From f1b5e9a68e4a00615755753778043fed2e8925c6 Mon Sep 17 00:00:00 2001
From: khalid <khalid.belkhir@umontpellier.fr>
Date: Wed, 1 Dec 2021 17:29:20 +0100
Subject: [PATCH] debug accel_align
---
tools/accel_align/accel_align.rule.snakefile | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/tools/accel_align/accel_align.rule.snakefile b/tools/accel_align/accel_align.rule.snakefile
index e80bf361..46745566 100755
--- a/tools/accel_align/accel_align.rule.snakefile
+++ b/tools/accel_align/accel_align.rule.snakefile
@@ -29,7 +29,7 @@ if config["SeOrPe"] == "PE":
"-o {params.tmp_sam} "
"{params.indexPrefix} "
"{input.read} {input.read2} 2> {log}; "
- "samtools view -b {params.tmp_sam}/ 2>> {log} "
+ "samtools view -hb {params.tmp_sam} 2>> {log} "
"| samtools sort -@ {threads} > {output.bam} 2>> {log} && "
"samtools index -@ {threads} {output.bam} 2>> {log}; "
"rm -f {params.tmp_sam} "
@@ -63,7 +63,7 @@ elif config["SeOrPe"] == "SE":
"-o {params.tmp_sam} "
"{params.indexPrefix} "
"{input.read} 2> {log}; "
- "| samtools view -b {params.tmp_sam} 2>> {log} "
+ "| samtools view -hb {params.tmp_sam} 2>> {log} "
"| samtools sort -@ {threads} > {output.bam} 2>> {log} && "
"samtools index -@ {threads} {output.bam} 2>> {log}; "
"rm -f {params.tmp_sam} "
--
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