generate index if not provided

anand-imcm · Jul 26, 2024 · 2ccb9b0 · 2ccb9b0
1 parent 3545ab3
commit 2ccb9b0
Showing 1 changed file with 2 additions and 2 deletions.
diff --git 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