diff --git a/Snakefile b/Snakefile index f3ec9a99261d6f59f6a5d20067673b80345ad0ab..daa0e348ea8417b0773aab4b909c315446ed3695 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