From e4e4c1bccd400171d579f2a96d00eaf113041e6f Mon Sep 17 00:00:00 2001
From: rlegendr <rachel.legendre@pasteur.fr>
Date: Mon, 13 Sep 2021 12:07:51 +0200
Subject: [PATCH] bug in path
---
Snakefile | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/Snakefile b/Snakefile
index b980edd..f7e3619 100755
--- a/Snakefile
+++ b/Snakefile
@@ -174,14 +174,14 @@ if config["bowtie2_mapping"]["do"]:
bowtie2_index_fasta = unpack(mapping_index)
bowtie2_index_log = "02-Mapping/bowtie2/logs/bowtie2_{REF}_indexing.log"
if config["genome"]["host_mapping"] and config["genome"]["rRNA_mapping"] :
- bowtie2_index_output_done = config["genome"]["genome_directory"]+"{}/bowtie2/{{REF}}.1.bt2".format(config["genome"]["host_name"])
- bowtie2_index_output_prefix = config["genome"]["genome_directory"]+"{}/bowtie2/{{REF}}".format(config["genome"]["host_name"])
+ bowtie2_index_output_done = os.path.join(config["genome"]["genome_directory"],"{}/bowtie2/{{REF}}.1.bt2".format(config["genome"]["host_name"]))
+ bowtie2_index_output_prefix = os.path.join(config["genome"]["genome_directory"]+"{}/bowtie2/{{REF}}".format(config["genome"]["host_name"]))
elif not config["genome"]["host_mapping"] and config["genome"]["rRNA_mapping"] :
- bowtie2_index_output_done = config["genome"]["genome_directory"]+"{}/bowtie2/{{REF}}.1.bt2".format(config["genome"]["name"])
- bowtie2_index_output_prefix = config["genome"]["genome_directory"]+"{}/bowtie2/{{REF}}".format(config["genome"]["name"])
+ bowtie2_index_output_done = os.path.join(config["genome"]["genome_directory"]+"{}/bowtie2/{{REF}}.1.bt2".format(config["genome"]["name"]))
+ bowtie2_index_output_prefix = os.path.join(config["genome"]["genome_directory"]+"{}/bowtie2/{{REF}}".format(config["genome"]["name"]))
else:
- bowtie2_index_output_done = config["genome"]["genome_directory"]+"{REF}/bowtie2/{REF}.1.bt2"
- bowtie2_index_output_prefix = config["genome"]["genome_directory"]+"{REF}/bowtie2/{REF}"
+ bowtie2_index_output_done = os.path.join(config["genome"]["genome_directory"]+"{REF}/bowtie2/{REF}.1.bt2")
+ bowtie2_index_output_prefix = os.path.join(config["genome"]["genome_directory"]+"{REF}/bowtie2/{REF}")
include: os.path.join(RULES, "bowtie2_index.rules")
--
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