From 6f027a2eeb0f5517735fbb874177e9e2a2d4f523 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 14 Apr 2021 10:40:29 +0200
Subject: [PATCH] kallisto: fix warning in mapping_fastq about single-end
parameters
---
src/nf_modules/kallisto/main.nf | 6 ++----
1 file changed, 2 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/kallisto/main.nf b/src/nf_modules/kallisto/main.nf
index d25f085a..9c85118a 100644
--- a/src/nf_modules/kallisto/main.nf
+++ b/src/nf_modules/kallisto/main.nf
@@ -50,22 +50,20 @@ process mapping_fastq {
pair_id = file_id
}
- if (reads instanceof List) {
+ if (reads instanceof List)
"""
mkdir ${pair_id}
kallisto quant -i ${index} -t ${task.cpus} \
${params.mapping_fastq} -o ${pair_id} \
${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_mapping_report.txt
"""
- } else {
+ else
"""
mkdir ${pair_id}
kallisto quant -i ${index} -t ${task.cpus} --single \
${params.mapping_fastq} -o ${pair_id} \
- -l ${params.mean} -s ${params.sd} \
${reads} &> ${reads.simpleName}_kallisto_mapping_report.txt
"""
- }
}
params.mapping_fastq_pairedend = "--bias --bootstrap-samples 100"
--
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