fixe path in star index

Snakefile

@@ -86,7 +86,7 @@ final_output = []
 #----------------------------------
 
 fastqc_input_fastq = input_data
-fastqc_output_done = "00-Fastqc/{{SAMPLE}}{}_fastqc{}".format(rt1,config["input_extension"])
+fastqc_output_done = "00-Fastqc/{{SAMPLE}}{}_fastqc.done".format(rt1)
 fastqc_wkdir = "00-Fastqc"
 fastqc_log = "00-Fastqc/logs/{{SAMPLE}}{}_fastqc_raw.log".format(rt1)
 final_output.extend(expand(fastqc_output_done, SAMPLE=samples))
@@ -212,8 +212,8 @@ if config["star_mapping"]["do"]:
     star_index_fasta = unpack(mapping_index)
     star_mapping_splice_file = unpack(annot_index)
     star_index_log = "02-Mapping/{REF}/STAR/logs/STAR_{REF}_indexing.log"
-    star_index_output_done = config["genome"]["genome_directory"]+"/{REF}/STAR/SAindex"
-    star_index_output_dir = config["genome"]["genome_directory"]+"/{REF}/STAR/" 
+    star_index_output_done = os.path.join(config["genome"]["genome_directory"], "/{REF}/STAR/SAindex")
+    star_index_output_dir = os.path.join(config["genome"]["genome_directory"], "/{REF}/STAR/")
  
     include: os.path.join(RULES, "star_index.rules")