From e5648eb269491393d43e7bc1bc4ccf95f745d689 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Sat, 6 Oct 2018 10:40:22 +0200
Subject: [PATCH] SNP_calling.nf: change RG tag order
---
src/SNP_calling.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/SNP_calling.nf b/src/SNP_calling.nf
index 9fd40b14..945b4450 100644
--- a/src/SNP_calling.nf
+++ b/src/SNP_calling.nf
@@ -146,8 +146,8 @@ process mapping_fastq {
"""
bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
--rg-id ${sample_name} \
---rg SM:${sample_name} \
--rg PL:Illumina \
+--rg SM:${sample_name} \
-1 ${reads[0]} -2 ${reads[1]} 2> \
${pair_id}_bowtie2_report.txt | \
samtools view -Sb - > ${pair_id}.bam
--
GitLab