From 9514876eb167111c0ea549d9aeba69e16a52faa1 Mon Sep 17 00:00:00 2001
From: Rachel  LEGENDRE <rachel.legendre@pasteur.fr>
Date: Wed, 10 Nov 2021 11:45:21 +0100
Subject: [PATCH] remove double / in path

---
 Snakefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Snakefile b/Snakefile
index f3ec9a9..daa0e34 100755
--- a/Snakefile
+++ b/Snakefile
@@ -234,7 +234,7 @@ if config["star_mapping"]["do"]:
     star_mapping_pass2_input = adapters_output
     star_mapping_pass2_done = star_index_output_done
     star_mapping_pass2_index = star_index_output_dir
-    star_mapping_pass2_logs = "02-Mapping/{REF}/STAR//logs/{SAMPLE}_{REF}.out"
+    star_mapping_pass2_logs = "02-Mapping/{REF}/STAR/logs/{SAMPLE}_{REF}.out"
     star_mapping_pass2_output_prefix =  "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_"
     star_mapping_pass2_junctions = expand("02-Mapping/{{REF}}/STAR/{SAMPLE}_{{REF}}_init_SJ.out.tab", SAMPLE=samples)
     star_mapping_pass2_bam = star_mapping_pass1_bam
-- 
GitLab