diff --git a/Snakefile b/Snakefile index b980edd9559fe6f103727734718c0e6e27251ce3..f7e3619a1d7a60f66c6ed491c6e438c9a2f12f51 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")