Remove functions file

software/fastqc/main.nf

@@ -1,21 +1,25 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process FASTQC {
     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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0"
+    } else {
         container "quay.io/biocontainers/fastqc:0.11.9--0"
-    //container "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0"
+    }
-
-    conda (params.conda ? "bioconda::fastqc=0.11.9" : null)
     
     input:
     tuple val(meta), path(reads)
-    val   options
     
     output:
     tuple val(meta), path("*.html"), emit: html
@@ -25,19 +29,18 @@ process FASTQC {
     script:
     // Add soft-links to original FastQs for consistent naming in pipeline
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}.${ioptions.suffix}" : "${meta.id}"
     if (meta.single_end) {
         """
         [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
-        fastqc $ioptions.args --threads $task.cpus ${prefix}.fastq.gz
+        fastqc $options.args --threads $task.cpus ${prefix}.fastq.gz
         fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
         """
     } else {
         """
         [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
         [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
-        fastqc $ioptions.args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
+        fastqc $options.args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
         fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
         """
     }

software/gffread/main.nf

@@ -1,20 +1,24 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
+    conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0"
+    } else {
         container "quay.io/biocontainers/gffread:0.12.1--h8b12597_0"
-    //container https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0
+    }
-
-    conda (params.conda ? "bioconda::gffread=0.12.1" : null)
 
     input:
     path gff
-    val  options
     
     output:
     path "*.gtf"        , emit: gtf
@@ -22,9 +26,8 @@ process GFFREAD {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
     """
-    gffread $gff $ioptions.args -o ${gff.baseName}.gtf
+    gffread $gff $options.args -o ${gff.baseName}.gtf
     echo \$(gffread --version 2>&1) > ${software}.version.txt
     """
 }

software/hisat2/align/main.nf

@@ -1,6 +1,9 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 def VERSION = '2.2.0'
 
 process HISAT2_ALIGN {
@@ -8,18 +11,19 @@ process HISAT2_ALIGN {
     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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::hisat2=2.2.0 bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2880dd9d8ad0a7b221d4eacda9a818e92983128d-0"
+    } else {
         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
@@ -30,8 +34,7 @@ process HISAT2_ALIGN {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
 
     def strandedness = ''
     if (meta.strandedness == 'forward') {
@@ -53,7 +56,7 @@ process HISAT2_ALIGN {
             --threads $task.cpus \\
             $seq_center \\
             $unaligned \\
-            $ioptions.args \\
+            $options.args \\
             | samtools view -bS -F 4 -F 256 - > ${prefix}.bam
 
         echo $VERSION > ${software}.version.txt
@@ -74,7 +77,7 @@ process HISAT2_ALIGN {
             $unaligned \\
             --no-mixed \\
             --no-discordant \\
-            $ioptions.args \\
+            $options.args \\
             | samtools view -bS -F 4 -F 8 -F 256 - > ${prefix}.bam
 
         if [ -f ${prefix}.unmapped.fastq.1.gz ]; then

software/hisat2/build/main.nf

@@ -1,24 +1,28 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
+    conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
+    } else {
         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
@@ -47,7 +51,6 @@ process HISAT2_BUILD {
     }
 
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
     """
     mkdir hisat2
     $extract_exons
@@ -55,7 +58,7 @@ process HISAT2_BUILD {
         -p $task.cpus \\
         $ss \\
         $exon \\
-        $ioptions.args \\
+        $options.args \\
         $fasta \\
         hisat2/${fasta.baseName}
 

software/hisat2/extractsplicesites/main.nf

@@ -1,22 +1,25 @@
 // Import generic module functions
 include { saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+
 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:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
+    conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/hisat2:2.2.0--py37hfa133b6_4"
+    } else {
         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

software/macs2/functions.nf

@@ -1,59 +0,0 @@
-/*
- * -----------------------------------------------------
- *  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/preseq/lcextrap/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process PRESEQ_LCEXTRAP {
     tag "$meta.id"
     label 'process_medium'
     label 'error_ignore'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::preseq=2.0.3" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/preseq:2.0.3--hf53bd2b_3"
+    } else {
         container "quay.io/biocontainers/preseq:2.0.3--hf53bd2b_3"
-    //container "https://depot.galaxyproject.org/singularity/preseq:2.0.3--hf53bd2b_3"
+    }
-
-    conda (params.conda ? "bioconda::preseq=2.0.3" : null)
 
     input:
     tuple val(meta), path(bam)
-    val   options
     
     output:
     tuple val(meta), path("*.ccurve.txt"), emit: ccurve
@@ -25,13 +29,12 @@ process PRESEQ_LCEXTRAP {
 
     script:
     def software   = getSoftwareName(task.process)
-    def ioptions   = initOptions(options)
+    def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix     = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     def paired_end = meta.single_end ? '' : '-pe'
     """
     preseq \\
         lc_extrap \\
-        $ioptions.args \\
+        $options.args \\
         $paired_end \\
         -output ${prefix}.ccurve.txt \\
         $bam

software/qualimap/rnaseq/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::qualimap=2.2.2d" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1"
+    } else {
         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
@@ -24,8 +28,7 @@ process QUALIMAP_RNASEQ {
 
     script:
     def software   = getSoftwareName(task.process)
-    def ioptions   = initOptions(options)
+    prefix         = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    prefix         = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     def paired_end = meta.single_end ? '' : '-pe'
     def memory     = task.memory.toGiga() + "G"
 
@@ -42,7 +45,7 @@ process QUALIMAP_RNASEQ {
     qualimap \\
         --java-mem-size=$memory \\
         rnaseq \\
-        $ioptions.args \\
+        $options.args \\
         -bam $bam \\
         -gtf $gtf \\
         -p $strandedness \\

software/rsem/calculateexpression/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
+    } else {
         container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
-    //container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
+    }
-
-    conda (params.conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
 
     input:
     tuple val(meta), path(reads)
     path  index
-    val   options
     
     output:
     tuple val(meta), path("*.genes.results")   , emit: counts_gene
@@ -31,8 +35,7 @@ process RSEM_CALCULATEEXPRESSION {
 
     script:
     def software   = getSoftwareName(task.process)
-    def ioptions   = initOptions(options)
+    prefix         = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    prefix         = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
 
     def strandedness = ''
     if (meta.strandedness == 'forward') {
@@ -48,7 +51,7 @@ process RSEM_CALCULATEEXPRESSION {
         --temporary-folder ./tmp/ \\
         $strandedness \\
         $paired_end \\
-        $ioptions.args \\
+        $options.args \\
         $reads \\
         \$INDEX \\
         $prefix

software/rsem/preparereference/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
+    conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
+    } else {
         container "quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
-    //container "https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0"
+    }
-
-    conda (params.conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
 
     input:
     path fasta
     path gtf
-    val  options
     
     output:
     path "rsem"         , emit: index
@@ -24,13 +28,12 @@ process RSEM_PREPAREREFERENCE {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
     """
     mkdir rsem
     rsem-prepare-reference \\
         --gtf $gtf \\
         --num-threads $task.cpus \\
-        $ioptions.args \\
+        $options.args \\
         $fasta \\
         rsem/genome
 

software/rseqc/bamstat/main.nf

@@ -1,21 +1,25 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         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
@@ -23,12 +27,11 @@ process RSEQC_BAMSTAT {
 
     script:
     def software = getSoftwareName(task.process) 
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     """
     bam_stat.py \\
         -i $bam \\
-        $ioptions.args \\
+        $options.args \\
         > ${prefix}.bam_stat.txt
 
     bam_stat.py --version | sed -e "s/bam_stat.py //g" > ${software}.version.txt

software/rseqc/inferexperiment/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         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
@@ -24,13 +28,12 @@ process RSEQC_INFEREXPERIMENT {
 
     script:
     def software = getSoftwareName(task.process) 
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     """
     infer_experiment.py \\
         -i $bam \\
         -r $bed \\
-        $ioptions.args \\
+        $options.args \\
         > ${prefix}.infer_experiment.txt
 
     infer_experiment.py --version | sed -e "s/infer_experiment.py //g" > ${software}.version.txt

software/rseqc/innerdistance/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         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
@@ -28,15 +32,14 @@ process RSEQC_INNERDISTANCE {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     if (!meta.single_end) {
         """
         inner_distance.py \\
             -i $bam \\
             -r $bed \\
             -o $prefix \\
-            $ioptions.args \\
+            $options.args \\
             > stdout.txt
         head -n 2 stdout.txt > ${prefix}.inner_distance_mean.txt
 

software/rseqc/junctionannotation/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         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
@@ -30,14 +34,13 @@ process RSEQC_JUNCTIONANNOTATION {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     """
     junction_annotation.py \\
         -i $bam \\
         -r $bed \\
         -o $prefix \\
-        $ioptions.args \\
+        $options.args \\
         2> ${prefix}.junction_annotation.log
 
     junction_annotation.py --version | sed -e "s/junction_annotation.py //g" > ${software}.version.txt

software/rseqc/junctionsaturation/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         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
@@ -25,14 +29,13 @@ process RSEQC_JUNCTIONSATURATION {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     """
     junction_saturation.py \\
         -i $bam \\
         -r $bed \\
         -o $prefix \\
-        $ioptions.args
+        $options.args
 
     junction_saturation.py --version | sed -e "s/junction_saturation.py //g" > ${software}.version.txt
     """

software/rseqc/readdistribution/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         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
@@ -24,8 +28,7 @@ process RSEQC_READDISTRIBUTION {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     """
     read_distribution.py \\
         -i $bam \\

software/rseqc/readduplication/main.nf

@@ -1,21 +1,25 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
+    } else {
         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
@@ -26,13 +30,12 @@ process RSEQC_READDUPLICATION {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     """
     read_duplication.py \\
         -i $bam \\
         -o $prefix \\
-        $ioptions.args
+        $options.args
 
     read_duplication.py --version | sed -e "s/read_duplication.py //g" > ${software}.version.txt
     """

software/salmon/index/main.nf

@@ -1,21 +1,25 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
+    conda (params.enable_conda ? "bioconda::salmon=1.3.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/salmon:1.3.0--hf69c8f4_0"
+    } else {
         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
@@ -23,13 +27,12 @@ process SALMON_INDEX {
 
     script:
     def software = getSoftwareName(task.process) 
-    def ioptions = initOptions(options)
     """
     salmon \\
         index \\
         --threads $task.cpus \\
         -t $fasta \\
-        $ioptions.args \\
+        $options.args \\
         -i salmon
     salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
     """

software/salmon/quant/main.nf

@@ -1,23 +1,27 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::salmon=1.3.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/salmon:1.3.0--hf69c8f4_0"
+    } else {
         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
@@ -25,8 +29,7 @@ process SALMON_QUANT {
 
     script:
     def software  = getSoftwareName(task.process)
-    def ioptions  = initOptions(options)
+    prefix        = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    prefix        = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     def endedness = meta.single_end ? "-r $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
 
     def strandedness = meta.single_end ? 'U' : 'IU'
@@ -42,7 +45,7 @@ process SALMON_QUANT {
         --libType=$strandedness \\
         --index $index \\
         $endedness \\
-        $ioptions.args \\
+        $options.args \\
         -o $prefix
 
     salmon --version | sed -e "s/salmon //g" > ${software}.version.txt

software/samtools/flagstat/main.nf

@@ -1,20 +1,23 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
 
 process SAMTOOLS_FLAGSTAT {
     tag "$meta.id"
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    } else {
         container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
-    //container " https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    }
-
-    conda (params.conda ? "bioconda::samtools=1.10" : null)
 
     input:
     tuple val(meta), path(bam), path(bai)
-    val   options
     
     output:
     tuple val(meta), path("*.flagstat"), emit: flagstat

software/samtools/idxstats/main.nf

@@ -1,20 +1,23 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
 
 process SAMTOOLS_IDXSTATS {
     tag "$meta.id"
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    } else {
         container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
-    //container " https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    }
-
-    conda (params.conda ? "bioconda::samtools=1.10" : null)
 
     input:
     tuple val(meta), path(bam), path(bai)
-    val   options
     
     output:
     tuple val(meta), path("*.idxstats"), emit: idxstats

software/samtools/index/main.nf

@@ -1,20 +1,23 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
 
 process SAMTOOLS_INDEX {
     tag "$meta.id"
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    } else {
         container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
-    //container " https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    }
-
-    conda (params.conda ? "bioconda::samtools=1.10" : null)
 
     input:
     tuple val(meta), path(bam)
-    val   options
     
     output:
     tuple val(meta), path("*.bai"), emit: bai

software/samtools/sort/main.nf

@@ -1,21 +1,25 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process SAMTOOLS_SORT {
     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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    } else {
         container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
-    //container " https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    }
-
-    conda (params.conda ? "bioconda::samtools=1.10" : null)
 
     input:
     tuple val(meta), path(bam)
-    val   options
     
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -23,10 +27,9 @@ process SAMTOOLS_SORT {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     """
-    samtools sort $ioptions.args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam
+    samtools sort $options.args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam
     echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
     """
 }

software/samtools/stats/main.nf

@@ -1,20 +1,23 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
 
 process SAMTOOLS_STATS {
     tag "$meta.id"
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    } else {
         container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
-    //container " https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+    }
-
-    conda (params.conda ? "bioconda::samtools=1.10" : null)
 
     input:
     tuple val(meta), path(bam), path(bai)
-    val   options
     
     output:
     tuple val(meta), path("*.stats"), emit: stats

software/sortmerna/main.nf

@@ -1,22 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::sortmerna=4.2.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/sortmerna:4.2.0--0"
+    } else {
         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
@@ -25,8 +29,7 @@ process SORTMERNA {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
 
     def Refs = ""
     for (i=0; i<fasta.size(); i++) { Refs+= " --ref ${fasta[i]}" }
@@ -39,7 +42,7 @@ process SORTMERNA {
             --workdir . \\
             --aligned rRNA_reads \\
             --other non_rRNA_reads \\
-            $ioptions.args
+            $options.args
 
         gzip -f < non_rRNA_reads.fq > ${prefix}.fastq.gz
         mv rRNA_reads.log ${prefix}.sortmerna.log
@@ -58,7 +61,7 @@ process SORTMERNA {
             --other non_rRNA_reads \\
             --paired_in \\
             --out2 \\
-            $ioptions.args
+            $options.args
 
         gzip -f < non_rRNA_reads_fwd.fq > ${prefix}_1.fastq.gz
         gzip -f < non_rRNA_reads_rev.fq > ${prefix}_2.fastq.gz

software/star/align/main.nf

@@ -1,24 +1,28 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    // Don't upgrade me - 2.7X indices incompatible with iGenomes.
+    // Note: 2.7X indices incompatible with AWS iGenomes.
+    conda (params.enable_conda ? "bioconda::star=2.6.1d" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0"
+    } else {
         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
@@ -34,8 +38,7 @@ process STAR_ALIGN {
 
     script:
     def software   = getSoftwareName(task.process)
-    def ioptions   = initOptions(options)
+    def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix     = ioptions.suffix ? "${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'"
     """
@@ -46,7 +49,7 @@ process STAR_ALIGN {
         --outFileNamePrefix $prefix. \\
         $ignore_gtf \\
         $seq_center \\
-        $ioptions.args
+        $options.args
 
     if [ -f ${prefix}.Unmapped.out.mate1 ]; then
         mv ${prefix}.Unmapped.out.mate1 ${prefix}.unmapped_1.fastq

software/star/genomegenerate/main.nf

@@ -1,23 +1,27 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
 
-    // Don't upgrade me - 2.7X indices incompatible with iGenomes.
+    // Note: 2.7X indices incompatible with AWS iGenomes.
+    conda (params.enable_conda ? "bioconda::star=2.6.1d" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/star:2.6.1d--0"
+    } else {
         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
@@ -25,7 +29,6 @@ process STAR_GENOMEGENERATE {
 
     script:
     def software  = getSoftwareName(task.process)
-    def ioptions  = initOptions(options)
     def memory    = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
     """
     mkdir star
@@ -36,7 +39,7 @@ process STAR_GENOMEGENERATE {
         --sjdbGTFfile $gtf \\
         --runThreadN $task.cpus \\
         $memory \\
-        $ioptions.args
+        $options.args
 
     STAR --version | sed -e "s/STAR_//g" > ${software}.version.txt
     """

software/stringtie/main.nf

@@ -1,22 +1,27 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    // Note: 2.7X indices incompatible with AWS iGenomes.
+    conda (params.enable_conda ? "bioconda::stringtie=2.1.4" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/stringtie:2.1.4--h7e0af3c_0"
+    } else {
         container "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0"
-    //container "https://depot.galaxyproject.org/singularity/stringtie:2.1.4--h7e0af3c_0"
+    }
-
-    conda (params.conda ? "bioconda::stringtie=2.1.4" : null)
 
     input:
     tuple val(meta), path(bam)
     path  gtf
-    val   options
     
     output:
     tuple val(meta), path("*.coverage.gtf")   , emit: coverage_gtf
@@ -27,8 +32,7 @@ process STRINGTIE {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
 
     def strandedness = ''
     if (meta.strandedness == 'forward') {
@@ -45,7 +49,7 @@ process STRINGTIE {
         -A ${prefix}.gene_abundance.txt \\
         -C ${prefix}.coverage.gtf \\
         -b ${prefix}.ballgown \\
-        $ioptions.args
+        $options.args
 
     stringtie --version > ${software}.version.txt
     """

software/subread/featurecounts/main.nf

@@ -1,21 +1,26 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process SUBREAD_FEATURECOUNTS {
     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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    // Note: 2.7X indices incompatible with AWS iGenomes.
+    conda (params.enable_conda ? "bioconda::subread=2.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0"
+    } else {
         container "quay.io/biocontainers/subread:2.0.1--hed695b0_0"
-    //container "https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0"
+    }
-
-    conda (params.conda ? "bioconda::subread=2.0.1" : null)
 
     input:
     tuple val(meta), path(bams), path(annotation)
-    val   options
     
     output:
     tuple val(meta), path("*featureCounts.txt")        , emit: counts
@@ -24,8 +29,7 @@ process SUBREAD_FEATURECOUNTS {
 
     script:
     def software   = getSoftwareName(task.process)
-    def ioptions   = initOptions(options)
+    def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix     = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     def paired_end = meta.single_end ? '' : '-p'
 
     def strandedness = 0
@@ -36,7 +40,7 @@ process SUBREAD_FEATURECOUNTS {
     }
     """
     featureCounts \\
-        $ioptions.args \\
+        $options.args \\
         $paired_end \\
         -T $task.cpus \\
         -a $annotation \\

software/trimgalore/main.nf

@@ -1,21 +1,25 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 process TRIMGALORE {
     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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::trim-galore=0.6.6" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.6--0"
+    } else {
         container "quay.io/biocontainers/trim-galore:0.6.6--0"
-    //container "https://depot.galaxyproject.org/singularity/trim-galore:0.6.6--0"
+    }
-
-    conda (params.conda ? "bioconda::trim-galore=0.6.6" : null)
 
     input:
     tuple val(meta), path(reads)
-    val   options
 
     output:
     tuple val(meta), path("*.fq.gz")    , emit: reads
@@ -45,13 +49,12 @@ process TRIMGALORE {
 
     // Added soft-links to original fastqs for consistent naming in MultiQC
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     if (meta.single_end) {
         """
         [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
         trim_galore \\
-            $ioptions.args \\
+            $options.args \\
             --cores $cores \\
             --gzip \\
             $c_r1 \\
@@ -64,7 +67,7 @@ process TRIMGALORE {
         [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
         [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
         trim_galore \\
-            $ioptions.args \\
+            $options.args \\
             --cores $cores \\
             --paired \\
             --gzip \\

software/umitools/dedup/main.nf

@@ -1,21 +1,25 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::umi_tools=1.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/umi_tools:1.0.1--py37h516909a_1"
+    } else {
         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
@@ -24,14 +28,13 @@ process UMITOOLS_DEDUP {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     """
     umi_tools dedup \\
         -I $bam \\
         -S ${prefix}.bam \\
         --output-stats=$prefix \\
-        $ioptions.args \\
+        $options.args \\
 
     umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
     """

software/umitools/extract/main.nf

@@ -1,21 +1,25 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
+params.options = [:]
+def options    = initOptions(params.options)
+
 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) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
+    conda (params.enable_conda ? "bioconda::umi_tools=1.0.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/umi_tools:1.0.1--py37h516909a_1"
+    } else {
         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
@@ -24,15 +28,14 @@ process UMITOOLS_EXTRACT {
 
     script:
     def software = getSoftwareName(task.process)
-    def ioptions = initOptions(options)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     if (meta.single_end) {
         """
         umi_tools \\
             extract \\
             -I $reads \\
             -S ${prefix}.umi_extract.fastq.gz \\
-            $ioptions.args \\
+            $options.args \\
             > ${prefix}.umi_extract.log
 
         umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt
@@ -45,7 +48,7 @@ process UMITOOLS_EXTRACT {
             --read2-in=${reads[1]} \\
             -S ${prefix}.umi_extract_1.fastq.gz \\
             --read2-out=${prefix}.umi_extract_2.fastq.gz \\
-            $ioptions.args \\
+            $options.args \\
             > ${prefix}.umi_extract.log
 
         umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt