From 9d265049973a895da3276742e39f48a350fe0cc4 Mon Sep 17 00:00:00 2001
From: Floreal Cabanettes <floreal.cabanettes@inra.fr>
Date: Mon, 6 Aug 2018 14:34:21 +0200
Subject: [PATCH] Fix for snakemake >= 5.0
---
snakecnv/align.snk | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/snakecnv/align.snk b/snakecnv/align.snk
index f610c49..d8067cc 100644
--- a/snakecnv/align.snk
+++ b/snakecnv/align.snk
@@ -69,8 +69,8 @@ rule bamindex:
threads:
1
log:
- stdout = "logs/mapindex_{sample}.o",
- stderr = "logs/mapindex_{sample}.e"
+ stdout = "logs/mapindex_{sample}_{folder}.o",
+ stderr = "logs/mapindex_{sample}_{folder}.e"
shell:
"samtools index {input}; "
"samtools flagstat {input} > {output.summary}"
--
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