fix bad wdl

Author: Jose Soto

pipelines/wdl/arrays/imputation_beagle/ImputationBeagle.wdl

@@ -321,20 +321,20 @@ workflow ImputationBeagle {
 
     call beagleTasks.SelectVariantRecordsOnly {
       input:
-        vcf = UpdateHeader.output_vcf,
-        vcf_index = UpdateHeader.output_vcf_index,
+        vcf = CreateIndexForGatheredChunkVcfs.output_vcf,
+        vcf_index = CreateIndexForGatheredChunkVcfs.output_vcf_index,
         basename = referencePanelContig_2.contig + ".imputed.no_overlaps.update_header.only_variants",
     }
 
     call beagleTasks.CreateHomRefSitesOnlyVcf {
       input:
-        vcf = UpdateHeader.output_vcf,
-        vcf_index = UpdateHeader.output_vcf_index,
+        vcf = CreateIndexForGatheredChunkVcfs.output_vcf,
+        vcf_index = CreateIndexForGatheredChunkVcfs.output_vcf_index,
         basename = referencePanelContig_2.contig + ".imputed.no_overlaps.update_header.only_hom_ref.sites_only",
     }
 
     File chromosome_vcf = SelectVariantRecordsOnly.output_vcf
-    File chromsome_hom_ref_sites_only_vcfs = CreateHomRefSitesOnlyVcf.output_vcf
+    File chromsome_hom_ref_sites_only_vcf = CreateHomRefSitesOnlyVcf.output_vcf
   }
 
   call beagleTasks.GatherVcfsNoIndex {
@@ -353,7 +353,7 @@ workflow ImputationBeagle {
 
   call beagleTasks.GatherVcfsNoIndex as GatherHomRefSitesOnlyVcfs {
     input:
-      input_vcfs = chromsome_hom_ref_sites_only_vcfs,
+      input_vcfs = chromsome_hom_ref_sites_only_vcf,
       output_vcf_basename = output_basename + ".imputed.hom_ref_sites_only",
       gatk_docker = gatk_docker
   }

tasks/wdl/ImputationBeagleTasks.wdl

@@ -1022,8 +1022,6 @@ task SelectVariantRecordsOnly {
     set -e -o pipefail
 
     bcftools view -i 'GT[*]="alt"' -Oz -o ~{basename}.vcf.gz ~{vcf}
-
-    bcftools index -t ~{basename}.vcf.gz
   }
 
   runtime {
@@ -1037,7 +1035,6 @@ task SelectVariantRecordsOnly {
 
   output {
     File output_vcf = "~{basename}.vcf.gz"
-    File output_vcf_index = "~{basename}.vcf.gz.tbi"
   }
 }
 
@@ -1065,8 +1062,6 @@ task CreateHomRefSitesOnlyVcf {
     bcftools query -e 'GT[*]="alt"' -f '%CHROM\t%POS\t%ID\t%REF\t%ALT\t%QUAL\t%FILTER\t%INFO\n' ~{vcf} >> ~{basename}.vcf
 
     bgzip ~{basename}.vcf
-
-    bcftools index -t ~{basename}.vcf.gz
   }
 
   runtime {
@@ -1080,6 +1075,5 @@ task CreateHomRefSitesOnlyVcf {
 
   output {
     File output_vcf = "~{basename}.vcf.gz"
-    File output_vcf_index = "~{basename}.vcf.gz.tbi"
   }
 }