From fbed90fcf4848bcb3a3d11db018d19152c369a36 Mon Sep 17 00:00:00 2001
From: Emmanuel Labaronne <emmanuel.labaronne@ens-lyon.fr>
Date: Mon, 28 Sep 2020 16:46:54 +0200
Subject: [PATCH] src/RNAseq.nf : add --paired option in dedup process
---
src/RNAseq.nf | 2 ++
1 file changed, 2 insertions(+)
diff --git a/src/RNAseq.nf b/src/RNAseq.nf
index 47f028d8..97a95fe2 100644
--- a/src/RNAseq.nf
+++ b/src/RNAseq.nf
@@ -346,6 +346,7 @@ process dedup_genome {
"""
umi_tools dedup -I ${bam[0]} \
-S ${file_id}.dedup.bam \
+ --paired \
2> ${file_id}_dedup.log
"""
}
@@ -505,6 +506,7 @@ process dedup_postgenome {
"""
umi_tools dedup -I ${bam[0]} \
-S ${file_id}.dedup.bam \
+ --paired \
2> ${file_id}_dedup.log
"""
}
--
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