From d671e35f60d012e8d05b725ff799e0f7c0e5a0e8 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 19 Sep 2023 13:08:46 +0200
Subject: [PATCH] split.nf: change detection of file truncation
---
src/modules/split.nf | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/src/modules/split.nf b/src/modules/split.nf
index 3088a21..a22360e 100644
--- a/src/modules/split.nf
+++ b/src/modules/split.nf
@@ -17,11 +17,17 @@ 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 echo "1" > error.txt; fi")}'
ls -l ${fastq.simpleName}_* | \\
awk '{system("gzip -c "\$9" > "\$9".fastq.gz && rm "\$9)}'
+ if [ -e "error.txt" ]
+ then
+ echo "file truncation detected" >&2
+ exit 1
+ fi
+
cat <<-END_VERSIONS > versions.yml
"${task.process}":
split: v1.35.0
--
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