RNAseq.nf : add trimming

src/RNAseq.nf

@@ -23,4 +23,25 @@ process adaptor_removal {
   -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
   ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
   """
+}
+
+
+process trimming {
+  tag "${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
+"""
 }
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