RNASeq.nf: remove single-end process

src/RNASeq.nf

@@ -36,35 +36,3 @@ process adaptor_removal {
   ${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"
-  publishDir "results/fastq/adaptor_removal/", mode: 'copy'
-
-  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
-  """
-}
-