From d1229d3e746ce804d627e1e4af0ab09917e49923 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 4 Jun 2019 11:55:32 +0200
Subject: [PATCH] rewrite tabix
---
samtools.wdl | 13 ++++++++++---
1 file changed, 10 insertions(+), 3 deletions(-)
diff --git a/samtools.wdl b/samtools.wdl
index c4c8126..befa335 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -182,17 +182,24 @@ task Fastq {
task Tabix {
input {
- String inputFile
+ File inputFile
+ String outputFilePath = "indexed.vcf.gz"
String type = "vcf"
String dockerTag = "0.2.6--ha92aebf_0"
}
command {
- tabix ~{inputFile} -p ~{type}
+ set -e
+ if [ ! -f ~{outputFilePath} ]
+ then
+ ln ~{inputFile} ~{outputFilePath}
+ fi
+ tabix ~{outputFilePath} -p ~{type}
}
output {
- File index = inputFile + ".tbi"
+ File indexedFile = outputFilePath
+ File index = outputFilePath + ".tbi"
}
runtime {
--
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