RNAseq.nf : add UrQt block

src/RNAseq.nf

@@ -25,3 +25,24 @@ process adaptor_removal {
   """
 }
 
+process trimming {
+  tag "${reads}"
+  cpus 4
+  publishDir "results/fastq/trimming/", mode: 'copy'
+
+  input:
+  file reads from fastq_files_cut
+
+  output:
+  file "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
+
+  script:
+"""
+UrQt --t 20 --m ${task.cpus} --gz \
+--in ${reads[0]} --inpair ${reads[1]} \
+--out ${reads[0].baseName}_trim_R1.fastq.gz --outpair ${reads[1].baseName}_trim_R2.fastq.gz \
+> ${reads[0].baseName}_trimming_report.txt
+"""
+}
+
+