From 0dba9f2bf7ac9f01393deab069d081b553323589 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 6 Jun 2018 11:01:26 +0200
Subject: [PATCH] Kallisto.nf: fix paired end
---
src/nf_modules/Kallisto/kallisto.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/nf_modules/Kallisto/kallisto.nf b/src/nf_modules/Kallisto/kallisto.nf
index aa92350..b158eee 100644
--- a/src/nf_modules/Kallisto/kallisto.nf
+++ b/src/nf_modules/Kallisto/kallisto.nf
@@ -70,7 +70,7 @@ process mapping_fastq {
mkdir ${reads[0].baseName}
kallisto quant -i ${index} -t ${task.cpus} \
--bias --bootstrap-samples 100 -o ${reads[0].baseName} \
-${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_report.txt
+${reads[0]} ${reads[1]} &> ${reads[0].baseName}_kallisto_report.txt
"""
}
--
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