Merge branch 'nf-core:master' into maxquant

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 \\

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)

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' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
-        'quay.io/biocontainers/bcftools:1.11--h7c999a4_0' }"
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(vcfs)

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' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_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
+    cat $fasta \\
-    header=\$(head -n 1 ${prefix}.fa | sed 's/>//g')
+        | bcftools \\
-    sed -i 's/\${header}/${meta.id}/g' ${prefix}.fa
+            consensus \\
+            $vcf \\
+            $args \\
+            > ${prefix}.fa
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

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' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(vcf)

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' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_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 ?: ''

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' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(vcfs), path(tbis)

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' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(vcfs), path(tbis)

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' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_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

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

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' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(vcf)

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' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(vcf), path(index)

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' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(vcf)

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
+    """
+}

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"

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' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(vcf)

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' :
+        'https://depot.galaxyproject.org/singularity/bcftools:1.14--h88f3f91_0' :
-        'quay.io/biocontainers/bcftools:1.13--h3a49de5_0' }"
+        'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
     tuple val(meta), path(vcf), path(index)

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' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:4d235f41348a00533f18e47c9669f1ecb327f629-0' :
-        'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0' }"
+        '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('*.bam')    , emit: bam
-    tuple val(meta), path('*.log'), emit: log
+    tuple val(meta), path('*.log')    , emit: log
-    path  "versions.yml"          , emit: versions
+    tuple val(meta), path('*fastq.gz'), emit: fastq, optional:true
-    tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq
+    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 \\

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

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 |
+    // | input     | output     | command1 | command2 |
-        // |-----------|------------|----------|----------|
+    // |-----------|------------|----------|----------|
-        // | gzipped   | gzipped    | cat      |          |
+    // | gzipped   | gzipped    | cat      |          |
-        // | ungzipped | ungzipped  | cat      |          |
+    // | ungzipped | ungzipped  | cat      |          |
-        // | gzipped   | ungzipped  | zcat     |          |
+    // | gzipped   | ungzipped  | zcat     |          |
-        // | ungzipped | gzipped    | cat      | pigz     |
+    // | ungzipped | gzipped    | cat      | pigz     |
 
-        def in_zip   = file_list[0].endsWith('.gz')
+    def in_zip   = file_list[0].endsWith('.gz')
-        def out_zip  = file_out.endsWith('.gz')
+    def out_zip  = file_out.endsWith('.gz')
-        def command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
+    def command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
-        def command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
+    def command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
-        """
+    """
-        $command1 \\
+    $command1 \\
-            $args \\
+        $args \\
-            ${file_list.join(' ')} \\
+        ${file_list.join(' ')} \\
-            $command2 \\
+        $command2 \\
-            > $file_out
+        > $file_out
 
-        cat <<-END_VERSIONS > versions.yml
+    cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
+    "${task.process}":
-            pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
-        END_VERSIONS
+    END_VERSIONS
-        """
+    """
-    }
 }

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' :
+        'https://depot.galaxyproject.org/singularity/chromap:0.1.5--h9a82719_0' :
-        'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0' }"
+        '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
+        chromap: \$(echo \$(chromap --version 2>&1))
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
 }

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)

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
+    """
+}

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"

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' :
+        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
-        'quay.io/biocontainers/dsh-bio:2.0.6--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}":

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
+        description: Assembly segments in uncompressed or compressed GFA 1.0 format
-        pattern: "*.{gfa}"
+        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
+        description: Assembly segment sequences in gzipped FASTA format
-        pattern: "*.{fa}"
+        pattern: "*.{fa.gz}"
     - versions:
         type: file
         description: File containing software versions

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' :
+        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
-        'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
+        'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bed)

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' :
+        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
-        'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
+        'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gff3)

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' :
+        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
-        'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
+        'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bed)

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' :
+        'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
-        'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
+        'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gff3)

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' :
+        'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' :
-        'quay.io/biocontainers/fastp:0.20.1--h8b12597_0' }"
+        'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }"
 
     input:
     tuple val(meta), path(reads)

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 ?: ''

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--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)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--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)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bed)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(pileup), path(matched)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     path fasta

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(genomicsdb)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(cram)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--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)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(recal_table)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--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)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gvcf), path(gvcf_index), path(intervals)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(feature_file)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(interval_list)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(f1r2)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bams)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(aligned)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcfs)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta) , path(input) , path(input_index) , val(which_norm)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

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' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(vcf_tbi)

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)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
-        container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-            'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-            'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
+        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf) , path(tbi)

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 ?

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

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 | \\
+        $bam \\
-        $save_mpileup \\
+        $mpileup \\
-        ivar consensus \\
+        | ivar \\
+            consensus \\
             $args \\
             -p $prefix
 

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

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 = gff ? "-g $gff" : ""
-    def features     = params.gff ? "-g $gff" : ""
+    def mpileup = save_mpileup ? "| tee ${prefix}.mpileup" : ""
     """
-    samtools mpileup \\
+    samtools \\
+        mpileup \\
         $args2 \\
         --reference $fasta \\
-        $bam | \\
+        $bam \\
-        $save_mpileup  \\
+        $mpileup \\
-        ivar variants \\
+        | ivar \\
+            variants \\
             $args \\
             $features \\
             -r $fasta \\

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

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:

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' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' :
-        'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:941789bd7fe00db16531c26de8bf3c5c985242a5-0' }"
+        'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' }"
 
     input:
     tuple val(meta), path(reads)

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

modules/malt/run/main.nf

@@ -1,6 +1,5 @@
 process MALT_RUN {
-
+    label 'process_high'
-    label 'process_high_memory'
 
     conda (params.enable_conda ? "bioconda::malt=0.53" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

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
+    """
+}

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"

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' :
+        'https://depot.galaxyproject.org/singularity/minia:3.2.6--h9a82719_0' :
-        'quay.io/biocontainers/minia:3.2.4--he513fc3_0' }"
+        'quay.io/biocontainers/minia:3.2.6--h9a82719_0' }"
 
     input:
     tuple val(meta), path(reads)

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' :
+        'https://depot.galaxyproject.org/singularity/nanoplot:1.39.0--pyhdfd78af_0' :
-        'quay.io/biocontainers/nanoplot:1.38.0--pyhdfd78af_0' }"
+        'quay.io/biocontainers/nanoplot:1.39.0--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(ontfile)

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
+    """
+}

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"

modules/nextclade/main.nf

@@ -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
-    """
-}

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
+    """
+}

modules/nextclade/run/meta.yml

@@ -1,17 +1,17 @@
-name: nextclade
+name: nextclade_run
-description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (Javascript implementation)
+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)
+      description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks
-      homepage: https://clades.nextstrain.org
+      homepage: https://github.com/nextstrain/nextclade
-      documentation: None
+      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"

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' :
+        'https://depot.galaxyproject.org/singularity/pangolin:3.1.17--pyhdfd78af_0' :
-        'quay.io/biocontainers/pangolin:3.1.11--pyhdfd78af_1' }"
+        'quay.io/biocontainers/pangolin:3.1.17--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)

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:

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' :
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

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' :
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

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' :
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)

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' :
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(readlist)

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' :
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

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' :
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bams)

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' :
+        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

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:

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)

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:

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 rejects = save_cliprejects ? "--rejects-file ${prefix}.cliprejects.bam" : ""
-    def stats    = save_clipstats   ? "-f ${prefix}.clipstats.txt"               : ""
+    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 \\

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
         """
     }
-
 }

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 \\

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
+    tuple val(meta), path ("*.fai"), emit: fai
-    path "versions.yml"             , emit: versions
+    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.*\$//')

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.*\$//')

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  \\

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.*\$//')

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.*\$//')

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}":

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}":