From 6a290f9fef04e71f36194c9fdf2e2a1e98bc0c5b Mon Sep 17 00:00:00 2001
From: lestrada <lilia.estrada-virrueta@ens-lyon.fr>
Date: Wed, 6 Jun 2018 13:56:06 +0000
Subject: [PATCH] RNQA_Seq.nf: cutadapt block
---
src/RNA_Seq.nf | 39 +++++++++++++++++++++++++++++++++++++++
1 file changed, 39 insertions(+)
create mode 100644 src/RNA_Seq.nf
diff --git a/src/RNA_Seq.nf b/src/RNA_Seq.nf
new file mode 100644
index 0000000..0eb73bb
--- /dev/null
+++ b/src/RNA_Seq.nf
@@ -0,0 +1,39 @@
+/*
+* cutadapt :
+* Imputs : fastq files
+* Output : fastq files
+*/
+
+/* Illumina adaptor removal */
+
+/*
+* 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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