From 600ee64ed3478b5736ce322824902b71ef84fd35 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 1 Mar 2022 16:47:03 +0100
Subject: [PATCH] hisat2: change report file name
---
src/nf_modules/hisat2/main.nf | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/nf_modules/hisat2/main.nf b/src/nf_modules/hisat2/main.nf
index 34492a11..5d7ac491 100644
--- a/src/nf_modules/hisat2/main.nf
+++ b/src/nf_modules/hisat2/main.nf
@@ -76,9 +76,9 @@ process mapping_fastq {
-x ${index_id} \
-1 ${reads[0]} \
-2 ${reads[1]} 2> \
- ${file_prefix}_ht2_mapping_report_tmp.txt \
+ ${file_prefix}_ht2_mapping_report.txt \
| samtools view -@ ${task.cpus} -bS - 2>> \
- ${file_prefix}_ht2_mapping_report_tmp.txt \
+ ${file_prefix}_ht2_mapping_report.txt \
| samtools sort -@ ${task.cpus} -o ${file_prefix}.bam - 2>> \
${file_prefix}_ht2_mapping_report.txt
@@ -92,7 +92,7 @@ process mapping_fastq {
-p ${task.cpus} \
-x ${index_id} \
-U ${reads} 2> \
- ${file_prefix}_ht2_mapping_report_tmp.txt \
+ ${file_prefix}_ht2_mapping_report.txt \
| samtools view -@ ${task.cpus} -bS - 2>> \
${file_prefix}_ht2_mapping_report.txt \
| samtools sort -@ ${task.cpus} -o ${file_prefix}.bam - 2>> \
--
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