From f089ea6ba83625934eda532b7d2dee3c42e20a28 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 5 May 2021 08:46:08 +0200
Subject: [PATCH] flexi_splitter: fix awk cmd
---
src/nf_modules/flexi_splitter/main.nf | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/nf_modules/flexi_splitter/main.nf b/src/nf_modules/flexi_splitter/main.nf
index 86b9bbd6..47e67604 100644
--- a/src/nf_modules/flexi_splitter/main.nf
+++ b/src/nf_modules/flexi_splitter/main.nf
@@ -34,7 +34,7 @@ process split_file {
tuple val(config_id), path(config)
output:
- tuple val(file_id), path("split/*/*"), emit: fastq
+ tuple val(file_id), path("results/*"), emit: fastq
script:
if (file_id instanceof List){
@@ -50,7 +50,7 @@ process split_file {
mkdir -p results/
find split -type "f" | \
sed -E "s|(.*/split/(.*)/(.*))|\1 \2_\3|g" |
- awk '{"mv "\$1" results/"\$2}'
+ awk '{system("mv "\$1" results/"\$2)}'
rm -Rf split
"""
else
@@ -60,7 +60,7 @@ process split_file {
mkdir -p results/
find split -type "f" | \
sed -E "s|(.*/split/(.*)/(.*))|\1 \2_\3|g" |
- awk '{"mv "\$1" results/"\$2}'
+ awk '{system("mv "\$1" results/"\$2)}'
rm -Rf split
"""
}
--
GitLab