules/cutadapt/main.nf
@@ -5,7 +5,7 @@ process CUTADAPT {
     conda (params.enable_conda ? 'bioconda::cutadapt=3.4' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/cutadapt:3.4--py39h38f01e4_1' :
-        'quay.io/biocontainers/cutadapt:3.4--py37h73a75cf_1' }"
+        'quay.io/biocontainers/cutadapt:3.4--py39h38f01e4_1' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/deepvariant/main.nf b/modules/deepvariant/main.nf
new file mode 100644
index 00000000..98345c83
--- /dev/null
+++ b/modules/deepvariant/main.nf
@@ -0,0 +1,44 @@
+process DEEPVARIANT {
+    tag "$meta.id"
+    label 'process_medium'
+
+
+    if (params.enable_conda) {
+        exit 1, "Conda environments cannot be used when using the DeepVariant tool. Please use docker or singularity containers."
+    }
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'google/deepvariant:1.3.0' :
+        'google/deepvariant:1.3.0' }"
+
+    input:
+    tuple val(meta), path(input), path(index), path(intervals)
+    path(fasta)
+    path(fai)
+
+    output:
+    tuple val(meta), path("*.vcf.gz") ,  emit: vcf
+    tuple val(meta), path("*g.vcf.gz"),  emit: gvcf
+    path "versions.yml"               ,  emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def regions = intervals ? "--regions ${intervals}" : ""
+
+    """
+    /opt/deepvariant/bin/run_deepvariant \\
+        --ref=${fasta} \\
+        --reads=${input} \\
+        --output_vcf=${prefix}.vcf.gz \\
+        --output_gvcf=${prefix}.g.vcf.gz \\
+        ${args} \\
+        ${regions} \\
+        --num_shards=${task.cpus}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' )
+    END_VERSIONS
+    """
+}
diff --git a/modules/deepvariant/meta.yml b/modules/deepvariant/meta.yml
new file mode 100644
index 00000000..d4423d69
--- /dev/null
+++ b/modules/deepvariant/meta.yml
@@ -0,0 +1,62 @@
+name: deepvariant
+description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
+keywords:
+  - variant calling
+  - machine learning
+tools:
+  - deepvariant:
+      description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
+      homepage: https://github.com/google/deepvariant
+      documentation: https://github.com/google/deepvariant
+      tool_dev_url: https://github.com/google/deepvariant
+      doi: "https://doi.org/10.1038/nbt.4235"
+      licence: ['BSD-3-clause']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - input:
+      type: file
+      description: BAM/CRAM file
+      pattern: "*.bam/cram"
+  - index:
+      type: file
+      description: Index of BAM/CRAM file
+      pattern: "*.bai/crai"
+  - interval:
+      type: file
+      description: Interval file for targeted regions
+      pattern: "*.bed"
+  - fasta:
+      type: file
+      description: The reference fasta file
+      pattern: "*.fasta"
+  - fai:
+      type: file
+      description: Index of reference fasta file
+      pattern: "*.fai"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: Compressed VCF file
+      pattern: "*.vcf.gz"
+  - gvcf:
+      type: file
+      description: Compressed GVCF file
+      pattern: "*.g.vcf.gz"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+
+authors:
+  - "@abhi18av"
diff --git a/modules/dshbio/exportsegments/main.nf b/modules/dshbio/exportsegments/main.nf
index d506a4b6..0a1920a6 100644
--- a/modules/dshbio/exportsegments/main.nf
+++ b/modules/dshbio/exportsegments/main.nf
@@ -2,16 +2,16 @@ process DSHBIO_EXPORTSEGMENTS {
     tag "${meta.id}"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.6" : null)
+    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0' :
-        'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
+        'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gfa)
 
     output:
-    tuple val(meta), path("*.fa"), emit: fasta
+    tuple val(meta), path("*.fa.gz"), emit: fasta
     path "versions.yml"              , emit: versions
 
     script:
@@ -22,7 +22,7 @@ process DSHBIO_EXPORTSEGMENTS {
         export-segments \\
         $args \\
         -i $gfa \\
-        -o ${prefix}.fa
+        -o ${prefix}.fa.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/dshbio/exportsegments/meta.yml b/modules/dshbio/exportsegments/meta.yml
index da5455c7..eddb6d09 100644
--- a/modules/dshbio/exportsegments/meta.yml
+++ b/modules/dshbio/exportsegments/meta.yml
@@ -21,8 +21,8 @@ input:
             e.g. [ id:'test', single_end:false ]
     - gfa:
         type: file
-        description: Assembly segments in GFA 1.0 format
-        pattern: "*.{gfa}"
+        description: Assembly segments in uncompressed or compressed GFA 1.0 format
+        pattern: "*.{gfa|gfa.bgz|gfa.gz|gfa.zst}"
 output:
     - meta:
         type: map
@@ -31,8 +31,8 @@ output:
             e.g. [ id:'test', single_end:false ]
     - fasta:
         type: file
-        description: Assembly segment sequences in FASTA format
-        pattern: "*.{fa}"
+        description: Assembly segment sequences in gzipped FASTA format
+        pattern: "*.{fa.gz}"
     - versions:
         type: file
         description: File containing software versions
diff --git a/modules/dshbio/filterbed/main.nf b/modules/dshbio/filterbed/main.nf
index 6480f4a4..6efe07e8 100644
--- a/modules/dshbio/filterbed/main.nf
+++ b/modules/dshbio/filterbed/main.nf
@@ -2,10 +2,10 @@ process DSHBIO_FILTERBED {
     tag "${meta.id}"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.6" : null)
+    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0' :
-        'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
+        'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bed)
diff --git a/modules/dshbio/filtergff3/main.nf b/modules/dshbio/filtergff3/main.nf
index a0bbf3af..5214ce23 100644
--- a/modules/dshbio/filtergff3/main.nf
+++ b/modules/dshbio/filtergff3/main.nf
@@ -2,10 +2,10 @@ process DSHBIO_FILTERGFF3 {
     tag "${meta.id}"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.6" : null)
+    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0' :
-        'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
+        'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gff3)
diff --git a/modules/dshbio/splitbed/main.nf b/modules/dshbio/splitbed/main.nf
index 8dbf1104..c0ca6a8b 100644
--- a/modules/dshbio/splitbed/main.nf
+++ b/modules/dshbio/splitbed/main.nf
@@ -2,10 +2,10 @@ process DSHBIO_SPLITBED {
     tag "${meta.id}"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.6" : null)
+    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0' :
-        'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
+        'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bed)
diff --git a/modules/dshbio/splitgff3/main.nf b/modules/dshbio/splitgff3/main.nf
index fc868a39..012afec7 100644
--- a/modules/dshbio/splitgff3/main.nf
+++ b/modules/dshbio/splitgff3/main.nf
@@ -2,10 +2,10 @@ process DSHBIO_SPLITGFF3 {
     tag "${meta.id}"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.6" : null)
+    conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0' :
-        'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
+        'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gff3)
diff --git a/modules/fastp/main.nf b/modules/fastp/main.nf
index 33603842..a406036a 100644
--- a/modules/fastp/main.nf
+++ b/modules/fastp/main.nf
@@ -2,10 +2,10 @@ process FASTP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::fastp=0.20.1' : null)
+    conda (params.enable_conda ? 'bioconda::fastp=0.23.2' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fastp:0.20.1--h8b12597_0' :
-        'quay.io/biocontainers/fastp:0.20.1--h8b12597_0' }"
+        'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' :
+        'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/fgbio/fastqtobam/main.nf b/modules/fgbio/fastqtobam/main.nf
index 126c3dd8..3060d715 100644
--- a/modules/fgbio/fastqtobam/main.nf
+++ b/modules/fgbio/fastqtobam/main.nf
@@ -13,7 +13,7 @@ process FGBIO_FASTQTOBAM {
 
     output:
     tuple val(meta), path("*_umi_converted.bam"), emit: umibam
-    path "versions.yml"                         , emit: version
+    path "versions.yml"                         , emit: versions
 
     script:
     def args = task.ext.args ?: ''
diff --git a/modules/gatk4/applybqsr/main.nf b/modules/gatk4/applybqsr/main.nf
index 22702211..c246190a 100644
--- a/modules/gatk4/applybqsr/main.nf
+++ b/modules/gatk4/applybqsr/main.nf
@@ -2,10 +2,10 @@ process GATK4_APPLYBQSR {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
diff --git a/modules/gatk4/applyvqsr/main.nf b/modules/gatk4/applyvqsr/main.nf
index 9e61ba4b..99233975 100644
--- a/modules/gatk4/applyvqsr/main.nf
+++ b/modules/gatk4/applyvqsr/main.nf
@@ -2,10 +2,10 @@ process GATK4_APPLYVQSR {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi), path(recal), path(recalidx), path(tranches)
diff --git a/modules/gatk4/baserecalibrator/main.nf b/modules/gatk4/baserecalibrator/main.nf
index 3a26d6cc..42391d62 100644
--- a/modules/gatk4/baserecalibrator/main.nf
+++ b/modules/gatk4/baserecalibrator/main.nf
@@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals)
diff --git a/modules/gatk4/bedtointervallist/main.nf b/modules/gatk4/bedtointervallist/main.nf
index 76d0f8a4..37f46f48 100644
--- a/modules/gatk4/bedtointervallist/main.nf
+++ b/modules/gatk4/bedtointervallist/main.nf
@@ -2,10 +2,10 @@ process GATK4_BEDTOINTERVALLIST {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bed)
diff --git a/modules/gatk4/calculatecontamination/main.nf b/modules/gatk4/calculatecontamination/main.nf
index 7fc88076..f4e98f64 100644
--- a/modules/gatk4/calculatecontamination/main.nf
+++ b/modules/gatk4/calculatecontamination/main.nf
@@ -2,10 +2,10 @@ process GATK4_CALCULATECONTAMINATION {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(pileup), path(matched)
diff --git a/modules/gatk4/createsequencedictionary/main.nf b/modules/gatk4/createsequencedictionary/main.nf
index 4d82a643..2cbd8948 100644
--- a/modules/gatk4/createsequencedictionary/main.nf
+++ b/modules/gatk4/createsequencedictionary/main.nf
@@ -2,10 +2,10 @@ process GATK4_CREATESEQUENCEDICTIONARY {
     tag "$fasta"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     path fasta
diff --git a/modules/gatk4/createsomaticpanelofnormals/main.nf b/modules/gatk4/createsomaticpanelofnormals/main.nf
index c094084f..8ab578c4 100644
--- a/modules/gatk4/createsomaticpanelofnormals/main.nf
+++ b/modules/gatk4/createsomaticpanelofnormals/main.nf
@@ -2,10 +2,10 @@ process GATK4_CREATESOMATICPANELOFNORMALS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(genomicsdb)
diff --git a/modules/gatk4/estimatelibrarycomplexity/main.nf b/modules/gatk4/estimatelibrarycomplexity/main.nf
index 78079c20..744ebf21 100644
--- a/modules/gatk4/estimatelibrarycomplexity/main.nf
+++ b/modules/gatk4/estimatelibrarycomplexity/main.nf
@@ -2,10 +2,10 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(cram)
diff --git a/modules/gatk4/fastqtosam/main.nf b/modules/gatk4/fastqtosam/main.nf
index 2c13890f..f0116b41 100644
--- a/modules/gatk4/fastqtosam/main.nf
+++ b/modules/gatk4/fastqtosam/main.nf
@@ -2,10 +2,10 @@ process GATK4_FASTQTOSAM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/gatk4/filtermutectcalls/main.nf b/modules/gatk4/filtermutectcalls/main.nf
index e68d01db..2f5f8dcb 100644
--- a/modules/gatk4/filtermutectcalls/main.nf
+++ b/modules/gatk4/filtermutectcalls/main.nf
@@ -2,10 +2,10 @@ process GATK4_FILTERMUTECTCALLS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi), path(stats), path(orientationbias), path(segmentation), path(contaminationfile), val(contaminationest)
diff --git a/modules/gatk4/gatherbqsrreports/main.nf b/modules/gatk4/gatherbqsrreports/main.nf
index 721f5634..b084ab00 100644
--- a/modules/gatk4/gatherbqsrreports/main.nf
+++ b/modules/gatk4/gatherbqsrreports/main.nf
@@ -2,10 +2,10 @@ process GATK4_GATHERBQSRREPORTS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(recal_table)
diff --git a/modules/gatk4/genomicsdbimport/main.nf b/modules/gatk4/genomicsdbimport/main.nf
index f1a606cb..94a589cd 100644
--- a/modules/gatk4/genomicsdbimport/main.nf
+++ b/modules/gatk4/genomicsdbimport/main.nf
@@ -2,10 +2,10 @@ process GATK4_GENOMICSDBIMPORT {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi), path(intervalfile), val(intervalval), path(wspace)
diff --git a/modules/gatk4/genotypegvcfs/main.nf b/modules/gatk4/genotypegvcfs/main.nf
index f9107b1e..016da1f5 100644
--- a/modules/gatk4/genotypegvcfs/main.nf
+++ b/modules/gatk4/genotypegvcfs/main.nf
@@ -2,10 +2,10 @@ process GATK4_GENOTYPEGVCFS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gvcf), path(gvcf_index), path(intervals)
diff --git a/modules/gatk4/getpileupsummaries/main.nf b/modules/gatk4/getpileupsummaries/main.nf
index 896e23bd..a81ae635 100644
--- a/modules/gatk4/getpileupsummaries/main.nf
+++ b/modules/gatk4/getpileupsummaries/main.nf
@@ -2,10 +2,10 @@ process GATK4_GETPILEUPSUMMARIES {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
diff --git a/modules/gatk4/haplotypecaller/main.nf b/modules/gatk4/haplotypecaller/main.nf
index 8b4c0e64..8c22da68 100644
--- a/modules/gatk4/haplotypecaller/main.nf
+++ b/modules/gatk4/haplotypecaller/main.nf
@@ -2,10 +2,10 @@ process GATK4_HAPLOTYPECALLER {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals)
diff --git a/modules/gatk4/indexfeaturefile/main.nf b/modules/gatk4/indexfeaturefile/main.nf
index 63633e5f..ecd24173 100644
--- a/modules/gatk4/indexfeaturefile/main.nf
+++ b/modules/gatk4/indexfeaturefile/main.nf
@@ -2,10 +2,10 @@ process GATK4_INDEXFEATUREFILE {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(feature_file)
diff --git a/modules/gatk4/intervallisttools/main.nf b/modules/gatk4/intervallisttools/main.nf
index b1881932..17412160 100644
--- a/modules/gatk4/intervallisttools/main.nf
+++ b/modules/gatk4/intervallisttools/main.nf
@@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOOLS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(interval_list)
diff --git a/modules/gatk4/learnreadorientationmodel/main.nf b/modules/gatk4/learnreadorientationmodel/main.nf
index 961b6a75..d1bce19f 100644
--- a/modules/gatk4/learnreadorientationmodel/main.nf
+++ b/modules/gatk4/learnreadorientationmodel/main.nf
@@ -2,10 +2,10 @@ process GATK4_LEARNREADORIENTATIONMODEL {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(f1r2)
diff --git a/modules/gatk4/markduplicates/main.nf b/modules/gatk4/markduplicates/main.nf
index 5f6f127e..c101d042 100644
--- a/modules/gatk4/markduplicates/main.nf
+++ b/modules/gatk4/markduplicates/main.nf
@@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bams)
diff --git a/modules/gatk4/mergebamalignment/main.nf b/modules/gatk4/mergebamalignment/main.nf
index b13b9ae8..b0b9daa1 100644
--- a/modules/gatk4/mergebamalignment/main.nf
+++ b/modules/gatk4/mergebamalignment/main.nf
@@ -2,10 +2,10 @@ process GATK4_MERGEBAMALIGNMENT {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(aligned)
diff --git a/modules/gatk4/mergevcfs/main.nf b/modules/gatk4/mergevcfs/main.nf
index 9158a242..b2e584a8 100644
--- a/modules/gatk4/mergevcfs/main.nf
+++ b/modules/gatk4/mergevcfs/main.nf
@@ -2,10 +2,10 @@ process GATK4_MERGEVCFS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcfs)
diff --git a/modules/gatk4/mutect2/main.nf b/modules/gatk4/mutect2/main.nf
index 1abf44ea..c33cee18 100644
--- a/modules/gatk4/mutect2/main.nf
+++ b/modules/gatk4/mutect2/main.nf
@@ -2,10 +2,10 @@ process GATK4_MUTECT2 {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta) , path(input) , path(input_index) , val(which_norm)
diff --git a/modules/gatk4/revertsam/main.nf b/modules/gatk4/revertsam/main.nf
index 585d2063..5a13d61d 100644
--- a/modules/gatk4/revertsam/main.nf
+++ b/modules/gatk4/revertsam/main.nf
@@ -2,10 +2,10 @@ process GATK4_REVERTSAM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/gatk4/samtofastq/main.nf b/modules/gatk4/samtofastq/main.nf
index 9b73299f..0a75f604 100644
--- a/modules/gatk4/samtofastq/main.nf
+++ b/modules/gatk4/samtofastq/main.nf
@@ -2,10 +2,10 @@ process GATK4_SAMTOFASTQ {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/gatk4/splitncigarreads/main.nf b/modules/gatk4/splitncigarreads/main.nf
index c27c393f..29483fb5 100644
--- a/modules/gatk4/splitncigarreads/main.nf
+++ b/modules/gatk4/splitncigarreads/main.nf
@@ -2,10 +2,10 @@ process GATK4_SPLITNCIGARREADS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/gatk4/variantfiltration/main.nf b/modules/gatk4/variantfiltration/main.nf
index 32e4aae1..beaec0c0 100644
--- a/modules/gatk4/variantfiltration/main.nf
+++ b/modules/gatk4/variantfiltration/main.nf
@@ -2,10 +2,10 @@ process GATK4_VARIANTFILTRATION {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(vcf_tbi)
diff --git a/modules/gatk4/variantrecalibrator/main.nf b/modules/gatk4/variantrecalibrator/main.nf
index 5641d6de..c4aa5535 100644
--- a/modules/gatk4/variantrecalibrator/main.nf
+++ b/modules/gatk4/variantrecalibrator/main.nf
@@ -2,10 +2,10 @@ process GATK4_VARIANTRECALIBRATOR {
     tag "$meta.id"
     label 'process_low'
 
-        conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
-        container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-            'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
-            'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf) , path(tbi)
diff --git a/modules/gtdbtk/classifywf/main.nf b/modules/gtdbtk/classifywf/main.nf
index 4a4b3a01..009efa8d 100644
--- a/modules/gtdbtk/classifywf/main.nf
+++ b/modules/gtdbtk/classifywf/main.nf
@@ -2,6 +2,7 @@ def VERSION = '1.5.0' // Version information not provided by tool on CLI
 
 process GTDBTK_CLASSIFYWF {
     tag "${meta.assembler}-${meta.id}"
+    label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::gtdbtk=1.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/idr/main.nf b/modules/idr/main.nf
index 44b07be4..7e377878 100644
--- a/modules/idr/main.nf
+++ b/modules/idr/main.nf
@@ -5,7 +5,7 @@ process IDR {
     conda (params.enable_conda ? "bioconda::idr=2.0.4.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/idr:2.0.4.2--py39hcbe4a3b_5' :
-        'quay.io/biocontainers/idr:2.0.4.2--py38h9af456f_5' }"
+        'quay.io/biocontainers/idr:2.0.4.2--py39hcbe4a3b_5' }"
 
     input:
     path peaks
diff --git a/modules/ivar/consensus/main.nf b/modules/ivar/consensus/main.nf
index 58d97c8c..96d00ce2 100644
--- a/modules/ivar/consensus/main.nf
+++ b/modules/ivar/consensus/main.nf
@@ -9,7 +9,8 @@ process IVAR_CONSENSUS {
 
     input:
     tuple val(meta), path(bam)
-    path  fasta
+    path fasta
+    val save_mpileup
 
     output:
     tuple val(meta), path("*.fa")      , emit: fasta
@@ -21,14 +22,16 @@ process IVAR_CONSENSUS {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
+    def mpileup = save_mpileup ? "| tee ${prefix}.mpileup" : ""
     """
-    samtools mpileup \\
+    samtools \\
+        mpileup \\
         --reference $fasta \\
         $args2 \\
-        $bam | \\
-        $save_mpileup \\
-        ivar consensus \\
+        $bam \\
+        $mpileup \\
+        | ivar \\
+            consensus \\
             $args \\
             -p $prefix
 
diff --git a/modules/ivar/consensus/meta.yml b/modules/ivar/consensus/meta.yml
index 2ee5f2c6..aa08ad98 100644
--- a/modules/ivar/consensus/meta.yml
+++ b/modules/ivar/consensus/meta.yml
@@ -25,6 +25,10 @@ input:
         type: file
         description: The reference sequence used for mapping and generating the BAM file
         pattern: "*.fa"
+    - save_mpileup:
+        type: boolean
+        description: Save mpileup file generated by ivar consensus
+        patter: "*.mpileup"
 output:
     - meta:
         type: map
diff --git a/modules/ivar/variants/main.nf b/modules/ivar/variants/main.nf
index ce4abd4d..bb6e402b 100644
--- a/modules/ivar/variants/main.nf
+++ b/modules/ivar/variants/main.nf
@@ -11,6 +11,7 @@ process IVAR_VARIANTS {
     tuple val(meta), path(bam)
     path  fasta
     path  gff
+    val   save_mpileup
 
     output:
     tuple val(meta), path("*.tsv")    , emit: tsv
@@ -21,15 +22,17 @@ process IVAR_VARIANTS {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
-    def features     = params.gff ? "-g $gff" : ""
+    def features = gff ? "-g $gff" : ""
+    def mpileup = save_mpileup ? "| tee ${prefix}.mpileup" : ""
     """
-    samtools mpileup \\
+    samtools \\
+        mpileup \\
         $args2 \\
         --reference $fasta \\
-        $bam | \\
-        $save_mpileup  \\
-        ivar variants \\
+        $bam \\
+        $mpileup \\
+        | ivar \\
+            variants \\
             $args \\
             $features \\
             -r $fasta \\
diff --git a/modules/ivar/variants/meta.yml b/modules/ivar/variants/meta.yml
index fd3fce9e..29cbd958 100644
--- a/modules/ivar/variants/meta.yml
+++ b/modules/ivar/variants/meta.yml
@@ -29,6 +29,10 @@ input:
         type: file
         description: A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.
         patter: "*.gff"
+    - save_mpileup:
+        type: boolean
+        description: Save mpileup file generated by ivar variants
+        patter: "*.mpileup"
 output:
     - meta:
         type: map
diff --git a/modules/jupyternotebook/main.nf b/modules/jupyternotebook/main.nf
index e4bdf98b..871d6ccd 100644
--- a/modules/jupyternotebook/main.nf
+++ b/modules/jupyternotebook/main.nf
@@ -9,7 +9,7 @@ process JUPYTERNOTEBOOK {
     //ipykernel, jupytext, papermill and nbconvert Python packages.
     conda (params.enable_conda ? "ipykernel=6.0.3 jupytext=1.11.4 nbconvert=6.1.0 papermill=2.3.3 matplotlib=3.4.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963%3A879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' :
         'quay.io/biocontainers/mulled-v2-514b1a5d280c7043110b2a8d0a87b57ba392a963:879972fc8bdc81ee92f2bce3b4805d89a772bf84-0' }"
 
     input:
diff --git a/modules/kraken2/kraken2/main.nf b/modules/kraken2/kraken2/main.nf
index 3c4d1caf..eaabb229 100644
--- a/modules/kraken2/kraken2/main.nf
+++ b/modules/kraken2/kraken2/main.nf
@@ -2,10 +2,10 @@ process KRAKEN2_KRAKEN2 {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? 'bioconda::kraken2=2.1.1 conda-forge::pigz=2.6' : null)
+    conda (params.enable_conda ? 'bioconda::kraken2=2.1.2 conda-forge::pigz=2.6' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:941789bd7fe00db16531c26de8bf3c5c985242a5-0' :
-        'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:941789bd7fe00db16531c26de8bf3c5c985242a5-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' :
+        'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/krona/kronadb/main.nf b/modules/krona/kronadb/main.nf
index ca7fc3d3..d8156035 100644
--- a/modules/krona/kronadb/main.nf
+++ b/modules/krona/kronadb/main.nf
@@ -8,8 +8,6 @@ process KRONA_KRONADB {
         'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' :
         'quay.io/biocontainers/krona:2.7.1--pl526_5' }"
 
-    input:
-
     output:
     path 'taxonomy/taxonomy.tab', emit: db
     path "versions.yml"         , emit: versions
diff --git a/modules/malt/run/main.nf b/modules/malt/run/main.nf
index 8b8f05cc..5e81667e 100644
--- a/modules/malt/run/main.nf
+++ b/modules/malt/run/main.nf
@@ -1,6 +1,5 @@
 process MALT_RUN {
-
-    label 'process_high_memory'
+    label 'process_high'
 
     conda (params.enable_conda ? "bioconda::malt=0.53" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/mash/dist/main.nf b/modules/mash/dist/main.nf
new file mode 100644
index 00000000..323bd339
--- /dev/null
+++ b/modules/mash/dist/main.nf
@@ -0,0 +1,34 @@
+process MASH_DIST {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::mash=2.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1' :
+        'quay.io/biocontainers/mash:2.3--he348c14_1' }"
+
+    input:
+    tuple val(meta), path(query)
+    path reference
+
+    output:
+    tuple val(meta), path("*.txt"), emit: dist
+    path "versions.yml"           , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mash \\
+        dist \\
+        -p $task.cpus \\
+        $args \\
+        $reference \\
+        $query > ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mash: \$(mash --version 2>&1)
+    END_VERSIONS
+    """
+}
diff --git a/modules/mash/dist/meta.yml b/modules/mash/dist/meta.yml
new file mode 100644
index 00000000..8cbaa63c
--- /dev/null
+++ b/modules/mash/dist/meta.yml
@@ -0,0 +1,45 @@
+name: mash_dist
+description: Calculate Mash distances between reference and query seqeunces
+keywords:
+  - mash/dist
+tools:
+  - mash:
+      description: Fast sequence distance estimator that uses MinHash
+      homepage: https://github.com/marbl/Mash
+      documentation: https://mash.readthedocs.io/en/latest/sketches.html
+      tool_dev_url: https://github.com/marbl/Mash
+      doi: "10.1186/s13059-016-0997-x"
+      licence: ['https://github.com/marbl/Mash/blob/master/LICENSE.txt']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reference:
+      type: file
+      description: FASTA, FASTQ or Mash sketch
+      pattern: "*.{fasta,fasta.gz,fastq,fastq.gz,msh}"
+  - query:
+      type: file
+      description: FASTA, FASTQ or Mash sketch
+      pattern: "*.{fasta,fasta.gz,fastq,fastq.gz,msh}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - dist:
+      type: file
+      description: The results from mash dist
+      pattern: "*.txt"
+
+authors:
+  - "@rpetit3"
diff --git a/modules/minia/main.nf b/modules/minia/main.nf
index ceff67c5..968cafa5 100644
--- a/modules/minia/main.nf
+++ b/modules/minia/main.nf
@@ -2,10 +2,10 @@ process MINIA {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::minia=3.2.4" : null)
+    conda (params.enable_conda ? "bioconda::minia=3.2.6" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/minia:3.2.4--he513fc3_0' :
-        'quay.io/biocontainers/minia:3.2.4--he513fc3_0' }"
+        'https://depot.galaxyproject.org/singularity/minia:3.2.6--h9a82719_0' :
+        'quay.io/biocontainers/minia:3.2.6--h9a82719_0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nanoplot/main.nf b/modules/nanoplot/main.nf
index 36577d8a..c3fb8a37 100644
--- a/modules/nanoplot/main.nf
+++ b/modules/nanoplot/main.nf
@@ -2,10 +2,10 @@ process NANOPLOT {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? 'bioconda::nanoplot=1.38.0' : null)
+    conda (params.enable_conda ? 'bioconda::nanoplot=1.39.0' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/nanoplot:1.38.0--pyhdfd78af_0' :
-        'quay.io/biocontainers/nanoplot:1.38.0--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/nanoplot:1.39.0--pyhdfd78af_0' :
+        'quay.io/biocontainers/nanoplot:1.39.0--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(ontfile)
diff --git a/modules/nextclade/datasetget/main.nf b/modules/nextclade/datasetget/main.nf
new file mode 100644
index 00000000..55371168
--- /dev/null
+++ b/modules/nextclade/datasetget/main.nf
@@ -0,0 +1,39 @@
+process NEXTCLADE_DATASETGET {
+    tag "$dataset"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::nextclade=1.9.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/nextclade:1.9.0--h9ee0642_0' :
+        'quay.io/biocontainers/nextclade:1.9.0--h9ee0642_0' }"
+
+    input:
+    val dataset
+    val reference
+    val tag
+
+    output:
+    path "$prefix"     , emit: dataset
+    path "versions.yml", emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${dataset}"
+    def fasta = reference ? "--reference ${reference}" : ''
+    def version = tag ? "--tag ${tag}" : ''
+    """
+    nextclade \\
+        dataset \\
+        get \\
+        $args \\
+        --name $dataset \\
+        $fasta \\
+        $version \\
+        --output-dir $prefix
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        nextclade: \$(nextclade --version 2>&1)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nextclade/datasetget/meta.yml b/modules/nextclade/datasetget/meta.yml
new file mode 100644
index 00000000..1246d918
--- /dev/null
+++ b/modules/nextclade/datasetget/meta.yml
@@ -0,0 +1,42 @@
+name: nextclade_datasetget
+description: Get dataset for SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation)
+keywords:
+  - nextclade
+  - variant
+  - consensus
+tools:
+  - nextclade:
+      description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks
+      homepage: https://github.com/nextstrain/nextclade
+      documentation: https://github.com/nextstrain/nextclade
+      tool_dev_url: https://github.com/nextstrain/nextclade
+      doi: ""
+      licence: ['MIT']
+
+input:
+  - dataset:
+      type: string
+      description: Name of dataset to retrieve. A list of available datasets can be obtained using the nextclade dataset list command.
+      pattern: ".+"
+  - reference:
+      type: string
+      description: Accession id to download dataset based on a particular reference sequence. A list of available datasets can be obtained using the nextclade dataset list command.
+      pattern: ".+"
+  - tag:
+      type: string
+      description: Version tag of the dataset to download. A list of available datasets can be obtained using the nextclade dataset list command.
+      pattern: ".+"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - prefix:
+      type: path
+      description: A directory containing the dataset files needed for nextclade run
+      pattern: "prefix"
+
+authors:
+  - "@antunderwood"
+  - "@drpatelh"
diff --git a/modules/nextclade/main.nf b/modules/nextclade/main.nf
deleted file mode 100755
index f60af57b..00000000
--- a/modules/nextclade/main.nf
+++ /dev/null
@@ -1,40 +0,0 @@
-process NEXTCLADE {
-    tag "$meta.id"
-    label 'process_low'
-
-    conda (params.enable_conda ? "bioconda::nextclade_js=0.14.4" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/nextclade_js:0.14.4--h9ee0642_0' :
-        'quay.io/biocontainers/nextclade_js:0.14.4--h9ee0642_0' }"
-
-    input:
-    tuple val(meta), path(fasta)
-
-    output:
-    tuple val(meta), path("${prefix}.csv")       , emit: csv
-    tuple val(meta), path("${prefix}.json")      , emit: json
-    tuple val(meta), path("${prefix}.tree.json") , emit: json_tree
-    tuple val(meta), path("${prefix}.tsv")       , emit: tsv
-    tuple val(meta), path("${prefix}.clades.tsv"), optional:true, emit: tsv_clades
-    path "versions.yml"                          , emit: versions
-
-    script:
-    def args = task.ext.args   ?: ''
-    prefix   = task.ext.prefix ?: "${meta.id}"
-    """
-    nextclade \\
-        $args \\
-        --jobs $task.cpus \\
-        --input-fasta $fasta \\
-        --output-json ${prefix}.json \\
-        --output-csv ${prefix}.csv \\
-        --output-tsv ${prefix}.tsv \\
-        --output-tsv-clades-only ${prefix}.clades.tsv \\
-        --output-tree ${prefix}.tree.json
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        nextclade: \$(nextclade --version 2>&1)
-    END_VERSIONS
-    """
-}
diff --git a/modules/nextclade/run/main.nf b/modules/nextclade/run/main.nf
new file mode 100644
index 00000000..e29dd8ce
--- /dev/null
+++ b/modules/nextclade/run/main.nf
@@ -0,0 +1,42 @@
+process NEXTCLADE_RUN {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::nextclade=1.9.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/nextclade:1.9.0--h9ee0642_0' :
+        'quay.io/biocontainers/nextclade:1.9.0--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+    path dataset
+
+    output:
+    tuple val(meta), path("${prefix}.csv")      , emit: csv
+    tuple val(meta), path("${prefix}.tsv")      , emit: tsv
+    tuple val(meta), path("${prefix}.json")     , emit: json
+    tuple val(meta), path("${prefix}.tree.json"), emit: json_tree
+    path "versions.yml"                         , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    nextclade \\
+        run \\
+        $args \\
+        --jobs $task.cpus \\
+        --input-fasta $fasta \\
+        --input-dataset $dataset \\
+        --output-csv ${prefix}.csv \\
+        --output-tsv ${prefix}.tsv \\
+        --output-json ${prefix}.json \\
+        --output-tree ${prefix}.tree.json \\
+        --output-basename ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        nextclade: \$(nextclade --version 2>&1)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nextclade/meta.yml b/modules/nextclade/run/meta.yml
old mode 100755
new mode 100644
similarity index 75%
rename from modules/nextclade/meta.yml
rename to modules/nextclade/run/meta.yml
index 1b4a435a..40a863e6
--- a/modules/nextclade/meta.yml
+++ b/modules/nextclade/run/meta.yml
@@ -1,17 +1,17 @@
-name: nextclade
-description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (Javascript implementation)
+name: nextclade_run
+description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation)
 keywords:
   - nextclade
   - variant
   - consensus
 tools:
   - nextclade:
-      description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (Javascript implementation)
-      homepage: https://clades.nextstrain.org
-      documentation: None
+      description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks
+      homepage: https://github.com/nextstrain/nextclade
+      documentation: https://github.com/nextstrain/nextclade
       tool_dev_url: https://github.com/nextstrain/nextclade
       doi: ""
-      licence: ["MIT"]
+      licence: ['MIT']
 
 input:
   - meta:
@@ -19,6 +19,10 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
+  - dataset:
+      type: path
+      description: Path containing the dataset files obtained by running nextclade dataset get
+      pattern: "*"
   - fasta:
       type: file
       description: FASTA file containing one or more consensus sequences
@@ -50,10 +54,7 @@ output:
       type: file
       description: TSV file containing nextclade results
       pattern: "*.{tsv}"
-  - tsv_clades:
-      type: file
-      description: TSV file containing nextclade results for clades only
-      pattern: "*.{clades.tsv}"
 
 authors:
+  - "@antunderwood"
   - "@drpatelh"
diff --git a/modules/pangolin/main.nf b/modules/pangolin/main.nf
index 5ee2b2e0..40d6d78e 100644
--- a/modules/pangolin/main.nf
+++ b/modules/pangolin/main.nf
@@ -2,10 +2,10 @@ process PANGOLIN {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::pangolin=3.1.11' : null)
+    conda (params.enable_conda ? 'bioconda::pangolin=3.1.17' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pangolin:3.1.11--pyhdfd78af_1' :
-        'quay.io/biocontainers/pangolin:3.1.11--pyhdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/pangolin:3.1.17--pyhdfd78af_0' :
+        'quay.io/biocontainers/pangolin:3.1.17--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/paraclu/main.nf b/modules/paraclu/main.nf
index 1623ea89..cc16674e 100644
--- a/modules/paraclu/main.nf
+++ b/modules/paraclu/main.nf
@@ -6,7 +6,7 @@ process PARACLU {
 
     conda (params.enable_conda ? "bioconda::paraclu=10" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/paraclu%3A10--h9a82719_1' :
+        'https://depot.galaxyproject.org/singularity/paraclu:10--h9a82719_1' :
         'quay.io/biocontainers/paraclu:10--h9a82719_1' }"
 
     input:
diff --git a/modules/picard/collecthsmetrics/main.nf b/modules/picard/collecthsmetrics/main.nf
index 9dabc3aa..ae3e4d96 100644
--- a/modules/picard/collecthsmetrics/main.nf
+++ b/modules/picard/collecthsmetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/picard/collectmultiplemetrics/main.nf b/modules/picard/collectmultiplemetrics/main.nf
index 481761e3..9511f7a4 100644
--- a/modules/picard/collectmultiplemetrics/main.nf
+++ b/modules/picard/collectmultiplemetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf
index 361ca1b5..dd9da1b6 100644
--- a/modules/picard/collectwgsmetrics/main.nf
+++ b/modules/picard/collectwgsmetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTWGSMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
diff --git a/modules/picard/filtersamreads/main.nf b/modules/picard/filtersamreads/main.nf
index 70bd2fa7..6a9c9c72 100644
--- a/modules/picard/filtersamreads/main.nf
+++ b/modules/picard/filtersamreads/main.nf
@@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(readlist)
diff --git a/modules/picard/markduplicates/main.nf b/modules/picard/markduplicates/main.nf
index 3087bff4..7990d7e6 100644
--- a/modules/picard/markduplicates/main.nf
+++ b/modules/picard/markduplicates/main.nf
@@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/picard/mergesamfiles/main.nf b/modules/picard/mergesamfiles/main.nf
index 952d6331..96616a44 100644
--- a/modules/picard/mergesamfiles/main.nf
+++ b/modules/picard/mergesamfiles/main.nf
@@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bams)
diff --git a/modules/picard/sortsam/main.nf b/modules/picard/sortsam/main.nf
index 7728484c..6676eed6 100644
--- a/modules/picard/sortsam/main.nf
+++ b/modules/picard/sortsam/main.nf
@@ -2,10 +2,10 @@ process PICARD_SORTSAM {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/pirate/main.nf b/modules/pirate/main.nf
index 70de52e6..c7d7476c 100644
--- a/modules/pirate/main.nf
+++ b/modules/pirate/main.nf
@@ -4,7 +4,7 @@ process PIRATE {
 
     conda (params.enable_conda ? "bioconda::pirate=1.0.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/pirate%3A1.0.4--hdfd78af_1' :
+        'https://depot.galaxyproject.org/singularity/pirate:1.0.4--hdfd78af_1' :
         'quay.io/biocontainers/pirate:1.0.4--hdfd78af_1' }"
 
     input:
diff --git a/modules/porechop/main.nf b/modules/porechop/main.nf
index 249efad9..f5ad93f8 100644
--- a/modules/porechop/main.nf
+++ b/modules/porechop/main.nf
@@ -5,7 +5,7 @@ process PORECHOP {
     conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2' :
-        'quay.io/biocontainers/porechop:0.2.4--py38h8c62d01_2' }"
+        'quay.io/biocontainers/porechop:0.2.4--py39h7cff6ad_2' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/rmarkdownnotebook/main.nf b/modules/rmarkdownnotebook/main.nf
index f8183216..18d8e150 100644
--- a/modules/rmarkdownnotebook/main.nf
+++ b/modules/rmarkdownnotebook/main.nf
@@ -9,7 +9,7 @@ process RMARKDOWNNOTEBOOK {
     //yaml and rmarkdown R packages.
     conda (params.enable_conda ? "r-base=4.1.0 r-rmarkdown=2.9 r-yaml=2.2.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5%3A0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' :
         'quay.io/biocontainers/mulled-v2-31ad840d814d356e5f98030a4ee308a16db64ec5:0e852a1e4063fdcbe3f254ac2c7469747a60e361-0' }"
 
     input:
diff --git a/modules/samtools/ampliconclip/main.nf b/modules/samtools/ampliconclip/main.nf
index 55a2f736..e553f218 100644
--- a/modules/samtools/ampliconclip/main.nf
+++ b/modules/samtools/ampliconclip/main.nf
@@ -22,8 +22,9 @@ process SAMTOOLS_AMPLICONCLIP {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def rejects  = save_cliprejects ? "--rejects-file ${prefix}.cliprejects.bam" : ""
-    def stats    = save_clipstats   ? "-f ${prefix}.clipstats.txt"               : ""
+    def rejects = save_cliprejects ? "--rejects-file ${prefix}.cliprejects.bam" : ""
+    def stats   = save_clipstats   ? "-f ${prefix}.clipstats.txt"               : ""
+    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     samtools \\
         ampliconclip \\
diff --git a/modules/samtools/bam2fq/main.nf b/modules/samtools/bam2fq/main.nf
index 689eb960..32588dd7 100644
--- a/modules/samtools/bam2fq/main.nf
+++ b/modules/samtools/bam2fq/main.nf
@@ -9,11 +9,11 @@ process SAMTOOLS_BAM2FQ {
 
     input:
     tuple val(meta), path(inputbam)
-    val(split)
+    val split
 
     output:
     tuple val(meta), path("*.fq.gz"), emit: reads
-    path "versions.yml"          , emit: versions
+    path "versions.yml"             , emit: versions
 
     script:
     def args = task.ext.args ?: ''
@@ -50,5 +50,4 @@ process SAMTOOLS_BAM2FQ {
         END_VERSIONS
         """
     }
-
 }
diff --git a/modules/samtools/depth/main.nf b/modules/samtools/depth/main.nf
index ebf029aa..50b2ed5d 100644
--- a/modules/samtools/depth/main.nf
+++ b/modules/samtools/depth/main.nf
@@ -12,12 +12,11 @@ process SAMTOOLS_DEPTH {
 
     output:
     tuple val(meta), path("*.tsv"), emit: tsv
-    path "versions.yml"          , emit: versions
+    path "versions.yml"           , emit: versions
 
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
     """
     samtools \\
         depth \\
diff --git a/modules/samtools/faidx/main.nf b/modules/samtools/faidx/main.nf
index d8308b03..58c445d8 100644
--- a/modules/samtools/faidx/main.nf
+++ b/modules/samtools/faidx/main.nf
@@ -11,13 +11,16 @@ process SAMTOOLS_FAIDX {
     tuple val(meta), path(fasta)
 
     output:
-    tuple val(meta), path ("*.fai") , emit: fai
-    path "versions.yml"             , emit: versions
+    tuple val(meta), path ("*.fai"), emit: fai
+    path "versions.yml"            , emit: versions
 
     script:
     def args = task.ext.args ?: ''
     """
-    samtools faidx $fasta
+    samtools \\
+        faidx \\
+        $fasta
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
diff --git a/modules/samtools/fastq/main.nf b/modules/samtools/fastq/main.nf
index 212e804e..a2dae087 100644
--- a/modules/samtools/fastq/main.nf
+++ b/modules/samtools/fastq/main.nf
@@ -18,13 +18,14 @@ process SAMTOOLS_FASTQ {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def endedness = meta.single_end ? "-0 ${prefix}.fastq.gz" : "-1 ${prefix}_1.fastq.gz -2 ${prefix}_2.fastq.gz"
-
     """
-    samtools fastq \\
+    samtools \\
+        fastq \\
         $args \\
         --threads ${task.cpus-1} \\
         $endedness \\
         $bam
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
diff --git a/modules/samtools/fixmate/main.nf b/modules/samtools/fixmate/main.nf
index d108f8d6..89ac666d 100644
--- a/modules/samtools/fixmate/main.nf
+++ b/modules/samtools/fixmate/main.nf
@@ -18,7 +18,6 @@ process SAMTOOLS_FIXMATE {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
-
     """
     samtools \\
         fixmate  \\
diff --git a/modules/samtools/flagstat/main.nf b/modules/samtools/flagstat/main.nf
index 03721d0b..119adf77 100644
--- a/modules/samtools/flagstat/main.nf
+++ b/modules/samtools/flagstat/main.nf
@@ -17,7 +17,12 @@ process SAMTOOLS_FLAGSTAT {
     script:
     def args = task.ext.args ?: ''
     """
-    samtools flagstat --threads ${task.cpus-1} $bam > ${bam}.flagstat
+    samtools \\
+        flagstat \\
+        --threads ${task.cpus-1} \\
+        $bam \\
+        > ${bam}.flagstat
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
diff --git a/modules/samtools/idxstats/main.nf b/modules/samtools/idxstats/main.nf
index cd068679..fc54e676 100644
--- a/modules/samtools/idxstats/main.nf
+++ b/modules/samtools/idxstats/main.nf
@@ -17,7 +17,11 @@ process SAMTOOLS_IDXSTATS {
     script:
     def args = task.ext.args ?: ''
     """
-    samtools idxstats $bam > ${bam}.idxstats
+    samtools \\
+        idxstats \\
+        $bam \\
+        > ${bam}.idxstats
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
diff --git a/modules/samtools/index/main.nf b/modules/samtools/index/main.nf
index db025a8f..c4fa2c63 100644
--- a/modules/samtools/index/main.nf
+++ b/modules/samtools/index/main.nf
@@ -19,7 +19,11 @@ process SAMTOOLS_INDEX {
     script:
     def args = task.ext.args ?: ''
     """
-    samtools index -@ ${task.cpus-1} $args $input
+    samtools \\
+        index \\
+        -@ ${task.cpus-1} \\
+        $args \\
+        $input
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/samtools/merge/main.nf b/modules/samtools/merge/main.nf
index fcfcf61f..a318bfc4 100644
--- a/modules/samtools/merge/main.nf
+++ b/modules/samtools/merge/main.nf
@@ -12,7 +12,7 @@ process SAMTOOLS_MERGE {
     path fasta
 
     output:
-    tuple val(meta), path("${prefix}.bam"),  optional:true, emit: bam
+    tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam
     tuple val(meta), path("${prefix}.cram"), optional:true, emit: cram
     path  "versions.yml"                                  , emit: versions
 
@@ -22,7 +22,13 @@ process SAMTOOLS_MERGE {
     def file_type = input_files[0].getExtension()
     def reference = fasta ? "--reference ${fasta}" : ""
     """
-    samtools merge --threads ${task.cpus-1} $args ${reference} ${prefix}.${file_type} $input_files
+    samtools \\
+        merge \\
+        --threads ${task.cpus-1} \\
+        $args \\
+        ${reference} \\
+        ${prefix}.${file_type} \\
+        $input_files
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/samtools/sort/main.nf b/modules/samtools/sort/main.nf
index 0c2cf25e..42c7bbf4 100644
--- a/modules/samtools/sort/main.nf
+++ b/modules/samtools/sort/main.nf
@@ -17,6 +17,7 @@ process SAMTOOLS_SORT {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     samtools sort $args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/samtools/stats/main.nf b/modules/samtools/stats/main.nf
index 83c87002..7209070d 100644
--- a/modules/samtools/stats/main.nf
+++ b/modules/samtools/stats/main.nf
@@ -19,7 +19,12 @@ process SAMTOOLS_STATS {
     def args = task.ext.args ?: ''
     def reference = fasta ? "--reference ${fasta}" : ""
     """
-    samtools stats --threads ${task.cpus-1} ${reference} ${input} > ${input}.stats
+    samtools \\
+        stats \\
+        --threads ${task.cpus-1} \\
+        ${reference} \\
+        ${input} \\
+        > ${input}.stats
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/samtools/view/main.nf b/modules/samtools/view/main.nf
index 619b84dc..cb205d0b 100644
--- a/modules/samtools/view/main.nf
+++ b/modules/samtools/view/main.nf
@@ -18,11 +18,20 @@ process SAMTOOLS_VIEW {
 
     script:
     def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     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} $args $input > ${prefix}.${file_type}
+    samtools \\
+        view \\
+        --threads ${task.cpus-1} \\
+        ${reference} \\
+        $args \\
+        $input \\
+        $args2 \\
+        > ${prefix}.${file_type}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/spatyper/main.nf b/modules/spatyper/main.nf
index e0ba8d13..d04fd265 100644
--- a/modules/spatyper/main.nf
+++ b/modules/spatyper/main.nf
@@ -4,7 +4,7 @@ process SPATYPER {
 
     conda (params.enable_conda ? "bioconda::spatyper=0.3.3" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/spatyper%3A0.3.3--pyhdfd78af_3' :
+        'https://depot.galaxyproject.org/singularity/spatyper:0.3.3--pyhdfd78af_3' :
         'quay.io/biocontainers/spatyper:0.3.3--pyhdfd78af_3' }"
 
     input:
diff --git a/modules/ucsc/wigtobigwig/main.nf b/modules/ucsc/wigtobigwig/main.nf
index 4c596c9a..6a1847b6 100644
--- a/modules/ucsc/wigtobigwig/main.nf
+++ b/modules/ucsc/wigtobigwig/main.nf
@@ -1,7 +1,7 @@
 def VERSION = '377' // Version information not provided by tool on CLI
 
 process UCSC_WIGTOBIGWIG {
-    tag '$wig'
+    tag "$meta.id"
     label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::ucsc-wigtobigwig=377" : null)
@@ -10,21 +10,22 @@ process UCSC_WIGTOBIGWIG {
         'quay.io/biocontainers/ucsc-wigtobigwig:377--h0b8a92a_2' }"
 
     input:
-    path wig
+    tuple val(meta), path(wig)
     path sizes
 
     output:
-    path "*.bw"        , emit: bw
-    path "versions.yml", emit: versions
+    tuple val(meta), path("*.bw"), emit: bw
+    path "versions.yml"          , emit: versions
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     wigToBigWig \\
         $args \\
         $wig \\
         $sizes \\
-        ${wig.getSimpleName()}.bw
+        ${prefix}.bw
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/ucsc/wigtobigwig/meta.yml b/modules/ucsc/wigtobigwig/meta.yml
index 4723ff2b..5ca94bb4 100644
--- a/modules/ucsc/wigtobigwig/meta.yml
+++ b/modules/ucsc/wigtobigwig/meta.yml
@@ -15,6 +15,11 @@ tools:
       licence: ['varies; see http://genome.ucsc.edu/license']
 
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - wig:
       type: file
       description: wig file
@@ -35,3 +40,4 @@ output:
 
 authors:
   - "@jianhong"
+  - "@projectoriented"
diff --git a/modules/vcflib/vcfuniq/main.nf b/modules/vcflib/vcfuniq/main.nf
new file mode 100644
index 00000000..37fc51bc
--- /dev/null
+++ b/modules/vcflib/vcfuniq/main.nf
@@ -0,0 +1,32 @@
+def VERSION = '1.0.2' // Version information not provided by tool on CLI
+
+process VCFLIB_VCFUNIQ {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::vcflib=1.0.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/vcflib:1.0.2--h3198e80_5':
+        'quay.io/biocontainers/vcflib:1.0.2--h3198e80_5' }"
+
+    input:
+    tuple val(meta), path(vcf), path(tbi)
+
+    output:
+    tuple val(meta), path("*.gz"), emit: vcf
+    path "versions.yml"          , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    vcfuniq \\
+        $vcf \\
+        | bgzip -c $args > ${prefix}.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vcflib: $VERSION
+    END_VERSIONS
+    """
+}
diff --git a/modules/vcflib/vcfuniq/meta.yml b/modules/vcflib/vcfuniq/meta.yml
new file mode 100644
index 00000000..3bfc679b
--- /dev/null
+++ b/modules/vcflib/vcfuniq/meta.yml
@@ -0,0 +1,46 @@
+name: vcflib_vcfuniq
+description: List unique genotypes. Like GNU uniq, but for VCF records. Remove records which have the same position, ref, and alt as the previous record.
+keywords:
+  - vcf
+  - uniq
+  - deduplicate
+tools:
+  - vcflib:
+      description: Command-line tools for manipulating VCF files
+      homepage: https://github.com/vcflib/vcflib
+      documentation: https://github.com/vcflib/vcflib#USAGE
+      doi: "https://doi.org/10.1101/2021.05.21.445151"
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: Compressed VCF file
+      pattern: "*.vcf.gz"
+  - tbi:
+      type: file
+      description: Index of VCF file
+      pattern: "*.vcf.gz.tbi"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - vcf:
+      type: file
+      description: Compressed VCF file
+      pattern: "*.vcf.gz"
+
+authors:
+  - "@drpatelh"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 04be83db..89ed82ad 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -114,6 +114,10 @@ bcftools/reheader:
   - modules/bcftools/reheader/**
   - tests/modules/bcftools/reheader/**
 
+bcftools/sort:
+  - modules/bcftools/sort/**
+  - tests/modules/bcftools/sort/**
+
 bcftools/stats:
   - modules/bcftools/stats/**
   - tests/modules/bcftools/stats/**
@@ -282,6 +286,14 @@ cellranger/gtf:
   - modules/cellranger/gtf/**
   - tests/modules/cellranger/gtf/**
 
+cellranger/mkfastq:
+  - modules/cellranger/mkfastq/**
+  - tests/modules/cellranger/mkfastq/**
+
+cellranger/mkgtf:
+  - modules/cellranger/mkgtf/**
+  - tests/modules/cellranger/mkgtf/**
+
 cellranger/mkref:
   - modules/cellranger/mkref/**
   - tests/modules/cellranger/mkref/**
@@ -384,6 +396,10 @@ deeptools/plotprofile:
   - modules/deeptools/plotprofile/**
   - tests/modules/deeptools/plotprofile/**
 
+deepvariant:
+  - modules/deepvariant/**
+  - tests/modules/deepvariant/**
+
 delly/call:
   - modules/delly/call/**
   - tests/modules/delly/call/**
@@ -892,6 +908,10 @@ mapdamage2:
   - modules/mapdamage2/**
   - tests/modules/mapdamage2/**
 
+mash/dist:
+  - modules/mash/dist/**
+  - tests/modules/mash/dist/**
+
 mash/sketch:
   - modules/mash/sketch/**
   - tests/modules/mash/sketch/**
@@ -1001,9 +1021,13 @@ ncbigenomedownload:
   - modules/ncbigenomedownload/**
   - tests/modules/ncbigenomedownload/**
 
-nextclade:
-  - modules/nextclade/**
-  - tests/modules/nextclade/**
+nextclade/datasetget:
+  - modules/nextclade/datasetget/**
+  - tests/modules/nextclade/datasetget/**
+
+nextclade/run:
+  - modules/nextclade/run/**
+  - tests/modules/nextclade/run/**
 
 ngmaster:
   - modules/ngmaster/**
@@ -1473,6 +1497,10 @@ variantbam:
   - modules/variantbam/**
   - tests/modules/variantbam/**
 
+vcflib/vcfuniq:
+  - modules/vcflib/vcfuniq/**
+  - tests/modules/vcflib/vcfuniq/**
+
 vcftools:
   - modules/vcftools/**
   - tests/modules/vcftools/**
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index fde5dc42..f453baa6 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -82,6 +82,9 @@ params {
                 scaffolds_fasta                                = "${test_data_dir}/genomics/sarscov2/illumina/fasta/scaffolds.fasta"
 
                 assembly_gfa                                   = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa"
+                assembly_gfa_bgz                               = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa.bgz"
+                assembly_gfa_gz                                = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa.gz"
+                assembly_gfa_zst                               = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa.zst"
 
                 test_single_end_bam_readlist_txt               = "${test_data_dir}/genomics/sarscov2/illumina/picard/test.single_end.bam.readlist.txt"
 
@@ -149,6 +152,19 @@ params {
                 justhusky_minimal_vcf_gz_tbi                   = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz.tbi"
 
             }
+            'pangenome' {
+                pangenome_fa                                  = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa"
+                pangenome_fa_gz                               = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa.gz"
+                pangenome_paf                                 = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf"
+                pangenome_paf_gz                              = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf.gz"
+                pangenome_seqwish_gfa                         = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.seqwish.gfa"
+                pangenome_smoothxg_gfa                        = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.smoothxg.gfa"
+                pangenome_gfaffix_gfa                         = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.gfaffix.gfa"
+                'odgi' {
+                    pangenome_og                                  = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.og"
+                    pangenome_lay                                 = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.lay"
+                }
+            }
             'illumina' {
                 test_paired_end_sorted_bam                              = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam"
                 test_paired_end_sorted_bam_bai                          = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai"
diff --git a/tests/modules/bcftools/concat/test.yml b/tests/modules/bcftools/concat/test.yml
index fee6158f..7d04ebc6 100644
--- a/tests/modules/bcftools/concat/test.yml
+++ b/tests/modules/bcftools/concat/test.yml
@@ -5,4 +5,4 @@
     - bcftools
   files:
     - path: output/bcftools/test3.vcf.gz
-      md5sum: c400c7458524d889e0967b06ed72534f
+      md5sum: 35c88bfaad20101062e98beb217d7137
diff --git a/tests/modules/bcftools/consensus/main.nf b/tests/modules/bcftools/consensus/main.nf
index ab00fbce..b2ee899b 100644
--- a/tests/modules/bcftools/consensus/main.nf
+++ b/tests/modules/bcftools/consensus/main.nf
@@ -5,11 +5,13 @@ nextflow.enable.dsl = 2
 include { BCFTOOLS_CONSENSUS } from '../../../../modules/bcftools/consensus/main.nf'
 
 workflow test_bcftools_consensus {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ],
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) ],
-              [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
-            ]
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
 
     BCFTOOLS_CONSENSUS ( input )
 }
diff --git a/tests/modules/bcftools/mpileup/main.nf b/tests/modules/bcftools/mpileup/main.nf
index 813ca408..1568f157 100644
--- a/tests/modules/bcftools/mpileup/main.nf
+++ b/tests/modules/bcftools/mpileup/main.nf
@@ -5,9 +5,25 @@ nextflow.enable.dsl = 2
 include { BCFTOOLS_MPILEUP } from '../../../../modules/bcftools/mpileup/main.nf'
 
 workflow test_bcftools_mpileup {
-    input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]]
-    fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
 
-    BCFTOOLS_MPILEUP ( input, fasta )
+    input = [
+        [ id:'test' ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_mpileup = false
+
+    BCFTOOLS_MPILEUP ( input, fasta, save_mpileup )
+}
+
+workflow test_bcftools_save_mpileup {
+
+    input = [
+        [ id:'test' ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_mpileup = true
+
+    BCFTOOLS_MPILEUP ( input, fasta, save_mpileup )
 }
diff --git a/tests/modules/bcftools/mpileup/test.yml b/tests/modules/bcftools/mpileup/test.yml
index f081c543..35c33553 100644
--- a/tests/modules/bcftools/mpileup/test.yml
+++ b/tests/modules/bcftools/mpileup/test.yml
@@ -5,8 +5,23 @@
     - bcftools
   files:
     - path: output/bcftools/test.bcftools_stats.txt
-      md5sum: 74863ef525eef8d87e3119146d281bcf
+      md5sum: 72c506e633413c6b439f95336933984e
     - path: output/bcftools/test.vcf.gz.tbi
-      md5sum: 0772419c5d819b4caa4aebfcad010c6e
+      md5sum: ae0f17dcc2cb27034d848699b824c516
     - path: output/bcftools/test.vcf.gz
-      md5sum: 9811674bb8da7ff30581319a910f2396
+      md5sum: e9e520663875c66296f3bff0fa226c40
+
+- name: bcftools mpileup test_bcftools_save_mpileup
+  command: nextflow run ./tests/modules/bcftools/mpileup -entry test_bcftools_save_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/mpileup/nextflow.config
+  tags:
+    - bcftools/mpileup
+    - bcftools
+  files:
+    - path: output/bcftools/test.bcftools_stats.txt
+      md5sum: 72c506e633413c6b439f95336933984e
+    - path: output/bcftools/test.vcf.gz.tbi
+      md5sum: ae0f17dcc2cb27034d848699b824c516
+    - path: output/bcftools/test.vcf.gz
+      md5sum: e9e520663875c66296f3bff0fa226c40
+    - path: output/bcftools/test.mpileup
+      md5sum: fe0e45a57ffdfb253ed6794f8356a3f0
diff --git a/tests/modules/bcftools/sort/main.nf b/tests/modules/bcftools/sort/main.nf
new file mode 100644
index 00000000..fadb8270
--- /dev/null
+++ b/tests/modules/bcftools/sort/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_SORT } from '../../../../modules/bcftools/sort/main.nf'
+
+workflow test_bcftools_sort {
+
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+    ]
+
+    BCFTOOLS_SORT ( input )
+}
diff --git a/tests/modules/nextclade/nextflow.config b/tests/modules/bcftools/sort/nextflow.config
similarity index 95%
rename from tests/modules/nextclade/nextflow.config
rename to tests/modules/bcftools/sort/nextflow.config
index 8730f1c4..50f50a7a 100644
--- a/tests/modules/nextclade/nextflow.config
+++ b/tests/modules/bcftools/sort/nextflow.config
@@ -1,5 +1,5 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
+    
+}
\ No newline at end of file
diff --git a/tests/modules/bcftools/sort/test.yml b/tests/modules/bcftools/sort/test.yml
new file mode 100644
index 00000000..694fc307
--- /dev/null
+++ b/tests/modules/bcftools/sort/test.yml
@@ -0,0 +1,10 @@
+- name: bcftools sort test_bcftools_sort
+  command: nextflow run tests/modules/bcftools/sort -entry test_bcftools_sort -c tests/config/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/sort
+  files:
+    - path: output/bcftools/test.vcf.gz
+      md5sum: fc178eb342a91dc0d1d568601ad8f8e2
+    - path: output/bcftools/versions.yml
+      md5sum: f1bb553befa5108f81135b8fec613b6b
diff --git a/tests/modules/bcftools/stats/test.yml b/tests/modules/bcftools/stats/test.yml
index d3587f95..59f3b991 100644
--- a/tests/modules/bcftools/stats/test.yml
+++ b/tests/modules/bcftools/stats/test.yml
@@ -5,4 +5,4 @@
     - bcftools/stats
   files:
     - path: output/bcftools/test.bcftools_stats.txt
-      md5sum: d3543531396cf7012f13ebdce639cbc8
+      md5sum: 1f948177196b09806782e1ee801463a2
diff --git a/tests/modules/bowtie2/align/main.nf b/tests/modules/bowtie2/align/main.nf
index 8c8e3ab8..2d3945e5 100644
--- a/tests/modules/bowtie2/align/main.nf
+++ b/tests/modules/bowtie2/align/main.nf
@@ -13,9 +13,10 @@ workflow test_bowtie2_align_single_end {
         ]
     ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_unaligned = false
 
     BOWTIE2_BUILD ( fasta )
-    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
+    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned )
 }
 
 workflow test_bowtie2_align_paired_end {
@@ -27,7 +28,8 @@ workflow test_bowtie2_align_paired_end {
         ]
     ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_unaligned = false
 
     BOWTIE2_BUILD ( fasta )
-    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
+    BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned )
 }
diff --git a/tests/modules/cat/cat/main.nf b/tests/modules/cat/cat/main.nf
index 430c71fa..1fd56851 100644
--- a/tests/modules/cat/cat/main.nf
+++ b/tests/modules/cat/cat/main.nf
@@ -43,3 +43,12 @@ workflow test_cat_unzipped_zipped {
 
     CAT_CAT ( input, 'cat.txt.gz' )
 }
+
+workflow test_cat_one_file_unzipped_zipped {
+
+    input = [
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+    ]
+
+    CAT_CAT ( input, 'cat.txt.gz' )
+}
diff --git a/tests/modules/cat/cat/test.yml b/tests/modules/cat/cat/test.yml
index d7973042..1244d8d2 100644
--- a/tests/modules/cat/cat/test.yml
+++ b/tests/modules/cat/cat/test.yml
@@ -31,3 +31,11 @@
     - cat/cat
   files:
     - path: output/cat/cat.txt.gz
+
+- name: cat one file unzipped zipped
+  command: nextflow run ./tests/modules/cat/cat -entry test_cat_one_file_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
+  tags:
+    - cat
+    - cat/cat
+  files:
+    - path: output/cat/cat.txt.gz
diff --git a/tests/modules/chromap/index/test.yml b/tests/modules/chromap/index/test.yml
index 74cfadfc..dde1aa1b 100644
--- a/tests/modules/chromap/index/test.yml
+++ b/tests/modules/chromap/index/test.yml
@@ -5,4 +5,3 @@
     - chromap
   files:
     - path: output/chromap/genome.index
-      md5sum: f889d5f61d80823766af33277d27d386
diff --git a/tests/modules/deepvariant/main.nf b/tests/modules/deepvariant/main.nf
new file mode 100644
index 00000000..3b1b90e6
--- /dev/null
+++ b/tests/modules/deepvariant/main.nf
@@ -0,0 +1,36 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DEEPVARIANT                          } from '../../../modules/deepvariant/main.nf'
+include { DEEPVARIANT as DEEPVARIANT_INTERVALS } from '../../../modules/deepvariant/main.nf'
+
+workflow test_deepvariant {
+
+    bam_tuple_ch = Channel.of([ [ id:'test', single_end:false ], // meta map
+                               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                               []
+                                ])
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    DEEPVARIANT ( bam_tuple_ch, fasta, fai)
+}
+
+workflow test_deepvariant_cram_intervals {
+
+    cram_tuple_ch = Channel.of([[ id:'test', single_end:false ], // meta map
+                               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
+                               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
+                               file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
+                            ])
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    DEEPVARIANT_INTERVALS ( cram_tuple_ch, fasta, fai)
+}
diff --git a/tests/modules/deepvariant/nextflow.config b/tests/modules/deepvariant/nextflow.config
new file mode 100644
index 00000000..a7e90c82
--- /dev/null
+++ b/tests/modules/deepvariant/nextflow.config
@@ -0,0 +1,14 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: DEEPVARIANT {
+         ext.args = ' --regions=\"chr22:0-40001\" --model_type=WGS '
+         ext.prefix = { "${meta.id}_out" }
+     }
+     withName: DEEPVARIANT_INTERVALS {
+         ext.args = '--model_type=WGS '
+         ext.prefix = { "${meta.id}_out" }
+     }
+
+}
diff --git a/tests/modules/deepvariant/test.yml b/tests/modules/deepvariant/test.yml
new file mode 100644
index 00000000..30a0b1b3
--- /dev/null
+++ b/tests/modules/deepvariant/test.yml
@@ -0,0 +1,23 @@
+- name: deepvariant test_deepvariant
+  command: nextflow run tests/modules/deepvariant -entry test_deepvariant -c tests/config/nextflow.config
+  tags:
+    - deepvariant
+  files:
+    - path: output/deepvariant/test_out.g.vcf.gz
+      md5sum: c4c65a3eaf62d6fbe0aba0a414318c8d
+    - path: output/deepvariant/test_out.vcf.gz
+      md5sum: ad964f68ac1d1b2720a9a4e0b6a3a389
+    - path: output/deepvariant/versions.yml
+      md5sum: 51572055ca5c07fc4001b25a9c273bf8
+
+- name: deepvariant test_deepvariant_cram_intervals
+  command: nextflow run tests/modules/deepvariant -entry test_deepvariant_cram_intervals -c tests/config/nextflow.config
+  tags:
+    - deepvariant
+  files:
+    - path: output/deepvariant/test_out.g.vcf.gz
+      md5sum: c4c65a3eaf62d6fbe0aba0a414318c8d
+    - path: output/deepvariant/test_out.vcf.gz
+      md5sum: ad964f68ac1d1b2720a9a4e0b6a3a389
+    - path: output/deepvariant/versions.yml
+      md5sum: 7d9293db0d44423b114abc7116feb967
diff --git a/tests/modules/dshbio/exportsegments/main.nf b/tests/modules/dshbio/exportsegments/main.nf
index c213dc54..0460950a 100644
--- a/tests/modules/dshbio/exportsegments/main.nf
+++ b/tests/modules/dshbio/exportsegments/main.nf
@@ -11,3 +11,27 @@ workflow test_dshbio_exportsegments {
 
     DSHBIO_EXPORTSEGMENTS ( input )
 }
+
+workflow test_dshbio_exportsegments_bgz {
+    input = [ [ id:'test_bgz' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['assembly_gfa_bgz'], checkIfExists: true) ]
+            ]
+
+    DSHBIO_EXPORTSEGMENTS ( input )
+}
+
+workflow test_dshbio_exportsegments_gz {
+    input = [ [ id:'test_gz' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['assembly_gfa_gz'], checkIfExists: true) ]
+            ]
+
+    DSHBIO_EXPORTSEGMENTS ( input )
+}
+
+workflow test_dshbio_exportsegments_zst {
+    input = [ [ id:'test_zst' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['assembly_gfa_zst'], checkIfExists: true) ]
+            ]
+
+    DSHBIO_EXPORTSEGMENTS ( input )
+}
diff --git a/tests/modules/dshbio/exportsegments/test.yml b/tests/modules/dshbio/exportsegments/test.yml
index c811df03..85406f8f 100644
--- a/tests/modules/dshbio/exportsegments/test.yml
+++ b/tests/modules/dshbio/exportsegments/test.yml
@@ -4,5 +4,32 @@
     - dshbio
     - dshbio/exportsegments
   files:
-    - path: ./output/dshbio/test.fa
-      md5sum: 19ed0b69970ed3fbb641c5c510ebef61
+    - path: ./output/dshbio/test.fa.gz
+      md5sum: 2b8471e1ccf84169ccb75a1c1bb9109c
+
+- name: dshbio exportsegments bgz
+  command: nextflow run ./tests/modules/dshbio/exportsegments -entry test_dshbio_exportsegments_bgz -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/exportsegments/nextflow.config
+  tags:
+    - dshbio
+    - dshbio/exportsegments
+  files:
+    - path: ./output/dshbio/test_bgz.fa.gz
+      md5sum: 2b8471e1ccf84169ccb75a1c1bb9109c
+
+- name: dshbio exportsegments gz
+  command: nextflow run ./tests/modules/dshbio/exportsegments -entry test_dshbio_exportsegments_gz -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/exportsegments/nextflow.config
+  tags:
+    - dshbio
+    - dshbio/exportsegments
+  files:
+    - path: ./output/dshbio/test_gz.fa.gz
+      md5sum: 2b8471e1ccf84169ccb75a1c1bb9109c
+
+- name: dshbio exportsegments zst
+  command: nextflow run ./tests/modules/dshbio/exportsegments -entry test_dshbio_exportsegments_zst -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/exportsegments/nextflow.config
+  tags:
+    - dshbio
+    - dshbio/exportsegments
+  files:
+    - path: ./output/dshbio/test_zst.fa.gz
+      md5sum: 2b8471e1ccf84169ccb75a1c1bb9109c
diff --git a/tests/modules/fastp/test.yml b/tests/modules/fastp/test.yml
index cd7ddeed..0863259b 100644
--- a/tests/modules/fastp/test.yml
+++ b/tests/modules/fastp/test.yml
@@ -12,9 +12,9 @@
         - "Q20 bases: 12922(92.9841%)"
         - "reads passed filter: 99"
     - path: output/fastp/test.trim.fastq.gz
-      md5sum: e2257263668dc8a75d95475099fb472d
+      md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
     - path: output/fastp/test.fastp.json
-      md5sum: e0d856ebb3da9e4462c3ce9683efe01d
+      md5sum: a517ba37b17a342b5428f2c1f8fe3dd7
 
 - name: fastp test_fastp_paired_end
   command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
@@ -33,9 +33,9 @@
       contains:
         - '"passed_filter_reads": 198'
     - path: output/fastp/test_1.trim.fastq.gz
-      md5sum: e2257263668dc8a75d95475099fb472d
+      md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
     - path: output/fastp/test_2.trim.fastq.gz
-      md5sum: 9eff7203596580cc5e42aceab4a469df
+      md5sum: 532b190fb4dc7b2277ee5cf1464e598c
 
 - name: fastp test_fastp_single_end_trim_fail
   command: nextflow run ./tests/modules/fastp -entry test_fastp_single_end_trim_fail -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
@@ -51,11 +51,11 @@
         - "Q20 bases: 12922(92.9841%)"
         - "reads passed filter: 99"
     - path: output/fastp/test.trim.fastq.gz
-      md5sum: e2257263668dc8a75d95475099fb472d
+      md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
     - path: output/fastp/test.fastp.json
-      md5sum: ee65a46d6e59fa556f112727b8a902ce
+      md5sum: 4be682c727942a45fc4c8600c28694a8
     - path: output/fastp/test.fail.fastq.gz
-      md5sum: de315d397c994d8e66bafc7a8dc11070
+      md5sum: b57f2026eb259a0b0c0b3960c270258d
 
 - name: fastp test_fastp_paired_end_trim_fail
   command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_trim_fail -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
@@ -74,13 +74,13 @@
       contains:
         - '"passed_filter_reads": 198'
     - path: output/fastp/test_1.trim.fastq.gz
-      md5sum: e2257263668dc8a75d95475099fb472d
+      md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
     - path: output/fastp/test_2.trim.fastq.gz
-      md5sum: 9eff7203596580cc5e42aceab4a469df
+      md5sum: 532b190fb4dc7b2277ee5cf1464e598c
     - path: output/fastp/test_1.fail.fastq.gz
-      md5sum: e62ff0123a74adfc6903d59a449cbdb0
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/fastp/test_2.fail.fastq.gz
-      md5sum: f52309b35a7c15cbd56a9c3906ef98a5
+      md5sum: 72d0002841967676ac936d08746a9128
 
 - name: fastp test_fastp_paired_end_merged
   command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_merged -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
@@ -101,8 +101,8 @@
         - "total reads: 75"
         - "total bases: 13683"
     - path: output/fastp/test.merged.fastq.gz
-      md5sum: ce88539076ced5aff11f866836ea1f40
+      md5sum: 4955ca2c899729b17bd526d2626a8d73
     - path: output/fastp/test_1.trim.fastq.gz
-      md5sum: 65d75c13abbfbfd993914e1379634100
+      md5sum: 4a03721ee252b7c6e81e007550e6ab63
     - path: output/fastp/test_2.trim.fastq.gz
-      md5sum: 0d87ce4d8ef29fb35f337eb0f6c9fcb4
+      md5sum: 7a4ddf8485c147cd7aaf0d4f6cd57ace
diff --git a/tests/modules/gatk4/applybqsr/test.yml b/tests/modules/gatk4/applybqsr/test.yml
index b4aef7ab..7449c210 100644
--- a/tests/modules/gatk4/applybqsr/test.yml
+++ b/tests/modules/gatk4/applybqsr/test.yml
@@ -5,9 +5,9 @@
     - gatk4/applybqsr
   files:
     - path: output/gatk4/test.bam
-      md5sum: 8fe7c4b5fcfb72d24ed8102eb26e42fb
+      md5sum: 908825edf1f229a072f91d8b753d95dd
     - path: output/gatk4/versions.yml
-      md5sum: 8a2fb7c7e38f24d3fefd5e84da701b00
+      md5sum: b65c46529ae9658db0c596cbc26505c2
 
 - name: gatk4 applybqsr test_gatk4_applybqsr_intervals
   command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config
@@ -16,9 +16,9 @@
     - gatk4/applybqsr
   files:
     - path: output/gatk4/test.bam
-      md5sum: a7a1d1373ac1529abbc5e05359718ab1
+      md5sum: 50f8a79c7d528e02470416f81eb582bc
     - path: output/gatk4/versions.yml
-      md5sum: 550eecbb88887fadf8c62c5992ae48af
+      md5sum: 17c8a40b3537e3400edebd1826d28385
 
 - name: gatk4 applybqsr test_gatk4_applybqsr_cram
   command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_cram -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config
@@ -27,6 +27,6 @@
     - gatk4/applybqsr
   files:
     - path: output/gatk4/test.cram
-      md5sum: b7659b3b2adaabbe73658dc059dbfdf6
+      md5sum: cd8d4ba6181f714e74641adeb2f9aa1d
     - path: output/gatk4/versions.yml
-      md5sum: 57933f27b3a31b05af3f7c248d365396
+      md5sum: 35218922e1929c699ea64de9f4c29fb5
diff --git a/tests/modules/gatk4/applyvqsr/test.yml b/tests/modules/gatk4/applyvqsr/test.yml
index 577da79d..b2acc6d8 100644
--- a/tests/modules/gatk4/applyvqsr/test.yml
+++ b/tests/modules/gatk4/applyvqsr/test.yml
@@ -7,7 +7,7 @@
     - path: output/gatk4/test.vcf.gz
     - path: output/gatk4/test.vcf.gz.tbi
     - path: output/gatk4/versions.yml
-      md5sum: 984c932ee9a5683b18e22a369aa5c9e7
+      md5sum: 524a78cdfa56c8b09a4ff3f4cb278261
 
 - name: gatk4 applyvqsr test_gatk4_applyvqsr_allele_specific
   command: nextflow run tests/modules/gatk4/applyvqsr -entry test_gatk4_applyvqsr_allele_specific -c tests/config/nextflow.config -c ./tests/modules/gatk4/applyvqsr/nextflow.config
@@ -18,4 +18,4 @@
     - path: output/gatk4/test.vcf.gz
     - path: output/gatk4/test.vcf.gz.tbi
     - path: output/gatk4/versions.yml
-      md5sum: 3b55f26c94c5f145f10ef4c5f83ec3cc
+      md5sum: 7a3c6e97628bd1f5f4e7fd429bf74a8e
diff --git a/tests/modules/gatk4/calculatecontamination/test.yml b/tests/modules/gatk4/calculatecontamination/test.yml
index 9370ffd4..d598d1c0 100644
--- a/tests/modules/gatk4/calculatecontamination/test.yml
+++ b/tests/modules/gatk4/calculatecontamination/test.yml
@@ -7,7 +7,7 @@
     - path:  output/gatk4/test.contamination.table
       md5sum: 46c708c943b453da89a3da08acfdb2a7
     - path:  output/gatk4/versions.yml
-      md5sum: 6f2396e71389cdfd184f91222c24fe8d
+      md5sum: 79575dc2e6a7f0361f2d8b090c496070
 
 - name: gatk4 calculatecontamination test_gatk4_calculatecontamination_matched_pair
   command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_matched_pair -c tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config
@@ -18,7 +18,7 @@
     - path:  output/gatk4/test.contamination.table
       md5sum: 46c708c943b453da89a3da08acfdb2a7
     - path:  output/gatk4/versions.yml
-      md5sum: 26863fa1e7e7d50d1a10761eced26062
+      md5sum: 733f15ef7eb504daec9fd8cd9beef71a
 
 - name: gatk4 calculatecontamination test_gatk4_calculatecontamination_segmentation
   command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_segmentation -c tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config
@@ -31,4 +31,4 @@
     - path:  output/gatk4/test.segmentation.table
       md5sum: f4643d9319bde4efbfbe516d6fb13052
     - path:  output/gatk4/versions.yml
-      md5sum: 8b1191953ff20660e06e2a5d79e96b02
+      md5sum: 5396e33146addbe4a59d0f30cb573a3a
diff --git a/tests/modules/gatk4/fastqtosam/test.yml b/tests/modules/gatk4/fastqtosam/test.yml
index 912633b5..7f6357e8 100644
--- a/tests/modules/gatk4/fastqtosam/test.yml
+++ b/tests/modules/gatk4/fastqtosam/test.yml
@@ -6,7 +6,7 @@
   files:
     - path: output/gatk4/test.bam
     - path: output/gatk4/versions.yml
-      md5sum: db3fa4b463427b08e32a5d8264be59c1
+      md5sum: 03f3accdc3e3c392c1179213286a0b67
 
 - name: gatk4 fastqtosam test_gatk4_fastqtosam_paired_end
   command: nextflow run tests/modules/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c tests/config/nextflow.config  -c ./tests/modules/gatk4/fastqtosam/nextflow.config
@@ -16,4 +16,4 @@
   files:
     - path: output/gatk4/test.bam
     - path: output/gatk4/versions.yml
-      md5sum: f4e35e46a29d8faebda5e852f9d0a132
+      md5sum: 144e7118d5f277ad5fba863213c810b0
diff --git a/tests/modules/gatk4/gatherbqsrreports/test.yml b/tests/modules/gatk4/gatherbqsrreports/test.yml
index 38b8cf54..521f2197 100644
--- a/tests/modules/gatk4/gatherbqsrreports/test.yml
+++ b/tests/modules/gatk4/gatherbqsrreports/test.yml
@@ -7,7 +7,7 @@
     - path: output/gatk4/test.table
       md5sum: 9603b69fdc3b5090de2e0dd78bfcc4bf
     - path: output/gatk4/versions.yml
-      md5sum: 2fa1214574359aa7c4e2212efbae3714
+      md5sum: b53101f71b0763e80855703ba4e1f101
 
 - name: gatk4 gatherbqsrreports test_gatk4_gatherbqsrreports_multiple
   command: nextflow run tests/modules/gatk4/gatherbqsrreports -entry test_gatk4_gatherbqsrreports_multiple -c tests/config/nextflow.config
@@ -18,4 +18,4 @@
     - path: output/gatk4/test.table
       md5sum: 0c1257eececf95db8ca378272d0f21f9
     - path: output/gatk4/versions.yml
-      md5sum: 92c17a728cef6d458491bcec6dac3e0c
+      md5sum: 584a6ebf04f54abcfcf4c8255e13ff2a
diff --git a/tests/modules/gatk4/genomicsdbimport/test.yml b/tests/modules/gatk4/genomicsdbimport/test.yml
index 059a561a..d1a8f073 100644
--- a/tests/modules/gatk4/genomicsdbimport/test.yml
+++ b/tests/modules/gatk4/genomicsdbimport/test.yml
@@ -19,7 +19,7 @@
     - path: output/gatk4/test/vidmap.json
       md5sum: 18d3f68bd2cb6f4474990507ff95017a
     - path: output/gatk4/versions.yml
-      md5sum: 92e9e7db68d22df72adc02e59fab1eb7
+      md5sum: 6fffaf981f099659cf820277d1f3c606
 
 - name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_get_intervalslist
   command: nextflow run tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_get_intervalslist -c tests/config/nextflow.config -c ./tests/modules/gatk4/genomicsdbimport/nextflow.config
@@ -30,7 +30,7 @@
     - path: output/gatk4/test.interval_list
       md5sum: 4c85812ac15fc1cd29711a851d23c0bf
     - path: output/gatk4/versions.yml
-      md5sum: b3fcd07c2f498a2ad503912524d74294
+      md5sum: 4a56022d6e08d54e8ba853637bf3b5f1
     - path: output/untar/versions.yml
       md5sum: 8f080677b109aea2cfca50208b077534
 
@@ -55,6 +55,6 @@
     - path: output/gatk4/test_genomicsdb/vidmap.json
       md5sum: 18d3f68bd2cb6f4474990507ff95017a
     - path: output/gatk4/versions.yml
-      md5sum: f204d259538a490b40c1fe787a3d6602
+      md5sum: da6a815b7340683b1a56bdfd7e66d463
     - path: output/untar/versions.yml
       md5sum: 9b2916aea9790bdf427c0cb38109110c
diff --git a/tests/modules/gatk4/indexfeaturefile/test.yml b/tests/modules/gatk4/indexfeaturefile/test.yml
index e4a7cd8a..04c71ea2 100644
--- a/tests/modules/gatk4/indexfeaturefile/test.yml
+++ b/tests/modules/gatk4/indexfeaturefile/test.yml
@@ -15,7 +15,7 @@
     - path: output/gatk4/genome.bed.gz.tbi
       md5sum: 4bc51e2351a6e83f20e13be75861f941
     - path: output/gatk4/versions.yml
-      md5sum: e574bd51e4c6d6ded5dcf3cd865dbf4a
+      md5sum: 9eb24dc17c96971b7991b3e154279aa7
 
 - name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf
   command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf -c tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config
@@ -25,7 +25,7 @@
   files:
     - path: output/gatk4/test.genome.vcf.idx
     - path: output/gatk4/versions.yml
-      md5sum: fee70d33f4379ced035d8e851a3e08c6
+      md5sum: f76543e715342bf1fcdeb20385e01fe9
 
 - name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf_gz
   command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf_gz -c tests/config/nextflow.config
@@ -36,4 +36,4 @@
     - path: output/gatk4/test.genome.vcf.gz.tbi
       md5sum: fedd68eaddf8d31257853d9da8325bd3
     - path: output/gatk4/versions.yml
-      md5sum: 29bddb019f0fe04218cfc07f8203e022
+      md5sum: a5d988cf62648f700ffac7257e72b2c0
diff --git a/tests/modules/gatk4/markduplicates/test.yml b/tests/modules/gatk4/markduplicates/test.yml
index d975113e..333de7c9 100644
--- a/tests/modules/gatk4/markduplicates/test.yml
+++ b/tests/modules/gatk4/markduplicates/test.yml
@@ -5,12 +5,12 @@
     - gatk4/markduplicates
   files:
     - path: output/gatk4/test.bai
-      md5sum: e9c125e82553209933883b4fe2b8d7c2
+      md5sum: c8f7a9e426c768577f88f59cb1336bf3
     - path: output/gatk4/test.bam
-      md5sum: 1c6b1372121eddccd086456aa1c174bf
+      md5sum: fba0c99a0b087c90113a210e4465f91b
     - path: output/gatk4/test.metrics
     - path: output/gatk4/versions.yml
-      md5sum: 0e46677bdf1e5df892578cec6bc26dba
+      md5sum: dacbab0e112d2403b09df138d4e62895
 
 - name: gatk4 markduplicates test_gatk4_markduplicates_multiple_bams
   command: nextflow run tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_bams -c tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicates/nextflow.config
@@ -19,9 +19,9 @@
     - gatk4/markduplicates
   files:
     - path: output/gatk4/test.bai
-      md5sum: bad71df9c876e72a5bc0a3e0fd755f92
+      md5sum: 325932c51f6898b02dfec469c984ba28
     - path: output/gatk4/test.bam
-      md5sum: d1b85fb578a97f05b484c0d241a9aaad
+      md5sum: f7cba8104e3a7024a5e00c02304f7dea
     - path: output/gatk4/test.metrics
     - path: output/gatk4/versions.yml
-      md5sum: 6844dc08e677455205e2270ac291c951
+      md5sum: 14d0d085df7d2f9e770578d92c329299
diff --git a/tests/modules/gatk4/splitncigarreads/test.yml b/tests/modules/gatk4/splitncigarreads/test.yml
index 47a2abe2..a18fbb04 100644
--- a/tests/modules/gatk4/splitncigarreads/test.yml
+++ b/tests/modules/gatk4/splitncigarreads/test.yml
@@ -5,6 +5,6 @@
     - gatk4/splitncigarreads
   files:
     - path: output/gatk4/test.bam
-      md5sum: 03068d510523c996814256d9811dc272
+      md5sum: 1d54057d9f403fba2068ac1aaa4b8a28
     - path: output/gatk4/versions.yml
-      md5sum: de130e0ab817304404f296b2e512b3b8
+      md5sum: f0f29af552075dc6bf8a13028e09f8e4
diff --git a/tests/modules/ivar/consensus/main.nf b/tests/modules/ivar/consensus/main.nf
index d0807984..27ac83f9 100644
--- a/tests/modules/ivar/consensus/main.nf
+++ b/tests/modules/ivar/consensus/main.nf
@@ -2,14 +2,28 @@
 
 nextflow.enable.dsl = 2
 
-params.save_mpileup = true
 include { IVAR_CONSENSUS } from '../../../../modules/ivar/consensus/main.nf'
 
 workflow test_ivar_consensus {
-    input = [ [ id:'test'],
-                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) 
-            ]
+
+    input = [
+        [ id:'test'],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    
-    IVAR_CONSENSUS ( input, fasta )
+    save_mpileup = false
+
+    IVAR_CONSENSUS ( input, fasta, save_mpileup)
+}
+
+workflow test_ivar_consensus_mpileup {
+
+    input = [
+        [ id:'test'],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    save_mpileup = true
+
+    IVAR_CONSENSUS ( input, fasta, save_mpileup)
 }
diff --git a/tests/modules/ivar/consensus/test.yml b/tests/modules/ivar/consensus/test.yml
index caaa640f..c045eebb 100644
--- a/tests/modules/ivar/consensus/test.yml
+++ b/tests/modules/ivar/consensus/test.yml
@@ -1,5 +1,16 @@
-- name: ivar consensus
+- name: ivar consensus test_ivar_consensus
   command: nextflow run ./tests/modules/ivar/consensus -entry test_ivar_consensus -c ./tests/config/nextflow.config -c ./tests/modules/ivar/consensus/nextflow.config
+  tags:
+    - ivar
+    - ivar/consensus
+  files:
+    - path: output/ivar/test.fa
+      md5sum: 9e21a64818f4302b4dece5480fa5e8b8
+    - path: output/ivar/test.qual.txt
+      md5sum: 68b329da9893e34099c7d8ad5cb9c940
+
+- name: ivar consensus test_ivar_consensus_mpileup
+  command: nextflow run ./tests/modules/ivar/consensus -entry test_ivar_consensus_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/ivar/consensus/nextflow.config
   tags:
     - ivar
     - ivar/consensus
diff --git a/tests/modules/ivar/variants/main.nf b/tests/modules/ivar/variants/main.nf
index f603b5e5..96835c60 100644
--- a/tests/modules/ivar/variants/main.nf
+++ b/tests/modules/ivar/variants/main.nf
@@ -5,40 +5,40 @@ nextflow.enable.dsl = 2
 include { IVAR_VARIANTS } from '../../../../modules/ivar/variants/main.nf'
 
 workflow test_ivar_variants_no_gff_no_mpileup {
-    params.gff          = false
-    params.save_mpileup = false
 
-    input = [ [ id:'test'],
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) 
-            ]
+    input = [
+        [ id:'test'],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    dummy = file("dummy_file.txt")
-    
-    IVAR_VARIANTS ( input, fasta, dummy )
+    gff = []
+    save_mpileup = false
+
+    IVAR_VARIANTS ( input, fasta, gff, save_mpileup )
 }
 
 workflow test_ivar_variants_no_gff_with_mpileup {
-    params.gff          = false
-    params.save_mpileup = true
 
-    input = [ [ id:'test'],
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) 
-            ]
+    input = [
+        [ id:'test'],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    dummy = file("dummy_file.txt")
+    gff = []
+    save_mpileup = true
 
-    IVAR_VARIANTS ( input, fasta, dummy )
+    IVAR_VARIANTS ( input, fasta, gff, save_mpileup )
 }
 
 workflow test_ivar_variants_with_gff_with_mpileup {
-    params.gff          = true
-    params.save_mpileup = true
-    
-    input = [ [ id:'test'],
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) 
-            ]
+
+    input = [
+        [ id:'test'],
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    gff   = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
-    
-    IVAR_VARIANTS ( input, fasta, gff )
+    gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
+    save_mpileup = true
+
+    IVAR_VARIANTS ( input, fasta, gff, save_mpileup )
 }
diff --git a/tests/modules/mash/dist/main.nf b/tests/modules/mash/dist/main.nf
new file mode 100644
index 00000000..10c9c9fa
--- /dev/null
+++ b/tests/modules/mash/dist/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MASH_DIST } from '../../../../modules/mash/dist/main.nf'
+
+workflow test_mash_dist {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
+    ]
+
+    reference =  file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    MASH_DIST ( input, reference )
+}
diff --git a/tests/modules/mash/dist/nextflow.config b/tests/modules/mash/dist/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/mash/dist/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}
\ No newline at end of file
diff --git a/tests/modules/mash/dist/test.yml b/tests/modules/mash/dist/test.yml
new file mode 100644
index 00000000..2602f87d
--- /dev/null
+++ b/tests/modules/mash/dist/test.yml
@@ -0,0 +1,10 @@
+- name: mash dist test_mash_dist
+  command: nextflow run tests/modules/mash/dist -entry test_mash_dist -c tests/config/nextflow.config
+  tags:
+    - mash
+    - mash/dist
+  files:
+    - path: output/mash/test.txt
+      md5sum: 1dfd5b53e1996f9fdb9d260b3e81c4d6
+    - path: output/mash/versions.yml
+      md5sum: f786d48a9af59e823d19c171969d0d50
diff --git a/tests/modules/nextclade/datasetget/main.nf b/tests/modules/nextclade/datasetget/main.nf
new file mode 100644
index 00000000..0fc38a5b
--- /dev/null
+++ b/tests/modules/nextclade/datasetget/main.nf
@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { NEXTCLADE_DATASETGET } from '../../../../modules/nextclade/datasetget/main.nf'
+
+workflow test_nextclade_datasetget {
+
+    dataset = 'sars-cov-2'
+    reference = 'MN908947'
+    tag = '2022-01-05T19:54:31Z'
+
+    NEXTCLADE_DATASETGET ( dataset, reference, tag )
+}
diff --git a/tests/modules/nextclade/datasetget/nextflow.config b/tests/modules/nextclade/datasetget/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/nextclade/datasetget/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}
\ No newline at end of file
diff --git a/tests/modules/nextclade/datasetget/test.yml b/tests/modules/nextclade/datasetget/test.yml
new file mode 100644
index 00000000..7e798a11
--- /dev/null
+++ b/tests/modules/nextclade/datasetget/test.yml
@@ -0,0 +1,20 @@
+- name: nextclade datasetget
+  command: nextflow run ./tests/modules/nextclade/datasetget -entry test_nextclade_datasetget -c ./tests/config/nextflow.config -c ./tests/modules/nextclade/datasetget/nextflow.config
+  tags:
+    - nextclade
+    - nextclade/datasetget
+  files:
+    - path: output/nextclade/sars-cov-2/genemap.gff
+      md5sum: 21ebebfd0f416eeb959e55ebffd808e8
+    - path: output/nextclade/sars-cov-2/primers.csv
+      md5sum: 5990c3483bf66ce607aeb90a44e7ef2e
+    - path: output/nextclade/sars-cov-2/qc.json
+      md5sum: 018fa0c0b0d2e824954e37e01495d549
+    - path: output/nextclade/sars-cov-2/reference.fasta
+      md5sum: c7ce05f28e4ec0322c96f24e064ef55c
+    - path: output/nextclade/sars-cov-2/sequences.fasta
+      md5sum: 41129d255b99e0e92bdf20e866b99a1b
+    - path: output/nextclade/sars-cov-2/tag.json
+      md5sum: 2f6d8e806d9064571ee4188ef1304c9c
+    - path: output/nextclade/sars-cov-2/tree.json
+      md5sum: f8fb33ed62b59142ac20998eb599df6c
\ No newline at end of file
diff --git a/tests/modules/nextclade/main.nf b/tests/modules/nextclade/main.nf
deleted file mode 100755
index 15750990..00000000
--- a/tests/modules/nextclade/main.nf
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { NEXTCLADE } from '../../../modules/nextclade/main.nf'
-
-workflow test_nextclade {
-    input = [ 
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    ]
-    
-    NEXTCLADE ( input )
-}
diff --git a/tests/modules/nextclade/run/main.nf b/tests/modules/nextclade/run/main.nf
new file mode 100644
index 00000000..35b52317
--- /dev/null
+++ b/tests/modules/nextclade/run/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { NEXTCLADE_DATASETGET } from '../../../../modules/nextclade/datasetget/main.nf'
+include { NEXTCLADE_RUN        } from '../../../../modules/nextclade/run/main.nf'
+
+workflow test_nextclade_run {
+
+    dataset = 'sars-cov-2'
+    reference = 'MN908947'
+    tag = '2022-01-05T19:54:31Z'
+
+    NEXTCLADE_DATASETGET ( dataset, reference, tag )
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    NEXTCLADE_RUN ( input, NEXTCLADE_DATASETGET.out.dataset )
+}
diff --git a/tests/modules/nextclade/run/nextflow.config b/tests/modules/nextclade/run/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/nextclade/run/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}
\ No newline at end of file
diff --git a/tests/modules/nextclade/run/test.yml b/tests/modules/nextclade/run/test.yml
new file mode 100644
index 00000000..37f7d8ae
--- /dev/null
+++ b/tests/modules/nextclade/run/test.yml
@@ -0,0 +1,13 @@
+- name: nextclade run
+  command: nextflow run ./tests/modules/nextclade/run -entry test_nextclade_run -c ./tests/config/nextflow.config -c ./tests/modules/nextclade/run/nextflow.config
+  tags:
+    - nextclade
+    - nextclade/run
+  files:
+    - path: output/nextclade/test.json
+    - path: output/nextclade/test.csv
+      md5sum: 3b87a4da190ba2e1fdc8418dc3a7ffdb
+    - path: output/nextclade/test.tsv
+      md5sum: 449393288e8734a02def139c550a8d9b
+    - path: output/nextclade/test.tree.json
+      md5sum: 9c6e33cb7ff860bee6194847bd2c855c
diff --git a/tests/modules/nextclade/test.yml b/tests/modules/nextclade/test.yml
deleted file mode 100755
index 36218aad..00000000
--- a/tests/modules/nextclade/test.yml
+++ /dev/null
@@ -1,13 +0,0 @@
-- name: nextclade test_nextclade
-  command: nextflow run ./tests/modules/nextclade -entry test_nextclade -c ./tests/config/nextflow.config -c ./tests/modules/nextclade/nextflow.config
-  tags:
-    - nextclade
-  files:
-    - path: output/nextclade/test.json
-      md5sum: cab92830c5cb66076e7d6c054ea98362
-    - path: output/nextclade/test.csv
-      md5sum: 4f7096df9be51f99a0d62a38653b29cf
-    - path: output/nextclade/test.tsv
-      md5sum: fe07dc4ffcd81742ca9bef93f88e8836
-    - path: output/nextclade/test.tree.json
-      md5sum: 5c57dd724bc2b5cfde8f42a17ff2865a
diff --git a/tests/modules/pangolin/test.yml b/tests/modules/pangolin/test.yml
index c77e4912..15be6973 100644
--- a/tests/modules/pangolin/test.yml
+++ b/tests/modules/pangolin/test.yml
@@ -4,4 +4,4 @@
     - pangolin
   files:
     - path: ./output/pangolin/test.pangolin.csv
-      md5sum: 4eaff46b5b11cd59fb44d4e8e7c4945e
+      md5sum: 2563856ee31ba2a4a05705ff940a28cc
diff --git a/tests/modules/samtools/stats/test.yml b/tests/modules/samtools/stats/test.yml
index 178eba72..d3444f02 100644
--- a/tests/modules/samtools/stats/test.yml
+++ b/tests/modules/samtools/stats/test.yml
@@ -14,4 +14,4 @@
     - samtools
   files:
     - path: output/samtools/test.paired_end.recalibrated.sorted.cram.stats
-      md5sum: 62377b29c3f6253e37308a28d13a496d
+      md5sum: ab49e7380714b7033e374ba1114e5e54
diff --git a/tests/modules/ucsc/wigtobigwig/main.nf b/tests/modules/ucsc/wigtobigwig/main.nf
index 614d4150..2abbe5b2 100644
--- a/tests/modules/ucsc/wigtobigwig/main.nf
+++ b/tests/modules/ucsc/wigtobigwig/main.nf
@@ -6,7 +6,8 @@ include { UCSC_WIGTOBIGWIG } from '../../../../modules/ucsc/wigtobigwig/main.nf'
 
 workflow test_ucsc_wigtobigwig {
 
-    input = file(params.test_data['sarscov2']['illumina']['test_wig_gz'], checkIfExists: true)
+    input = [ [ id:'test', single_end:false ], // meta map,
+                file(params.test_data['sarscov2']['illumina']['test_wig_gz'], checkIfExists: true) ]
 
     sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
 
diff --git a/tests/modules/ucsc/wigtobigwig/test.yml b/tests/modules/ucsc/wigtobigwig/test.yml
index 08d4bce4..ea1e12b0 100644
--- a/tests/modules/ucsc/wigtobigwig/test.yml
+++ b/tests/modules/ucsc/wigtobigwig/test.yml
@@ -6,3 +6,5 @@
   files:
     - path: output/ucsc/test.bw
       md5sum: b64af7003665dc51fae958216b06ed95
+    - path: output/ucsc/versions.yml
+      md5sum: 7e14421c65faf5165389f34806acdb12
diff --git a/tests/modules/vcflib/vcfuniq/main.nf b/tests/modules/vcflib/vcfuniq/main.nf
new file mode 100644
index 00000000..f2c8e6f8
--- /dev/null
+++ b/tests/modules/vcflib/vcfuniq/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { VCFLIB_VCFUNIQ } from '../../../../modules/vcflib/vcfuniq/main.nf'
+
+workflow test_vcflib_vcfuniq {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+    ]
+
+    VCFLIB_VCFUNIQ ( input )
+}
diff --git a/tests/modules/vcflib/vcfuniq/nextflow.config b/tests/modules/vcflib/vcfuniq/nextflow.config
new file mode 100644
index 00000000..ca824085
--- /dev/null
+++ b/tests/modules/vcflib/vcfuniq/nextflow.config
@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+    withName: VCFLIB_VCFUNIQ {
+        ext.prefix = { "${meta.id}.uniq" }
+    }
+
+}
diff --git a/tests/modules/vcflib/vcfuniq/test.yml b/tests/modules/vcflib/vcfuniq/test.yml
new file mode 100644
index 00000000..6d998225
--- /dev/null
+++ b/tests/modules/vcflib/vcfuniq/test.yml
@@ -0,0 +1,8 @@
+- name: vcflib vcfuniq
+  command: nextflow run ./tests/modules/vcflib/vcfuniq -entry test_vcflib_vcfuniq -c ./tests/config/nextflow.config -c ./tests/modules/vcflib/vcfuniq/nextflow.config
+  tags:
+    - vcflib
+    - vcflib/vcfuniq
+  files:
+    - path: output/vcflib/test.uniq.vcf.gz
+      md5sum: fc178eb342a91dc0d1d568601ad8f8e2