From 0977ef071a377de78f712d3be8e479709f923782 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 7 Jun 2019 09:51:43 +0200
Subject: [PATCH] bowtie2: nf, only keep last 15 lines of report
---
src/nf_modules/bowtie/mapping_paired.nf | 5 +++--
src/nf_modules/bowtie2/mapping_single.nf | 5 +++--
2 files changed, 6 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/bowtie/mapping_paired.nf b/src/nf_modules/bowtie/mapping_paired.nf
index e92cb3d1..a2429167 100644
--- a/src/nf_modules/bowtie/mapping_paired.nf
+++ b/src/nf_modules/bowtie/mapping_paired.nf
@@ -41,12 +41,13 @@ process mapping_fastq {
# reads
bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
-1 ${reads[0]} -2 ${reads[1]} 2> \
-${pair_id}_bowtie_report.txt | \
+${pair_id}_bowtie_report_tmp.txt | \
samtools view -Sb - > ${pair_id}.bam
-if grep -q "Error" ${pair_id}_bowtie_report.txt; then
+if grep -q "Error" ${pair_id}_bowtie_report_tmp.txt; then
exit 1
fi
+tail -n 15 ${file_id}_bowtie2_report_tmp.txt > ${file_id}_bowtie2_report.txt
"""
}
diff --git a/src/nf_modules/bowtie2/mapping_single.nf b/src/nf_modules/bowtie2/mapping_single.nf
index 1b7954ec..a264cb72 100644
--- a/src/nf_modules/bowtie2/mapping_single.nf
+++ b/src/nf_modules/bowtie2/mapping_single.nf
@@ -35,11 +35,12 @@ process mapping_fastq {
"""
bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
-U ${reads} 2> \
-${file_id}_bowtie2_report.txt | \
+${file_id}_bowtie2_report_tmp.txt | \
samtools view -Sb - > ${file_id}.bam
-if grep -q "Error" ${file_id}_bowtie2_report.txt; then
+if grep -q "Error" ${file_id}_bowtie2_report_tmp.txt; then
exit 1
fi
+tail -n 15 ${file_id}_bowtie2_report_tmp.txt > ${file_id}_bowtie2_report.txt
"""
}
--
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