Unify syntax

software/bwa/mem/main.nf

@@ -27,11 +27,11 @@ process BWA_MEM {
     def software   = getSoftwareName(task.process)
     def ioptions   = initOptions(options)
     def prefix     = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
-    def rg       = meta.read_group ? "-R ${meta.read_group}" : ""
+    def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
     """
     bwa mem \\
         $ioptions.args \\
-        $rg \\
+        $read_group \\
         -t $task.cpus \\
         $fasta \\
         $reads \\

software/deeptools/plotprofile/main.nf

@@ -25,7 +25,7 @@ process DEEPTOOLS_PLOTPROFILE {
     script:
     def software = getSoftwareName(task.process)
     def ioptions = initOptions(options)
-    prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     """
     plotProfile \\
         $ioptions.args \\

software/hisat2/extractsplicesites/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { saveFiles; getSoftwareName } from './functions'
 
 def VERSION = '2.2.0'
 

software/macs2/callpeak/main.nf

@@ -21,11 +21,12 @@ process MACS2_CALLPEAK {
     output:
     tuple val(meta), path("*.{narrowPeak,broadPeak}"), emit: peak
     tuple val(meta), path("*.xls")                   , emit: xls
-    tuple val(meta), path("*.gappedPeak"), emit: gapped optional true
-    tuple val(meta), path("*.bed"), emit: bed optional true
-    tuple val(meta), path("*.bdg"), emit: bdg optional true
     path  "*.version.txt"                            , emit: version
 
+    tuple val(meta), path("*.gappedPeak"), optional:true, emit: gapped
+    tuple val(meta), path("*.bed")       , optional:true, emit: bed
+    tuple val(meta), path("*.bdg")       , optional:true, emit: bdg
+
     script:
     def software = getSoftwareName(task.process)
     def ioptions = initOptions(options)

software/preseq/lcextrap/main.nf

@@ -27,12 +27,12 @@ process PRESEQ_LCEXTRAP {
     def software   = getSoftwareName(task.process)
     def ioptions   = initOptions(options)
     def prefix     = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
-    def pe       = meta.single_end ? '' : '-pe'
+    def paired_end = meta.single_end ? '' : '-pe'
     """
     preseq \\
         lc_extrap \\
         $ioptions.args \\
-        $pe \\
+        $paired_end \\
         -output ${prefix}.ccurve.txt \\
         $bam
     cp .command.err ${prefix}.command.log

software/qualimap/rnaseq/main.nf

@@ -26,6 +26,8 @@ process QUALIMAP_RNASEQ {
     def software   = getSoftwareName(task.process)
     def ioptions   = initOptions(options)
     prefix         = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    def paired_end = meta.single_end ? '' : '-pe'
+    def memory     = task.memory.toGiga() + "G"
 
     def strandedness = 'non-strand-specific'
     if (meta.strandedness == 'forward') {
@@ -33,8 +35,6 @@ process QUALIMAP_RNASEQ {
     } 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

software/salmon/quant/main.nf

@@ -27,6 +27,7 @@ process SALMON_QUANT {
     def software  = getSoftwareName(task.process)
     def ioptions  = initOptions(options)
     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'
     if (meta.strandedness == 'forward') {
@@ -34,7 +35,6 @@ process SALMON_QUANT {
     } 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 \\

software/star/genomegenerate/main.nf

@@ -26,7 +26,7 @@ process STAR_GENOMEGENERATE {
     script:
     def software  = getSoftwareName(task.process)
     def ioptions  = initOptions(options)
-    def avail_mem = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
+    def memory    = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
     """
     mkdir star
     STAR \\
@@ -35,7 +35,7 @@ process STAR_GENOMEGENERATE {
         --genomeFastaFiles $fasta \\
         --sjdbGTFfile $gtf \\
         --runThreadN $task.cpus \\
-        $avail_mem \\
+        $memory \\
         $ioptions.args
 
     STAR --version | sed -e "s/STAR_//g" > ${software}.version.txt

software/subread/featurecounts/main.nf

@@ -26,6 +26,7 @@ process SUBREAD_FEATURECOUNTS {
     def software   = getSoftwareName(task.process)
     def ioptions   = initOptions(options)
     def prefix     = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    def paired_end = meta.single_end ? '' : '-p'
 
     def strandedness = 0
     if (meta.strandedness == 'forward') {
@@ -33,7 +34,6 @@ process SUBREAD_FEATURECOUNTS {
     } else if (meta.strandedness == 'reverse') {
         strandedness = 2
     }
-    def paired_end = meta.single_end ? '' : '-p'
     """
     featureCounts \\
         $ioptions.args \\

software/trimgalore/main.nf

@@ -19,11 +19,12 @@ process TRIMGALORE {
 
     output:
     tuple val(meta), path("*.fq.gz")    , emit: reads
-    tuple val(meta), path("*.html"), emit: html optional true
-    tuple val(meta), path("*.zip"), emit: zip optional true
     tuple val(meta), path("*report.txt"), emit: log
     path "*.version.txt"                , emit: version
 
+    tuple val(meta), path("*.html"), emit: html optional true
+    tuple val(meta), path("*.zip") , emit: zip optional true
+
     script:
     // Calculate number of --cores for TrimGalore based on value of task.cpus
     // See: https://github.com/FelixKrueger/TrimGalore/blob/master/Changelog.md#version-060-release-on-1-mar-2019