From 79b0bfad5e6033d1e342cc14dd86d1e1d8a84ef6 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 19 Sep 2023 09:18:38 +0200
Subject: [PATCH] remove bash integer convertion
---
src/modules/sample_reads.nf | 10 +++++-----
src/modules/split.nf | 2 +-
2 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/src/modules/sample_reads.nf b/src/modules/sample_reads.nf
index e10d4ec..70e135e 100644
--- a/src/modules/sample_reads.nf
+++ b/src/modules/sample_reads.nf
@@ -120,15 +120,15 @@ process SAMPLE_READS {
error "SEQTK/SAMPLE must have a sample_size value included"
}
"""
- SAMPLE_SIZE=\$((cat $sample_size | tr -d '\\n'))
- CURRENT_READ_NUMBER=\$((cat $read_number | tr -d '\\n'))
+ SAMPLE_SIZE=\$(cat $sample_size | tr -d '\\n')
+ CURRENT_READ_NUMBER=\$(cat $read_number | tr -d '\\n')
if [\$SAMPLE_SIZE -eq \$CURRENT_READ_NUMBER]; then
ln -s ${reads} sample_${reads}
- READ_NUMBER=\$((cat $sample_size | tr -d '\\n'))
+ READ_NUMBER=\$(cat $sample_size | tr -d '\\n')
else
- zcat ${reads} | head -n \$((cat $sample_size | tr -d '\\n')) | gzip -c > sample_${reads}
- READ_NUMBER=\$((zcat sample_${reads} | wc -l))
+ zcat ${reads} | head -n \$(cat $sample_size | tr -d '\\n') | gzip -c > sample_${reads}
+ READ_NUMBER=\$(zcat sample_${reads} | wc -l)
fi
if [\$SAMPLE_SIZE -ne \$READ_NUMBER]; then
exit 1
diff --git a/src/modules/split.nf b/src/modules/split.nf
index 9a8b72f..3088a21 100644
--- a/src/modules/split.nf
+++ b/src/modules/split.nf
@@ -17,7 +17,7 @@ process SPLIT {
zcat ${fastq} | split -l 4000000 - ${fastq.simpleName}_
ls -l ${fastq.simpleName}_* | \\
- awk '{system("if [\$((wc -l "\$9")) -ne 4000000]; then exit 1; fi")}'
+ awk '{system("if [\$(wc -l "\$9") -ne 4000000]; then exit 1; fi")}'
ls -l ${fastq.simpleName}_* | \\
awk '{system("gzip -c "\$9" > "\$9".fastq.gz && rm "\$9)}'
--
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