From ced99c460c501a62c57a2baa367ad6fab2d9c646 Mon Sep 17 00:00:00 2001
From: kdc715 <kedic@LIT-PF3VB193.localdomain>
Date: Fri, 13 Dec 2024 14:15:44 +0100
Subject: [PATCH] fix file path for python script
---
snakemodules/kraken.smk | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/snakemodules/kraken.smk b/snakemodules/kraken.smk
index d499b12..186f8b1 100644
--- a/snakemodules/kraken.smk
+++ b/snakemodules/kraken.smk
@@ -1,3 +1,4 @@
+import os
rule kraken_map:
input:
@@ -57,7 +58,7 @@ rule obtain_classified_human_reads:
single_fq = rules.kraken_map.output.c_single,
paired_fq1 = rules.kraken_map.output.c_paired_1,
paired_fq2 = rules.kraken_map.output.c_paired_2,
- script= WORKFLOW_PATH + config["python_script"]
+ script= os.path.join(WORKFLOW_PATH,config["python_script"])
output:
hc_single = WORK_DIR + "/{sample}/contaminate_info/human_classified_single.fastq",
hc_paired_1 = WORK_DIR + "/{sample}/contaminate_info/human_classified_paired_1.fastq",
--
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