From 9b59f32dcfeec9553e027bff35a2d43f3169f959 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 20 Sep 2023 21:16:05 +0200
Subject: [PATCH] fix sample_reads.nf
---
src/modules/sample_reads.nf | 9 ++-------
1 file changed, 2 insertions(+), 7 deletions(-)
diff --git a/src/modules/sample_reads.nf b/src/modules/sample_reads.nf
index 70e135e..6f68317 100644
--- a/src/modules/sample_reads.nf
+++ b/src/modules/sample_reads.nf
@@ -122,14 +122,9 @@ process SAMPLE_READS {
"""
SAMPLE_SIZE=\$(cat $sample_size | tr -d '\\n')
CURRENT_READ_NUMBER=\$(cat $read_number | tr -d '\\n')
+ zcat ${reads} | head -n \$(cat $sample_size | tr -d '\\n') | gzip -c > sample_${reads}
+ READ_NUMBER=\$(zcat sample_${reads} | wc -l)
- if [\$SAMPLE_SIZE -eq \$CURRENT_READ_NUMBER]; then
- ln -s ${reads} sample_${reads}
- 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)
- fi
if [\$SAMPLE_SIZE -ne \$READ_NUMBER]; then
exit 1
fi
--
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