src/RNAseq_sen1∆.nf

+/*
+* cutadapt :
+* Imputs : fastq files
+* Output : fastq files
+*/
+
+/*                     Small RNA-seq Illumina adaptor removal NEXTflex Small RNA Seq Kit v3                            */
+
+/*
+* for paired-end data
+*/
+
+params.fastq = "$baseDir/data/fastq/*_R{1,2}_001.fastq.gz"
+
+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:
+  set pair_id, "*_cut_R{1,2}_001.fastq.gz" into fastq_files_cut
+
+  script:
+  """
+  cutadapt -a TGGAATTCTCGGGTGCCAAGG -A GTTCAGAGTTCTACAGTCCGACGATC \
+  -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
+  ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
+  """
+}