Replace sv_pipeline_base_docker with sv_pipeline_docker (#634)

broadinstitute · Feb 2, 2024 · 8e2828b · 8e2828b
1 parent b1c6b98
commit 8e2828b
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Showing 57 changed files with 122 additions and 180 deletions.
diff --git a/...lates/terra_workspaces/cohort_mode/workflow_configurations/CleanVcf.SingleBatch.json.tmpl b/...lates/terra_workspaces/cohort_mode/workflow_configurations/CleanVcf.SingleBatch.json.tmpl
@@ -11,7 +11,6 @@
   "CleanVcf.clean_vcf5_records_per_shard": 5000,
 
   "CleanVcf.primary_contigs_list": "${workspace.primary_contigs_list}",
-  "CleanVcf.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
 
   "CleanVcf.linux_docker": "${workspace.linux_docker}",
   "CleanVcf.sv_pipeline_docker": "${workspace.sv_pipeline_docker}",

diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/CleanVcf.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/CleanVcf.json.tmpl
@@ -11,7 +11,6 @@
   "CleanVcf.clean_vcf5_records_per_shard": 5000,
 
   "CleanVcf.primary_contigs_list": "${workspace.primary_contigs_list}",
-  "CleanVcf.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
 
   "CleanVcf.linux_docker": "${workspace.linux_docker}",
   "CleanVcf.sv_pipeline_docker": "${workspace.sv_pipeline_docker}",

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
@@ -18,7 +18,6 @@
   "ClusterBatch.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
   "ClusterBatch.sv_pipeline_docker": "${workspace.sv_pipeline_docker}",
   "ClusterBatch.gatk_docker": "${workspace.gatk_docker}",
-  "ClusterBatch.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
   "ClusterBatch.linux_docker": "${workspace.linux_docker}",
 
   "ClusterBatch.batch": "${this.sample_set_id}",

diff --git a/...lates/terra_workspaces/cohort_mode/workflow_configurations/GatherSampleEvidence.json.tmpl b/...lates/terra_workspaces/cohort_mode/workflow_configurations/GatherSampleEvidence.json.tmpl
@@ -27,7 +27,6 @@
   "GatherSampleEvidence.cloud_sdk_docker": "${workspace.cloud_sdk_docker}",
 
   "GatherSampleEvidence.primary_contigs_fai": "${workspace.primary_contigs_fai}",
-  "GatherSampleEvidence.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
 
   "GatherSampleEvidence.bam_or_cram_file": "${this.bam_or_cram_file}",
   "GatherSampleEvidence.sample_id": "${this.sample_id}"

diff --git a/...lates/terra_workspaces/cohort_mode/workflow_configurations/GenerateBatchMetrics.json.tmpl b/...lates/terra_workspaces/cohort_mode/workflow_configurations/GenerateBatchMetrics.json.tmpl
@@ -3,7 +3,6 @@
   "GenerateBatchMetrics.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}",
   "GenerateBatchMetrics.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
   "GenerateBatchMetrics.sv_base_docker": "${workspace.sv_base_docker}",
-  "GenerateBatchMetrics.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
   "GenerateBatchMetrics.linux_docker" : "${workspace.linux_docker}",
 
   "GenerateBatchMetrics.BAF_split_size": "10000",

diff --git a/.../terra_workspaces/cohort_mode/workflow_configurations/GenotypeBatch.SingleBatch.json.tmpl b/.../terra_workspaces/cohort_mode/workflow_configurations/GenotypeBatch.SingleBatch.json.tmpl
@@ -12,7 +12,6 @@
   "GenotypeBatch.ref_dict": "${workspace.reference_dict}",
 
   "GenotypeBatch.primary_contigs_list": "${workspace.primary_contigs_list}",
-  "GenotypeBatch.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
 
   "GenotypeBatch.batch": "${this.sample_set_id}",
   "GenotypeBatch.rf_cutoffs": "${this.cutoffs}",

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
@@ -12,7 +12,6 @@
   "GenotypeBatch.ref_dict": "${workspace.reference_dict}",
 
   "GenotypeBatch.primary_contigs_list": "${workspace.primary_contigs_list}",
-  "GenotypeBatch.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
 
   "GenotypeBatch.batch": "${this.sample_set_id}",
   "GenotypeBatch.rf_cutoffs": "${this.cutoffs}",

diff --git a/.../terra_workspaces/cohort_mode/workflow_configurations/MakeCohortVcf.SingleBatch.json.tmpl b/.../terra_workspaces/cohort_mode/workflow_configurations/MakeCohortVcf.SingleBatch.json.tmpl
@@ -34,7 +34,6 @@
   "MakeCohortVcf.sv_pipeline_qc_docker": "${workspace.sv_pipeline_qc_docker}",
 
   "MakeCohortVcf.primary_contigs_list": "${workspace.primary_contigs_list}",
-  "MakeCohortVcf.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
 
   "MakeCohortVcf.chr_x": "${workspace.chr_x}",
   "MakeCohortVcf.chr_y": "${workspace.chr_y}",

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
@@ -34,7 +34,6 @@
   "MakeCohortVcf.sv_pipeline_qc_docker": "${workspace.sv_pipeline_qc_docker}",
 
   "MakeCohortVcf.primary_contigs_list": "${workspace.primary_contigs_list}",
-  "MakeCohortVcf.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
 
   "MakeCohortVcf.chr_x": "${workspace.chr_x}",
   "MakeCohortVcf.chr_y": "${workspace.chr_y}",

diff --git a/...terra_workspaces/cohort_mode/workflow_configurations/RegenotypeCNVs.SingleBatch.json.tmpl b/...terra_workspaces/cohort_mode/workflow_configurations/RegenotypeCNVs.SingleBatch.json.tmpl
@@ -1,6 +1,5 @@
 {
   "RegenotypeCNVs.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}",
-  "RegenotypeCNVs.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_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
@@ -1,6 +1,5 @@
 {
   "RegenotypeCNVs.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}",
-  "RegenotypeCNVs.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_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/workflow_configurations/TrainGCNV.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/TrainGCNV.json.tmpl
@@ -62,5 +62,5 @@
   "TrainGCNV.samples": "${this.samples.sample_id}",
 
   "TrainGCNV.n_samples_subsample": 100,
-  "TrainGCNV.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}"
+  "TrainGCNV.sv_pipeline_docker": "${workspace.sv_pipeline_docker}"
 }
diff --git a/inputs/templates/terra_workspaces/cohort_mode/workspace.tsv.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workspace.tsv.tmpl
@@ -10,7 +10,6 @@ manta_docker	{{ dockers.manta_docker }}
 samtools_cloud_docker	{{ dockers.samtools_cloud_docker }}
 sv_base_docker	{{ dockers.sv_base_docker }}
 sv_base_mini_docker	{{ dockers.sv_base_mini_docker }}
-sv_pipeline_base_docker	{{ dockers.sv_pipeline_base_docker }}
 sv_pipeline_docker	{{ dockers.sv_pipeline_docker }}
 sv_pipeline_hail_docker	{{ dockers.sv_pipeline_hail_docker }}
 sv_pipeline_updates_docker	{{ dockers.sv_pipeline_updates_docker }}

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
@@ -33,7 +33,6 @@
   "GATKSVPipelineSingleSample.linux_docker" : "${workspace.linux_docker}",
   "GATKSVPipelineSingleSample.manta_docker": "${workspace.manta_docker}",
   "GATKSVPipelineSingleSample.sv_base_docker": "${workspace.sv_base_docker}",
-  "GATKSVPipelineSingleSample.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
   "GATKSVPipelineSingleSample.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
   "GATKSVPipelineSingleSample.sv_pipeline_docker": "${workspace.sv_pipeline_docker}",
   "GATKSVPipelineSingleSample.sv_pipeline_hail_docker": "${workspace.sv_pipeline_hail_docker}",

diff --git a/inputs/templates/terra_workspaces/single_sample/workspace.tsv.tmpl b/inputs/templates/terra_workspaces/single_sample/workspace.tsv.tmpl
@@ -9,7 +9,6 @@ manta_docker	{{ dockers.manta_docker }}
 samtools_cloud_docker	{{ dockers.samtools_cloud_docker }}
 sv_base_docker	{{ dockers.sv_base_docker }}
 sv_base_mini_docker	{{ dockers.sv_base_mini_docker }}
-sv_pipeline_base_docker	{{ dockers.sv_pipeline_base_docker }}
 sv_pipeline_docker	{{ dockers.sv_pipeline_docker }}
 sv_pipeline_hail_docker	{{ dockers.sv_pipeline_hail_docker }}
 sv_pipeline_updates_docker	{{ dockers.sv_pipeline_updates_docker }}

diff --git a/inputs/templates/test/ClusterBatch/ClusterBatch.json.tmpl b/inputs/templates/test/ClusterBatch/ClusterBatch.json.tmpl
@@ -20,7 +20,6 @@
   "ClusterBatch.depth_clustering_algorithm": "SINGLE_LINKAGE",
 
   "ClusterBatch.gatk_docker": {{ dockers.gatk_docker | tojson }},
-  "ClusterBatch.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }},
   "ClusterBatch.linux_docker": {{ dockers.linux_docker | tojson }},
 
   "ClusterBatch.batch": {{ test_batch.name | tojson }},

diff --git a/inputs/templates/test/FilterBatch/FilterBatch.json.tmpl b/inputs/templates/test/FilterBatch/FilterBatch.json.tmpl
@@ -6,7 +6,6 @@
   "FilterBatch.outlier_cutoff_nIQR": "10000",
 
   "FilterBatch.primary_contigs_list": {{ reference_resources.primary_contigs_list | tojson }},
-  "FilterBatch.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }},
   "FilterBatch.ped_file": {{ test_batch.ped_file | tojson }},
 
   "FilterBatch.batch": {{ test_batch.name | tojson }},

diff --git a/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.FromSampleEvidence.json.tmpl b/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.FromSampleEvidence.json.tmpl
@@ -29,7 +29,6 @@
   "GATKSVPipelineBatch.condense_counts_docker" : {{ dockers.condense_counts_docker | tojson }},
   "GATKSVPipelineBatch.genomes_in_the_cloud_docker" : {{ dockers.genomes_in_the_cloud_docker | tojson }},
   "GATKSVPipelineBatch.sv_base_docker": {{ dockers.sv_base_docker | tojson }},
-  "GATKSVPipelineBatch.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }},
   "GATKSVPipelineBatch.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
   "GATKSVPipelineBatch.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
   "GATKSVPipelineBatch.sv_pipeline_hail_docker": {{ dockers.sv_pipeline_hail_docker | tojson }},

diff --git a/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.json.tmpl b/inputs/templates/test/GATKSVPipelineBatch/GATKSVPipelineBatch.json.tmpl
@@ -23,7 +23,6 @@
   "GATKSVPipelineBatch.genomes_in_the_cloud_docker" : {{ dockers.genomes_in_the_cloud_docker | tojson }},
   "GATKSVPipelineBatch.scramble_docker" : {{ dockers.scramble_docker | tojson }},
   "GATKSVPipelineBatch.sv_base_docker": {{ dockers.sv_base_docker | tojson }},
-  "GATKSVPipelineBatch.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }},
   "GATKSVPipelineBatch.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
   "GATKSVPipelineBatch.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
   "GATKSVPipelineBatch.sv_pipeline_hail_docker": {{ dockers.sv_pipeline_hail_docker | tojson }},

diff --git a/inputs/templates/test/GATKSVPipelinePhase1/GATKSVPipelinePhase1.json.tmpl b/inputs/templates/test/GATKSVPipelinePhase1/GATKSVPipelinePhase1.json.tmpl
@@ -1,7 +1,6 @@
 {
   "GATKSVPipelinePhase1.sv_base_mini_docker":{{ dockers.sv_base_mini_docker | tojson }},
   "GATKSVPipelinePhase1.sv_base_docker": {{ dockers.sv_base_docker | tojson }},
-  "GATKSVPipelinePhase1.sv_pipeline_base_docker": {{ dockers.sv_pipeline_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 }},

diff --git a/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl b/inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl
@@ -31,7 +31,6 @@
   "GATKSVPipelineSingleSample.melt_docker" : {{ dockers.melt_docker | tojson }},
   "GATKSVPipelineSingleSample.scramble_docker" : {{ dockers.scramble_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_base_docker": {{ dockers.sv_base_docker | tojson }},
-  "GATKSVPipelineSingleSample.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_pipeline_hail_docker": {{ dockers.sv_pipeline_hail_docker | tojson }},

diff --git a/...ts/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.no_melt.json.tmpl b/...ts/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.no_melt.json.tmpl
@@ -34,7 +34,6 @@
   "GATKSVPipelineSingleSample.melt_docker": {{ dockers.melt_docker | tojson }},
   "GATKSVPipelineSingleSample.scramble_docker": {{ dockers.scramble_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_base_docker": {{ dockers.sv_base_docker | tojson }},
-  "GATKSVPipelineSingleSample.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
   "GATKSVPipelineSingleSample.sv_pipeline_hail_docker": {{ dockers.sv_pipeline_hail_docker | tojson }},

diff --git a/inputs/templates/test/GatherSampleEvidence/GatherSampleEvidence.json.tmpl b/inputs/templates/test/GatherSampleEvidence/GatherSampleEvidence.json.tmpl
@@ -21,7 +21,6 @@
   "GatherSampleEvidence.samtools_cloud_docker": {{ dockers.samtools_cloud_docker | tojson }},
   "GatherSampleEvidence.sv_base_mini_docker":{{ dockers.sv_base_mini_docker | tojson }},
   "GatherSampleEvidence.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
-  "GatherSampleEvidence.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }},
   "GatherSampleEvidence.manta_docker": {{ dockers.manta_docker | tojson }},
   "GatherSampleEvidence.melt_docker" : {{ dockers.melt_docker | tojson }},
   "GatherSampleEvidence.scramble_docker" : {{ dockers.scramble_docker | tojson }},

diff --git a/inputs/templates/test/GatherSampleEvidenceBatch/GatherSampleEvidenceBatch.json.tmpl b/inputs/templates/test/GatherSampleEvidenceBatch/GatherSampleEvidenceBatch.json.tmpl
@@ -29,7 +29,6 @@
 
   "GatherSampleEvidenceBatch.batch": {{ test_batch.name | tojson }},
   "GatherSampleEvidenceBatch.primary_contigs_fai": {{ reference_resources.primary_contigs_fai | tojson }},
-  "GatherSampleEvidenceBatch.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }},
   "GatherSampleEvidenceBatch.linux_docker": {{ dockers.linux_docker | tojson }},
 
   "GatherSampleEvidenceBatch.bam_or_cram_files": {{ test_batch.bam_or_cram_files | tojson }},

diff --git a/inputs/templates/test/GenerateBatchMetrics/GenerateBatchMetrics.json.tmpl b/inputs/templates/test/GenerateBatchMetrics/GenerateBatchMetrics.json.tmpl
@@ -3,7 +3,6 @@
   "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.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }},
   "GenerateBatchMetrics.linux_docker" : {{ dockers.linux_docker | tojson }},
 
   "GenerateBatchMetrics.BAF_split_size": "10000",

diff --git a/inputs/templates/test/GenotypeBatch/GenotypeBatch.json.tmpl b/inputs/templates/test/GenotypeBatch/GenotypeBatch.json.tmpl
@@ -12,7 +12,6 @@
   "GenotypeBatch.ref_dict": {{ reference_resources.reference_dict | tojson }},
 
   "GenotypeBatch.primary_contigs_list": {{ reference_resources.primary_contigs_list | tojson }},
-  "GenotypeBatch.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }},
 
   "GenotypeBatch.batch": {{ test_batch.name | tojson }},
   "GenotypeBatch.rf_cutoffs": {{ test_batch.cutoffs | tojson }},

diff --git a/inputs/templates/test/MakeCohortVcf/CleanVcf.json.tmpl b/inputs/templates/test/MakeCohortVcf/CleanVcf.json.tmpl
@@ -11,7 +11,6 @@
   "CleanVcf.clean_vcf5_records_per_shard": 5000,
 
   "CleanVcf.primary_contigs_list": {{ reference_resources.primary_contigs_list | tojson }},
-  "CleanVcf.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }},
 
   "CleanVcf.linux_docker": {{ dockers.linux_docker | tojson }},
   "CleanVcf.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},

diff --git a/inputs/templates/test/MakeCohortVcf/MakeCohortVcf.json.tmpl b/inputs/templates/test/MakeCohortVcf/MakeCohortVcf.json.tmpl
@@ -29,7 +29,6 @@
   "MakeCohortVcf.random_seed": 0,
 
   "MakeCohortVcf.primary_contigs_list": {{ reference_resources.primary_contigs_list | tojson }},
-  "MakeCohortVcf.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }},
 
   "MakeCohortVcf.linux_docker": {{ dockers.linux_docker | tojson }},
   "MakeCohortVcf.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},

diff --git a/inputs/templates/test/RegenotypeCNVs/RegenotypeCNVs.json.tmpl b/inputs/templates/test/RegenotypeCNVs/RegenotypeCNVs.json.tmpl
@@ -1,6 +1,5 @@
 {
   "RegenotypeCNVs.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }},
-  "RegenotypeCNVs.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_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
@@ -12,7 +12,6 @@
   "samtools_cloud_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/samtools-cloud:2024-01-24-v0.28.4-beta-9debd6d7",
   "sv_base_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-base:2024-01-24-v0.28.4-beta-9debd6d7",
   "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_base_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7",
   "sv_pipeline_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7",
   "sv_pipeline_hail_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7",
   "sv_pipeline_updates_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7",

diff --git a/inputs/values/dockers_azure.json b/inputs/values/dockers_azure.json
@@ -12,7 +12,6 @@
   "samtools_cloud_docker": "vahid.azurecr.io/gatk-sv/samtools-cloud:2024-01-24-v0.28.4-beta-9debd6d7",
   "sv_base_docker": "vahid.azurecr.io/gatk-sv/sv-base:2024-01-24-v0.28.4-beta-9debd6d7",
   "sv_base_mini_docker": "vahid.azurecr.io/gatk-sv/sv-base-mini:2024-01-24-v0.28.4-beta-9debd6d7",
-  "sv_pipeline_base_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7",
   "sv_pipeline_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7",
   "sv_pipeline_hail_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7",
   "sv_pipeline_updates_docker": "vahid.azurecr.io/gatk-sv/sv-pipeline:2024-01-24-v0.28.4-beta-9debd6d7",

diff --git a/wdl/CleanVcf.wdl b/wdl/CleanVcf.wdl
@@ -35,7 +35,6 @@ workflow CleanVcf {
     # Module metrics parameters
     # Run module metrics workflow at the end - on by default
     Boolean? run_module_metrics
-    String? sv_pipeline_base_docker  # required if run_module_metrics = true
     File? primary_contigs_list  # required if run_module_metrics = true
     File? baseline_cluster_vcf  # baseline files are optional for metrics workflow
     File? baseline_complex_resolve_vcf
@@ -222,7 +221,7 @@ workflow CleanVcf {
         baseline_cleaned_vcf = baseline_cleaned_vcf,
         contig_list = select_first([primary_contigs_list]),
         linux_docker = linux_docker,
-        sv_pipeline_base_docker = select_first([sv_pipeline_base_docker]),
+        sv_pipeline_docker = sv_pipeline_docker,
         sv_base_mini_docker = sv_base_mini_docker
     }
   }

diff --git a/wdl/ClusterBatch.wdl b/wdl/ClusterBatch.wdl
@@ -56,7 +56,6 @@ workflow ClusterBatch {
     # Run module metrics workflow at the end - on by default
     Boolean? run_module_metrics
     String? linux_docker  # required if run_module_metrics = true
-    String? sv_pipeline_base_docker  # required if run_module_metrics = true
     File? baseline_depth_vcf  # baseline files are optional for metrics workflow
     File? baseline_manta_vcf
     File? baseline_wham_vcf
@@ -284,7 +283,7 @@ workflow ClusterBatch {
         baseline_melt_vcf = baseline_melt_vcf,
         contig_list = select_first([contig_list]),
         sv_base_mini_docker = sv_base_mini_docker,
-        sv_pipeline_base_docker = select_first([sv_pipeline_base_docker]),
+        sv_pipeline_docker = sv_pipeline_docker,
         linux_docker = select_first([linux_docker])
     }
   }

diff --git a/wdl/ClusterBatchMetrics.wdl b/wdl/ClusterBatchMetrics.wdl
@@ -22,7 +22,7 @@ workflow ClusterBatchMetrics {
 
     File contig_list
     String? sv_base_mini_docker  # required if not providing samples array
-    String sv_pipeline_base_docker
+    String sv_pipeline_docker
     String linux_docker
 
     RuntimeAttr? runtime_attr_sample_ids_from_vcf
@@ -51,7 +51,7 @@ workflow ClusterBatchMetrics {
       prefix = "depth_clustered",
       types = "DEL,DUP",
       contig_list = contig_list,
-      sv_pipeline_base_docker = sv_pipeline_base_docker,
+      sv_pipeline_docker = sv_pipeline_docker,
       runtime_attr_override = runtime_attr_depth_metrics
   }
   if (defined(manta_vcf)) {
@@ -63,7 +63,7 @@ workflow ClusterBatchMetrics {
         prefix = "manta_clustered",
         types = "DEL,DUP,INS,INV,BND",
         contig_list = contig_list,
-        sv_pipeline_base_docker = sv_pipeline_base_docker,
+        sv_pipeline_docker = sv_pipeline_docker,
         runtime_attr_override = runtime_attr_manta_metrics
     }
   }
@@ -76,7 +76,7 @@ workflow ClusterBatchMetrics {
         prefix = "melt_clustered",
         types = "INS",
         contig_list = contig_list,
-        sv_pipeline_base_docker = sv_pipeline_base_docker,
+        sv_pipeline_docker = sv_pipeline_docker,
         runtime_attr_override = runtime_attr_melt_metrics
     }
   }
@@ -89,7 +89,7 @@ workflow ClusterBatchMetrics {
         prefix = "scramble_clustered",
         types = "INS",
         contig_list = contig_list,
-        sv_pipeline_base_docker = sv_pipeline_base_docker,
+        sv_pipeline_docker = sv_pipeline_docker,
         runtime_attr_override = runtime_attr_scramble_metrics
     }
   }
@@ -102,7 +102,7 @@ workflow ClusterBatchMetrics {
         prefix = "wham_clustered",
         types = "DEL,DUP",
         contig_list = contig_list,
-        sv_pipeline_base_docker = sv_pipeline_base_docker,
+        sv_pipeline_docker = sv_pipeline_docker,
         runtime_attr_override = runtime_attr_wham_metrics
     }
   }

diff --git a/wdl/CombineReassess.wdl b/wdl/CombineReassess.wdl
@@ -10,7 +10,6 @@ workflow CombineReassess {
     Array[File] vcfs 
     Int min_var_per_sample_outlier_threshold
     Float regeno_sample_overlap
-    String sv_pipeline_base_docker
     String sv_pipeline_docker
     RuntimeAttr? runtime_attr_vcf2bed
     RuntimeAttr? runtime_attr_merge_list_creassess
@@ -33,7 +32,7 @@ workflow CombineReassess {
       min_var_per_sample_outlier_threshold = min_var_per_sample_outlier_threshold,
       regeno_sample_overlap = regeno_sample_overlap,
       runtime_attr_override = runtime_attr_merge_list_creassess,
-      sv_pipeline_base_docker = sv_pipeline_base_docker
+      sv_pipeline_docker = sv_pipeline_docker
   }
   output {
     File regeno_variants = MergeList.regeno_var
@@ -88,7 +87,7 @@ task MergeList {
     File regeno_sample_ids_lookup
     Int min_var_per_sample_outlier_threshold
     Float regeno_sample_overlap
-    String sv_pipeline_base_docker
+    String sv_pipeline_docker
     RuntimeAttr? runtime_attr_override
   }
   RuntimeAttr default_attr = object {
@@ -175,7 +174,7 @@ task MergeList {
     memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB"
     disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD"
     bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb])
-    docker: sv_pipeline_base_docker
+    docker: sv_pipeline_docker
     preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
     maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])
   }