From 92f8f6050f4f2c82f6d904e09b29b78143525f58 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 7 Jun 2019 09:54:29 +0200
Subject: [PATCH] bowtie: nf, only keep 15 last lines of report
---
src/nf_modules/bowtie/mapping_paired.nf | 2 +-
src/nf_modules/bowtie/mapping_single.nf | 5 +++--
src/nf_modules/bowtie2/mapping_paired.nf | 5 +++--
3 files changed, 7 insertions(+), 5 deletions(-)
diff --git a/src/nf_modules/bowtie/mapping_paired.nf b/src/nf_modules/bowtie/mapping_paired.nf
index a2429167..ae533a41 100644
--- a/src/nf_modules/bowtie/mapping_paired.nf
+++ b/src/nf_modules/bowtie/mapping_paired.nf
@@ -47,7 +47,7 @@ samtools view -Sb - > ${pair_id}.bam
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
+tail -n 15 ${file_id}_bowtie_report_tmp.txt > ${file_id}_bowtie_report.txt
"""
}
diff --git a/src/nf_modules/bowtie/mapping_single.nf b/src/nf_modules/bowtie/mapping_single.nf
index 490cb1d0..a86e424c 100644
--- a/src/nf_modules/bowtie/mapping_single.nf
+++ b/src/nf_modules/bowtie/mapping_single.nf
@@ -39,11 +39,12 @@ for (index_file in index) {
"""
bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
-q ${reads} 2> \
-${file_id}_bowtie_report.txt | \
+${file_id}_bowtie_report_tmp.txt | \
samtools view -Sb - > ${file_id}.bam
-if grep -q "Error" ${file_id}_bowtie_report.txt; then
+if grep -q "Error" ${file_id}_bowtie_report_tmp.txt; then
exit 1
fi
+tail -n 15 ${file_id}_bowtie_report_tmp.txt > ${file_id}_bowtie_report.txt
"""
}
diff --git a/src/nf_modules/bowtie2/mapping_paired.nf b/src/nf_modules/bowtie2/mapping_paired.nf
index dc466740..2a97ed62 100644
--- a/src/nf_modules/bowtie2/mapping_paired.nf
+++ b/src/nf_modules/bowtie2/mapping_paired.nf
@@ -35,12 +35,13 @@ process mapping_fastq {
"""
bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
-1 ${reads[0]} -2 ${reads[1]} 2> \
-${pair_id}_bowtie2_report.txt | \
+${pair_id}_bowtie2_report_tmp.txt | \
samtools view -Sb - > ${pair_id}.bam
-if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
+if grep -q "Error" ${pair_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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