From ac55982a7acf3c06460ae0b8ac2c394865eeaa4c Mon Sep 17 00:00:00 2001
From: dcats <d.cats@lumc.nl>
Date: Fri, 18 Mar 2022 12:46:53 +0100
Subject: [PATCH] run tabix if vcf index is missing in gridss
---
gridss.wdl | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/gridss.wdl b/gridss.wdl
index d3d251a..92d7df1 100644
--- a/gridss.wdl
+++ b/gridss.wdl
@@ -116,6 +116,12 @@ task GRIDSS {
~{normalBam} \
~{tumorBam}
samtools index ~{outputPrefix}_assembly.bam ~{outputPrefix}_assembly.bai
+
+ # For some reason the VCF index is sometimes missing
+ if [ ! -e ~{outputPrefix}.vcf.gz.tbi ]
+ then
+ tabix ~{outputPrefix}.vcf.gz
+ fi
}
output {
--
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