From 2ccb9b0ffdbe9885bc129eeba3cac39e1080d945 Mon Sep 17 00:00:00 2001
From: anand-imcm <anand.maurya@well.ox.ac.uk>
Date: Fri, 26 Jul 2024 16:42:49 +0100
Subject: [PATCH] generate index if not provided

---
 workflows/tasks/extract_info.wdl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflows/tasks/extract_info.wdl b/workflows/tasks/extract_info.wdl
index 461cc3c..4af3989 100644
--- a/workflows/tasks/extract_info.wdl
+++ b/workflows/tasks/extract_info.wdl
@@ -19,8 +19,8 @@ task extract {
         for vcf in ~{sep=' ' imputed_vcf}; do
             ln -s $vcf $(basename $vcf)
             if [[ $vcf == *.vcf.gz ]]; then
-                if [ ! -f $vcf.csi ]; then
-                    bcftools index -c $vcf
+                if [ ! -f $vcf.csi ] && [ ! -f $vcf.tbi ]; then
+                    bcftools index -c $(basename $vcf)
                 fi
             fi
         done