From c836ffda0caaefd3bf156b06b1fb51db7b43a619 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Wed, 22 Nov 2017 17:44:01 +0100
Subject: [PATCH 1/2] add tabix version

---
 tool_collections/vcftools/vcftools_compare/vcftools_compare.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tool_collections/vcftools/vcftools_compare/vcftools_compare.xml b/tool_collections/vcftools/vcftools_compare/vcftools_compare.xml
index 29850bd4..ccc41364 100644
--- a/tool_collections/vcftools/vcftools_compare/vcftools_compare.xml
+++ b/tool_collections/vcftools/vcftools_compare/vcftools_compare.xml
@@ -2,7 +2,7 @@
     <description>multiple VCF datasets</description>
 
     <requirements>
-        <requirement type="package">tabix</requirement>
+        <requirement type="package" version="0.2.5">tabix</requirement>
         <requirement type="package" version="0.1.11">vcftools</requirement>
     </requirements>
     

From ffc370135fff194fe6711fcc0a5e6313ee68febc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Wed, 22 Nov 2017 18:18:14 +0100
Subject: [PATCH 2/2] quote filenames

---
 .../vcftools/vcftools_compare/vcftools_compare.xml          | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tool_collections/vcftools/vcftools_compare/vcftools_compare.xml b/tool_collections/vcftools/vcftools_compare/vcftools_compare.xml
index ccc41364..044b22fd 100644
--- a/tool_collections/vcftools/vcftools_compare/vcftools_compare.xml
+++ b/tool_collections/vcftools/vcftools_compare/vcftools_compare.xml
@@ -11,13 +11,13 @@
         #set dataset_names = []
         #for $input in $inputs:
             ## Sort file.                                     
-            sort -k1,1 -k2,2n ${input.file} > ${input.name}.vcf.sorted ;
+            sort -k1,1 -k2,2n '${input.file}' > '${input.name}.vcf.sorted' ;
 
             ## Compress.
-            bgzip ${input.name}.vcf.sorted ;
+            bgzip '${input.name}.vcf.sorted' ;
 
             ## Index.
-            tabix -p vcf ${input.name}.vcf.sorted.gz ;
+            tabix -p vcf '${input.name}.vcf.sorted.gz' ;
 
             #silent dataset_names.append( str($input.name) + '.vcf.sorted.gz' )
         #end for