From 5f9751a9ec2bd23de5109c8a3c1d812a1cd968ea Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Thu, 15 Feb 2018 16:56:50 +0100
Subject: [PATCH] Chunks may have quirky names. Wrap in quotes to prevent shell
oddities.
---
Snakefile | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/Snakefile b/Snakefile
index 6bd0b70..82566ee 100644
--- a/Snakefile
+++ b/Snakefile
@@ -261,13 +261,13 @@ rule gvcf_gather:
ref=REFERENCE,
gatk=GATK
params:
- gvcfs=" -V ".join(expand(out_path("{{sample}}/vcf/{{sample}}.{chunk}.part.vcf.gz"),
+ gvcfs="' -V '".join(expand(out_path("{{sample}}/vcf/{{sample}}.{chunk}.part.vcf.gz"),
chunk=CHUNKS))
output:
gvcf=out_path("{sample}/vcf/{sample}.g.vcf.gz")
conda: "envs/gatk.yml"
shell: "java -Xmx4G -cp {input.gatk} org.broadinstitute.gatk.tools.CatVariants "\
- "-R {input.ref} -V {params.gvcfs} -out {output.gvcf} "\
+ "-R {input.ref} -V '{params.gvcfs}' -out {output.gvcf} "\
"-assumeSorted"
@@ -295,13 +295,13 @@ rule genotype_gather:
ref=REFERENCE,
gatk=GATK
params:
- vcfs=" -V ".join(expand(out_path("multisample/genotype.{chunk}.part.vcf.gz"),
+ vcfs="' -V '".join(expand(out_path("multisample/genotype.{chunk}.part.vcf.gz"),
chunk=CHUNKS))
output:
combined=out_path("multisample/genotyped.vcf.gz")
conda: "envs/gatk.yml"
shell: "java -Xmx4G -cp {input.gatk} org.broadinstitute.gatk.tools.CatVariants "\
- "-R {input.ref} -V {params.vcfs} -out {output.combined} "\
+ "-R {input.ref} -V '{params.vcfs}' -out {output.combined} "\
"-assumeSorted"
--
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