From 572e5b054e34c0128e4215c564aaf96632047c06 Mon Sep 17 00:00:00 2001
From: hpolvech <helene.polveche@ens-lyon.fr>
Date: Wed, 6 Jun 2018 13:58:13 +0000
Subject: [PATCH] RNASeq.nf:Cutadapt
---
src/RNASeq.nf | 31 +++++++++++++++++++++++++++++++
1 file changed, 31 insertions(+)
create mode 100644 src/RNASeq.nf
diff --git a/src/RNASeq.nf b/src/RNASeq.nf
new file mode 100644
index 0000000..354f00e
--- /dev/null
+++ b/src/RNASeq.nf
@@ -0,0 +1,31 @@
+/*
+* Cutadapt
+* 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: ${params.fastq}" }
+ .set { fastq_files }
+
+process adaptor_removal {
+ tag "$pair_id"
+ publishDir "results/fastq/adaptor_removal/", mode: 'copy'
+
+ input:
+ set pair_id, file(reads) from fastq_files
+
+ output:
+ file "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
+
+ script:
+ """
+ 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
+ """
+}
--
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