From 742e683a6552a73de08e44820740d04626ba08e7 Mon Sep 17 00:00:00 2001
From: vvanoost <vincent.vanoosthuyse@ens-lyon.fr>
Date: Wed, 18 Jul 2018 13:45:47 +0000
Subject: [PATCH] change adapter sequences for Nextflex 3' adapter
---
"src/RNAseq sen1\342\210\206.nf" | 38 ++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
create mode 100644 "src/RNAseq sen1\342\210\206.nf"
diff --git "a/src/RNAseq sen1\342\210\206.nf" "b/src/RNAseq sen1\342\210\206.nf"
new file mode 100644
index 0000000..8695b03
--- /dev/null
+++ "b/src/RNAseq sen1\342\210\206.nf"
@@ -0,0 +1,38 @@
+/*
+* cutadapt :
+* Imputs : fastq files
+* Output : fastq files
+*/
+
+/* Small RNA-seq Illumina adaptor removal NEXTflex Small RNA Seq Kit v3 */
+
+/*
+* for paired-end data
+*/
+
+params.fastq = "$baseDir/data/fastq/*_R{1,2}_001.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:
+ set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
+
+ script:
+ """
+ cutadapt -a TGGAATTCTCGGGTGCCAAGG -g CCTTGGCACCCGAGAATTCCA -A TGGAATTCTCGGGTGCCAAGG -G CCTTGGCACCCGAGAATTCCA \
+ -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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