From 39775a6cd33609d4859bf3f452cd95f2c9d18437 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 8 Oct 2021 17:02:44 +0200
Subject: [PATCH] agat: unzip gz file
---
src/nf_modules/agat/main.nf | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/src/nf_modules/agat/main.nf b/src/nf_modules/agat/main.nf
index a2e3d420..b12d2b84 100644
--- a/src/nf_modules/agat/main.nf
+++ b/src/nf_modules/agat/main.nf
@@ -18,6 +18,7 @@ process gff_to_bed {
script:
"""
-agat_convert_sp_gff2bed.pl --gff ${gff} --sub cds -o ${gff.simpleName}.bed
+zcat ${gff} > ${gff.baseName}.gff
+agat_convert_sp_gff2bed.pl --gff ${gff.baseName}.gff --sub cds -o ${gff.simpleName}.bed
"""
}
\ No newline at end of file
--
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