From fca7dda8d917513eff8c035a38787127525b97fe Mon Sep 17 00:00:00 2001
From: magodfroid <maxime.godfroid@sciensano.be>
Date: Thu, 26 Oct 2023 16:09:22 +0200
Subject: [PATCH] [mg] fixed the conflicts in the Snakefile

---
 workflow/Snakefile | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/workflow/Snakefile b/workflow/Snakefile
index 8a5ed226..ad3616ea 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -413,7 +413,8 @@ if common_config["platform"] =="RNA-Seq":
             genome = genome_dir / pipeline_config["genome_filename"]
         params:
             annotations = genome_dir / pipeline_config["annotation_filename"],
-            genome_name = pipeline_config["genome_name"]
+            genome_name = pipeline_config["genome_name"],
+            genome_dir = pipeline_config["genomedir"]
         output:
             directory(genome_dir / "RSEM_index")
         conda:
@@ -421,7 +422,7 @@ if common_config["platform"] =="RNA-Seq":
         benchmark: log_dir / "benchmark.RSEM_make_index.txt"
         shell:
             '''
-            mkdir RSEM_index
+            mkdir {params.genome_dir}/RSEM_index
             rsem-prepare-reference --gtf {params.annotations} {input.genome} {output}/{params.genome_name}
             '''