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Verified Commit f089ea6b authored by Laurent Modolo's avatar Laurent Modolo
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flexi_splitter: fix awk cmd

parent ef62cf28
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...@@ -34,7 +34,7 @@ process split_file { ...@@ -34,7 +34,7 @@ process split_file {
tuple val(config_id), path(config) tuple val(config_id), path(config)
output: output:
tuple val(file_id), path("split/*/*"), emit: fastq tuple val(file_id), path("results/*"), emit: fastq
script: script:
if (file_id instanceof List){ if (file_id instanceof List){
...@@ -50,7 +50,7 @@ process split_file { ...@@ -50,7 +50,7 @@ process split_file {
mkdir -p results/ mkdir -p results/
find split -type "f" | \ find split -type "f" | \
sed -E "s|(.*/split/(.*)/(.*))|\1 \2_\3|g" | sed -E "s|(.*/split/(.*)/(.*))|\1 \2_\3|g" |
awk '{"mv "\$1" results/"\$2}' awk '{system("mv "\$1" results/"\$2)}'
rm -Rf split rm -Rf split
""" """
else else
...@@ -60,7 +60,7 @@ process split_file { ...@@ -60,7 +60,7 @@ process split_file {
mkdir -p results/ mkdir -p results/
find split -type "f" | \ find split -type "f" | \
sed -E "s|(.*/split/(.*)/(.*))|\1 \2_\3|g" | sed -E "s|(.*/split/(.*)/(.*))|\1 \2_\3|g" |
awk '{"mv "\$1" results/"\$2}' awk '{system("mv "\$1" results/"\$2)}'
rm -Rf split rm -Rf split
""" """
} }
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