From 4a29c9e0c9fa0a32220dfbb60e9f30e8e7ed8c69 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 15 Oct 2021 14:30:49 +0200
Subject: [PATCH] agat: add gff_to_gtf convertion
---
src/nf_modules/agat/main.nf | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
diff --git a/src/nf_modules/agat/main.nf b/src/nf_modules/agat/main.nf
index b12d2b84..bdf142f8 100644
--- a/src/nf_modules/agat/main.nf
+++ b/src/nf_modules/agat/main.nf
@@ -21,4 +21,26 @@ process gff_to_bed {
zcat ${gff} > ${gff.baseName}.gff
agat_convert_sp_gff2bed.pl --gff ${gff.baseName}.gff --sub cds -o ${gff.simpleName}.bed
"""
+}
+
+params.gff_to_gtf = ""
+params.gff_to_gtf_out = ""
+process gff_to_gtf {
+ container = "${container_url}"
+ label "big_mem_mono_cpus"
+ tag "$file_id"
+ if (params.gff_to_gtf_out != "") {
+ publishDir "results/${params.gff_to_gtf_out}", mode: 'copy'
+ }
+
+ input:
+ tuple val(file_id), path(gff)
+ output:
+ tuple val(file_id), path("*.gtf"), emit: gtf
+
+ script:
+"""
+zcat ${gff} > ${gff.baseName}.gff
+agat_convert_sp_gff2gtf.pl --gff ${gff.baseName}.gff -o ${gff.simpleName}.gtf
+"""
}
\ No newline at end of file
--
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