From 7d92ce73ba86e74ac329c2d8525be42fce6a0f86 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 29 Apr 2021 11:09:25 +0200
Subject: [PATCH] alntools: escape awk $
---
src/nf_modules/alntools/main.nf | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/nf_modules/alntools/main.nf b/src/nf_modules/alntools/main.nf
index a667f101..df2f0f77 100644
--- a/src/nf_modules/alntools/main.nf
+++ b/src/nf_modules/alntools/main.nf
@@ -22,10 +22,10 @@ process bam2ec {
script:
"""
awk -F"\t" '
-$3=="exon"
+\$3=="exon"
{
- ID=substr($9, length($9)-16, 15);
- L[ID]+=$5-$4+1
+ ID=substr(\$9, length(\$9)-16, 15);
+ L[ID]+=\$5-\$4+1
}
END{
for(i in L)
--
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