Unify syntax

software/SOFTWARE/TOOL/main.nf

@@ -60,7 +60,7 @@ process SOFTWARE_TOOL {
     // TODO nf-core: If meta is provided in "input:" section then it MUST be added to ALL output channels (except version)
     tuple val(meta), path("*.bam"), emit: bam
     // TODO nf-core: List additional required output channels/values here
-    path "*.version.txt", emit: version
+    path "*.version.txt"          , emit: version
 
     script:
     def software = getSoftwareName(task.process)

software/bwa/index/main.nf

@@ -18,7 +18,7 @@ process BWA_INDEX {
     val  options
 
     output:
-    path "${fasta}.*", emit: index
+    path "${fasta}.*"   , emit: index
     path "*.version.txt", emit: version
 
     script:

software/bwa/mem/main.nf

@@ -21,17 +21,17 @@ process BWA_MEM {
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
-    path "*.version.txt", emit: version
+    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 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/computematrix/main.nf

@@ -19,9 +19,9 @@ process DEEPTOOLS_COMPUTEMATRIX {
     val   options
 
     output:
-    tuple val(meta), path("*.mat.gz"), emit: matrix
+    tuple val(meta), path("*.mat.gz") , emit: matrix
     tuple val(meta), path("*.mat.tab"), emit: table
-    path "*.version.txt", emit: version
+    path  "*.version.txt"             , emit: version
 
     script:
     def software = getSoftwareName(task.process)

software/deeptools/plotfingerprint/main.nf

@@ -18,10 +18,10 @@ process DEEPTOOLS_PLOTFINGERPRINT {
     val   options
 
     output:
-    tuple val(meta), path("*.pdf"), emit: pdf
+    tuple val(meta), path("*.pdf")          , emit: pdf
-    tuple val(meta), path("*.raw.txt"), emit: matrix
+    tuple val(meta), path("*.raw.txt")      , emit: matrix
     tuple val(meta), path("*.qcmetrics.txt"), emit: metrics
-    path "*.version.txt", emit: version
+    path  "*.version.txt"                   , emit: version
 
     script:
     def software = getSoftwareName(task.process)

software/deeptools/plotheatmap/main.nf

@@ -20,7 +20,7 @@ process DEEPTOOLS_PLOTHEATMAP {
     output:
     tuple val(meta), path("*.pdf"), emit: pdf
     tuple val(meta), path("*.tab"), emit: table
-    path "*.version.txt", emit: version
+    path  "*.version.txt"         , emit: version
 
     script:
     def software = getSoftwareName(task.process)

software/deeptools/plotprofile/main.nf

@@ -20,12 +20,12 @@ process DEEPTOOLS_PLOTPROFILE {
     output:
     tuple val(meta), path("*.pdf"), emit: pdf
     tuple val(meta), path("*.tab"), emit: table
-    path "*.version.txt", emit: version
+    path  "*.version.txt"         , emit: version
 
     script:
     def software = getSoftwareName(task.process)
     def ioptions = initOptions(options)
-    prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
     """
     plotProfile \\
         $ioptions.args \\

software/fastqc/main.nf

@@ -19,8 +19,8 @@ process FASTQC {
 
     output:
     tuple val(meta), path("*.html"), emit: html
-    tuple val(meta), path("*.zip"), emit: zip
+    tuple val(meta), path("*.zip") , emit: zip
-    path "*.version.txt", emit: version
+    path  "*.version.txt"          , emit: version
 
     script:
     // Add soft-links to original FastQs for consistent naming in pipeline

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/homer/annotatepeaks/main.nf

@@ -23,7 +23,7 @@ process HOMER_ANNOTATEPEAKS {
 
     output:
     tuple val(meta), path("*annotatePeaks.txt"), emit: txt
-    path "*.version.txt", emit: version
+    path  "*.version.txt"                      , emit: version
 
     script:
     def software = getSoftwareName(task.process)

software/macs2/callpeak/main.nf

@@ -20,11 +20,12 @@ process MACS2_CALLPEAK {
 
     output:
     tuple val(meta), path("*.{narrowPeak,broadPeak}"), emit: peak
-    tuple val(meta), path("*.xls"), emit: xls
+    tuple val(meta), path("*.xls")                   , emit: xls
-    tuple val(meta), path("*.gappedPeak"), emit: gapped optional true
+    path  "*.version.txt"                            , emit: version
-    tuple val(meta), path("*.bed"), emit: bed optional true
+
-    tuple val(meta), path("*.bdg"), emit: bdg optional true
+    tuple val(meta), path("*.gappedPeak"), optional:true, emit: gapped
-    path "*.version.txt", emit: version
+    tuple val(meta), path("*.bed")       , optional:true, emit: bed
+    tuple val(meta), path("*.bdg")       , optional:true, emit: bdg
 
     script:
     def software = getSoftwareName(task.process)

software/phantompeakqualtools/main.nf

@@ -20,10 +20,10 @@ process PHANTOMPEAKQUALTOOLS {
     val   options
 
     output:
-    tuple val(meta), path("*.out"), emit: spp
+    tuple val(meta), path("*.out")  , emit: spp
-    tuple val(meta), path("*.pdf"), emit: pdf
+    tuple val(meta), path("*.pdf")  , emit: pdf
     tuple val(meta), path("*.Rdata"), emit: rdata
-    path "*.version.txt", emit: version
+    path  "*.version.txt"           , emit: version
 
     script:
     def software = getSoftwareName(task.process)

software/picard/collectmultiplemetrics/main.nf

@@ -20,8 +20,8 @@ process PICARD_COLLECTMULTIPLEMETRICS {
 
     output:
     tuple val(meta), path("*_metrics"), emit: metrics
-    tuple val(meta), path("*.pdf"), emit: pdf
+    tuple val(meta), path("*.pdf")    , emit: pdf
-    path "*.version.txt", emit: version
+    path  "*.version.txt"             , emit: version
 
     script:
     def software  = getSoftwareName(task.process)

software/picard/markduplicates/main.nf

@@ -18,9 +18,9 @@ process PICARD_MARKDUPLICATES {
     val   options
 
     output:
-    tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.bam")        , emit: bam
     tuple val(meta), path("*.metrics.txt"), emit: metrics
-    path "*.version.txt", emit: version
+    path  "*.version.txt"                 , emit: version
 
     script:
     def software  = getSoftwareName(task.process)

software/picard/mergesamfiles/main.nf

@@ -19,7 +19,7 @@ process PICARD_MERGESAMFILES {
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
-    path "*.version.txt", emit: version
+    path  "*.version.txt"         , emit: version
 
     script:
     def software  = getSoftwareName(task.process)

software/preseq/lcextrap/main.nf

@@ -20,19 +20,19 @@ process PRESEQ_LCEXTRAP {
 
     output:
     tuple val(meta), path("*.ccurve.txt"), emit: ccurve
-    tuple val(meta), path("*.log"), emit: log
+    tuple val(meta), path("*.log")       , emit: log
-    path "*.version.txt", emit: version
+    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 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/samtools/flagstat/main.nf

@@ -18,7 +18,7 @@ process SAMTOOLS_FLAGSTAT {
 
     output:
     tuple val(meta), path("*.flagstat"), emit: flagstat
-    path "*.version.txt", emit: version
+    path  "*.version.txt"              , emit: version
 
     script:
     def software = getSoftwareName(task.process)

software/samtools/idxstats/main.nf

@@ -18,7 +18,7 @@ process SAMTOOLS_IDXSTATS {
 
     output:
     tuple val(meta), path("*.idxstats"), emit: idxstats
-    path "*.version.txt", emit: version
+    path  "*.version.txt"              , emit: version
 
     script:
     def software = getSoftwareName(task.process)

software/samtools/index/main.nf

@@ -18,7 +18,7 @@ process SAMTOOLS_INDEX {
 
     output:
     tuple val(meta), path("*.bai"), emit: bai
-    path "*.version.txt", emit: version
+    path  "*.version.txt"         , emit: version
 
     script:
     def software = getSoftwareName(task.process)

software/samtools/sort/main.nf

@@ -19,7 +19,7 @@ process SAMTOOLS_SORT {
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
-    path "*.version.txt", emit: version
+    path  "*.version.txt"         , emit: version
 
     script:
     def software = getSoftwareName(task.process)

software/samtools/stats/main.nf

@@ -18,7 +18,7 @@ process SAMTOOLS_STATS {
 
     output:
     tuple val(meta), path("*.stats"), emit: stats
-    path "*.version.txt", emit: version
+    path  "*.version.txt"           , emit: version
 
     script:
     def software = getSoftwareName(task.process)

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

@@ -18,11 +18,12 @@ process TRIMGALORE {
     val   options
 
     output:
-    tuple val(meta), path("*.fq.gz"), emit: reads
+    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
+    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

software/ucsc/bedgraphtobigwig/main.nf

@@ -22,7 +22,7 @@ process UCSC_BEDRAPHTOBIGWIG {
 
     output:
     tuple val(meta), path("*.bigWig"), emit: bigwig
-    path "*.version.txt", emit: version
+    path "*.version.txt"             , emit: version
 
     script:
     def software = getSoftwareName(task.process)