From 4e063da00dc525b1464c1c4b6fc70ce3a8ea419b Mon Sep 17 00:00:00 2001
From: vvanoost <vincent.vanoosthuyse@ens-lyon.fr>
Date: Wed, 18 Jul 2018 14:43:24 +0000
Subject: [PATCH] =?UTF-8?q?Add=20urqt=20to=20RNAseq=5Fsen1=E2=88=86.nf?=
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---
"src/RNAseq_sen1\342\210\206.nf" | 40 ++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
diff --git "a/src/RNAseq_sen1\342\210\206.nf" "b/src/RNAseq_sen1\342\210\206.nf"
index eda4e8a..7d3fb5a 100644
--- "a/src/RNAseq_sen1\342\210\206.nf"
+++ "b/src/RNAseq_sen1\342\210\206.nf"
@@ -36,3 +36,43 @@ process adaptor_removal {
${reads[0]} ${reads[1]} > ${pair_id}_report.txt
"""
}
+
+/*
+* urqt :
+* Imputs : fastq files
+* Output : fastq files
+*/
+/* quality trimming */
+
+/*
+* for paired-end data
+*/
+
+params.fastq = "$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:
+ set pair_id, file(reads) from fastq_files_cut
+
+ output:
+ set pair_id, "*_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 ${pair_id}_trim_R1.fastq.gz --outpair ${pair_id}_trim_R2.fastq.gz \
+> ${pair_id}_trimming_report.txt
+"""
+}
--
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