Replace sv_pipeline_rdtest_docker with sv_pipeline_docker. (#645)

* Replace sv_pipeline_rdtest_docker with sv_pipeline_docker. * Remove duplicate input definition. * Update the docker image to use the current latest version.
broadinstitute · Apr 30, 2024 · a42dfeb · a42dfeb
1 parent 9dd0777
commit a42dfeb
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Showing 54 changed files with 58 additions and 130 deletions.
diff --git a/...lates/terra_workspaces/cohort_mode/workflow_configurations/GenerateBatchMetrics.json.tmpl b/...lates/terra_workspaces/cohort_mode/workflow_configurations/GenerateBatchMetrics.json.tmpl
@@ -1,6 +1,5 @@
 {
   "GenerateBatchMetrics.sv_pipeline_docker": "${workspace.sv_pipeline_docker}",
-  "GenerateBatchMetrics.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}",
   "GenerateBatchMetrics.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
   "GenerateBatchMetrics.sv_base_docker": "${workspace.sv_base_docker}",
   "GenerateBatchMetrics.linux_docker" : "${workspace.linux_docker}",

diff --git a/.../terra_workspaces/cohort_mode/workflow_configurations/GenotypeBatch.SingleBatch.json.tmpl b/.../terra_workspaces/cohort_mode/workflow_configurations/GenotypeBatch.SingleBatch.json.tmpl
@@ -1,7 +1,6 @@
 {
   "GenotypeBatch.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
   "GenotypeBatch.sv_pipeline_docker": "${workspace.sv_pipeline_docker}",
-  "GenotypeBatch.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}",
   "GenotypeBatch.linux_docker" : "${workspace.linux_docker}",
 
   "GenotypeBatch.n_RD_genotype_bins": "100000", 

diff --git a/...ts/templates/terra_workspaces/cohort_mode/workflow_configurations/GenotypeBatch.json.tmpl b/...ts/templates/terra_workspaces/cohort_mode/workflow_configurations/GenotypeBatch.json.tmpl
@@ -1,7 +1,6 @@
 {
   "GenotypeBatch.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
   "GenotypeBatch.sv_pipeline_docker": "${workspace.sv_pipeline_docker}",
-  "GenotypeBatch.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}",
   "GenotypeBatch.linux_docker" : "${workspace.linux_docker}",
 
   "GenotypeBatch.n_RD_genotype_bins": "100000", 

diff --git a/...kspaces/cohort_mode/workflow_configurations/GenotypeComplexVariants.SingleBatch.json.tmpl b/...kspaces/cohort_mode/workflow_configurations/GenotypeComplexVariants.SingleBatch.json.tmpl
@@ -6,7 +6,6 @@
   "GenotypeComplexVariants.linux_docker": "${workspace.linux_docker}",
   "GenotypeComplexVariants.sv_pipeline_docker": "${workspace.sv_pipeline_docker}",
   "GenotypeComplexVariants.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
-  "GenotypeComplexVariants.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}",
 
   "GenotypeComplexVariants.cohort_name": "${this.sample_set_id}",
   "GenotypeComplexVariants.batches": "${this.sample_set_id}",

diff --git a/...es/terra_workspaces/cohort_mode/workflow_configurations/GenotypeComplexVariants.json.tmpl b/...es/terra_workspaces/cohort_mode/workflow_configurations/GenotypeComplexVariants.json.tmpl
@@ -6,7 +6,6 @@
   "GenotypeComplexVariants.linux_docker": "${workspace.linux_docker}",
   "GenotypeComplexVariants.sv_pipeline_docker": "${workspace.sv_pipeline_docker}",
   "GenotypeComplexVariants.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
-  "GenotypeComplexVariants.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}",
 
   "GenotypeComplexVariants.cohort_name": "${this.sample_set_set_id}",
   "GenotypeComplexVariants.batches": "${this.sample_sets.sample_set_id}",

diff --git a/.../terra_workspaces/cohort_mode/workflow_configurations/MakeCohortVcf.SingleBatch.json.tmpl b/.../terra_workspaces/cohort_mode/workflow_configurations/MakeCohortVcf.SingleBatch.json.tmpl
@@ -28,7 +28,6 @@
   "MakeCohortVcf.linux_docker": "${workspace.linux_docker}",
   "MakeCohortVcf.sv_pipeline_docker": "${workspace.sv_pipeline_docker}",
   "MakeCohortVcf.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
-  "MakeCohortVcf.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}",
   "MakeCohortVcf.sv_pipeline_qc_docker": "${workspace.sv_pipeline_qc_docker}",
 
   "MakeCohortVcf.primary_contigs_list": "${workspace.primary_contigs_list}",

diff --git a/...ts/templates/terra_workspaces/cohort_mode/workflow_configurations/MakeCohortVcf.json.tmpl b/...ts/templates/terra_workspaces/cohort_mode/workflow_configurations/MakeCohortVcf.json.tmpl
@@ -28,7 +28,6 @@
   "MakeCohortVcf.linux_docker": "${workspace.linux_docker}",
   "MakeCohortVcf.sv_pipeline_docker": "${workspace.sv_pipeline_docker}",
   "MakeCohortVcf.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
-  "MakeCohortVcf.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}",
   "MakeCohortVcf.sv_pipeline_qc_docker": "${workspace.sv_pipeline_qc_docker}",
 
   "MakeCohortVcf.primary_contigs_list": "${workspace.primary_contigs_list}",

diff --git a/...terra_workspaces/cohort_mode/workflow_configurations/RegenotypeCNVs.SingleBatch.json.tmpl b/...terra_workspaces/cohort_mode/workflow_configurations/RegenotypeCNVs.SingleBatch.json.tmpl
@@ -1,5 +1,4 @@
 {
-  "RegenotypeCNVs.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}",
   "RegenotypeCNVs.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
   "RegenotypeCNVs.sv_pipeline_docker": "${workspace.sv_pipeline_docker}",
   "RegenotypeCNVs.n_RdTest_bins": "100000",

diff --git a/...s/templates/terra_workspaces/cohort_mode/workflow_configurations/RegenotypeCNVs.json.tmpl b/...s/templates/terra_workspaces/cohort_mode/workflow_configurations/RegenotypeCNVs.json.tmpl
@@ -1,5 +1,4 @@
 {
-  "RegenotypeCNVs.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}",
   "RegenotypeCNVs.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
   "RegenotypeCNVs.sv_pipeline_docker": "${workspace.sv_pipeline_docker}",
   "RegenotypeCNVs.n_RdTest_bins": "100000",

diff --git a/inputs/templates/terra_workspaces/cohort_mode/workspace.tsv.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workspace.tsv.tmpl
@@ -12,7 +12,6 @@ sv_base_docker	{{ dockers.sv_base_docker }}
 sv_base_mini_docker	{{ dockers.sv_base_mini_docker }}
 sv_pipeline_docker	{{ dockers.sv_pipeline_docker }}
 sv_pipeline_qc_docker	{{ dockers.sv_pipeline_qc_docker }}
-sv_pipeline_rdtest_docker	{{ dockers.sv_pipeline_rdtest_docker }}
 wham_docker	{{ dockers.wham_docker }}
 scramble_docker	{{ dockers.scramble_docker }}
 allosome_file	{{ reference_resources.allosome_file }}

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
@@ -36,7 +36,6 @@
   "GATKSVPipelineSingleSample.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
   "GATKSVPipelineSingleSample.sv_pipeline_docker": "${workspace.sv_pipeline_docker}",
   "GATKSVPipelineSingleSample.sv_pipeline_qc_docker": "${workspace.sv_pipeline_qc_docker}",
-  "GATKSVPipelineSingleSample.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}",
   "GATKSVPipelineSingleSample.wham_docker": "${workspace.wham_docker}",
   "GATKSVPipelineSingleSample.samtools_cloud_docker": "${workspace.samtools_cloud_docker}",
 

diff --git a/inputs/templates/terra_workspaces/single_sample/workspace.tsv.tmpl b/inputs/templates/terra_workspaces/single_sample/workspace.tsv.tmpl
@@ -11,7 +11,6 @@ sv_base_docker	{{ dockers.sv_base_docker }}
 sv_base_mini_docker	{{ dockers.sv_base_mini_docker }}
 sv_pipeline_docker	{{ dockers.sv_pipeline_docker }}
 sv_pipeline_qc_docker	{{ dockers.sv_pipeline_qc_docker }}
-sv_pipeline_rdtest_docker	{{ dockers.sv_pipeline_rdtest_docker }}
 wham_docker	{{ dockers.wham_docker }}
 ref_panel_name	{{ ref_panel.name }}
 ref_panel_bincov_matrix	{{ ref_panel.merged_coverage_file }}

diff --git a/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.FromSampleEvidence.json.tmpl b/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.FromSampleEvidence.json.tmpl
@@ -32,7 +32,6 @@
   "GATKSVPipelineBatch.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
   "GATKSVPipelineBatch.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
   "GATKSVPipelineBatch.sv_pipeline_qc_docker": {{ dockers.sv_pipeline_qc_docker | tojson }},
-  "GATKSVPipelineBatch.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }},
   "GATKSVPipelineBatch.samtools_cloud_docker": {{ dockers.samtools_cloud_docker | tojson }},
   "GATKSVPipelineBatch.cloud_sdk_docker": {{ dockers.cloud_sdk_docker | tojson }},
 

diff --git a/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.json.tmpl b/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.json.tmpl
@@ -26,7 +26,6 @@
   "GATKSVPipelineBatch.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
   "GATKSVPipelineBatch.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
   "GATKSVPipelineBatch.sv_pipeline_qc_docker": {{ dockers.sv_pipeline_qc_docker | tojson }},
-  "GATKSVPipelineBatch.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }},
   "GATKSVPipelineBatch.samtools_cloud_docker": {{ dockers.samtools_cloud_docker | tojson }},
   "GATKSVPipelineBatch.cloud_sdk_docker": {{ dockers.cloud_sdk_docker | tojson }},
 

diff --git a/inputs/templates/test/GATKSVPipelinePhase1/GATKSVPipelinePhase1.json.tmpl b/inputs/templates/test/GATKSVPipelinePhase1/GATKSVPipelinePhase1.json.tmpl
@@ -2,7 +2,6 @@
   "GATKSVPipelinePhase1.sv_base_mini_docker":{{ dockers.sv_base_mini_docker | tojson }},
   "GATKSVPipelinePhase1.sv_base_docker": {{ dockers.sv_base_docker | tojson }},
   "GATKSVPipelinePhase1.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
-  "GATKSVPipelinePhase1.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }},
   "GATKSVPipelinePhase1.sv_pipeline_qc_docker": {{ dockers.sv_pipeline_qc_docker | tojson }},
   "GATKSVPipelinePhase1.linux_docker" : {{ dockers.linux_docker | tojson }},
   "GATKSVPipelinePhase1.cnmops_docker": {{ dockers.cnmops_docker | tojson }},

diff --git a/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl b/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl
@@ -34,7 +34,6 @@
   "GATKSVPipelineSingleSample.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_pipeline_qc_docker": {{ dockers.sv_pipeline_qc_docker | tojson }},
-  "GATKSVPipelineSingleSample.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }},
   "GATKSVPipelineSingleSample.wham_docker": {{ dockers.wham_docker | tojson }},
   "GATKSVPipelineSingleSample.samtools_cloud_docker": {{ dockers.samtools_cloud_docker | tojson }},
   "GATKSVPipelineSingleSample.cloud_sdk_docker": {{ dockers.cloud_sdk_docker | tojson }},

diff --git a/...ts/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.no_melt.json.tmpl b/...ts/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.no_melt.json.tmpl
@@ -37,7 +37,6 @@
   "GATKSVPipelineSingleSample.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_pipeline_qc_docker": {{ dockers.sv_pipeline_qc_docker | tojson }},
-  "GATKSVPipelineSingleSample.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }},
   "GATKSVPipelineSingleSample.wham_docker": {{ dockers.wham_docker | tojson }},
   "GATKSVPipelineSingleSample.samtools_cloud_docker": {{ dockers.samtools_cloud_docker | tojson }},
   "GATKSVPipelineSingleSample.cloud_sdk_docker": {{ dockers.cloud_sdk_docker | tojson }},

diff --git a/inputs/templates/test/GenerateBatchMetrics/GenerateBatchMetrics.json.tmpl b/inputs/templates/test/GenerateBatchMetrics/GenerateBatchMetrics.json.tmpl
@@ -1,6 +1,5 @@
 {
   "GenerateBatchMetrics.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
-  "GenerateBatchMetrics.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }},
   "GenerateBatchMetrics.sv_base_mini_docker":{{ dockers.sv_base_mini_docker | tojson }},
   "GenerateBatchMetrics.sv_base_docker": {{ dockers.sv_base_docker | tojson }},
   "GenerateBatchMetrics.linux_docker" : {{ dockers.linux_docker | tojson }},

diff --git a/inputs/templates/test/GenotypeBatch/GenotypeBatch.json.tmpl b/inputs/templates/test/GenotypeBatch/GenotypeBatch.json.tmpl
@@ -1,7 +1,6 @@
 {
   "GenotypeBatch.sv_base_mini_docker":{{ dockers.sv_base_mini_docker | tojson }},
   "GenotypeBatch.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
-  "GenotypeBatch.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }},
   "GenotypeBatch.linux_docker" : {{ dockers.linux_docker | tojson }},
 
   "GenotypeBatch.n_RD_genotype_bins": "100000", 

diff --git a/inputs/templates/test/MakeCohortVcf/GenotypeComplexVariants.json.tmpl b/inputs/templates/test/MakeCohortVcf/GenotypeComplexVariants.json.tmpl
@@ -6,7 +6,6 @@
   "GenotypeComplexVariants.linux_docker": {{ dockers.linux_docker | tojson }},
   "GenotypeComplexVariants.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
   "GenotypeComplexVariants.sv_base_mini_docker":{{ dockers.sv_base_mini_docker | tojson }},
-  "GenotypeComplexVariants.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }},
 
   "GenotypeComplexVariants.cohort_name": {{ test_batch.name | tojson }},
   "GenotypeComplexVariants.batches": [

diff --git a/inputs/templates/test/MakeCohortVcf/MakeCohortVcf.json.tmpl b/inputs/templates/test/MakeCohortVcf/MakeCohortVcf.json.tmpl
@@ -33,7 +33,6 @@
   "MakeCohortVcf.linux_docker": {{ dockers.linux_docker | tojson }},
   "MakeCohortVcf.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
   "MakeCohortVcf.sv_base_mini_docker":{{ dockers.sv_base_mini_docker | tojson }},
-  "MakeCohortVcf.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }},
   "MakeCohortVcf.sv_pipeline_qc_docker": {{ dockers.sv_pipeline_qc_docker | tojson }},
 
   "MakeCohortVcf.cohort_name": {{ test_batch.name | tojson }},

diff --git a/inputs/templates/test/Module09/Module09VisualizeSingleSample.json.tmpl b/inputs/templates/test/Module09/Module09VisualizeSingleSample.json.tmpl
@@ -1,6 +1,6 @@
 {
         "Module09VisualizeSingleSample.sv_base_mini_docker" : "us.gcr.io/broad-dsde-methods/gatk-sv/sv-base-mini:mw-gnomad-02-6a66c96",
-        "Module09VisualizeSingleSample.sv_pipeline_rdtest_docker" : "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline-rdtest:mw-gnomad-02-6a66c96",
+        "Module09VisualizeSingleSample.sv_pipeline_docker" : "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-04-29-v0.28.4-beta-7fd43657",
         "Module09VisualizeSingleSample.igv_docker" : "us.gcr.io/broad-dsde-methods/gatk-sv/igv:mw-xz-fixes-2-b1be6a9",
 
         "Module09VisualizeSingleSample.Fasta" : "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",

diff --git a/inputs/templates/test/Mosaic/Mosaic.json.tmpl b/inputs/templates/test/Mosaic/Mosaic.json.tmpl
@@ -2,7 +2,6 @@
   "MosaicManualCheck.rare_cutoff":2,
   "MosaicManualCheck.outlier": "gs://gatk-sv-resources/resources/outlier.txt",
   "MosaicManualCheck.fam_file": {{ test_batch.ped_file | tojson }},
-  "MosaicManualCheck.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }},
   "MosaicManualCheck.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
   "MosaicManualCheck.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
   "MosaicManualCheck.agg_metrics": [{{ test_batch.evidence_metrics | tojson }}],

diff --git a/inputs/templates/test/RegenotypeCNVs/RegenotypeCNVs.json.tmpl b/inputs/templates/test/RegenotypeCNVs/RegenotypeCNVs.json.tmpl
@@ -1,5 +1,4 @@
 {
-  "RegenotypeCNVs.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }},
   "RegenotypeCNVs.sv_base_mini_docker":{{ dockers.sv_base_mini_docker | tojson }},
   "RegenotypeCNVs.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
   "RegenotypeCNVs.n_RdTest_bins": "100000",

diff --git a/inputs/values/dockers.json b/inputs/values/dockers.json
@@ -14,7 +14,6 @@
   "sv_base_mini_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-base-mini:2024-01-24-v0.28.4-beta-9debd6d7",
   "sv_pipeline_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-04-29-v0.28.4-beta-7fd43657",
   "sv_pipeline_qc_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-04-29-v0.28.4-beta-7fd43657",
-  "sv_pipeline_rdtest_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-04-29-v0.28.4-beta-7fd43657",
   "wham_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/wham:2024-01-24-v0.28.4-beta-9debd6d7",
   "igv_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/igv:mw-xz-fixes-2-b1be6a9",
   "duphold_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/duphold:mw-xz-fixes-2-b1be6a9",

diff --git a/inputs/values/dockers_azure.json b/inputs/values/dockers_azure.json
@@ -14,7 +14,6 @@
   "sv_base_mini_docker": "vahid.azurecr.io/gatk-sv/sv-base-mini:2024-01-24-v0.28.4-beta-9debd6d7",
   "sv_pipeline_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2024-04-29-v0.28.4-beta-7fd43657",
   "sv_pipeline_qc_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2024-04-29-v0.28.4-beta-7fd43657",
-  "sv_pipeline_rdtest_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2024-04-29-v0.28.4-beta-7fd43657",
   "wham_docker": "vahid.azurecr.io/gatk-sv/wham:2024-01-24-v0.28.4-beta-9debd6d7",
   "igv_docker": "vahid.azurecr.io/gatk-sv/igv:mw-xz-fixes-2-b1be6a9",
   "duphold_docker": "vahid.azurecr.io/gatk-sv/duphold:mw-xz-fixes-2-b1be6a9",

diff --git a/wdl/GATKSVPipelineBatch.wdl b/wdl/GATKSVPipelineBatch.wdl
@@ -89,7 +89,6 @@ workflow GATKSVPipelineBatch {
     String sv_base_mini_docker
     String sv_base_docker
     String sv_pipeline_docker
-    String sv_pipeline_rdtest_docker
     String sv_pipeline_qc_docker
     String linux_docker
     String cnmops_docker
@@ -224,7 +223,6 @@ workflow GATKSVPipelineBatch {
       sv_base_mini_docker=sv_base_mini_docker,
       sv_base_docker=sv_base_docker,
       sv_pipeline_docker=sv_pipeline_docker,
-      sv_pipeline_rdtest_docker=sv_pipeline_rdtest_docker,
       sv_pipeline_qc_docker=sv_pipeline_qc_docker,
       linux_docker=linux_docker,
       cnmops_docker=cnmops_docker,
@@ -253,7 +251,6 @@ workflow GATKSVPipelineBatch {
       primary_contigs_list = primary_contigs_list,
       sv_base_mini_docker=sv_base_mini_docker,
       sv_pipeline_docker=sv_pipeline_docker,
-      sv_pipeline_rdtest_docker=sv_pipeline_rdtest_docker,
       linux_docker=linux_docker
   }
 
@@ -271,8 +268,7 @@ workflow GATKSVPipelineBatch {
       contig_list=primary_contigs_list,
       regeno_coverage_medians=[GenotypeBatch.regeno_coverage_medians],
       sv_base_mini_docker=sv_base_mini_docker,
-      sv_pipeline_docker=sv_pipeline_docker,
-      sv_pipeline_rdtest_docker=sv_pipeline_rdtest_docker
+      sv_pipeline_docker=sv_pipeline_docker
   }
 
 
@@ -302,7 +298,6 @@ workflow GATKSVPipelineBatch {
       primary_contigs_list = primary_contigs_list,
       linux_docker=linux_docker,
       sv_pipeline_docker=sv_pipeline_docker,
-      sv_pipeline_rdtest_docker=sv_pipeline_rdtest_docker,
       sv_pipeline_qc_docker=sv_pipeline_qc_docker,
       sv_base_mini_docker=sv_base_mini_docker
   }

diff --git a/wdl/GATKSVPipelinePhase1.wdl b/wdl/GATKSVPipelinePhase1.wdl
@@ -27,7 +27,6 @@ workflow GATKSVPipelinePhase1 {
     String sv_base_mini_docker
     String sv_base_docker
     String sv_pipeline_docker
-    String sv_pipeline_rdtest_docker
     String sv_pipeline_qc_docker
     String linux_docker
     String cnmops_docker
@@ -420,7 +419,6 @@ workflow GATKSVPipelinePhase1 {
       sv_base_mini_docker=sv_base_mini_docker,
       sv_base_docker=sv_base_docker,
       sv_pipeline_docker=sv_pipeline_docker,
-      sv_pipeline_rdtest_docker=sv_pipeline_rdtest_docker,
       linux_docker=linux_docker,
       runtime_attr_sample_list=runtime_attr_sample_list,
       runtime_attr_petest=runtime_attr_petest,

diff --git a/wdl/GATKSVPipelineSingleSample.wdl b/wdl/GATKSVPipelineSingleSample.wdl
@@ -66,7 +66,6 @@ workflow GATKSVPipelineSingleSample {
     String sv_base_mini_docker
     String sv_base_docker
     String sv_pipeline_docker
-    String sv_pipeline_rdtest_docker
     String sv_pipeline_qc_docker
     String linux_docker
     String cnmops_docker
@@ -1076,7 +1075,6 @@ workflow GATKSVPipelineSingleSample {
       run_module_metrics = run_genotypebatch_metrics,
       sv_base_mini_docker=sv_base_mini_docker,
       sv_pipeline_docker=sv_pipeline_docker,
-      sv_pipeline_rdtest_docker=sv_pipeline_rdtest_docker,
       linux_docker=linux_docker,
       runtime_attr_split_vcf=runtime_attr_split_vcf_genotypebatch,
       runtime_attr_merge_counts=runtime_attr_merge_counts,
@@ -1157,7 +1155,6 @@ workflow GATKSVPipelineSingleSample {
 
       linux_docker=linux_docker,
       sv_pipeline_docker=sv_pipeline_docker,
-      sv_pipeline_rdtest_docker=sv_pipeline_rdtest_docker,
       sv_pipeline_qc_docker=sv_pipeline_qc_docker,
       sv_base_mini_docker=sv_base_mini_docker,
 

diff --git a/wdl/GenerateBatchMetrics.wdl b/wdl/GenerateBatchMetrics.wdl
@@ -44,7 +44,6 @@ workflow GenerateBatchMetrics {
     File? primary_contigs_list  # required if run_module_metrics = true
 
     String sv_pipeline_docker
-    String sv_pipeline_rdtest_docker
     String sv_base_mini_docker
     String sv_base_docker
     String linux_docker
@@ -131,7 +130,6 @@ workflow GenerateBatchMetrics {
             female_samples = GetSampleLists.female_samples,
             male_only_variant_ids = GetMaleOnlyVariantIDs.male_only_variant_ids,
             sv_pipeline_docker = sv_pipeline_docker,
-            sv_pipeline_rdtest_docker = sv_pipeline_rdtest_docker,
             linux_docker = linux_docker,
             runtime_attr_rdtest = runtime_attr_rdtest,
             runtime_attr_split_rd_vcf = runtime_attr_split_rd_vcf,

diff --git a/wdl/GenotypeBatch.wdl b/wdl/GenotypeBatch.wdl
@@ -52,7 +52,6 @@ workflow GenotypeBatch {
 
     String sv_base_mini_docker
     String sv_pipeline_docker
-    String sv_pipeline_rdtest_docker
     String linux_docker
 
     # Common
@@ -152,7 +151,6 @@ workflow GenotypeBatch {
         ref_dict = ref_dict,
         sv_base_mini_docker = sv_base_mini_docker,
         sv_pipeline_docker = sv_pipeline_docker,
-        sv_pipeline_rdtest_docker = sv_pipeline_rdtest_docker,
         runtime_attr_split_vcf = runtime_attr_split_vcf,
         runtime_attr_merge_counts = runtime_attr_merge_counts,
         runtime_attr_make_batch_bed = runtime_attr_make_batch_bed,
@@ -194,7 +192,6 @@ workflow GenotypeBatch {
       sr_median_hom_ins = sr_median_hom_ins,
       sv_base_mini_docker = sv_base_mini_docker,
       sv_pipeline_docker = sv_pipeline_docker,
-      sv_pipeline_rdtest_docker = sv_pipeline_rdtest_docker,
       linux_docker = linux_docker,
       runtime_attr_split_variants = runtime_attr_split_variants,
       runtime_attr_make_subset_vcf = runtime_attr_make_subset_vcf,
@@ -228,7 +225,6 @@ workflow GenotypeBatch {
         ref_dict = ref_dict,
         sv_base_mini_docker = sv_base_mini_docker,
         sv_pipeline_docker = sv_pipeline_docker,
-        sv_pipeline_rdtest_docker = sv_pipeline_rdtest_docker,
         runtime_attr_training_bed = runtime_attr_training_bed,
         runtime_attr_genotype_train = runtime_attr_genotype_train,
         runtime_attr_generate_cutoff = runtime_attr_generate_cutoff,
@@ -254,7 +250,6 @@ workflow GenotypeBatch {
       ref_dict = ref_dict,
       sv_base_mini_docker = sv_base_mini_docker,
       sv_pipeline_docker = sv_pipeline_docker,
-      sv_pipeline_rdtest_docker = sv_pipeline_rdtest_docker,
       runtime_attr_split_variants = runtime_attr_split_variants,
       runtime_attr_rdtest_genotype = runtime_attr_rdtest_genotype,
       runtime_attr_make_subset_vcf = runtime_attr_make_subset_vcf,

diff --git a/wdl/GenotypeComplexVariants.wdl b/wdl/GenotypeComplexVariants.wdl
@@ -32,7 +32,6 @@ workflow GenotypeComplexVariants {
     String linux_docker
     String sv_base_mini_docker
     String sv_pipeline_docker
-    String sv_pipeline_rdtest_docker
 
     # overrides for mini tasks
     RuntimeAttr? runtime_override_concat
@@ -99,7 +98,6 @@ workflow GenotypeComplexVariants {
         linux_docker=linux_docker,
         sv_base_mini_docker=sv_base_mini_docker,
         sv_pipeline_docker=sv_pipeline_docker,
-        sv_pipeline_rdtest_docker=sv_pipeline_rdtest_docker,
         runtime_override_ids_from_median=runtime_override_ids_from_median,
         runtime_override_split_vcf_to_genotype=runtime_override_split_vcf_to_genotype,
         runtime_override_concat_cpx_cnv_vcfs=runtime_override_concat_cpx_cnv_vcfs,