fix chrX/Y swap in json templates, make GatherBatchEv output names un…

…ique for Terra (#378)
broadinstitute · Jul 28, 2022 · ef29ea1 · ef29ea1
1 parent bb25222
commit ef29ea1
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Showing 5 changed files with 8 additions and 44 deletions.
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
@@ -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/...t_mode/workflow_configurations/output_configurations/GatherBatchEvidenceOutputs.json.tmpl b/...t_mode/workflow_configurations/output_configurations/GatherBatchEvidenceOutputs.json.tmpl
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
@@ -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
@@ -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
@@ -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