From 38ec6a6d1a5dad07f66806ba306565856a97ba83 Mon Sep 17 00:00:00 2001
From: Sascha Meiers <meiers@embl.de>
Date: Thu, 11 Jan 2018 13:42:13 +0100
Subject: [PATCH] small fixes
---
Snakefile | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/Snakefile b/Snakefile
index 88cc308..1d58145 100644
--- a/Snakefile
+++ b/Snakefile
@@ -425,9 +425,9 @@ rule split_external_snv_calls:
vcf = lambda wc: config["snv_calls"][wc.sample]
output:
vcf = "external_snv_calls/{sample}/{chrom}.vcf"
- log: "external_snv_calls/{sample}/{chrom}.vcf.log"
+ log: "log/{sample}/external_snv_calls.{chrom}.vcf.log"
params:
bcftools = config["bcftools"]
shell:
- "({params.bcftools} view --samples {wildcards.sample} --types snps {input.vcf} {wildcards.chrom} | bcftools view --genotype het - > {output.vcf}) > {log} 2>&1"
+ "({params.bcftools} view --samples {wildcards.sample} --types snps {input.vcf} {wildcards.chrom} | {params.bcftools} view --genotype het - > {output.vcf}) > {log} 2>&1"
--
GitLab