Merge branch 'master' into tkhalilullah/issue946

modules/adapterremoval/main.nf

@@ -49,7 +49,7 @@ process ADAPTERREMOVAL {
         """
         AdapterRemoval  \\
             --file1 ${reads[0]} \\
-            --file2 ${reads[0]} \\
+            --file2 ${reads[1]} \\
             $options.args \\
             --basename $prefix \\
             --threads $task.cpus \\
@@ -68,7 +68,7 @@ process ADAPTERREMOVAL {
         """
         AdapterRemoval  \\
             --file1 ${reads[0]} \\
-            --file2 ${reads[0]} \\
+            --file2 ${reads[1]} \\
             --collapse \\
             $options.args \\
             --basename $prefix \\

modules/agrvate/main.nf

@@ -11,11 +11,11 @@ process AGRVATE {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::agrvate=1.0.1" : null)
+    conda (params.enable_conda ? "bioconda::agrvate=1.0.2" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/agrvate:1.0.1--hdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/agrvate:1.0.2--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/agrvate:1.0.1--hdfd78af_0"
+        container "quay.io/biocontainers/agrvate:1.0.2--hdfd78af_0"
     }
 
     input:

modules/allelecounter/main.nf

@@ -19,8 +19,9 @@ process ALLELECOUNTER {
     }
 
     input:
-    tuple val(meta), path(bam), path(bai)
+    tuple val(meta), path(input), path(input_index)
     path loci
+    path fasta
 
     output:
     tuple val(meta), path("*.alleleCount"), emit: allelecount
@@ -28,11 +29,14 @@ process ALLELECOUNTER {
 
     script:
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def reference_options = fasta ? "-r $fasta": ""
+
     """
     alleleCounter \\
         $options.args \\
         -l $loci \\
-        -b $bam \\
+        -b $input \\
+        $reference_options \\
         -o ${prefix}.alleleCount
 
     cat <<-END_VERSIONS > versions.yml

modules/allelecounter/meta.yml

@@ -19,11 +19,11 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - bam:
+  - input:
       type: file
       description: BAM/CRAM/SAM file
       pattern: "*.{bam,cram,sam}"
-  - bai:
+  - input_index:
       type: file
       description: BAM/CRAM/SAM index file
       pattern: "*.{bai,crai,sai}"
@@ -31,7 +31,9 @@ input:
       type: file
       description: loci file <CHR><tab><POS1>
       pattern: "*.{tsv}"
-
+  - fasta:
+    type: file
+    description: Input genome fasta file. Required when passing CRAM files.
 
 output:
   - meta:
@@ -50,3 +52,4 @@ output:
 
 authors:
   - "@fullama"
+  - "@fbdtemme"

modules/assemblyscan/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/assemblyscan/main.nf

@@ -0,0 +1,38 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process ASSEMBLYSCAN {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::assembly-scan=0.4.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/assembly-scan:0.4.1--pyhdfd78af_0"
+    } else {
+        container "quay.io/biocontainers/assembly-scan:0.4.1--pyhdfd78af_0"
+    }
+
+    input:
+    tuple val(meta), path(assembly)
+
+    output:
+    tuple val(meta), path("*.json"), emit: json
+    path "versions.yml"            , emit: versions
+
+    script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    assembly-scan $assembly > ${prefix}.json
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( assembly-scan --version 2>&1 | sed 's/^.*assembly-scan //; s/Using.*\$//' )
+    END_VERSIONS
+    """
+}

modules/assemblyscan/meta.yml

@@ -0,0 +1,43 @@
+name: assemblyscan
+description: Assembly summary statistics in JSON format
+keywords:
+  - assembly
+  - statistics
+tools:
+  - assemblyscan:
+      description: Assembly summary statistics in JSON format
+      homepage: https://github.com/rpetit3/assembly-scan
+      documentation: https://github.com/rpetit3/assembly-scan
+      tool_dev_url: https://github.com/rpetit3/assembly-scan
+      doi: ""
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - assembly:
+      type: file
+      description: FASTA file for a given assembly
+      pattern: "*.fasta"
+
+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"
+  - json:
+      type: file
+      description: Assembly statistics in JSON format
+      pattern: "*.json"
+
+authors:
+  - "@sateeshperi"
+  - "@mjcipriano"

modules/ataqv/ataqv/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/ataqv/ataqv/main.nf

@@ -0,0 +1,56 @@
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process ATAQV_ATAQV {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::ataqv=1.2.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/ataqv:1.2.1--py39ha23c084_2"
+    } else {
+        container "quay.io/biocontainers/ataqv:1.2.1--py36hfdecbe1_2"
+    }
+
+    input:
+    tuple val(meta), path(bam), path(bai), path(peak_file)
+    val organism
+    path tss_file
+    path excl_regs_file
+    path autosom_ref_file
+
+    output:
+    tuple val(meta), path("*.ataqv.json"), emit: json
+    tuple val(meta), path("*.problems")  , emit: problems, optional: true
+    path "versions.yml"                  , emit: versions
+
+    script:
+    def prefix      = options.suffix   ? "${meta.id}${options.suffix}"                  : "${meta.id}"
+    def peak        = peak_file        ? "--peak-file $peak_file"                       : ''
+    def tss         = tss_file         ? "--tss-file $tss_file"                         : ''
+    def excl_regs   = excl_regs_file   ? "--excluded-region-file $excl_regs_file"       : ''
+    def autosom_ref = autosom_ref_file ? "--autosomal-reference-file $autosom_ref_file" : ''
+    """
+    ataqv \\
+        $options.args \\
+        $peak \\
+        $tss \\
+        $excl_regs \\
+        $autosom_ref \\
+        --metrics-file "${prefix}.ataqv.json" \\
+        --threads $task.cpus \\
+        --name $prefix \\
+        $organism \\
+        $bam
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( ataqv --version )
+    END_VERSIONS
+    """
+}

modules/ataqv/ataqv/meta.yml

@@ -0,0 +1,66 @@
+name: ataqv_ataqv
+description: ataqv function of a corresponding ataqv tool
+keywords:
+  - ataqv
+tools:
+  - ataqv:
+      description: ataqv is a toolkit for measuring and comparing ATAC-seq results. It was written to help understand how well ATAC-seq assays have worked, and to make it easier to spot differences that might be caused by library prep or sequencing.
+      homepage: https://github.com/ParkerLab/ataqv/blob/master/README.rst
+      documentation: https://github.com/ParkerLab/ataqv/blob/master/README.rst
+      tool_dev_url: https://github.com/ParkerLab/ataqv
+      doi: "https://doi.org/10.1016/j.cels.2020.02.009"
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM file
+      pattern: "*.bam"
+  - bai:
+      type: file
+      description: BAM index file with the same prefix as bam file. Required if tss_file input is provided.
+      pattern: "*.bam.bai"
+  - peak_file:
+      type: file
+      description: A BED file of peaks called for alignments in the BAM file
+      pattern: "*.bed"
+  - organism:
+      type: string
+      description: The subject of the experiment, which determines the list of autosomes (see "Reference Genome Configuration" section at https://github.com/ParkerLab/ataqv).
+  - tss_file:
+      type: file
+      description: A BED file of transcription start sites for the experiment organism. If supplied, a TSS enrichment score will be calculated according to the ENCODE data standards. This calculation requires that the BAM file of alignments be indexed.
+      pattern: "*.bed"
+  - excl_regs_file:
+      type: file
+      description: A BED file containing excluded regions. Peaks or TSS overlapping these will be ignored.
+      pattern: "*.bed"
+  - autosom_ref_file:
+      type: file
+      description: A file containing autosomal reference names, one per line. The names must match the reference names in the alignment file exactly, or the metrics based on counts of autosomal alignments will be wrong.
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - json:
+      type: file
+      description: The JSON file to which metrics will be written.
+  - problems:
+      type: file
+      description: If given, problematic reads will be logged to a file per read group, with names derived from the read group IDs, with ".problems" appended. If no read groups are found, the reads will be written to one file named after the BAM file.
+      pattern: "*.problems"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@i-pletenev"

modules/bamutil/trimbam/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/bamutil/trimbam/main.nf

@@ -0,0 +1,44 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process BAMUTIL_TRIMBAM {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::bamutil=1.0.15" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bamutil:1.0.15--h2e03b76_1"
+    } else {
+        container "quay.io/biocontainers/bamutil:1.0.15--h2e03b76_1"
+    }
+
+    input:
+    tuple val(meta), path(bam), val(trim_left), val(trim_right)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "versions.yml"           , emit: versions
+
+    script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    bam \\
+        trimBam \\
+        $bam \\
+        ${prefix}.bam \\
+        $options.args \\
+        -L $trim_left \\
+        -R $trim_right
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( echo \$( bam trimBam 2>&1 ) | sed 's/^Version: //;s/;.*//' )
+    END_VERSIONS
+    """
+}

modules/bamutil/trimbam/meta.yml

@@ -0,0 +1,51 @@
+name: bamutil_trimbam
+description: trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’, or by soft clipping
+keywords:
+  - bam
+  - trim
+  - clipping
+  - bamUtil
+  - trimBam
+tools:
+  - bamutil:
+      description: Programs that perform operations on SAM/BAM files, all built into a single executable, bam.
+      homepage: https://genome.sph.umich.edu/wiki/BamUtil
+      documentation: https://genome.sph.umich.edu/wiki/BamUtil:_trimBam
+      tool_dev_url: https://github.com/statgen/bamUtil
+      doi: "10.1101/gr.176552.114"
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM file
+      pattern: "*.bam"
+  - trim_left:
+      type: integer
+      description: Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming.
+  - trim_right:
+      type: integer
+      description: Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming.
+
+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"
+  - bam:
+      type: file
+      description: Trimmed but unsorted BAM file
+      pattern: "*.bam"
+
+authors:
+  - "@jfy133"

modules/bbmap/align/main.nf

@@ -24,6 +24,7 @@ process BBMAP_ALIGN {
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.log"), emit: log
     path "versions.yml"           , emit: versions
 
     script:
@@ -51,7 +52,8 @@ process BBMAP_ALIGN {
         out=${prefix}.bam \\
         $options.args \\
         threads=$task.cpus \\
-        -Xmx${task.memory.toGiga()}g
+        -Xmx${task.memory.toGiga()}g \\
+        &> ${prefix}.bbmap.log
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:

modules/bedtools/genomecov/main.nf

@@ -19,7 +19,7 @@ process BEDTOOLS_GENOMECOV {
     }
 
     input:
-    tuple val(meta), path(intervals)
+    tuple val(meta), path(intervals), val(scale)
     path  sizes
     val   extension
 
@@ -28,13 +28,21 @@ process BEDTOOLS_GENOMECOV {
     path  "versions.yml"                   , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def args_token = options.args.tokenize()
+    def args       = options.args
+    args += (scale > 0 && scale != 1) ? " -scale $scale" : ""
+
+    if (!args_token.contains('-bg') && (scale > 0 && scale != 1)) {
+        args += " -bg"
+    }
+
     if (intervals.name =~ /\.bam/) {
         """
         bedtools \\
             genomecov \\
             -ibam $intervals \\
-            $options.args \\
+            $args \\
             > ${prefix}.${extension}
 
         cat <<-END_VERSIONS > versions.yml
@@ -48,7 +56,7 @@ process BEDTOOLS_GENOMECOV {
             genomecov \\
             -i $intervals \\
             -g $sizes \\
-            $options.args \\
+            $args \\
             > ${prefix}.${extension}
 
         cat <<-END_VERSIONS > versions.yml

modules/bedtools/genomecov/meta.yml

@@ -20,6 +20,9 @@ input:
         type: file
         description: BAM/BED/GFF/VCF
         pattern: "*.{bam|bed|gff|vcf}"
+    - scale:
+        type: value
+        description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch
     - sizes:
         type: file
         description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column
@@ -45,3 +48,4 @@ authors:
     - "@sruthipsuresh"
     - "@drpatelh"
     - "@sidorov-si"
+    - "@chris-cheshire"

modules/bedtools/sort/main.nf

@@ -19,20 +19,21 @@ process BEDTOOLS_SORT {
     }
 
     input:
-    tuple val(meta), path(bed)
+    tuple val(meta), path(intervals)
+    val   extension
 
     output:
-    tuple val(meta), path('*.bed'), emit: bed
-    path  "versions.yml"          , emit: versions
+    tuple val(meta), path("*.${extension}"), emit: sorted
+    path  "versions.yml"                   , emit: versions
 
     script:
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     bedtools \\
         sort \\
-        -i $bed \\
+        -i $intervals \\
         $options.args \\
-        > ${prefix}.bed
+        > ${prefix}.${extension}
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:

modules/bedtools/sort/meta.yml

@@ -15,20 +15,26 @@ input:
         description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-    - bed:
+    - intervals:
         type: file
-        description: Input BED file
-        pattern: "*.{bed}"
+        description: BED/BEDGRAPH
+        pattern: "*.{bed|bedGraph}"
+
+    - extension:
+        type: string
+        description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.
 output:
     - meta:
         type: map
         description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-    - bed:
+
+    - sorted:
         type: file
-        description: Sorted BED file
-        pattern: "*.{bed}"
+        description: Sorted output file
+        pattern: "*.${extension}"
+
     - versions:
         type: file
         description: File containing software versions
@@ -37,3 +43,4 @@ authors:
     - "@Emiller88"
     - "@sruthipsuresh"
     - "@drpatelh"
+    - "@chris-cheshire"

modules/bwa/index/main.nf

@@ -31,8 +31,8 @@ process BWA_INDEX {
     bwa \\
         index \\
         $options.args \\
-        $fasta \\
-        -p bwa/${fasta.baseName}
+        -p bwa/${fasta.baseName} \\
+        $fasta
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:

modules/bwameth/align/main.nf

@@ -32,6 +32,10 @@ process BWAMETH_ALIGN {
     """
     INDEX=`find -L ${index} -name "*.bwameth.c2t" | sed 's/.bwameth.c2t//'`
 
+    # Modify the timestamps so that bwameth doesn't complain about building the index
+    # See https://github.com/nf-core/methylseq/pull/217
+    touch -c -- *
+
     bwameth.py \\
         $options.args \\
         $read_group \\

modules/cellranger/Dockerfile

@@ -0,0 +1,21 @@
+FROM continuumio/miniconda3:4.8.2
+LABEL authors="Gisela Gabernet <gisela.gabernet@gmail.com>" \
+    description="Docker image containing Cell Ranger"
+# Disclaimer: this container is not provided nor supported by 10x Genomics.
+
+# Install procps and clean apt cache
+RUN apt-get update \
+    && apt-get install -y procps \
+    && apt-get clean -y && rm -rf /var/lib/apt/lists/*
+
+# Copy pre-downloaded cellranger file
+ENV CELLRANGER_VER 6.0.2
+COPY cellranger-$CELLRANGER_VER.tar.gz /opt/cellranger-$CELLRANGER_VER.tar.gz
+
+# Install cellranger
+RUN \
+    cd /opt && \
+    tar -xzvf cellranger-$CELLRANGER_VER.tar.gz && \
+    export PATH=/opt/cellranger-$CELLRANGER_VER:$PATH && \
+    ln -s /opt/cellranger-$CELLRANGER_VER/cellranger /usr/bin/cellranger && \
+    rm -rf /opt/cellranger-$CELLRANGER_VER.tar.gz

modules/cellranger/mkref/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/cellranger/mkref/main.nf

@@ -0,0 +1,40 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process CELLRANGER_MKREF {
+    tag 'mkref'
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    if (params.enable_conda) {
+        exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
+    }
+    container "nfcore/cellranger:6.0.2"
+
+    input:
+    path fasta
+    path gtf
+    val(reference_name)
+
+    output:
+    path "versions.yml"     , emit: versions
+    path "${reference_name}", emit: reference
+
+    script:
+    """
+    cellranger mkref \\
+        --genome=${reference_name} \\
+        --fasta=${fasta} \\
+        --genes=${gtf}
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
+    END_VERSIONS
+    """
+}

modules/cellranger/mkref/meta.yml

@@ -0,0 +1,39 @@
+name: cellranger_mkref
+description: Module to build the reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkref command.
+keywords:
+  - reference
+  - mkref
+  - index
+tools:
+  - cellranger:
+      description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
+      homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
+      documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
+      tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
+      doi: ""
+      licence: 10x Genomics EULA
+
+input:
+  - fasta:
+      type: file
+      description: fasta genome file
+      pattern: "*.{fasta,fa}"
+  - gtf:
+      type: file
+      description: gtf transcriptome file
+      pattern: "*.gtf"
+  - reference_name:
+      type: val
+      description: name to give the reference folder
+      pattern: str
+
+output:
+  - versions:
+      type: file
+      description: File containing software version
+      pattern: "versions.yml"
+  - reference:
+      type: folder
+      description: Folder containing all the reference indices needed by Cell Ranger
+authors:
+  - "@ggabernet"

modules/cellranger/readme.md

@@ -0,0 +1,18 @@
+# Updating the docker container and making a new module release
+
+Cell Ranger is a commercial tool by 10X Genomics. The container provided for the cellranger nf-core module is not provided nor supported by 10x Genomics. Updating the Cell Ranger version in the container and pushing the update to Dockerhub needs to be done manually.
+
+1. Navigate to the [Cell Ranger download page](https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest) and download the tar ball of the desired Cell Ranger version with `curl` or `wget`. Place this file in the same folder where the Dockerfile lies.
+
+2. Edit the Dockerfile: update the Cell Ranger version in this line:
+
+    ```bash
+    ENV CELLRANGER_VER <VERSION>
+    ```
+
+3. Create the container:
+
+    ```bash
+    docker build . -t nfcore/cellranger:<VERSION>
+    docker push nfcore/cellranger:<VERSION>
+    ```

modules/cmseq/polymut/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/cmseq/polymut/main.nf

@@ -0,0 +1,46 @@
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+def VERSION = '1.0.4'
+
+process CMSEQ_POLYMUT {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::cmseq=1.0.4" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/cmseq:1.0.4--pyhb7b1952_0"
+    } else {
+        container "quay.io/biocontainers/cmseq:1.0.4--pyhb7b1952_0"
+    }
+
+    input:
+    tuple val(meta), path(bam), path(bai), path(gff), path(fasta)
+
+    output:
+    tuple val(meta), path("*.txt"), emit: polymut
+    path "versions.yml"                   , emit: versions
+
+    script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def fasta_refid = fasta ? "-c $fasta" : ""
+    def sortindex = bai ? "" : "--sortindex"
+    """
+    polymut.py \\
+        $options.args \\
+        $sortindex \\
+        $fasta_refid \\
+        --gff_file $gff \\
+        $bam > ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( echo $VERSION )
+    END_VERSIONS
+    """
+}

modules/cmseq/polymut/meta.yml

@@ -0,0 +1,61 @@
+name: cmseq_polymut
+description: Calculates polymorphic site rates over protein coding genes
+keywords:
+  - polymut
+  - polymorphic
+  - mags
+  - assembly
+  - polymorphic sites
+  - estimation
+  - protein coding genes
+  - cmseq
+  - bam
+  - coverage
+tools:
+  - cmseq:
+      description: Set of utilities on sequences and BAM files
+      homepage: https://github.com/SegataLab/cmseq
+      documentation: https://github.com/SegataLab/cmseq
+      tool_dev_url: https://github.com/SegataLab/cmseq
+      licence: ['MIT License']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM file
+      pattern: "*.bam"
+  - bai:
+      type: file
+      description: BAM index file
+      pattern: "*.bai"
+  - gff:
+      type: file
+      description: GFF file used to extract protein-coding genes
+      pattern: "*.gff"
+  - fasta:
+      type: file
+      description: Optional fasta file to run on a subset of references in the BAM file.
+      pattern: .{fa,fasta,fas,fna}
+
+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"
+  - polymut:
+      type: file
+      description: Polymut report in `.txt` format.
+      pattern: "*.txt"
+
+authors:
+  - "@maxibor"

modules/cooler/dump/main.nf

@@ -20,18 +20,20 @@ process COOLER_DUMP {
 
     input:
     tuple val(meta), path(cool)
+    val resolution
 
     output:
     tuple val(meta), path("*.bedpe"), emit: bedpe
-    path "versions.yml"                  , emit: versions
+    path "versions.yml"             , emit: versions
 
     script:
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def suffix   = resolution     ? "::$resolution"               : ""
     """
     cooler dump \\
         $options.args \\
         -o ${prefix}.bedpe \\
-        $cool
+        $cool$suffix
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:

modules/cooler/merge/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/cooler/merge/main.nf

@@ -0,0 +1,41 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process COOLER_MERGE {
+    tag "$meta.id"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0"
+    } else {
+        container "quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0"
+    }
+
+    input:
+    tuple val(meta), path(cool)
+
+    output:
+    tuple val(meta), path("*.cool"), emit: cool
+    path "versions.yml"            , emit: versions
+
+    script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    cooler merge \\
+        $options.args \\
+        ${prefix}.cool \\
+        ${cool}
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(cooler --version 2>&1 | sed 's/cooler, version //')
+    END_VERSIONS
+    """
+}

modules/cooler/merge/meta.yml

@@ -0,0 +1,41 @@
+name: cooler_merge
+description: Merge multiple coolers with identical axes
+keywords:
+  - merge
+tools:
+  - cooler:
+      description: Sparse binary format for genomic interaction matrices
+      homepage: https://cooler.readthedocs.io/en/latest/index.html
+      documentation: https://cooler.readthedocs.io/en/latest/index.html
+      tool_dev_url: https://github.com/open2c/cooler
+      doi: "10.1093/bioinformatics/btz540"
+      licence: ['BSD-3-clause']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - cool:
+      type: file
+      description: Path to COOL file
+      pattern: "*.{cool,mcool}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software version
+      pattern: "versions.yml"
+  - cool:
+      type: file
+      description: Path to COOL file
+      pattern: "*.cool"
+
+authors:
+  - "@jianhong"

modules/cooler/zoomify/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/cooler/zoomify/main.nf

@@ -0,0 +1,42 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process COOLER_ZOOMIFY {
+    tag "$meta.id"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0"
+    } else {
+        container "quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0"
+    }
+
+    input:
+    tuple val(meta), path(cool)
+
+    output:
+    tuple val(meta), path("*.mcool"), emit: mcool
+    path "versions.yml"             , emit: versions
+
+    script:
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    cooler zoomify \\
+        $options.args \\
+        -n $task.cpus \\
+        -o ${prefix}.mcool \\
+        $cool
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(cooler --version 2>&1 | sed 's/cooler, version //')
+    END_VERSIONS
+    """
+}

modules/cooler/zoomify/meta.yml

@@ -0,0 +1,41 @@
+name: cooler_zoomify
+description: Generate a multi-resolution cooler file by coarsening
+keywords:
+  - mcool
+tools:
+  - cooler:
+      description: Sparse binary format for genomic interaction matrices
+      homepage: https://cooler.readthedocs.io/en/latest/index.html
+      documentation: https://cooler.readthedocs.io/en/latest/index.html
+      tool_dev_url: https://github.com/open2c/cooler
+      doi: "10.1093/bioinformatics/btz540"
+      licence: ['BSD-3-clause']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - cool:
+      type: file
+      description: Path to COOL file
+      pattern: "*.{cool,mcool}"
+
+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"
+  - mcool:
+      type: file
+      description: Output mcool file
+      pattern: "*.mcool"
+
+authors:
+  - "@jianhong"

modules/dedup/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/dedup/main.nf

@@ -0,0 +1,47 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process DEDUP {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::dedup=0.12.8" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/dedup:0.12.8--hdfd78af_1"
+    } else {
+        container "quay.io/biocontainers/dedup:0.12.8--hdfd78af_1"
+    }
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*_rmdup.bam"), emit: bam     // _rmdup is hardcoded output from dedup
+    tuple val(meta), path("*.json")     , emit: json
+    tuple val(meta), path("*.hist")     , emit: hist
+    tuple val(meta), path("*log")       , emit: log
+    path "versions.yml"                 , emit: versions
+
+    script:
+    prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+
+    """
+    dedup \\
+        -Xmx${task.memory.toGiga()}g  \\
+        -i $bam \\
+        -o . \\
+        $options.args
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( echo \$(dedup --version 2>&1) | tail -n 1 | sed 's/.* v//')
+
+    END_VERSIONS
+    """
+}

modules/dedup/meta.yml

@@ -0,0 +1,60 @@
+name: dedup
+description: DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).
+keywords:
+  - dedup
+  - deduplication
+  - pcr duplicates
+  - ancient DNA
+  - paired-end
+  - bam
+tools:
+  - dedup:
+      description: DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).
+      homepage: https://github.com/apeltzer/DeDup
+      documentation: https://dedup.readthedocs.io/en/latest/
+      tool_dev_url: https://github.com/apeltzer/DeDup
+      doi: "10.1186/s13059-016-0918-z"
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/SAM file
+      pattern: "*.{bam,sam}"
+
+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"
+  - bam:
+      type: file
+      description: Deduplicated BAM file
+      pattern: "*_rmdup.bam"
+  - json:
+      type: file
+      description: JSON file for MultiQC
+      pattern: "*.json"
+  - hist:
+      type: file
+      description: Histogram data of amount of deduplication
+      pattern: "*.hist"
+  - log:
+      type: file
+      description: Dedup log information
+      pattern: "*log"
+
+
+
+authors:
+  - "@jfy133"

modules/emmtyper/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/emmtyper/main.nf

@@ -0,0 +1,41 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process EMMTYPER {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::emmtyper=0.2.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/emmtyper:0.2.0--py_0"
+    } else {
+        container "quay.io/biocontainers/emmtyper:0.2.0--py_0"
+    }
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: tsv
+    path "versions.yml"           , emit: versions
+
+    script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    emmtyper \\
+        $options.args \\
+        $fasta \\
+        > ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( echo \$(emmtyper --version 2>&1) | sed 's/^.*emmtyper v//' )
+    END_VERSIONS
+    """
+}

modules/emmtyper/meta.yml

@@ -0,0 +1,43 @@
+name: emmtyper
+description: EMM typing of Streptococcus pyogenes assemblies
+keywords:
+  - fasta
+  - Streptococcus pyogenes
+  - typing
+tools:
+  - emmtyper:
+      description: Streptococcus pyogenes in silico EMM typer
+      homepage: https://github.com/MDU-PHL/emmtyper
+      documentation: https://github.com/MDU-PHL/emmtyper
+      tool_dev_url: https://github.com/MDU-PHL/emmtyper
+      doi: ""
+      licence: ['GNU General Public v3 (GPL v3)']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: FASTA assembly file
+      pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}"
+
+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"
+  - tsv:
+      type: file
+      description: Tab-delimited result file
+      pattern: "*.tsv"
+
+authors:
+  - "@rpetit3"

modules/fargene/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/fargene/main.nf

@@ -0,0 +1,63 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+def VERSION = '0.1'
+
+process FARGENE {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::fargene=0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/fargene:0.1--py27h21c881e_4"
+    } else {
+        container "quay.io/biocontainers/fargene:0.1--py27h21c881e_4"
+    }
+
+    input:
+    // input may be fasta (for genomes or longer contigs) or paired-end fastq (for metagenome), the latter in addition with --meta flag
+    tuple val(meta), path(input)
+    val hmm_model
+
+    output:
+    path "*.log"                                                                                 , emit: log
+    path "${prefix}/results_summary.txt"                                                         , emit: txt
+    tuple val(meta), path("${prefix}/hmmsearchresults/*.out")                                    , optional: true, emit: hmm
+    tuple val(meta), path("${prefix}/predictedGenes/predicted-orfs.fasta")                       , optional: true, emit: orfs
+    tuple val(meta), path("${prefix}/predictedGenes/predicted-orfs-amino.fasta")                 , optional: true, emit: orfs_amino
+    tuple val(meta), path("${prefix}/predictedGenes/retrieved-contigs.fasta")                    , optional: true, emit: contigs
+    tuple val(meta), path("${prefix}/predictedGenes/retrieved-contigs-peptides.fasta")           , optional: true, emit: contigs_pept
+    tuple val(meta), path("${prefix}/predictedGenes/*filtered.fasta")                            , optional: true, emit: filtered
+    tuple val(meta), path("${prefix}/predictedGenes/*filtered-peptides.fasta")                   , optional: true, emit: filtered_pept
+    tuple val(meta), path("${prefix}/retrievedFragments/all_retrieved_*.fastq")                  , optional: true, emit: fragments
+    tuple val(meta), path("${prefix}/retrievedFragments/retrievedFragments/trimmedReads/*.fasta"), optional: true, emit: trimmed
+    tuple val(meta), path("${prefix}/spades_assembly/*")                                         , optional: true, emit: spades
+    tuple val(meta), path("${prefix}/tmpdir/*.fasta")                                            , optional: true, emit: metagenome
+    tuple val(meta), path("${prefix}/tmpdir/*.out")                                              , optional: true, emit: tmp
+    path "versions.yml"                                                                          , emit: versions
+
+    script:
+    prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    gzip \\
+        -cdf $input \\
+        > unziped.fa |
+        fargene \\
+            $options.args \\
+            -p $task.cpus \\
+            -i unziped.fa \\
+            --hmm-model $hmm_model \\
+            -o $prefix
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo $VERSION)
+    END_VERSIONS
+    """
+}

modules/fargene/meta.yml

@@ -0,0 +1,101 @@
+name: fargene
+description: tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.
+keywords:
+  - antibiotic resistance genes
+  - ARGs
+  - identifier
+  - metagenomic
+  - contigs
+tools:
+  - fargene:
+      description: Fragmented Antibiotic Resistance Gene Identifier takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output
+      homepage: https://github.com/fannyhb/fargene
+      documentation: https://github.com/fannyhb/fargene
+      tool_dev_url: https://github.com/fannyhb/fargene
+      doi: ""
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - input:
+      type: file
+      description: fasta or paired-end fastq file containing either genomes or longer contigs as nucleotide or protein sequences (fasta) or fragmented metagenomic reads (fastq)
+      pattern: "*.{fasta}"
+  - hmm_model:
+      type: string
+      description: name of custom hidden markov model to be used [pre-defined class_a, class_b_1_2, class_b_3, class_c, class_d_1, class_d_2, qnr, tet_efflux, tet_rpg, tet_enzyme]
+
+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"
+  - log:
+      type: file
+      description: log file
+      pattern: "*.{log}"
+  - txt:
+      type: file
+      description: analysis summary text file
+      pattern: "*.{txt}"
+  - hmm:
+      type: file
+      description: output from hmmsearch
+      pattern: "*.{out}"
+  - orfs:
+      type: file
+      description: open reading frames (ORFs)
+      pattern: "*.{fasta}"
+  - orfs_amino:
+      type: file
+      description: protein translation of open reading frames (ORFs)
+      pattern: "*.{fasta}"
+  - contigs:
+      type: file
+      description: (complete) contigs that passed the final full-length classification
+      pattern: "*.{fasta}"
+  - contigs_pept:
+      type: file
+      description: parts of the contigs that passed the final classification step that aligned with the HMM, as amino acid sequences
+      pattern: "*.{fasta}"
+  - filtered:
+      type: file
+      description: sequences that passed the final classification step, but only the parts that where predicted by the HMM to be part of the gene
+      pattern: "*.{fasta}"
+  - filtered_pept:
+      type: file
+      description: sequences from filtered.fasta, translated in the same frame as the gene is predicted to be located
+      pattern: "*.{fasta}"
+  - fragments:
+      type: file
+      description: All quality controlled retrieved fragments that were classified as positive, together with its read-pair, gathered in two files
+      pattern: "*.{fastq}"
+  - trimmed:
+      type: file
+      description: The quality controlled retrieved fragments from each input file.
+      pattern: "*.{fasta}"
+  - spades:
+      type: directory
+      description: The output from the SPAdes assembly
+      pattern: "spades_assembly"
+  - metagenome:
+      type: file
+      description: The FASTQ to FASTA converted input files from metagenomic reads.
+      pattern: "*.{fasta}"
+  - tmp:
+      type: file
+      description: The from FASTQ to FASTA converted input files and their translated input sequences. Are only saved if option --store-peptides is used.
+      pattern: "*.{fasta}"
+
+
+authors:
+  - "@louperelo"

modules/fastqscan/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/fastqscan/main.nf

@@ -0,0 +1,40 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process FASTQSCAN {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::fastq-scan=0.4.4" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/fastq-scan:0.4.4--h7d875b9_0"
+    } else {
+        container "quay.io/biocontainers/fastq-scan:0.4.4--h7d875b9_0"
+    }
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("*.json"), emit: json
+    path "versions.yml"            , emit: versions
+
+    script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    zcat $reads | \\
+        fastq-scan \\
+        $options.args > ${prefix}.json
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( echo \$(fastq-scan -v 2>&1) | sed 's/^.*fastq-scan //' )
+    END_VERSIONS
+    """
+}

modules/fastqscan/meta.yml

@@ -0,0 +1,43 @@
+name: fastqscan
+description: FASTQ summary statistics in JSON format
+keywords:
+  - fastq
+  - summary
+  - statistics
+tools:
+  - fastqscan:
+      description: FASTQ summary statistics in JSON format
+      homepage: https://github.com/rpetit3/fastq-scan
+      documentation: https://github.com/rpetit3/fastq-scan
+      tool_dev_url: https://github.com/rpetit3/fastq-scan
+      doi: ""
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: FASTQ file
+      pattern: "*.{fastq.gz,fq.gz}"
+
+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"
+  - json:
+      type: file
+      description: JSON formatted file of summary statistics
+      pattern: "*.json"
+
+authors:
+  - "@rpetit3"

modules/fgbio/groupreadsbyumi/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/fgbio/groupreadsbyumi/main.nf

@@ -0,0 +1,50 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process FGBIO_GROUPREADSBYUMI {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::fgbio=1.4.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/fgbio:1.4.0--hdfd78af_0"
+    } else {
+        container "quay.io/biocontainers/fgbio:1.4.0--hdfd78af_0"
+    }
+
+    input:
+    tuple val(meta), path(taggedbam)
+    val(strategy)
+
+    output:
+    tuple val(meta), path("*_umi-grouped.bam")  , emit: bam
+    tuple val(meta), path("*_umi_histogram.txt"), emit: histogram
+    path "versions.yml"                         , emit: versions
+
+    script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+
+    """
+    mkdir tmp
+
+    fgbio \\
+        --tmp-dir=${PWD}/tmp \\
+        GroupReadsByUmi \\
+        -s $strategy \\
+        ${options.args} \\
+        -i $taggedbam \\
+        -o ${prefix}_umi-grouped.bam \\
+        -f ${prefix}_umi_histogram.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//')
+    END_VERSIONS
+    """
+}

modules/fgbio/groupreadsbyumi/meta.yml

@@ -0,0 +1,59 @@
+name: fgbio_groupreadsbyumi
+description: |
+      Groups reads together that appear to have come from the same original molecule.
+      Reads are grouped by template, and then templates are sorted by the 5’ mapping positions
+      of the reads from the template, used from earliest mapping position to latest.
+      Reads that have the same end positions are then sub-grouped by UMI sequence.
+      (!) Note: the MQ tag is required on reads with mapped mates (!)
+      This can be added using samblaster with the optional argument --addMateTags.
+keywords:
+  - UMI
+  - groupreads
+  - fgbio
+tools:
+  - fgbio:
+      description: A set of tools for working with genomic and high throughput sequencing data, including UMIs
+      homepage: http://fulcrumgenomics.github.io/fgbio/
+      documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/
+      tool_dev_url: https://github.com/fulcrumgenomics/fgbio
+      doi: ""
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: |
+        BAM file. Note: the MQ tag is required on reads with mapped mates (!)
+      pattern: "*.bam"
+  - strategy:
+      type: value
+      description: |
+        Reguired argument: defines the UMI assignment strategy.
+        Must be chosen among: Identity, Edit, Adjacency, Paired.
+
+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"
+  - bam:
+      type: file
+      description: UMI-grouped BAM
+      pattern: "*.bam"
+  - histogram:
+      type: file
+      description: A text file containing the tag family size counts
+      pattern: "*.txt"
+
+authors:
+  - "@lescai"

modules/freebayes/main.nf

@@ -19,24 +19,26 @@ process FREEBAYES {
     }
 
     input:
-    tuple val(meta), path(bam), path(bai)
-    tuple path(fasta), path(fai)
-    path(targets)
-    path(samples)
-    path(populations)
-    path(cnv)
-
+    tuple val(meta), path(input_1), path(input_1_index), path(input_2), path(input_2_index)
+    path fasta
+    path fai
+    path targets
+    path samples
+    path populations
+    path cnv
 
     output:
     tuple val(meta), path("*.vcf.gz")   , emit: vcf
     path  "versions.yml"                , emit: versions
 
     script:
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def targets_file = targets ? "--target ${targets}" : ""
-    def samples_file = samples ? "--samples ${samples}" : ""
-    def populations_file = populations ? "--populations ${populations}" : ""
-    def cnv_file = cnv ? "--cnv-map ${cnv}" : ""
+    def prefix           = options.suffix ? "${meta.id}${options.suffix}"  : "${meta.id}"
+    def input            = input_2        ? "${input_1} ${input_2}"        : "${input_1}"
+    def targets_file     = targets        ? "--target ${targets}"          : ""
+    def samples_file     = samples        ? "--samples ${samples}"         : ""
+    def populations_file = populations    ? "--populations ${populations}" : ""
+    def cnv_file         = cnv            ? "--cnv-map ${cnv}"             : ""
+
     if (task.cpus > 1) {
         """
         freebayes-parallel \\
@@ -47,7 +49,7 @@ process FREEBAYES {
             $populations_file \\
             $cnv_file \\
             $options.args \\
-            $bam  > ${prefix}.vcf
+            $input > ${prefix}.vcf
 
         gzip --no-name ${prefix}.vcf
 
@@ -66,7 +68,7 @@ process FREEBAYES {
             $populations_file \\
             $cnv_file \\
             $options.args \\
-            $bam > ${prefix}.vcf
+            $input > ${prefix}.vcf
 
         gzip --no-name ${prefix}.vcf
 

modules/freebayes/meta.yml

@@ -4,15 +4,18 @@ keywords:
   - variant caller
   - SNP
   - genotyping
-  - variant calling
+  - somatic variant calling
+  - germline variant calling
+  - bacterial variant calling
   - bayesian
+
 tools:
   - freebayes:
       description: Bayesian haplotype-based polymorphism discovery and genotyping
       homepage: https://github.com/freebayes/freebayes
       documentation: https://github.com/freebayes/freebayes
       tool_dev_url: https://github.com/freebayes/freebayes
-      doi: ""
+      doi: "arXiv:1207.3907"
       licence: ['MIT']
 
 input:
@@ -21,11 +24,11 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - bam:
+  - input:
       type: file
       description: BAM/CRAM/SAM file
       pattern: "*.{bam,cram,sam}"
-  - bai:
+  - input_index:
       type: file
       description: BAM/CRAM/SAM index file
       pattern: "*.bam.bai"
@@ -59,7 +62,6 @@ input:
           seq_name start end sample_name copy_number
       pattern: "*.bed"
 
-
 output:
   - meta:
       type: map
@@ -74,5 +76,8 @@ output:
       type: file
       description: Compressed VCF file
       pattern: "*.vcf.gz"
+
 authors:
   - "@maxibor"
+  - "@FriederikeHanssen"
+  - "@maxulysse"

modules/gatk4/applybqsr/main.nf

@@ -11,17 +11,17 @@ process GATK4_APPLYBQSR {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:
-    tuple val(meta), path(bam), path(bai), path(bqsr_table)
+    tuple val(meta), path(input), path(input_index), path(bqsr_table)
     path  fasta
-    path  fastaidx
+    path  fai
     path  dict
     path  intervals
 
@@ -32,12 +32,18 @@ process GATK4_APPLYBQSR {
     script:
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def interval = intervals ? "-L ${intervals}" : ""
+    if (!task.memory) {
+        log.info '[GATK ApplyBQSR] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
     """
     gatk ApplyBQSR \\
         -R $fasta \\
-        -I $bam \\
+        -I $input \\
         --bqsr-recal-file $bqsr_table \\
         $interval \\
+        --tmp-dir . \\
         -O ${prefix}.bam \\
         $options.args
 

modules/gatk4/applybqsr/meta.yml

@@ -20,22 +20,29 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - bam:
+  - input:
       type: file
-      description: BAM file from alignment
-      pattern: "*.{bam}"
+      description: BAM/CRAM file from alignment
+      pattern: "*.{bam,cram}"
+  - input_index:
+      type: file
+      description: BAI/CRAI file from alignment
+      pattern: "*.{bai,crai}"
   - bqsr_table:
       type: file
       description: Recalibration table from gatk4_baserecalibrator
   - fasta:
       type: file
       description: The reference fasta file
-  - fastaidx:
+      pattern: "*.fasta"
+  - fai:
       type: file
       description: Index of reference fasta file
+      pattern: "*.fasta.fai"
   - dict:
       type: file
       description: GATK sequence dictionary
+      pattern: "*.dict"
   - intervalsBed:
       type: file
       description: Bed file with the genomic regions included in the library (optional)
@@ -57,3 +64,4 @@ output:
 
 authors:
   - "@yocra3"
+  - "@FriederikeHanssen"

modules/gatk4/baserecalibrator/main.nf

@@ -11,17 +11,17 @@ process GATK4_BASERECALIBRATOR {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:
-    tuple val(meta), path(bam), path(bai)
+    tuple val(meta), path(input), path(input_index)
     path fasta
-    path fastaidx
+    path fai
     path dict
     path intervalsBed
     path knownSites
@@ -35,12 +35,19 @@ process GATK4_BASERECALIBRATOR {
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def intervalsCommand = intervalsBed ? "-L ${intervalsBed}" : ""
     def sitesCommand = knownSites.collect{"--known-sites ${it}"}.join(' ')
+
+    if (!task.memory) {
+        log.info '[GATK BaseRecalibrator] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
     """
     gatk BaseRecalibrator  \
         -R $fasta \
-        -I $bam \
+        -I $input \
         $sitesCommand \
         $intervalsCommand \
+        --tmp-dir . \
         $options.args \
         -O ${prefix}.table
 

modules/gatk4/baserecalibrator/meta.yml

@@ -20,19 +20,26 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - bam:
+  - input:
       type: file
-      description: BAM file from alignment
-      pattern: "*.{bam}"
+      description: BAM/CRAM file from alignment
+      pattern: "*.{bam,cram}"
+  - input_index:
+      type: file
+      description: BAI/CRAI file from alignment
+      pattern: "*.{bai,crai}"
   - fasta:
       type: file
       description: The reference fasta file
-  - fastaidx:
+      pattern: "*.fasta"
+  - fai:
       type: file
       description: Index of reference fasta file
+      pattern: "*.fasta.fai"
   - dict:
       type: file
       description: GATK sequence dictionary
+      pattern: "*.dict"
   - intervalsBed:
       type: file
       description: Bed file with the genomic regions included in the library (optional)
@@ -57,3 +64,4 @@ output:
 
 authors:
   - "@yocra3"
+  - "@FriederikeHanssen"

modules/gatk4/bedtointervallist/main.nf

@@ -11,11 +11,11 @@ process GATK4_BEDTOINTERVALLIST {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:

modules/gatk4/calculatecontamination/main.nf

@@ -11,11 +11,11 @@ process GATK4_CALCULATECONTAMINATION {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:

modules/gatk4/createsequencedictionary/main.nf

@@ -11,11 +11,11 @@ process GATK4_CREATESEQUENCEDICTIONARY {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:

modules/gatk4/createsomaticpanelofnormals/main.nf

@@ -11,17 +11,17 @@ process GATK4_CREATESOMATICPANELOFNORMALS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:
     tuple val(meta), path(genomicsdb)
     path fasta
-    path fastaidx
+    path fai
     path dict
 
     output:

modules/gatk4/createsomaticpanelofnormals/meta.yml

@@ -28,10 +28,10 @@ input:
       type: file
       description: The reference fasta file
       pattern: "*.fasta"
-  - fastaidx:
+  - fai:
       type: file
       description: Index of reference fasta file
-      pattern: "fasta.fai"
+      pattern: "*.fasta.fai"
   - dict:
       type: file
       description: GATK sequence dictionary

modules/gatk4/estimatelibrarycomplexity/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/gatk4/estimatelibrarycomplexity/main.nf

@@ -0,0 +1,54 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process GATK4_ESTIMATELIBRARYCOMPLEXITY {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
+    } else {
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
+    }
+
+    input:
+    tuple val(meta), path(cram)
+    path(fasta)
+    path(fai)
+    path(dict)
+
+    output:
+    tuple val(meta), path('*.metrics'), emit: metrics
+    path "versions.yml"                  , emit: versions
+
+    script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def crams = cram.collect(){ x -> "-I ".concat(x.toString()) }.join(" ")
+
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK EstimateLibraryComplexity] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    """
+    gatk EstimateLibraryComplexity \
+        ${crams} \
+        -O ${prefix}.metrics \
+        --REFERENCE_SEQUENCE ${fasta} \
+        --VALIDATION_STRINGENCY SILENT \
+        --TMP_DIR . $options.args
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/gatk4/estimatelibrarycomplexity/meta.yml

@@ -0,0 +1,56 @@
+name: gatk4_estimatelibrarycomplexity
+description: Estimates the numbers of unique molecules in a sequencing library.
+keywords:
+  - gatk4
+  - gatk4_estimatelibrarycomplexity
+  - duplication_metrics
+  - reporting
+tools:
+  - gatk4:
+      description: Genome Analysis Toolkit (GATK4)
+      homepage: https://gatk.broadinstitute.org/hc/en-us
+      documentation: https://gatk.broadinstitute.org/hc/en-us
+      tool_dev_url: https://github.com/broadinstitute/gatk
+      doi: "10.1158/1538-7445.AM2017-3590"
+      licence: ['Apache-2.0']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - cram:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+  - fasta:
+      type: file
+      description: The reference fasta file
+      pattern: "*.fasta"
+  - fai:
+      type: file
+      description: Index of reference fasta file
+      pattern: "fasta.fai"
+  - dict:
+      type: file
+      description: GATK sequence dictionary
+      pattern: "*.dict"
+
+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"
+  - metrics:
+      type: file
+      description: File containing metrics on the input files
+      pattern: "*.{metrics}"
+
+authors:
+  - "@FriederikeHanssen"

modules/gatk4/fastqtosam/main.nf

@@ -11,11 +11,11 @@ process GATK4_FASTQTOSAM {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:

modules/gatk4/filtermutectcalls/main.nf

@@ -11,17 +11,17 @@ process GATK4_FILTERMUTECTCALLS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:
     tuple val(meta), path(vcf), path(tbi), path(stats), path(orientationbias), path(segmentation), path(contaminationfile), val(contaminationest)
     path fasta
-    path fastaidx
+    path fai
     path dict
 
     output:

modules/gatk4/filtermutectcalls/meta.yml

@@ -53,10 +53,10 @@ input:
       type: file
       description: The reference fasta file
       pattern: "*.fasta"
-  - fastaidx:
+  - fai:
       type: file
       description: Index of reference fasta file
-      pattern: "fasta.fai"
+      pattern: "*.fasta.fai"
   - dict:
       type: file
       description: GATK sequence dictionary

modules/gatk4/genomicsdbimport/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/gatk4/genomicsdbimport/main.nf

@@ -0,0 +1,67 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process GATK4_GENOMICSDBIMPORT {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
+    } else {
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
+    }
+
+    input:
+    tuple val(meta), path(vcf), path(tbi), path(intervalfile), val(intervalval), path(wspace)
+    val run_intlist
+    val run_updatewspace
+    val input_map
+
+    output:
+    tuple val(meta), path("${prefix}")      , optional:true, emit: genomicsdb
+    tuple val(meta), path("$updated_db")    , optional:true, emit: updatedb
+    tuple val(meta), path("*.interval_list"), optional:true, emit: intervallist
+    path "versions.yml"                                    , emit: versions
+
+    script:
+    prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+
+    // settings for running default create gendb mode
+    inputs_command = input_map ? "--sample-name-map ${vcf[0]}" : "${'-V ' + vcf.join(' -V ')}"
+    dir_command = "--genomicsdb-workspace-path ${prefix}"
+    intervals_command = intervalfile ? " -L ${intervalfile} " : " -L ${intervalval} "
+
+    // settings changed for running get intervals list mode if run_intlist is true
+    if (run_intlist) {
+        inputs_command = ''
+        dir_command = "--genomicsdb-update-workspace-path ${wspace}"
+        intervals_command = "--output-interval-list-to-file ${prefix}.interval_list"
+    }
+
+    // settings changed for running update gendb mode. inputs_command same as default, update_db forces module to emit the updated gendb
+    if (run_updatewspace) {
+        dir_command = "--genomicsdb-update-workspace-path ${wspace}"
+        intervals_command = ''
+        updated_db = wspace.toString()
+    }
+
+    """
+    gatk GenomicsDBImport \\
+        $inputs_command \\
+        $dir_command \\
+        $intervals_command \\
+        $options.args
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/gatk4/genomicsdbimport/meta.yml

@@ -0,0 +1,84 @@
+name: gatk4_genomicsdbimport
+description: merge GVCFs from multiple samples. For use in joint genotyping or somatic panel of normal creation.
+keywords:
+  - gatk4
+  - genomicsdbimport
+  - genomicsdb
+  - panelofnormalscreation
+  - jointgenotyping
+tools:
+  - gatk4:
+      description: |
+        Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
+        with a primary focus on variant discovery and genotyping. Its powerful processing engine
+        and high-performance computing features make it capable of taking on projects of any size.
+      homepage: https://gatk.broadinstitute.org/hc/en-us
+      documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
+      doi: 10.1158/1538-7445.AM2017-3590
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+  - vcf:
+      type: list
+      description: either a list of vcf files to be used to create or update a genomicsdb, or a file that contains a map to vcf files to be used.
+      pattern: "*.vcf.gz"
+
+  - tbi:
+      type: list
+      description: list of tbi files that match with the input vcf files
+      pattern: "*.vcf.gz_tbi"
+
+  - wspace:
+      type: path
+      description: path to an existing genomicsdb to be used in update db mode or get intervals mode. This WILL NOT specify name of a new genomicsdb in create db mode.
+      pattern: "/path/to/existing/gendb"
+
+  - intervalfile:
+      type: file
+      description: file containing the intervals to be used when creating the genomicsdb
+      pattern: "*.interval_list"
+
+  - intervalval:
+      type: string
+      description: if an intervals file has not been spcified, the value enetered here will be used as an interval via the "-L" argument
+      pattern: "example: chr1:1000-10000"
+
+  - run_intlist:
+      type: boolean
+      description: Specify whether to run get interval list mode, this option cannot be specified at the same time as run_updatewspace.
+      pattern: "true/false"
+
+  - run_updatewspace:
+      type: boolean
+      description: Specify whether to run update genomicsdb mode, this option takes priority over run_intlist.
+      pattern: "true/false"
+
+  - input_map:
+      type: boolean
+      description: Specify whether the vcf input is providing a list of vcf file(s) or a single file containing a map of paths to vcf files to be used to create or update a genomicsdb.
+      pattern: "*.sample_map"
+
+output:
+  - genomicsdb:
+      type: directory
+      description: Directory containing the files that compose the genomicsdb workspace, this is only output for create mode, as update changes an existing db
+      pattern: "*/$prefix"
+  - updatedb:
+      type: directory
+      description: Directory containing the files that compose the updated genomicsdb workspace, this is only output for update mode, and should be the same path as the input wspace.
+      pattern: "same/path/as/wspace"
+  - intervallist:
+      type: file
+      description: File containing the intervals used to generate the genomicsdb, only created by get intervals mode.
+      pattern: "*.interval_list"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@GCJMackenzie"

modules/gatk4/genotypegvcfs/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/gatk4/genotypegvcfs/main.nf

@@ -0,0 +1,54 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process GATK4_GENOTYPEGVCFS {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+    } else {
+        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+    }
+
+    input:
+    tuple val(meta), path(gvcf), path(gvcf_index)
+    path  fasta
+    path  fasta_index
+    path  fasta_dict
+    path  dbsnp
+    path  dbsnp_index
+    path  intervals_bed
+
+    output:
+    tuple val(meta), path("*.vcf.gz"), emit: vcf
+    path  "versions.yml"             , emit: versions
+
+    script:
+    def prefix           = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def dbsnp_options    = dbsnp ? "-D ${dbsnp}" : ""
+    def interval_options = intervals_bed ? "-L ${intervals_bed}" : ""
+    def gvcf_options     = gvcf.name.endsWith(".vcf") || gvcf.name.endsWith(".vcf.gz") ? "$gvcf" : "gendb://$gvcf"
+    """
+    gatk \\
+        GenotypeGVCFs \\
+        $options.args \\
+        $interval_options \\
+        $dbsnp_options \\
+        -R $fasta \\
+        -V $gvcf_options \\
+        -O ${prefix}.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/gatk4/genotypegvcfs/meta.yml

@@ -0,0 +1,69 @@
+name: gatk4_genotypegvcfs
+description: |
+  Perform joint genotyping on one or more samples pre-called with HaplotypeCaller.
+keywords:
+  - joint genotyping
+  - genotype
+  - gvcf
+tools:
+  - gatk4:
+      description: Genome Analysis Toolkit (GATK4)
+      homepage: https://gatk.broadinstitute.org/hc/en-us
+      documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
+      tool_dev_url: https://github.com/broadinstitute/gatk
+      doi: "10.1158/1538-7445.AM2017-3590"
+      licence: ['BSD-3-clause']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - gvcf:
+      type: tuple of files
+      description: |
+        Tuple of gVCF(.gz) file (first) and its index (second) or the path to a GenomicsDB (and empty)
+      pattern: ["*.{vcf,vcf.gz}", "*.{idx,tbi}"]
+  - fasta:
+      type: file
+      description: Reference fasta file
+      pattern: "*.fasta"
+  - fasta_index:
+      type: file
+      description: Reference fasta index file
+      pattern: "*.fai"
+  - fasta_dict:
+      type: file
+      description: Reference fasta sequence dict file
+      pattern: "*.dict"
+  - dbsnp:
+      type: file
+      description: dbSNP VCF file
+      pattern: "*.vcf.gz"
+  - dbsnp_index:
+      type: tuple of files
+      description: dbSNP VCF index file
+      pattern: "*.tbi"
+  - intervals_bed:
+      type: file
+      description: An intevals BED file
+      pattern: "*.bed"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: Genotyped VCF file
+      pattern: "*.vcf.gz"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@santiagorevale"

modules/gatk4/getpileupsummaries/main.nf

@@ -11,17 +11,17 @@ process GATK4_GETPILEUPSUMMARIES {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:
     tuple val(meta), path(bam), path(bai)
     path variants
-    path variants_idx
+    path variants_tbi
     path sites
 
     output:

modules/gatk4/getpileupsummaries/meta.yml

@@ -35,7 +35,7 @@ input:
       type: file
       description: Population vcf of germline sequencing, containing allele fractions. Is also used as sites file if no separate sites file is specified.
       pattern: "*.vcf.gz"
-  - variants_idx:
+  - variants_tbi:
       type: file
       description: Index file for the germline resource.
       pattern: "*.vcf.gz.tbi"

modules/gatk4/haplotypecaller/main.nf

@@ -11,18 +11,21 @@ process GATK4_HAPLOTYPECALLER {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:
-    tuple val(meta), path(bam), path(bai)
+    tuple val(meta), path(input), path(input_index)
     path fasta
     path fai
     path dict
+    path dbsnp
+    path dbsnp_tbi
+    path interval
 
     output:
     tuple val(meta), path("*.vcf.gz"), emit: vcf
@@ -30,8 +33,10 @@ process GATK4_HAPLOTYPECALLER {
     path "versions.yml"              , emit: versions
 
     script:
-    def prefix    = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def avail_mem = 3
+    def prefix          = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def interval_option = interval ? "-L ${interval}" : ""
+    def dbsnp_option    = dbsnp ? "-D ${dbsnp}" : ""
+    def avail_mem       = 3
     if (!task.memory) {
         log.info '[GATK HaplotypeCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
     } else {
@@ -42,9 +47,12 @@ process GATK4_HAPLOTYPECALLER {
         --java-options "-Xmx${avail_mem}g" \\
         HaplotypeCaller \\
         -R $fasta \\
-        -I $bam \\
+        -I $input \\
+        ${dbsnp_option} \\
+        ${interval_option} \\
         -O ${prefix}.vcf.gz \\
-        $options.args
+        $options.args \\
+        --tmp-dir .
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:

modules/gatk4/haplotypecaller/meta.yml

@@ -21,14 +21,14 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - bam:
+  - input:
       type: file
-      description: BAM file
-      pattern: "*.bam"
-  - bai:
+      description: BAM/CRAM file from alignment
+      pattern: "*.{bam,cram}"
+  - input_index:
       type: file
-      description: Index of BAM file
-      pattern: "*.bam.bai"
+      description: BAI/CRAI file from alignment
+      pattern: "*.{bai,crai}"
   - fasta:
       type: file
       description: The reference fasta file
@@ -41,6 +41,16 @@ input:
       type: file
       description: GATK sequence dictionary
       pattern: "*.dict"
+  - dbsnp:
+      type: file
+      description: VCF file containing known sites (optional)
+  - dbsnp_tbi:
+      type: file
+      description: VCF index of dbsnp (optional)
+  - interval:
+      type: file
+      description: Bed file with the genomic regions included in the library (optional)
+
 output:
   - meta:
       type: map
@@ -62,3 +72,4 @@ output:
 
 authors:
   - "@suzannejin"
+  - "@FriederikeHanssen"

modules/gatk4/indexfeaturefile/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/gatk4/indexfeaturefile/main.nf

@@ -0,0 +1,40 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process GATK4_INDEXFEATUREFILE {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+    } else {
+        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+    }
+
+    input:
+    tuple val(meta), path(feature_file)
+
+    output:
+    tuple val(meta), path("*.{tbi,idx}"), emit: index
+    path  "versions.yml"                , emit: versions
+
+    script:
+    """
+    gatk \\
+        IndexFeatureFile \\
+        $options.args \\
+        -I $feature_file
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/gatk4/indexfeaturefile/meta.yml

@@ -0,0 +1,42 @@
+name: gatk4_indexfeaturefile
+description: Creates an index for a feature file, e.g. VCF or BED file.
+keywords:
+  - index
+  - feature
+tools:
+  - gatk4:
+      description: Genome Analysis Toolkit (GATK4)
+      homepage: https://gatk.broadinstitute.org/hc/en-us
+      documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
+      tool_dev_url: https://github.com/broadinstitute/gatk
+      doi: "10.1158/1538-7445.AM2017-3590"
+      licence: ['BSD-3-clause']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - feature_file:
+      type: file
+      description: VCF/BED file
+      pattern: "*.{vcf,vcf.gz,bed,bed.gz}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - index:
+      type: file
+      description: Index for VCF/BED file
+      pattern: "*.{tbi,idx}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@santiagorevale"

modules/gatk4/intervallisttools/main.nf

@@ -11,11 +11,11 @@ process GATK4_INTERVALLISTTOOLS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--hdfd78af_1"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--hdfd78af_1"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:

modules/gatk4/learnreadorientationmodel/main.nf

@@ -11,11 +11,11 @@ process GATK4_LEARNREADORIENTATIONMODEL {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:

modules/gatk4/markduplicates/main.nf

@@ -11,29 +11,36 @@ process GATK4_MARKDUPLICATES {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bams)
 
     output:
     tuple val(meta), path("*.bam")    , emit: bam
+    tuple val(meta), path("*.bai")    , emit: bai
     tuple val(meta), path("*.metrics"), emit: metrics
     path "versions.yml"               , emit: versions
 
     script:
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def bam_list = bams.collect(){ bam -> "--INPUT ".concat(bam.toString()) }.join(" ")
+    def avail_mem       = 3
+    if (!task.memory) {
+        log.info '[GATK HaplotypeCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
     """
     gatk MarkDuplicates \\
-        --INPUT $bam \\
+        $bam_list \\
         --METRICS_FILE ${prefix}.metrics \\
         --TMP_DIR . \\
-        --ASSUME_SORT_ORDER coordinate \\
         --CREATE_INDEX true \\
         --OUTPUT ${prefix}.bam \\
         $options.args

modules/gatk4/markduplicates/meta.yml

@@ -47,3 +47,4 @@ output:
 
 authors:
   - "@ajodeh-juma"
+  - "@FriederikeHanssen"

modules/gatk4/mergebamalignment/main.nf

@@ -11,11 +11,11 @@ process GATK4_MERGEBAMALIGNMENT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:

modules/gatk4/mergevcfs/main.nf

@@ -11,11 +11,11 @@ process GATK4_MERGEVCFS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:

modules/gatk4/mutect2/main.nf

@@ -11,24 +11,26 @@ process GATK4_MUTECT2 {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:
-    tuple val(meta) , path(bam) , path(bai) , val(which_norm)
-    val run_single
-    val run_pon
+    tuple val(meta) , path(input) , path(input_index) , val(which_norm)
+    val  run_single
+    val  run_pon
+    val  run_mito
+    val  interval_label
     path fasta
-    path fastaidx
+    path fai
     path dict
     path germline_resource
-    path germline_resource_idx
+    path germline_resource_tbi
     path panel_of_normals
-    path panel_of_normals_idx
+    path panel_of_normals_tbi
 
     output:
     tuple val(meta), path("*.vcf.gz")     , emit: vcf
@@ -39,35 +41,34 @@ process GATK4_MUTECT2 {
 
     script:
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def inputsList = []
-    def normalsList = []
-    def inputsCommand = ''
-    def panelsCommand = ''
-    def normalsCommand = ''
+    def panels_command = ''
+    def normals_command = ''
 
-    bam.each() {a -> inputsList.add(" -I " + a ) }
-    inputsCommand = inputsList.join( ' ')
+    def inputs_command = '-I ' + input.join( ' -I ')
 
     if(run_pon) {
-        panelsCommand = ''
-        normalsCommand = ''
+        panels_command = ''
+        normals_command = ''
 
     } else if(run_single) {
-        panelsCommand = " --germline-resource $germline_resource --panel-of-normals $panel_of_normals"
-        normalsCommand = ''
+        panels_command = " --germline-resource $germline_resource --panel-of-normals $panel_of_normals"
+        normals_command = ''
+
+    } else if(run_mito){
+        panels_command = "-L ${interval_label} --mitochondria-mode"
+        normals_command = ''
 
     } else {
-        panelsCommand = " --germline-resource $germline_resource --panel-of-normals $panel_of_normals --f1r2-tar-gz ${prefix}.f1r2.tar.gz"
-        which_norm.each() {a -> normalsList.add(" -normal " + a ) }
-        normalsCommand = normalsList.join( ' ')
+        panels_command = " --germline-resource $germline_resource --panel-of-normals $panel_of_normals --f1r2-tar-gz ${prefix}.f1r2.tar.gz"
+        normals_command = '-normal ' + which_norm.join( ' -normal ')
     }
 
     """
     gatk Mutect2 \\
         -R ${fasta} \\
-        ${inputsCommand} \\
-        ${normalsCommand} \\
-        ${panelsCommand} \\
+        ${inputs_command} \\
+        ${normals_command} \\
+        ${panels_command} \\
         -O ${prefix}.vcf.gz \\
         $options.args
 

modules/gatk4/mutect2/meta.yml

@@ -22,31 +22,42 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test']
-  - bam:
+  - input:
       type: list
-      description: list of BAM files
-      pattern: "*.bam"
-  - bai:
+      description: list of BAM files, also able to take CRAM as an input
+      pattern: "*.{bam/cram}"
+  - input_index:
       type: list
-      description: list of BAM file indexes
-      pattern: "*.bam.bai"
+      description: list of BAM file indexes, also able to take CRAM indexes as an input
+      pattern: "*.{bam.bai/cram.crai}"
   - which_norm:
       type: list
       description: optional list of sample headers contained in the normal sample bam files (these are required for tumor_normal_pair mode)
+      pattern: "testN"
   - run_single:
       type: boolean
       description: Specify whether or not to run in tumor_single mode instead of tumor_normal_pair mode (will be ignored if run_pon is also true)
+      pattern: "true/false"
   - run_pon:
       type: boolean
       description: Specify whether or not to run in panel_of_normal mode instead of tumor_normal_pair mode
+      pattern: "true/false"
+  - run_mito:
+      type: boolean
+      description: Specify whether or not to run in mitochondria-mode instead of tumor_normal_pair mode
+      pattern: "true/false"
+  - interval_label:
+      type: string
+      description: Specify the label used for mitochondrial chromosome when mutect2 is run in mitochondria mode.
+      pattern: "chrM"
   - fasta:
       type: file
       description: The reference fasta file
       pattern: "*.fasta"
-  - fastaidx:
+  - fai:
       type: file
       description: Index of reference fasta file
-      pattern: "fasta.fai"
+      pattern: "*.fasta.fai"
   - dict:
       type: file
       description: GATK sequence dictionary
@@ -55,18 +66,18 @@ input:
       type: file
       description: Population vcf of germline sequencing, containing allele fractions.
       pattern: "*.vcf.gz"
-  - germline_resource_idx:
+  - germline_resource_tbi:
       type: file
       description: Index file for the germline resource.
-      pattern: "*.vcf.gz_tbi"
+      pattern: "*.vcf.gz.tbi"
   - panel_of_normals:
       type: file
       description: vcf file to be used as a panel of normals.
       pattern: "*.vcf.gz"
-  - panel_of_normals_idx:
+  - panel_of_normals_tbi:
       type: file
       description: Index for the panel of normals.
-      pattern: "*.vcf.gz_tbi"
+      pattern: "*.vcf.gz.tbi"
 
 output:
   - vcf:

modules/gatk4/revertsam/main.nf

@@ -11,11 +11,11 @@ process GATK4_REVERTSAM {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:

modules/gatk4/samtofastq/main.nf

@@ -11,11 +11,11 @@ process GATK4_SAMTOFASTQ {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:

modules/gatk4/splitncigarreads/main.nf

@@ -11,11 +11,11 @@ process GATK4_SPLITNCIGARREADS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:

modules/gatk4/variantfiltration/main.nf

@@ -11,11 +11,11 @@ process GATK4_VARIANTFILTRATION {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
+        container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gatk4:4.2.0.0--0"
+        container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
     }
 
     input:

modules/genrich/main.nf

@@ -22,6 +22,10 @@ process GENRICH {
     tuple val(meta), path(treatment_bam)
     path  control_bam
     path  blacklist_bed
+    val   save_pvalues
+    val   save_pileup
+    val   save_bed
+    val   save_duplicates
 
     output:
     tuple val(meta), path("*narrowPeak")                     , emit: peaks
@@ -32,14 +36,14 @@ process GENRICH {
     path "versions.yml"                                      , emit: versions
 
     script:
-    def prefix     = options.suffix              ? "${meta.id}${options.suffix}"   : "${meta.id}"
-    def control    = params.control_bam          ? "-c $control_bam"               : ''
-    def pvalues    = params.pvalues              ? "-f ${prefix}.pvalues.bedGraph" : ""
-    def pileup     = params.pileup               ? "-k ${prefix}.pileup.bedGraph"  : ""
-    def bed        = params.bed                  ? "-b ${prefix}.intervals.bed"    : ""
-    def blacklist  = params.blacklist_bed        ? "-E $blacklist_bed"             : ""
+    def prefix     = options.suffix ? "${meta.id}${options.suffix}"   : "${meta.id}"
+    def control    = control_bam    ? "-c $control_bam"               : ''
+    def blacklist  = blacklist_bed  ? "-E $blacklist_bed"             : ""
+    def pvalues    = save_pvalues   ? "-f ${prefix}.pvalues.bedGraph" : ""
+    def pileup     = save_pileup    ? "-k ${prefix}.pileup.bedGraph"  : ""
+    def bed        = save_bed       ? "-b ${prefix}.intervals.bed"    : ""
     def duplicates = ""
-    if (params.save_duplicates) {
+    if (save_duplicates) {
         if (options.args.contains('-r')) {
             duplicates = "-R ${prefix}.duplicates.txt"
         } else {
@@ -58,7 +62,6 @@ process GENRICH {
         $pileup \\
         $bed \\
         $duplicates \\
-        $blacklist \\
         $control
 
     cat <<-END_VERSIONS > versions.yml

modules/genrich/meta.yml

@@ -15,7 +15,6 @@ tools:
       tool_dev_url: https://github.com/jsh58/Genrich
       doi: ""
       licence: ['MIT']
-
 input:
   - meta:
       type: map
@@ -34,7 +33,18 @@ input:
       type: file
       description: Bed file containing genomic intervals to exclude from the analysis
       pattern: "*.{bed}"
-
+  - save_pvalues:
+      type: boolean
+      description: Create bedgraph-ish file for p/q-values file
+  - save_pileup:
+      type: boolean
+      description: Create bedgraph-ish file for pileups and p-values
+  - save_bed:
+      type: boolean
+      description: Create BED file for reads/fragments/intervals
+  - save_duplicates:
+      type: boolean
+      description: Create PCR duplicates file (only works if -r option is set)
 output:
   - meta:
       type: map
@@ -65,7 +75,6 @@ output:
       type: file
       description: File containing software version
       pattern: "*.{version.txt}"
-
 authors:
   - "@JoseEspinosa"
 

modules/gstama/collapse/main.nf

@@ -11,11 +11,12 @@ process GSTAMA_COLLAPSE {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::gs-tama=1.0.2" : null)
+    conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/gs-tama:1.0.2--hdfd78af_0"
+        container "https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0"
     } else {
-        container "quay.io/biocontainers/gs-tama:1.0.2--hdfd78af_0"
+        container "quay.io/biocontainers/gs-tama:1.0.3--hdfd78af_0"
+
     }
 
     input:
@@ -23,7 +24,7 @@ process GSTAMA_COLLAPSE {
     path fasta
 
     output:
-    tuple val(meta), path("*.bed")                    , emit: bed
+    tuple val(meta), path("*_collapsed.bed")          , emit: bed
     tuple val(meta), path("*_trans_read.bed")         , emit: bed_trans_reads
     tuple val(meta), path("*_local_density_error.txt"), emit: local_density_error
     tuple val(meta), path("*_polya.txt")              , emit: polya

modules/gunc/downloaddb/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/gunc/downloaddb/main.nf

@@ -0,0 +1,37 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process GUNC_DOWNLOADDB {
+    tag '$db_name'
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0"
+    } else {
+        container "quay.io/biocontainers/gunc:1.0.5--pyhdfd78af_0"
+    }
+
+    input:
+    val db_name
+
+    output:
+    path "*.dmnd"       , emit: db
+    path "versions.yml" , emit: versions
+
+    script:
+    """
+    gunc download_db . -db $db_name $options.args
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( gunc --version )
+    END_VERSIONS
+    """
+}

modules/gunc/downloaddb/meta.yml

@@ -0,0 +1,36 @@
+name: gunc_downloaddb
+description: Download database for GUNC detection of Chimerism and Contamination in Prokaryotic Genomes
+keywords:
+  - download
+  - prokaryote
+  - assembly
+  - genome
+  - quality control
+  - chimeras
+tools:
+  - gunc:
+      description: Python package for detection of chimerism and contamination in prokaryotic genomes.
+      homepage: https://grp-bork.embl-community.io/gunc/
+      documentation: https://grp-bork.embl-community.io/gunc/
+      tool_dev_url: https://github.com/grp-bork/gunc
+      doi: "10.1186/s13059-021-02393-0"
+      licence: ['GNU General Public v3 or later (GPL v3+)']
+
+input:
+  - db_name:
+      type: string
+      description: "Which database to download. Options: progenomes or gtdb"
+      pattern: "progenomes|gtdb"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - db:
+      type: file
+      description: GUNC database file
+      pattern: "*.dmnd"
+
+authors:
+  - "@jfy133"

modules/gunc/run/functions.nf

@@ -0,0 +1,78 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    def ioptions  = initOptions(args.options)
+    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
+    if (ioptions.publish_by_meta) {
+        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+        for (key in key_list) {
+            if (args.meta && key instanceof String) {
+                def path = key
+                if (args.meta.containsKey(key)) {
+                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
+                }
+                path = path instanceof String ? path : ''
+                path_list.add(path)
+            }
+        }
+    }
+    if (ioptions.publish_files instanceof Map) {
+        for (ext in ioptions.publish_files) {
+            if (args.filename.endsWith(ext.key)) {
+                def ext_list = path_list.collect()
+                ext_list.add(ext.value)
+                return "${getPathFromList(ext_list)}/$args.filename"
+            }
+        }
+    } else if (ioptions.publish_files == null) {
+        return "${getPathFromList(path_list)}/$args.filename"
+    }
+}

modules/gunc/run/main.nf

@@ -0,0 +1,45 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process GUNC_RUN {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/gunc:1.0.5--pyhdfd78af_0"
+    } else {
+        container "quay.io/biocontainers/gunc:1.0.5--pyhdfd78af_0"
+    }
+
+    input:
+    tuple val(meta), path(fasta)
+    path(db)
+
+    output:
+    tuple val(meta), path("*maxCSS_level.tsv")                  , emit: maxcss_level_tsv
+    tuple val(meta), path("*all_levels.tsv")    , optional: true, emit: all_levels_tsv
+    path "versions.yml"                                         , emit: versions
+
+    script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    gunc \\
+        run \\
+        --input_fasta $fasta \\
+        --db_file $db \\
+        --threads $task.cpus \\
+        $options.args
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( gunc --version )
+    END_VERSIONS
+    """
+}