fix error with none option of pass2

Snakefile

@@ -236,6 +236,7 @@ if config["star_mapping"]["do"]:
     final_output.extend(expand(star_mapping_pass1_junctions, SAMPLE=samples, REF=ref))    
     include: os.path.join(RULES, "star_mapping_pass1.rules")  
     
+    if config["star_mapping"]["pass2"] != "none":
         #Second pass mapping
         star_mapping_pass2_input = adapters_output
         star_mapping_pass2_done = star_index_output_done
@@ -247,10 +248,11 @@ if config["star_mapping"]["do"]:
         elif config["star_mapping"]["pass2"] == "all-samples":
             star_mapping_pass2_junctions = expand("02-Mapping/{{REF}}/STAR/{SAMPLE}_{{REF}}_init_SJ.out.tab", SAMPLE=samples)
         else:
-        raise ValueError("Please provides a valid option to pass3 of STAR: must be by-sample, all-samples or none")
+            raise ValueError("Please provides a valid option to pass2 of STAR: must be by-sample, all-samples or none")
         star_mapping_pass2_bam = star_mapping_pass1_bam
         star_mapping_pass2_read_groups = "ID:{SAMPLE}"
         star_mapping_pass2_sort = "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_Aligned.sortedByCoord.out.bam"
+
         final_output.extend(expand(star_mapping_pass2_sort, SAMPLE=samples, REF=ref))    
         include: os.path.join(RULES, "star_mapping_pass2.rules")