Fix referencing HailMerge task instead of the workflow. (#445)

broadinstitute · Oct 12, 2022 · 09c618d · 09c618d
1 parent ed21680
commit 09c618d
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/wdl/CombineBatches.wdl b/wdl/CombineBatches.wdl
@@ -336,7 +336,7 @@ workflow CombineBatches {
 
     #Merge PESR & RD VCFs
     if (use_hail) {
-      call HailMerge.HailMergeTask as ConcatPesrDepthHail {
+      call HailMerge.HailMerge as ConcatPesrDepthHail {
         input:
           vcfs=[MergeDeletions.out, MergeDuplications.out, HarmonizeHeaders.out[2], HarmonizeHeaders.out[3], HarmonizeHeaders.out[4]],
           prefix="~{cohort_name}.~{contig}.concat_pesr_depth",

diff --git a/wdl/MergePesrDepth.wdl b/wdl/MergePesrDepth.wdl
@@ -72,7 +72,7 @@ workflow MergePesrDepth {
     }
 
     if (use_hail) {
-        call HailMerge.HailMergeTask as ConcatLargePesrDepthHail {
+        call HailMerge.HailMerge as ConcatLargePesrDepthHail {
             input:
                 vcfs=[SubsetLarge.filtered_vcf, subtyped_depth_vcf],
                 prefix="~{prefix}.large_pesr_depth",
@@ -157,7 +157,7 @@ workflow MergePesrDepth {
     }
 
     if (use_hail) {
-        call HailMerge.HailMergeTask as ConcatShardsHail {
+        call HailMerge.HailMerge as ConcatShardsHail {
             input:
                 vcfs=flatten([[SubsetSmall.filtered_vcf], SortVcf.out]),
                 prefix="~{prefix}.concat_shards",

diff --git a/wdl/ShardedCluster.wdl b/wdl/ShardedCluster.wdl
@@ -143,7 +143,7 @@ workflow ShardedCluster {
   }
   if (length(SvtkVcfCluster.out) > 0) {
     if (use_hail) {
-      call HailMerge.HailMergeTask as ConcatVcfsHail {
+      call HailMerge.HailMerge as ConcatVcfsHail {
         input:
           vcfs=SortVcf.out,
           prefix="~{prefix}.clustered",