From 5911d1201dd7a17e4693f51ecde2f68540fad4c3 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 20 Oct 2021 09:25:27 +0200
Subject: [PATCH] agat: add params to convertion processes
---
src/nf_modules/agat/main.nf | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/agat/main.nf b/src/nf_modules/agat/main.nf
index bdf142f8..e2d832e7 100644
--- a/src/nf_modules/agat/main.nf
+++ b/src/nf_modules/agat/main.nf
@@ -19,7 +19,7 @@ process gff_to_bed {
script:
"""
zcat ${gff} > ${gff.baseName}.gff
-agat_convert_sp_gff2bed.pl --gff ${gff.baseName}.gff --sub cds -o ${gff.simpleName}.bed
+agat_convert_sp_gff2bed.pl ${params.gff_to_bed} --gff ${gff.baseName}.gff -o ${gff.simpleName}.bed
"""
}
@@ -41,6 +41,6 @@ process gff_to_gtf {
script:
"""
zcat ${gff} > ${gff.baseName}.gff
-agat_convert_sp_gff2gtf.pl --gff ${gff.baseName}.gff -o ${gff.simpleName}.gtf
+agat_convert_sp_gff2gtf.pl ${params.gff_to_gtf} --gff ${gff.baseName}.gff -o ${gff.simpleName}.gtf
"""
}
\ No newline at end of file
--
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