From 16954d52a073a0fd045ec24c11cf6b9ed003e6a4 Mon Sep 17 00:00:00 2001
From: mherbett <marion.herbette@ens-lyon.fr>
Date: Wed, 6 Jun 2018 14:33:43 +0000
Subject: [PATCH] RNASeq.nf : addin code fo UrQt for quality timming
---
src/RNASeq.nf | 41 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 41 insertions(+)
diff --git a/src/RNASeq.nf b/src/RNASeq.nf
index c130936..244a734 100644
--- a/src/RNASeq.nf
+++ b/src/RNASeq.nf
@@ -38,3 +38,44 @@ process adaptor_removal {
"""
}
+/*
+* urqt :
+* Imputs : fastq files
+* Output : fastq files
+*/
+/* quality trimming */
+
+/*
+* for paired-end data
+*/
+
+params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
+
+log.info "fastq files : ${params.fastq}"
+
+Channel
+ .fromFilePairs( params.fastq )
+ .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+ .set { fastq_files }
+
+process trimming {
+ tag "${reads}"
+ cpus 4
+ publishDir "results/fastq/trimming/", mode: 'copy'
+
+ input:
+ file reads from fastq_files
+
+ 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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