From 7286daefed9fd53ff5e88c89ebbed4a0b5f3ffae Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 6 Oct 2021 15:41:16 +0200
Subject: [PATCH] samtools: fix bug :21
---
src/nf_modules/samtools/main.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index 1a402ba5..3c940314 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -18,7 +18,7 @@ process index_fasta {
script:
"""
-if gzip -t file.gz; then
+if gzip -t ${fasta}; then
zcat ${fasta} > ${fasta.simpleName}.fasta
samtools faidx ${params.index_fasta} ${fasta.simpleName}.fasta
else
--
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