cutadapt: update to last contributing guide version

src/nf_modules/cutadapt/main.nf

 version = "2.1"
 container_url = "lbmc/cutadapt:${version}"
 
-adapter_3_prim = "AGATCGGAAGAG"
-adapter_5_prim = "CTCTTCCGATCT"
-trim_quality = "20"
-
-params.adaptor_removal = "-a ${adapter_3_prim} -g ${adapter_5_prim} -A ${adapter_3_prim} -G ${adapter_5_prim}"
+params.adapter_3_prim = "AGATCGGAAGAG"
+params.adapter_5_prim = "CTCTTCCGATCT"
+params.adaptor_removal = "-a ${params.adapter_3_prim} -g ${params.adapter_5_prim} -A ${params.adapter_3_prim} -G ${params.adapter_5_prim}"
+params.adaptor_removal_out = ""
 process adaptor_removal {
   container = "${container_url}"
   label "big_mem_mono_cpus"
-  tag "$pair_id"
+  tag "$file_id"
+  if (params.adaptor_removal_out != "") {
+    publishDir "results/${params.adaptor_removal_out}", mode: 'copy'
+  }
 
   input:
-  tuple val(pair_id), path(reads)
+  tuple val(file_id), path(reads)
 
   output:
-  tuple val(pair_id), path("*_cut_R{1,2}.fastq.gz"), emit: fastq
+  tuple val(file_id), path("*_cut_R{1,2}.fastq.gz"), emit: fastq
   path "*_report.txt", emit: report
 
   script:
-  if (reads instanceof List)
+  if (file_id instanceof List){
+    file_prefix = file_id[0]
+  } else {
+    file_prefix = file_id
+  }
+  if (reads.size() == 2)
   """
   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
+  -o ${file_id}_cut_R1.fastq.gz -p ${file_id}_cut_R2.fastq.gz \
+  ${reads[0]} ${reads[1]} > ${file_id}_report.txt
   """
   else
   """
@@ -33,112 +40,40 @@ process adaptor_removal {
   """
 }
 
-params.adaptor_removal_pairedend = "-a ${adapter_3_prim} -g ${adapter_5_prim} -A ${adapter_3_prim} -G ${adapter_5_prim}"
-process adaptor_removal_pairedend {
-  container = "${container_url}"
-  label "big_mem_mono_cpus"
-  tag "$pair_id"
-
-  input:
-  tuple val(pair_id), path(reads)
-
-  output:
-  tuple val(pair_id), path("*_cut_R{1,2}.fastq.gz"), emit: fastq
-  path "*_report.txt", emit: report
-
-  script:
-  """
-  cutadapt ${params.adaptor_removal_pairedend} \
-  -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
-  ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
-  """
-}
-
-params.adaptor_removal_singleend = "-a ${adapter_3_prim} -g ${adapter_5_prim}"
-process adaptor_removal_singleend {
+params.trim_quality = "20"
+params.trimming = "-q ${params.trim_quality},${params.trim_quality}"
+params.trimming_out = ""
+process trimming {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$file_id"
+  if (params.trimming_out != "") {
+    publishDir "results/${params.trimming_out}", mode: 'copy'
+  }
 
   input:
   tuple val(file_id), path(reads)
 
   output:
-  tuple val(file_id), path("*_cut.fastq.gz"), emit: fastq
-  path "*_report.txt", emit: report
-
-  script:
-  """
-  cutadapt ${params.adaptor_removal_singleend} \
-  -o ${file_id}_cut.fastq.gz \
-  ${reads} > ${file_id}_report.txt
-  """
-}
-
-process trimming {
-  container = "${container_url}"
-  label "big_mem_mono_cpus"
-  tag "$pair_id"
-
-  input:
-  tuple val(pair_id), path(reads)
-
-  output:
-  tuple val(pair_id), path("*_trim_R{1,2}.fastq.gz"), emit:fastq
+  tuple val(file_id), path("*_trim_R{1,2}.fastq.gz"), emit:fastq
   path "*_report.txt", emit: report
 
   script:
-  if (reads instanceof List)
+  if (file_id instanceof List){
+    file_prefix = file_id[0]
+  } else {
+    file_prefix = file_id
+  }
+  if (reads.size() == 2)
   """
-  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
+  cutadapt ${params.trimming} \
+  -o ${file_id}_trim_R1.fastq.gz -p ${file_id}_trim_R2.fastq.gz \
+  ${reads[0]} ${reads[1]} > ${file_id}_report.txt
   """
   else
   """
-  cutadapt -q ${trim_quality},${trim_quality} \
-  -o ${file_id}_trim.fastq.gz \
-  ${reads} > ${file_id}_report.txt
-  """
-}
-
-process trimming_pairedend {
-  container = "${container_url}"
-  label "big_mem_mono_cpus"
-  tag "$pair_id"
-
-  input:
-  tuple val(pair_id), path(reads)
-
-  output:
-  tuple val(pair_id), path("*_trim_R{1,2}.fastq.gz"), emit:fastq
-  path "*_report.txt", emit: report
-
-  script:
-  """
-  cutadapt -q ${trim_quality},${trim_quality} \
-  -o ${pair_id}_trim_R1.fastq.gz -p ${pair_id}_trim_R2.fastq.gz \
-  ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
-  """
-}
-
-process trimming_singleend {
-  container = "${container_url}"
-  label "big_mem_mono_cpus"
-  tag "$file_id"
-
-  input:
-  tuple val(file_id), path(reads)
-
-  output:
-  tuple val(file_id), path("*_trim.fastq.gz"), emit: fastq
-  path "*_report.txt", emit: report
-
-  script:
-  """
-  cutadapt -q ${trim_quality},${trim_quality} \
+  cutadapt ${params.trimming} \
   -o ${file_id}_trim.fastq.gz \
   ${reads} > ${file_id}_report.txt
   """
 }
-