RNASeq.nf : removed co o sinle end triming

src/RNASeq.nf

@@ -6,36 +6,6 @@
 
 /*                      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"
-  publishDir "results/fastq/adaptor_removal/", mode: 'copy'
-
-  input:
-  set pair_id, file(reads) from fastq_files
-
-  output:
-  file "*_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