Add new modules

software/gffread/functions.nf

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+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/gffread/main.nf

@@ -0,0 +1,30 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process GFFREAD {
+    tag "$gff"
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    container "quay.io/biocontainers/gffread:0.11.7--h8b12597_0"
+    //container https://depot.galaxyproject.org/singularity/gffread:0.11.7--h8b12597_0
+
+    conda (params.conda ? "bioconda::gffread=0.11.7" : null)
+
+    input:
+    path gff
+    val  options
+
+    output:
+    path "*.gtf"        , emit: gtf
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    """
+    gffread $gff $ioptions.args -o ${gff.baseName}.gtf
+    echo \$(gffread --version 2>&1) > ${software}.version.txt
+    """
+}

software/hisat2/align/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/hisat2/align/main.nf

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+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+def VERSION = '2.2.0'
+
+process HISAT2_ALIGN {
+    tag "$meta.id"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0"
+    //container "https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0"
+
+    conda (params.conda ? "bioconda::hisat2=2.2.0 bioconda::samtools=1.10" : null)
+
+    input:
+    tuple val(meta), path(reads)
+    path  index
+    path  splicesites
+    val   options
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.log"), emit: summary
+    path  "*.version.txt"         , emit: version
+
+    tuple val(meta), path("*fastq.gz"), optional:true, emit: fastq
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+
+    def strandedness = ''
+    if (meta.strandedness == 'forward') {
+        strandedness = meta.single_end ? '--rna-strandness F' : '--rna-strandness FR'
+    } else if (meta.strandedness == 'reverse') {
+        strandedness = meta.single_end ? '--rna-strandness R' : '--rna-strandness RF'
+    }
+    def seq_center = params.seq_center ? "--rg-id ${prefix} --rg CN:${params.seq_center.replaceAll('\\s','_')} SM:$prefix" : "--rg-id ${prefix} --rg SM:$prefix"
+    if (meta.single_end) {
+        def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
+        """
+        INDEX=`find -L ./ -name "*.1.ht2" | sed 's/.1.ht2//'`
+        hisat2 \\
+            -x \$INDEX \\
+            -U $reads \\
+            $strandedness \\
+            --known-splicesite-infile $splicesites \\
+            --summary-file ${prefix}.hisat2.summary.log \\
+            --threads $task.cpus \\
+            $seq_center \\
+            $unaligned \\
+            $ioptions.args \\
+            | samtools view -bS -F 4 -F 256 - > ${prefix}.bam
+
+        echo $VERSION > ${software}.version.txt
+        """
+    } else {
+        def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
+        """
+        INDEX=`find -L ./ -name "*.1.ht2" | sed 's/.1.ht2//'`
+        hisat2 \\
+            -x \$INDEX \\
+            -1 ${reads[0]} \\
+            -2 ${reads[1]} \\
+            $strandedness \\
+            --known-splicesite-infile $splicesites \\
+            --summary-file ${prefix}.hisat2.summary.log \\
+            --threads $task.cpus \\
+            $seq_center \\
+            $unaligned \\
+            --no-mixed \\
+            --no-discordant \\
+            $ioptions.args \\
+            | samtools view -bS -F 4 -F 8 -F 256 - > ${prefix}.bam
+
+        if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
+            mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
+        fi
+        if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
+            mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
+        fi
+
+        echo $VERSION > ${software}.version.txt
+        """
+    }
+}

software/hisat2/build/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/hisat2/build/main.nf

@@ -0,0 +1,64 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+def VERSION = '2.2.0'
+
+process HISAT2_BUILD {
+    tag "$fasta"
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
+    //container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
+
+    conda (params.conda ? "bioconda::hisat2=2.2.0" : null)
+
+    input:
+    path fasta
+    path gtf
+    path splicesites
+    val  options
+
+    output:
+    path "hisat2",        emit: index
+    path "*.version.txt", emit: version
+
+    script:
+    def avail_mem = 0
+    if (!task.memory) {
+        log.info "[HISAT2 index build] Available memory not known - defaulting to 0. Specify process memory requirements to change this."
+    } else {
+        log.info "[HISAT2 index build] Available memory: ${task.memory}"
+        avail_mem = task.memory.toGiga()
+    }
+
+    def extract_exons = ''
+    def ss = ''
+    def exon = ''
+    if (avail_mem > params.hisat_build_memory) {
+        log.info "[HISAT2 index build] Over ${params.hisat_build_memory} GB available, so using splice sites and exons in HISAT2 index"
+        extract_exons = "hisat2_extract_exons.py $gtf > ${gtf.baseName}.exons.txt"
+        ss = "--ss $splicesites"
+        exon = "--exon ${gtf.baseName}.exons.txt"
+    } else {
+        log.info "[HISAT2 index build] Less than ${params.hisat_build_memory} GB available, so NOT using splice sites and exons in HISAT2 index."
+        log.info "[HISAT2 index build] Use --hisat_build_memory [small number] to skip this check."
+    }
+
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    """
+    mkdir hisat2
+    $extract_exons
+    hisat2-build \\
+        -p $task.cpus \\
+        $ss \\
+        $exon \\
+        $ioptions.args \\
+        $fasta \\
+        hisat2/${fasta.baseName}
+
+    echo $VERSION > ${software}.version.txt
+    """
+}

software/hisat2/extractsplicesites/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/hisat2/extractsplicesites/main.nf

@@ -0,0 +1,31 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+def VERSION = '2.2.0'
+
+process HISAT2_EXTRACTSPLICESITES {
+    tag "$gtf"
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    container "quay.io/biocontainers/hisat2:2.2.0--py37hfa133b6_4"
+    //container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
+
+    conda (params.conda ? "bioconda::hisat2=2.2.0" : null)
+
+    input:
+    path gtf
+    val  options
+
+    output:
+    path "*.splice_sites.txt", emit: txt
+    path "*.version.txt"     , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    hisat2_extract_splice_sites.py $gtf > ${gtf.baseName}.splice_sites.txt
+    echo $VERSION > ${software}.version.txt
+    """
+}

software/qualimap/rnaseq/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/qualimap/rnaseq/main.nf

@@ -0,0 +1,54 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process QUALIMAP_RNASEQ {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/qualimap:2.2.2d--1"
+    //container "https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1"
+
+    conda (params.conda ? "bioconda::qualimap=2.2.2d" : null)
+
+    input:
+    tuple val(meta), path(bam)
+    path  gtf
+    val   options
+
+    output:
+    tuple val(meta), path("${prefix}"), emit: results
+    path  "*.version.txt"             , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    prefix       = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+
+    def strandedness = 'non-strand-specific'
+    if (meta.strandedness == 'forward') {
+        strandedness = 'strand-specific-forward'
+    } else if (meta.strandedness == 'reverse') {
+        strandedness = 'strand-specific-reverse'
+    }
+    def paired_end = meta.single_end ? '' : '-pe'
+    def memory     = task.memory.toGiga() + "G"
+    """
+    unset DISPLAY
+    mkdir tmp
+    export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp
+    qualimap \\
+        --java-mem-size=$memory \\
+        rnaseq \\
+        $ioptions.args \\
+        -bam $bam \\
+        -gtf $gtf \\
+        -p $strandedness \\
+        $paired_end \\
+        -outdir $prefix
+
+    echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//' > ${software}.version.txt
+    """
+}

software/rsem/calculateexpression/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/rsem/calculateexpression/main.nf

@@ -0,0 +1,49 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process RSEM_CALCULATEEXPRESSION {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/rsem:1.3.3--pl526ha52163a_0"
+    //container "https://depot.galaxyproject.org/singularity/rsem:1.3.3--pl526ha52163a_0"
+
+    conda (params.conda ? "bioconda::rsem=1.3.3" : null)
+
+    input:
+    tuple val(meta), path(reads)
+    path  index
+    val   options
+
+    output:
+    tuple val(meta), path("*.genes.results")   , emit: counts_gene
+    tuple val(meta), path("*.isoforms.results"), emit: counts_transcript
+    tuple val(meta), path("*.stat")            , emit: stat
+    path  "*.version.txt"                      , emit: version
+
+    tuple val(meta), path("*.STAR.genome.bam")       , optional:true, emit: bam_star
+    tuple val(meta), path("${prefix}.genome.bam")    , optional:true, emit: bam_genome
+    tuple val(meta), path("${prefix}.transcript.bam"), optional:true, emit: bam_transcript
+
+    script:
+    def software   = getSoftwareName(task.process)
+    def ioptions   = initOptions(options)
+    prefix         = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    def paired_end = meta.single_end ? "" : "--paired-end"
+    """
+    INDEX=`find -L ./ -name "*.grp" | sed 's/.grp//'`
+    rsem-calculate-expression \\
+        --num-threads $task.cpus \\
+        --temporary-folder ./tmp/ \\
+        $paired_end \\
+        $ioptions.args \\
+        $reads \\
+        \$INDEX \\
+        $prefix
+
+    rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt
+    """
+}

software/rsem/preparereference/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/rsem/preparereference/main.nf

@@ -0,0 +1,39 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process RSEM_PREPAREREFERENCE {
+    tag "$fasta"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    container "quay.io/biocontainers/rsem:1.3.3--pl526ha52163a_0"
+    //container "https://depot.galaxyproject.org/singularity/rsem:1.3.3--pl526ha52163a_0"
+
+    conda (params.conda ? "bioconda::rsem=1.3.3" : null)
+
+    input:
+    path fasta
+    path gtf
+    val  options
+
+    output:
+    path "rsem"         , emit: index
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    """
+    mkdir rsem
+    rsem-prepare-reference \\
+        --gtf $gtf \\
+        --num-threads $task.cpus \\
+        $ioptions.args \\
+        $fasta \\
+        rsem/genome
+
+    rsem-calculate-expression --version | sed -e "s/Current version: RSEM v//g" > ${software}.version.txt
+    """
+}

software/rseqc/bamstat/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/rseqc/bamstat/main.nf

@@ -0,0 +1,36 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process RSEQC_BAMSTAT {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    //container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+
+    conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
+
+    input:
+    tuple val(meta), path(bam)
+    val   options
+
+    output:
+    tuple val(meta), path("*.bam_stat.txt"), emit: txt
+    path  "*.version.txt"                  , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    """
+    bam_stat.py \\
+        -i $bam \\
+        $ioptions.args \\
+        > ${prefix}.bam_stat.txt
+
+    bam_stat.py --version | sed -e "s/bam_stat.py //g" > ${software}.version.txt
+    """
+}

software/rseqc/inferexperiment/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/rseqc/inferexperiment/main.nf

@@ -0,0 +1,38 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process RSEQC_INFEREXPERIMENT {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    //container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+
+    conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
+
+    input:
+    tuple val(meta), path(bam)
+    path  bed
+    val   options
+
+    output:
+    tuple val(meta), path("*.infer_experiment.txt"), emit: txt
+    path  "*.version.txt"                          , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    """
+    infer_experiment.py \\
+        -i $bam \\
+        -r $bed \\
+        $ioptions.args \\
+        > ${prefix}.infer_experiment.txt
+
+    infer_experiment.py --version | sed -e "s/infer_experiment.py //g" > ${software}.version.txt
+    """
+}

software/rseqc/innerdistance/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/rseqc/innerdistance/main.nf

@@ -0,0 +1,50 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process RSEQC_INNERDISTANCE {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    //container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+
+    conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
+
+    input:
+    tuple val(meta), path(bam)
+    path  bed
+    val   options
+
+    output:
+    tuple val(meta), path("*distance.txt"), optional:true, emit: distance
+    tuple val(meta), path("*freq.txt")    , optional:true, emit: freq
+    tuple val(meta), path("*mean.txt")    , optional:true, emit: mean
+    tuple val(meta), path("*.pdf")        , optional:true, emit: pdf
+    tuple val(meta), path("*.r")          , optional:true, emit: rscript
+    path  "*.version.txt"                 , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    if (!meta.single_end) {
+        """
+        inner_distance.py \\
+            -i $bam \\
+            -r $bed \\
+            -o $prefix \\
+            $ioptions.args \\
+            > stdout.txt
+        head -n 2 stdout.txt > ${prefix}.inner_distance_mean.txt
+
+        inner_distance.py --version | sed -e "s/inner_distance.py //g" > ${software}.version.txt
+        """
+    } else {
+        """
+        inner_distance.py --version | sed -e "s/inner_distance.py //g" > ${software}.version.txt
+        """
+    }
+}

software/rseqc/junctionannotation/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/rseqc/junctionannotation/main.nf

@@ -0,0 +1,45 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process RSEQC_JUNCTIONANNOTATION {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    //container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+
+    conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
+
+    input:
+    tuple val(meta), path(bam)
+    path  bed
+    val   options
+
+    output:
+    tuple val(meta), path("*.junction.bed"), emit: bed
+    tuple val(meta), path("*.Interact.bed"), emit: interact_bed
+    tuple val(meta), path("*.xls")         , emit: xls
+    tuple val(meta), path("*junction.pdf") , emit: pdf
+    tuple val(meta), path("*events.pdf")   , emit: events_pdf
+    tuple val(meta), path("*.r")           , emit: rscript
+    tuple val(meta), path("*.log")         , emit: log
+    path  "*.version.txt"                  , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    """
+    junction_annotation.py \\
+        -i $bam \\
+        -r $bed \\
+        -o $prefix \\
+        $ioptions.args \\
+        2> ${prefix}.junction_annotation.log
+
+    junction_annotation.py --version | sed -e "s/junction_annotation.py //g" > ${software}.version.txt
+    """
+}

software/rseqc/junctionsaturation/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/rseqc/junctionsaturation/main.nf

@@ -0,0 +1,39 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process RSEQC_JUNCTIONSATURATION {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    //container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+
+    conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
+
+    input:
+    tuple val(meta), path(bam)
+    path  bed
+    val   options
+
+    output:
+    tuple val(meta), path("*.pdf"), emit: pdf
+    tuple val(meta), path("*.r")  , emit: rscript
+    path  "*.version.txt"         , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    """
+    junction_saturation.py \\
+        -i $bam \\
+        -r $bed \\
+        -o $prefix \\
+        $ioptions.args
+
+    junction_saturation.py --version | sed -e "s/junction_saturation.py //g" > ${software}.version.txt
+    """
+}

software/rseqc/readdistribution/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/rseqc/readdistribution/main.nf

@@ -0,0 +1,37 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process RSEQC_READDISTRIBUTION {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    //container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+
+    conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
+
+    input:
+    tuple val(meta), path(bam)
+    path  bed
+    val   options
+
+    output:
+    tuple val(meta), path("*.read_distribution.txt"), emit: txt
+    path  "*.version.txt"                           , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    """
+    read_distribution.py \\
+        -i $bam \\
+        -r $bed \\
+         > ${prefix}.read_distribution.txt
+
+    read_distribution.py --version | sed -e "s/read_distribution.py //g" > ${software}.version.txt
+    """
+}

software/rseqc/readduplication/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/rseqc/readduplication/main.nf

@@ -0,0 +1,39 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process RSEQC_READDUPLICATION {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
+    //container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+
+    conda (params.conda ? "bioconda::rseqc=3.0.1" : null)
+
+    input:
+    tuple val(meta), path(bam)
+    val   options
+
+    output:
+    tuple val(meta), path("*seq.DupRate.xls"), emit: seq_xls
+    tuple val(meta), path("*pos.DupRate.xls"), emit: pos_xls
+    tuple val(meta), path("*.pdf")           , emit: pdf
+    tuple val(meta), path("*.r")             , emit: rscript
+    path  "*.version.txt"                    , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    """
+    read_duplication.py \\
+        -i $bam \\
+        -o $prefix \\
+        $ioptions.args
+
+    read_duplication.py --version | sed -e "s/read_duplication.py //g" > ${software}.version.txt
+    """
+}

software/salmon/index/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/salmon/index/main.nf

@@ -0,0 +1,36 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process SALMON_INDEX {
+    tag "$fasta"
+    label "process_medium"
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0"
+    //container "https://depot.galaxyproject.org/singularity/salmon:1.3.0--hf69c8f4_0"
+
+    conda (params.conda ? "bioconda::salmon=1.3.0" : null)
+
+    input:
+    path fasta
+    val  options
+
+    output:
+    path "salmon"       , emit: index
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    """
+    salmon \\
+        index \\
+        --threads $task.cpus \\
+        -t $fasta \\
+        $ioptions.args \\
+        -i salmon
+    salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
+    """
+}

software/salmon/quant/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/salmon/quant/main.nf

@@ -0,0 +1,50 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process SALMON_QUANT {
+    tag "$meta.id"
+    label "process_medium"
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0"
+    //container "https://depot.galaxyproject.org/singularity/salmon:1.3.0--hf69c8f4_0"
+
+    conda (params.conda ? "bioconda::salmon=1.3.0" : null)
+
+    input:
+    tuple val(meta), path(reads)
+    path  index
+    path  gtf
+    val   options
+
+    output:
+    tuple val(meta), path("${prefix}"), emit: results
+    path  "*.version.txt"             , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    prefix       = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+
+    def strandedness = meta.single_end ? 'U' : 'IU'
+    if (meta.strandedness == 'forward') {
+        strandedness = meta.single_end ? 'SF' : 'ISF'
+    } else if (meta.strandedness == 'reverse') {
+        strandedness = meta.single_end ? 'SR' : 'ISR'
+    }
+    def endedness = meta.single_end ? "-r $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
+    """
+    salmon quant \\
+        --geneMap $gtf \\
+        --threads $task.cpus \\
+        --libType=$strandedness \\
+        --index $index \\
+        $endedness \\
+        $ioptions.args \\
+        -o $prefix
+
+    salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
+    """
+}

software/sortmerna/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/sortmerna/main.nf

@@ -0,0 +1,70 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process SORTMERNA {
+    tag "$meta.id"
+    label "process_high"
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/sortmerna:4.2.0--0"
+    //container "https://depot.galaxyproject.org/singularity/sortmerna:4.2.0--0"
+
+    conda (params.conda ? "bioconda::sortmerna=4.2.0" : null)
+
+    input:
+    tuple val(meta), path(reads)
+    path  fasta
+    val   options
+
+    output:
+    tuple val(meta), path("*.fastq.gz"), emit: reads
+    tuple val(meta), path("*.log")     , emit: log
+    path  "*.version.txt"              , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+
+    def Refs = ""
+    for (i=0; i<fasta.size(); i++) { Refs+= " --ref ${fasta[i]}" }
+    if (meta.single_end) {
+        """
+        sortmerna \\
+            $Refs \\
+            --reads $reads \\
+            --threads $task.cpus \\
+            --workdir . \\
+            --aligned rRNA_reads \\
+            --other non_rRNA_reads \\
+            $ioptions.args
+
+        gzip -f < non_rRNA_reads.fq > ${prefix}.fastq.gz
+        mv rRNA_reads.log ${prefix}.sortmerna.log
+
+        echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//' > ${software}.version.txt
+        """
+    } else {
+        """
+        sortmerna \\
+            $Refs \\
+            --reads ${reads[0]} \\
+            --reads ${reads[1]} \\
+            --threads $task.cpus \\
+            --workdir . \\
+            --aligned rRNA_reads \\
+            --other non_rRNA_reads \\
+            --paired_in \\
+            --out2 \\
+            $ioptions.args
+
+        gzip -f < non_rRNA_reads_fwd.fq > ${prefix}_1.fastq.gz
+        gzip -f < non_rRNA_reads_rev.fq > ${prefix}_2.fastq.gz
+        mv rRNA_reads.log ${prefix}.sortmerna.log
+
+        echo \$(sortmerna --version 2>&1) | sed 's/^.*SortMeRNA version //; s/ Build Date.*\$//' > ${software}.version.txt
+        """
+    }
+}

software/star/align/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/star/align/main.nf

@@ -0,0 +1,62 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process STAR_ALIGN {
+    tag "$meta.id"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    // Don't upgrade me - 2.7X indices incompatible with iGenomes.
+    container "quay.io/biocontainers/star:2.6.1d--0"
+    //container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0"
+
+    conda (params.conda ? "bioconda::star=2.6.1d" : null)
+
+    input:
+    tuple val(meta), path(reads)
+    path  index
+    path  gtf
+    val   options
+
+    output:
+    tuple val(meta), path("*Aligned.out.bam") , emit: bam
+    tuple val(meta), path("*Log.final.out")   , emit: log_final
+    tuple val(meta), path("*Log.out")         , emit: log_out
+    tuple val(meta), path("*Log.progress.out"), emit: log_progress
+    path  "*.version.txt"                     , emit: version
+
+    tuple val(meta), path("*sortedByCoord.out.bam")  , optional:true, emit: bam_sorted
+    tuple val(meta), path("*toTranscriptome.out.bam"), optional:true, emit: bam_transcript
+    tuple val(meta), path("*fastq.gz")               , optional:true, emit: fastq
+    tuple val(meta), path("*.tab")                   , optional:true, emit: tab
+
+    script:
+    def software   = getSoftwareName(task.process)
+    def ioptions   = initOptions(options)
+    def prefix     = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    def ignore_gtf = params.star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf"
+    def seq_center = params.seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$params.seq_center' 'SM:$prefix'" : "--outSAMattrRGline ID:$prefix 'SM:$prefix'"
+    """
+    STAR \\
+        --genomeDir $index \\
+        --readFilesIn $reads  \\
+        --runThreadN $task.cpus \\
+        --outFileNamePrefix $prefix. \\
+        $ignore_gtf \\
+        $seq_center \\
+        $ioptions.args
+
+    if [ -f ${prefix}.Unmapped.out.mate1 ]; then
+        mv ${prefix}.Unmapped.out.mate1 ${prefix}.unmapped_1.fastq
+        gzip ${prefix}.unmapped_1.fastq
+    fi
+    if [ -f ${prefix}.Unmapped.out.mate2 ]; then
+        mv ${prefix}.Unmapped.out.mate2 ${prefix}.unmapped_2.fastq
+        gzip ${prefix}.unmapped_2.fastq
+    fi
+
+    STAR --version | sed -e "s/STAR_//g" > ${software}.version.txt
+    """
+}

software/star/genomegenerate/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/star/genomegenerate/main.nf

@@ -0,0 +1,43 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process STAR_GENOMEGENERATE {
+    tag "$fasta"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    // Don't upgrade me - 2.7X indices incompatible with iGenomes.
+    container "quay.io/biocontainers/star:2.6.1d--0"
+    //container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0"
+
+    conda (params.conda ? "bioconda::star=2.6.1d" : null)
+
+    input:
+    path fasta
+    path gtf
+    val  options
+
+    output:
+    path "star"         , emit: index
+    path "*.version.txt", emit: version
+
+    script:
+    def software  = getSoftwareName(task.process)
+    def ioptions  = initOptions(options)
+    def avail_mem = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
+    """
+    mkdir star
+    STAR \\
+        --runMode genomeGenerate \\
+        --genomeDir star/ \\
+        --genomeFastaFiles $fasta \\
+        --sjdbGTFfile $gtf \\
+        --runThreadN $task.cpus \\
+        $avail_mem \\
+        $ioptions.args
+
+    STAR --version | sed -e "s/STAR_//g" > ${software}.version.txt
+    """
+}

software/stringtie/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/stringtie/main.nf

@@ -0,0 +1,52 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process STRINGTIE {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/stringtie:2.1.2--h7e0af3c_1"
+    //container "https://depot.galaxyproject.org/singularity/stringtie:2.1.2--h7e0af3c_1"
+
+    conda (params.conda ? "bioconda::stringtie=2.1.2" : null)
+
+    input:
+    tuple val(meta), path(bam)
+    path  gtf
+    val   options
+
+    output:
+    tuple val(meta), path("*.coverage.gtf")   , emit: coverage_gtf
+    tuple val(meta), path("*.transcripts.gtf"), emit: transcript_gtf
+    tuple val(meta), path("*.txt")            , emit: abundance
+    tuple val(meta), path("*.ballgown")       , emit: ballgown
+    path  "*.version.txt"                     , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+
+    def strandedness = ''
+    if (meta.strandedness == 'forward') {
+        strandedness = '--fr'
+    } else if (meta.strandedness == 'reverse') {
+        strandedness = '--rf'
+    }
+    """
+    stringtie \\
+        $bam \\
+        $strandedness \\
+        -G $gtf \\
+        -o ${prefix}.transcripts.gtf \\
+        -A ${prefix}.gene_abundance.txt \\
+        -C ${prefix}.coverage.gtf \\
+        -b ${prefix}.ballgown \\
+        $ioptions.args
+
+    stringtie --version > ${software}.version.txt
+    """
+}

software/umitools/dedup/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/umitools/dedup/main.nf

@@ -0,0 +1,38 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process UMITOOLS_DEDUP {
+    tag "$meta.id"
+    label "process_medium"
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/umi_tools:1.0.1--py37h516909a_1"
+    //container "https://depot.galaxyproject.org/singularity/umi_tools:1.0.1--py37h516909a_1"
+
+    conda (params.conda ? "bioconda::umi_tools=1.0.1" : null)
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    val   options
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.tsv"), emit: tsv
+    path  "*.version.txt"         , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    """
+    umi_tools dedup \\
+        -I $bam \\
+        -S ${prefix}.bam \\
+        --output-stats=$prefix \\
+        $ioptions.args \\
+
+    umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
+    """
+}

software/umitools/extract/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/umitools/extract/main.nf

@@ -0,0 +1,54 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+process UMITOOLS_EXTRACT {
+    tag "$meta.id"
+    label "process_low"
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/umi_tools:1.0.1--py37h516909a_1"
+    //container "https://depot.galaxyproject.org/singularity/umi_tools:1.0.1--py37h516909a_1"
+
+    conda (params.conda ? "bioconda::umi_tools=1.0.1" : null)
+
+    input:
+    tuple val(meta), path(reads)
+    val   options
+
+    output:
+    tuple val(meta), path("*.fastq.gz"), emit: reads
+    tuple val(meta), path("*.log")     , emit: log
+    path  "*.version.txt"              , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    if (meta.single_end) {
+        """
+        umi_tools \\
+            extract \\
+            -I $reads \\
+            -S ${prefix}.umi_extract.fastq.gz \\
+            $ioptions.args \\
+            > ${prefix}.umi_extract.log
+
+        umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
+        """
+    }  else {
+        """
+        umi_tools \\
+            extract \\
+            -I ${reads[0]} \\
+            --read2-in=${reads[1]} \\
+            -S ${prefix}.umi_extract_1.fastq.gz \\
+            --read2-out=${prefix}.umi_extract_2.fastq.gz \\
+            $ioptions.args \\
+            > ${prefix}.umi_extract.log
+
+        umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
+        """
+    }
+}