From 5f4bd25b8dc62c261dead05e849fe03d183f7fd6 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 5 Jun 2018 10:30:17 +0200
Subject: [PATCH] Kallisto: nf fix index for single-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 922d975..885f6ae 100644
--- a/src/nf_modules/Kallisto/kallisto.nf
+++ b/src/nf_modules/Kallisto/kallisto.nf
@@ -113,7 +113,7 @@ process mapping_fastq {
script:
"""
mkdir ${reads.baseName}
-kallisto quant -i ${index[0].baseName} -t ${task.cpus} --single
+kallisto quant -i ${index} -t ${task.cpus} --single
--bias --bootstrap-samples 100 -o ${reads.baseName} \
-l ${params.mean} -s ${params.sd} -o ./ \
${reads} > ${reads.baseName}_kallisto_report.txt
--
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