From c25de5f0091db7d24d2898ca1f5e05bd582ffbea Mon Sep 17 00:00:00 2001
From: Alexandria Pinto <pintoa1@mskcc.org>
Date: Wed, 18 Sep 2024 12:09:13 -0400
Subject: [PATCH] Name Genebed according to ensembl version

---
 modules/local/metafusion/genebed/main.nf | 3 ++-
 subworkflows/local/prepare_references.nf | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/modules/local/metafusion/genebed/main.nf b/modules/local/metafusion/genebed/main.nf
index 2314c40..34cba9c 100644
--- a/modules/local/metafusion/genebed/main.nf
+++ b/modules/local/metafusion/genebed/main.nf
@@ -9,6 +9,7 @@ process METAFUSION_GENEBED {
 
     input:
     tuple val(meta), path(gff)
+    val ensembl_version
 
     output:
     tuple val(meta), path("*.metafusion.gene.bed"), emit: metafusion_gene_bed
@@ -23,7 +24,7 @@ process METAFUSION_GENEBED {
     """
     final_generate_v75_gene_bed.R \\
         $gff \\
-        ${prefix}.metafusion.gene.bed
+        ${ensembl_version}.metafusion.gene.bed
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/subworkflows/local/prepare_references.nf b/subworkflows/local/prepare_references.nf
index b1d06a8..97e4124 100644
--- a/subworkflows/local/prepare_references.nf
+++ b/subworkflows/local/prepare_references.nf
@@ -90,7 +90,8 @@ workflow PREPARE_REFERENCES {
     )
 
     METAFUSION_GENEBED(
-        AGAT_SPADDINTRONS.out.gff
+        AGAT_SPADDINTRONS.out.gff,
+        params.ensembl_version
     )
 
     METAFUSION_GENEINFO(