cutadapt.nf: adaptator trimming code for paired and single-ends

src/nf_modules/cutadapt/cutadapt.nf

+/*
+* cutadapt :
+* Imputs : fastq files
+*/
+
+/*                      Illumina adaptor removal
+
+/*
+* for paired-end data
+*/
+
+params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
+
+log.info "fastq files : ${params.fastq}"
+
+Channel
+  .fromFilePairs( params.fastq )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .set { fastq_files }
+
+process adaptor_removal {
+  tag "$pair_id"
+
+  input:
+  set pair_id, file(reads) from fastq_files
+
+  output:
+  set "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
+
+  script:
+  """
+  cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT -A AGATCGGAAGAG -G CTCTTCCGATCT \
+  -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
+  ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
+  """
+}
+
+/*
+* for single-end data
+*/
+
+params.fastq = "$baseDir/data/fastq/*.fastq"
+
+log.info "fastq files : ${params.fastq}"
+
+Channel
+  .fromPath( params.fastq )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .set { fastq_files }
+
+process adaptor_removal {
+  tag "$reads.baseName"
+
+  input:
+  file reads from fastq_files
+
+  output:
+  file "*_cut.fastq.gz" into fastq_files_cut
+
+  script:
+  """
+  cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT\
+  -o ${reads.baseName}_cut.fastq.gz \
+  ${reads} > ${reads.baseName}_report.txt
+  """
+}
+