From 61d6bb79d0d8c68bdbaafb4a04c01f612ea4cef0 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 8 Mar 2021 10:45:16 +0100
Subject: [PATCH] gatk4: fix typo :264
---
src/nf_modules/gatk4/main.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf
index e616741f..f0b13262 100644
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -261,7 +261,7 @@ process personalized_genome {
gatk --java-options "-Xmx${xmx_memory}" -T FastaAlternateReferenceMaker\
-R ${reference} \
-V ${vcf} \
- -o ${file_id.library}_genome.fasta
+ -o ${file_id[0]}_genome.fasta
"""
}
--
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