From 81f280a02f4a73672b0d09946909cfa82a464701 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Fri, 8 Oct 2021 16:55:42 +0200
Subject: [PATCH] agat: add main.nf
---
src/nf_modules/agat/main.nf | 23 +++++++++++++++++++++++
1 file changed, 23 insertions(+)
create mode 100644 src/nf_modules/agat/main.nf
diff --git a/src/nf_modules/agat/main.nf b/src/nf_modules/agat/main.nf
new file mode 100644
index 00000000..03b1a3f5
--- /dev/null
+++ b/src/nf_modules/agat/main.nf
@@ -0,0 +1,23 @@
+version = "0.8.0"
+container_url = "lbmc/agat:${version}"
+
+params.gff_to_bed = ""
+params.gff_to_bed_out = ""
+process gff_to_bed {
+ container = "${container_url}"
+ label "big_mem_mono_cpus"
+ tag "$file_id"
+ if (params.gff_to_bed_out != "") {
+ publishDir "results/${params.gff_to_bed_out}", mode: 'copy'
+ }
+
+ input:
+ tuple val(file_id), path(gff)
+ output:
+ tuple val(file_id), path("*.bed"), emit: bed
+
+ script:
+"""
+agat_convert_sp_gff2bed.pl --gff ${gff} -o ${gff.simpleName}.bed
+"""
+}
\ No newline at end of file
--
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