From c68652064cfdb8c89be958abdc7777e6b1738946 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 1 Mar 2022 17:23:49 +0100
Subject: [PATCH] hisat2: remove samtools report
---
src/nf_modules/hisat2/main.nf | 13 ++++---------
1 file changed, 4 insertions(+), 9 deletions(-)
diff --git a/src/nf_modules/hisat2/main.nf b/src/nf_modules/hisat2/main.nf
index 2cdac569..e649bb6a 100644
--- a/src/nf_modules/hisat2/main.nf
+++ b/src/nf_modules/hisat2/main.nf
@@ -77,10 +77,8 @@ process mapping_fastq {
-1 ${reads[0]} \
-2 ${reads[1]} 2> \
${file_prefix}_ht2_mapping_report.txt \
- | samtools view -@ ${task.cpus} -bS - 2>> \
- ${file_prefix}_ht2_samtools_view_report.txt \
- | samtools sort -@ ${task.cpus} -o ${file_prefix}.bam - 2>> \
- ${file_prefix}_ht2_samtools_sort_report.txt
+ | samtools view -@ ${task.cpus} -bS - \
+ | samtools sort -@ ${task.cpus} -o ${file_prefix}.bam
if grep -q "Error" ${file_prefix}_ht2_mapping_report.txt; then
exit 1
@@ -93,11 +91,8 @@ process mapping_fastq {
-x ${index_id} \
-U ${reads} 2> \
${file_prefix}_ht2_mapping_report.txt \
- | samtools view -@ ${task.cpus} -bS - 2>> \
- ${file_prefix}_ht2_samtools_view_report.txt \
- | samtools sort -@ ${task.cpus} -o ${file_prefix}.bam - 2>> \
- ${file_prefix}_ht2_samtools_sort_report.txt
-
+ | samtools view -@ ${task.cpus} -bS - \
+ | samtools sort -@ ${task.cpus} -o ${file_prefix}.bam
if grep -q "Error" ${file_prefix}_ht2_mapping_report.txt; then
exit 1
fi
--
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