From 1592b47cd2846fdba74bfb53ca503322a7655bfe Mon Sep 17 00:00:00 2001
From: mherbett <marion.herbette@ens-lyon.fr>
Date: Wed, 6 Jun 2018 14:46:42 +0000
Subject: [PATCH] RNASEQ.nf miy fo paid nd
---
src/RNASeq.nf | 19 ++++++++++---------
1 file changed, 10 insertions(+), 9 deletions(-)
diff --git a/src/RNASeq.nf b/src/RNASeq.nf
index 8b03e38..57fa500 100644
--- a/src/RNASeq.nf
+++ b/src/RNASeq.nf
@@ -8,36 +8,37 @@
/*
-* for single-end data
+* for paired-end data
*/
-params.fastq = "$baseDir/data/fastq/*.fastq"
+params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
log.info "fastq files : ${params.fastq}"
Channel
- .fromPath( params.fastq )
+ .fromFilePairs( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
process adaptor_removal {
- tag "$reads.baseName"
+ tag "$pair_id"
publishDir "results/fastq/adaptor_removal/", mode: 'copy'
input:
- file reads from fastq_files
+ set pair_id, file(reads) from fastq_files
output:
- file "*_cut.fastq.gz" into fastq_files_cut
+ file "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
script:
"""
- cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT\
- -o ${reads.baseName}_cut.fastq.gz \
- ${reads} > ${reads.baseName}_report.txt
+ cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT -A AGATCGGAAGAG -G CTCTTCCGATCT \
+ -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
+ ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
"""
}
+
/*
* urqt :
* Imputs : fastq files
--
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