update solution_RNASeq.nf to match CONTRIBUTING.md

src/nf_modules/cutadapt/main.nf

@@ -19,19 +19,18 @@ process adaptor_removal {
   path "*_report.txt", emit: report
 
   script:
-  if (reads instanceof List) {
+  if (reads instanceof List)
   """
   cutadapt ${params.adaptor_removal} \
   -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
   ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
   """
-  } else {
+  else
   """
   cutadapt ${params.adaptor_removal} \
   -o ${file_id}_cut.fastq.gz \
   ${reads} > ${file_id}_report.txt
   """
-  }
 }
 
 params.adaptor_removal_pairedend = "-a ${adapter_3_prim} -g ${adapter_5_prim} -A ${adapter_3_prim} -G ${adapter_5_prim}"
@@ -76,7 +75,7 @@ process adaptor_removal_singleend {
   """
 }
 
-process trimming_pairedend {
+process trimming {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$pair_id"
@@ -89,13 +88,13 @@ process trimming_pairedend {
   path "*_report.txt", emit: report
 
   script:
-if (reads instanceof List)
+  if (reads instanceof List)
   """
   cutadapt -q ${trim_quality},${trim_quality} \
   -o ${pair_id}_trim_R1.fastq.gz -p ${pair_id}_trim_R2.fastq.gz \
   ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
   """
-else
+  else
   """
   cutadapt -q ${trim_quality},${trim_quality} \
   -o ${file_id}_trim.fastq.gz \

src/nf_modules/kallisto/main.nf

@@ -44,27 +44,28 @@ process mapping_fastq {
   tuple val(file_id), path("*_report.txt"), emit: report
 
   script:
-if (file_id instanceof List){
-  pair_id = file_id[0]
-} else {
-  pair_id = file_id
-}
+  if (file_id instanceof List){
+    pair_id = file_id[0]
+  } else {
+    pair_id = file_id
+  }
 
-if (reads instanceof List)
-"""
-mkdir ${pair_id}
-kallisto quant -i ${index} -t ${task.cpus} \
-${params.mapping_fastq} -o ${pair_id} \
-${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_mapping_report.txt
-"""
-else
-"""
-mkdir ${pair_id}
-kallisto quant -i ${index} -t ${task.cpus} --single \
-${params.mapping_fastq} -o ${pair_id} \
--l ${params.mean} -s ${params.sd} \
-${reads} &> ${reads.simpleName}_kallisto_mapping_report.txt
-"""
+  if (reads instanceof List) {
+  """
+  mkdir ${pair_id}
+  kallisto quant -i ${index} -t ${task.cpus} \
+  ${params.mapping_fastq} -o ${pair_id} \
+  ${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_mapping_report.txt
+  """
+  } else {
+  """
+  mkdir ${pair_id}
+  kallisto quant -i ${index} -t ${task.cpus} --single \
+  ${params.mapping_fastq} -o ${pair_id} \
+  -l ${params.mean} -s ${params.sd} \
+  ${reads} &> ${reads.simpleName}_kallisto_mapping_report.txt
+  """
+  }
 }
 
 params.mapping_fastq_pairedend = "--bias --bootstrap-samples 100"

src/solution_RNASeq.nf

@@ -11,13 +11,15 @@ log.info "bed file : ${params.bed}"
 Channel
   .fromPath( params.fasta )
   .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
+  .map { it -> [it.simpleName, it]}
   .set { fasta_files }
 Channel
   .fromPath( params.bed )
   .ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
+  .map { it -> [it.simpleName, it]}
   .set { bed_files }
 Channel
-  .fromFilePairs( params.fastq )
+  .fromFilePairs( params.fastq, size: -1)
   .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
   .set { fastq_files }
 
@@ -27,10 +29,10 @@ include { fasta_from_bed } from './nf_modules/bedtools/main'
 include { index_fasta; mapping_fastq } from './nf_modules/kallisto/main'
 
 workflow {
-    adaptor_removal(fastq_files)
-    trimming(adaptor_removal.out.fastq)
+    adaptor_removal(fastq_files.view())
+    trimming(adaptor_removal.out.fastq.view())
     fasta_from_bed(fasta_files, bed_files)
     index_fasta(fasta_from_bed.out.fasta)
-    mapping_fastq(index_fasta.out.index.collect(), trimming.out.fastq)
+    mapping_fastq(index_fasta.out.index.collect(), trimming.out.fastq.view())
 }