From f51e613e88188a686a1ba81a8707350e9da95920 Mon Sep 17 00:00:00 2001
From: fduveau <102-fduveau@users.noreply.gitlab.biologie.ens-lyon.fr>
Date: Fri, 13 Dec 2019 14:43:40 +0000
Subject: [PATCH] Update src/RNASeq.nf
---
src/RNASeq.nf | 18 ++++++++++++++++++
1 file changed, 18 insertions(+)
diff --git a/src/RNASeq.nf b/src/RNASeq.nf
index f78d5c2..4c5cb19 100644
--- a/src/RNASeq.nf
+++ b/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
+ """
+}
--
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