Update src/RNASeq.nf

src/RNASeq.nf

@@ -22,3 +22,21 @@ process adaptor_removal {
   ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
   """
 }
+
+process trimming {
+  tag "$pair_id"
+  publishDir "results/fastq/trimming/", mode: 'copy'
+
+  input:
+  set pair_id, file(reads) from fastq_files
+
+  output:
+  set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
+
+  script:
+  """
+  cutadapt -q 20,20 \
+  -o ${pair_id}_trim_R1.fastq.gz -p ${pair_id}_trim_R2.fastq.gz \
+  ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
+  """
+}