From b5b1582234852124a15d8230dd6b08bfef998fe2 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 5 Oct 2018 23:35:23 +0200
Subject: [PATCH] SNP_calling.nf: add RG info in bowtie22
---
src/SNP_calling.nf | 3 +++
1 file changed, 3 insertions(+)
diff --git a/src/SNP_calling.nf b/src/SNP_calling.nf
index cdc2782d..84027a8d 100644
--- a/src/SNP_calling.nf
+++ b/src/SNP_calling.nf
@@ -129,6 +129,9 @@ process mapping_fastq {
}
"""
bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
+--rg-id ${sample_name} \
+--rg SM:${sample_name} \
+--rg PL:Illumina \
-1 ${reads[0]} -2 ${reads[1]} 2> \
${pair_id}_bowtie2_report.txt | \
samtools view -Sb - > ${pair_id}.bam
--
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