From c064598e5b2775038148fbc316a2891343fae11d Mon Sep 17 00:00:00 2001
From: Mattias <m.dehollander@nioo.knaw.nl>
Date: Mon, 1 Oct 2018 12:33:27 +0200
Subject: [PATCH] Fix itsx log file

---
 Snakefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Snakefile b/Snakefile
index 3ab4ef6..b1bf380 100644
--- a/Snakefile
+++ b/Snakefile
@@ -310,7 +310,7 @@ if config['its'] == True:
             conda: "envs/itsx.yaml"
             # TODO: Filter on specific list of organisms? 
             # Only ITS2 region?
-            shell: "ITSx --cpu {threads} --preserve TRUE -i {input.fasta} -o {params.basename} > {params.dir}/{log}"
+            shell: "ITSx --cpu {threads} --preserve TRUE -i {input.fasta} -o {params.basename} 2> {log}"
 
 # Combine per sample files to a single project file
 rule mergefiles: