corrected stranded ALFA for rev. seq data

snakemake/Snakefile

@@ -211,8 +211,8 @@ rule run_alfa_bg_stranded:
 	shell:
 		""" 
 		cd {params.out_dir}; \
-		cp {params.in_file_str1} {params.rename_str1}; \
-		cp {params.in_file_str2} {params.rename_str2}; \
+		cp {params.in_file_str1} {params.rename_str2}; \
+		cp {params.in_file_str2} {params.rename_str1}; \
 		alfa -g {params.genome_index} \
 			--bedgraph {params.rename_str1} {params.rename_str2} {params.name} \
 			-s {params.stranded} &> {log}; \