From 44e1391dcb808cc206b3fc3ad58afc844e791293 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 7 Jun 2019 10:31:29 +0200
Subject: [PATCH] bowtie: nf fix pair_id var call
---
src/nf_modules/bowtie/mapping_paired.nf | 2 +-
src/nf_modules/bowtie2/mapping_paired.nf | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/bowtie/mapping_paired.nf b/src/nf_modules/bowtie/mapping_paired.nf
index ae533a41..46c2cd84 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}_bowtie_report_tmp.txt > ${file_id}_bowtie_report.txt
+tail -n 15 ${pair_id}_bowtie_report_tmp.txt > ${pair_id}_bowtie_report.txt
"""
}
diff --git a/src/nf_modules/bowtie2/mapping_paired.nf b/src/nf_modules/bowtie2/mapping_paired.nf
index 2a97ed62..bd03c7c3 100644
--- a/src/nf_modules/bowtie2/mapping_paired.nf
+++ b/src/nf_modules/bowtie2/mapping_paired.nf
@@ -41,7 +41,7 @@ samtools view -Sb - > ${pair_id}.bam
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
+tail -n 15 ${pair_id}_bowtie2_report_tmp.txt > ${pair_id}_bowtie2_report.txt
"""
}
--
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