From 666c81d16657c7d8db3517e678bb17a770834e24 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 13 Mar 2019 16:57:37 +0100
Subject: [PATCH] samblaster: fix test.sh
---
src/nf_modules/samblaster/dedup_sams.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/samblaster/dedup_sams.nf b/src/nf_modules/samblaster/dedup_sams.nf
index 24f4fc5a..bcfd829c 100644
--- a/src/nf_modules/samblaster/dedup_sams.nf
+++ b/src/nf_modules/samblaster/dedup_sams.nf
@@ -19,8 +19,8 @@ process dedup_sam {
script:
"""
samtools view -h ${bam} | \
-samblaster --addMateTags | \
-samtools view -Sb - > ${file_id}_dedub.bam
+samblaster --addMateTags 2> /dev/null | \
+samtools view -Sb - > ${file_id}_dedup.bam
"""
}
--
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