From 219529007df12ed4ab0e4ab6351785b32c46f788 Mon Sep 17 00:00:00 2001
From: burri0000 <dominik.burri@unibas.ch>
Date: Fri, 24 Jan 2020 17:36:34 +0100
Subject: [PATCH] corrected stranded ALFA for rev. seq data

---
 snakemake/Snakefile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/snakemake/Snakefile b/snakemake/Snakefile
index 4137bb8..db1b973 100644
--- a/snakemake/Snakefile
+++ b/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}; \
-- 
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