From 3b2112f624996f84b3580c0684d98c89dc95497f Mon Sep 17 00:00:00 2001
From: gbenoit <gerard.benoit11@ens-lyon.fr>
Date: Wed, 6 Jun 2018 14:40:49 +0000
Subject: [PATCH] RNAseq.nf : add trimming
---
src/RNAseq.nf | 21 +++++++++++++++++++++
1 file changed, 21 insertions(+)
diff --git a/src/RNAseq.nf b/src/RNAseq.nf
index 9ef25c8..0bfc242 100644
--- a/src/RNAseq.nf
+++ b/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
+"""
}
\ No newline at end of file
--
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