diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/ClusterBatch.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/ClusterBatch.json.tmpl
index e57187c1e..4198fbac7 100644
--- a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/ClusterBatch.json.tmpl
+++ b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/ClusterBatch.json.tmpl
@@ -4,8 +4,8 @@
   "ClusterBatch.reference_fasta_fai": "${workspace.reference_index}",
   "ClusterBatch.reference_dict": "${workspace.reference_dict}",
 
-  "ClusterBatch.chr_x": "${workspace.chr_y}",
-  "ClusterBatch.chr_y": "${workspace.chr_x}",
+  "ClusterBatch.chr_x": "${workspace.chr_x}",
+  "ClusterBatch.chr_y": "${workspace.chr_y}",
   "ClusterBatch.pesr_exclude_intervals": "${workspace.pesr_exclude_list}",
   "ClusterBatch.pesr_interval_overlap": "0.1",
   "ClusterBatch.pesr_breakend_window": "300",
diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/output_configurations/GatherBatchEvidenceOutputs.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/output_configurations/GatherBatchEvidenceOutputs.json.tmpl
deleted file mode 100644
index 0c3ec1d18..000000000
--- a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/output_configurations/GatherBatchEvidenceOutputs.json.tmpl
+++ /dev/null
@@ -1,36 +0,0 @@
-{
-  "GatherBatchEvidence.BAF_stats": "${this.BAF_stats}",
-  "GatherBatchEvidence.Matrix_QC_plot": "${this.Matrix_QC_plot}",
-  "GatherBatchEvidence.PE_stats": "${this.PE_stats}",
-  "GatherBatchEvidence.RD_stats": "${this.RD_stats}",
-  "GatherBatchEvidence.SR_stats": "${this.SR_stats}",
-  "GatherBatchEvidence.cnmops_del": "${this.cnmops_del}",
-  "GatherBatchEvidence.cnmops_del_index": "${this.cnmops_del_index}",
-  "GatherBatchEvidence.cnmops_dup": "${this.cnmops_dup}",
-  "GatherBatchEvidence.cnmops_dup_index": "${this.cnmops_dup_index}",
-  "GatherBatchEvidence.cnmops_large_del": "${this.cnmops_large_del}",
-  "GatherBatchEvidence.cnmops_large_del_index": "${this.cnmops_large_del_index}",
-  "GatherBatchEvidence.cnmops_large_dup": "${this.cnmops_large_dup}",
-  "GatherBatchEvidence.cnmops_large_dup_index": "${this.cnmops_large_dup_index}",
-  "GatherBatchEvidence.combined_ped_file": "${this.combined_ped_file}",
-  "GatherBatchEvidence.manta_tloc": "${this.manta_tloc}",
-  "GatherBatchEvidence.median_cov": "${this.median_cov}",
-  "GatherBatchEvidence.merged_BAF": "${this.merged_BAF}",
-  "GatherBatchEvidence.merged_BAF_index": "${this.merged_BAF_index}",
-  "GatherBatchEvidence.merged_PE": "${this.merged_PE}",
-  "GatherBatchEvidence.merged_PE_index": "${this.merged_PE_index}",
-  "GatherBatchEvidence.merged_SR": "${this.merged_SR}",
-  "GatherBatchEvidence.merged_SR_index": "${this.merged_SR_index}",
-  "GatherBatchEvidence.merged_bincov": "${this.merged_bincov}",
-  "GatherBatchEvidence.merged_bincov_index": "${this.merged_bincov_index}",
-  "GatherBatchEvidence.merged_dels": "${this.merged_dels}",
-  "GatherBatchEvidence.merged_dups": "${this.merged_dups}",
-  "GatherBatchEvidence.ploidy_matrix": "${this.ploidy_matrix_batchevidence}",
-  "GatherBatchEvidence.ploidy_plots": "${this.ploidy_plots_batchevidence}",
-  "GatherBatchEvidence.std_delly_vcf": "${this.std_delly_vcf}",
-  "GatherBatchEvidence.std_manta_vcf": "${this.std_manta_vcf}",
-  "GatherBatchEvidence.std_melt_vcf": "${this.std_melt_vcf}",
-  "GatherBatchEvidence.std_scramble_vcf": "${this.std_scramble_vcf}",
-  "GatherBatchEvidence.std_wham_vcf": "${this.std_wham_vcf}",
-  "GatherBatchEvidence.metrics_file_batchevidence": "${this.metrics_file_batchevidence}"
-}
diff --git a/inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.no_melt.json.tmpl b/inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.no_melt.json.tmpl
index 0f392ea1b..fd43deb90 100644
--- a/inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.no_melt.json.tmpl
+++ b/inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.no_melt.json.tmpl
@@ -75,8 +75,8 @@
   "GATKSVPipelineSingleSample.min_svsize" : 50,
   "GATKSVPipelineSingleSample.n_RD_genotype_bins" : 100000,
 
-  "GATKSVPipelineSingleSample.chr_x": "${workspace.chr_y}",
-  "GATKSVPipelineSingleSample.chr_y": "${workspace.chr_x}",
+  "GATKSVPipelineSingleSample.chr_x": "${workspace.chr_x}",
+  "GATKSVPipelineSingleSample.chr_y": "${workspace.chr_y}",
   "GATKSVPipelineSingleSample.pesr_exclude_intervals": "${workspace.pesr_exclude_list}",
   "GATKSVPipelineSingleSample.pesr_interval_overlap": "0.1",
   "GATKSVPipelineSingleSample.pesr_breakend_window": "300",
diff --git a/wdl/GATKSVPipelineSingleSample.wdl b/wdl/GATKSVPipelineSingleSample.wdl
index 00acf7876..078f55cd5 100644
--- a/wdl/GATKSVPipelineSingleSample.wdl
+++ b/wdl/GATKSVPipelineSingleSample.wdl
@@ -1501,8 +1501,8 @@ workflow GATKSVPipelineSingleSample {
     File pre_cleanup_vcf = AnnotateVcf.output_vcf
     File pre_cleanup_vcf_idx = AnnotateVcf.output_vcf_idx
 
-    File ploidy_matrix = select_first([GatherBatchEvidence.ploidy_matrix])
-    File ploidy_plots = select_first([GatherBatchEvidence.ploidy_plots])
+    File ploidy_matrix = select_first([GatherBatchEvidence.batch_ploidy_matrix])
+    File ploidy_plots = select_first([GatherBatchEvidence.batch_ploidy_plots])
     File metrics_file = SingleSampleMetrics.metrics_file
     File qc_file = SingleSampleQC.out
 
diff --git a/wdl/GatherBatchEvidence.wdl b/wdl/GatherBatchEvidence.wdl
index 8aa938690..b175bce4e 100644
--- a/wdl/GatherBatchEvidence.wdl
+++ b/wdl/GatherBatchEvidence.wdl
@@ -467,8 +467,8 @@ workflow GatherBatchEvidence {
     File merged_bincov = merged_bincov_
     File merged_bincov_index = merged_bincov_idx_
 
-    File? ploidy_matrix = Ploidy.ploidy_matrix
-    File? ploidy_plots = Ploidy.ploidy_plots
+    File? batch_ploidy_matrix = Ploidy.ploidy_matrix
+    File? batch_ploidy_plots = Ploidy.ploidy_plots
 
     File? combined_ped_file = AddCaseSampleToPed.combined_ped_file