From 6ea0517e3e2ec8546bb3bb9798587b25328d4dbd Mon Sep 17 00:00:00 2001
From: khalid <khalid.belkhir@umontpellier.fr>
Date: Mon, 29 Nov 2021 10:39:02 +0100
Subject: [PATCH] minimap2 redirect stderr bug
---
.../minimap2_reference_bam.rule.snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/tools/minimap2_reference_bam/minimap2_reference_bam.rule.snakefile b/tools/minimap2_reference_bam/minimap2_reference_bam.rule.snakefile
index b37325a4..3e4a57bd 100755
--- a/tools/minimap2_reference_bam/minimap2_reference_bam.rule.snakefile
+++ b/tools/minimap2_reference_bam/minimap2_reference_bam.rule.snakefile
@@ -16,7 +16,7 @@ rule <step_name>__minimap2_reference_bam:
"-t {threads} "
"{input.fasta} "
"{input.read} "
- "| samtools view -hb 2>> {log} "
+ "| samtools view -hb 2 > {log} "
"| samtools sort -@ {threads} > {output.reads_mapping} 2>> {log} &&"
" samtools index -@ {threads} {output.reads_mapping} 2>> {log}"
--
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