From 55144a92cf12575e480852f0d389e567960b5ff6 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 1 Sep 2021 15:29:40 +0200
Subject: [PATCH] bowtie2: simplify index name
---
src/nf_modules/bowtie2/main.nf | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/bowtie2/main.nf b/src/nf_modules/bowtie2/main.nf
index 4a670f17..3a0fc967 100644
--- a/src/nf_modules/bowtie2/main.nf
+++ b/src/nf_modules/bowtie2/main.nf
@@ -15,17 +15,17 @@ process index_fasta {
tuple val(file_id), path(fasta)
output:
- tuple val(file_id), path("*.index*"), emit: index
+ tuple val(file_id), path("*.bt2"), emit: index
tuple val(file_id), path("*_report.txt"), emit: report
script:
"""
bowtie2-build --threads ${task.cpus} \
${fasta} \
- ${fasta.baseName}.index &> \
- ${fasta.baseName}_bowtie2_index_report.txt
+ ${fasta.simpleName} &> \
+ ${fasta.simpleName}_bowtie2_index_report.txt
-if grep -q "Error" ${fasta.baseName}_bowtie2_index_report.txt; then
+if grep -q "Error" ${fasta.simpleName}_bowtie2_index_report.txt; then
exit 1
fi
"""
--
GitLab