From acb3143cf711a50db6e14f96ec4d405f61fa619b Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 5 May 2021 14:46:09 +0200
Subject: [PATCH] alntools: double escape awk script
---
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 a302ec2d..31e9c6ca 100644
--- a/src/nf_modules/alntools/main.nf
+++ b/src/nf_modules/alntools/main.nf
@@ -21,14 +21,14 @@ process bam2ec {
script:
"""
-awk -F"[\t;]" '
+awk -F"[\\t;]" '
\$3=="exon" {
- ID=gensub(/transcript_id \"(.*)\"/, "\\1", "g", \$11);
+ ID=gensub(/transcript_id \\"(.*)\\"/, "\\\\1", "g", \$11);
LEN[ID]+=\$5-\$4+1;
}
END{
for(i in LEN)
- {print i"\t"LEN[i]}
+ {print i"\\t"LEN[i]}
}
' ${gtf} > ${gtf.simpleName}_transcripts_lengths.tsv
alntools bam2ec ${params.bam2ec} -t ${gtf.simpleName}_transcripts_lengths.tsv -c 8 ${bam} ${bam.simpleName}.bin
--
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