SVConcordance workflows update (broadinstitute#540)

Genometric · Jun 27, 2023 · 517a882 · 517a882
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commit 517a882
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Showing 34 changed files with 581 additions and 626 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
@@ -20,7 +20,7 @@
   "CleanVcf.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
 
   "CleanVcf.cohort_name": "${this.sample_set_id}",
-  "CleanVcf.merged_ped_file": "${workspace.cohort_ped_file}",
+  "CleanVcf.ped_file": "${workspace.cohort_ped_file}",
   "CleanVcf.complex_genotype_vcfs": "${this.complex_genotype_vcfs}",
   "CleanVcf.complex_resolve_bothside_pass_lists": "${this.complex_resolve_bothside_pass_lists}",
   "CleanVcf.complex_resolve_background_fail_lists": "${this.complex_resolve_background_fail_lists}"

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
@@ -20,7 +20,7 @@
   "CleanVcf.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
 
   "CleanVcf.cohort_name": "${this.sample_set_set_id}",
-  "CleanVcf.merged_ped_file": "${workspace.cohort_ped_file}",
+  "CleanVcf.ped_file": "${workspace.cohort_ped_file}",
   "CleanVcf.complex_genotype_vcfs": "${this.complex_genotype_vcfs}",
   "CleanVcf.complex_resolve_bothside_pass_lists": "${this.complex_resolve_bothside_pass_lists}",
   "CleanVcf.complex_resolve_background_fail_lists": "${this.complex_resolve_background_fail_lists}"

diff --git a/...kspaces/cohort_mode/workflow_configurations/GenotypeComplexVariants.SingleBatch.json.tmpl b/...kspaces/cohort_mode/workflow_configurations/GenotypeComplexVariants.SingleBatch.json.tmpl
@@ -15,7 +15,7 @@
   "GenotypeComplexVariants.depth_vcfs": "${this.regenotyped_depth_vcfs}",
   "GenotypeComplexVariants.complex_resolve_vcfs": "${this.complex_resolve_vcfs}",
   "GenotypeComplexVariants.complex_resolve_vcf_indexes": "${this.complex_resolve_vcf_indexes}",
-  "GenotypeComplexVariants.merged_ped_file": "${workspace.cohort_ped_file}",
+  "GenotypeComplexVariants.ped_file": "${workspace.cohort_ped_file}",
   "GenotypeComplexVariants.bincov_files": "${this.merged_bincov}",
   "GenotypeComplexVariants.depth_gt_rd_sep_files": "${this.trained_genotype_depth_depth_sepcutoff}",
   "GenotypeComplexVariants.median_coverage_files": "${this.median_cov}"

diff --git a/...es/terra_workspaces/cohort_mode/workflow_configurations/GenotypeComplexVariants.json.tmpl b/...es/terra_workspaces/cohort_mode/workflow_configurations/GenotypeComplexVariants.json.tmpl
@@ -15,7 +15,7 @@
   "GenotypeComplexVariants.depth_vcfs": "${this.regenotyped_depth_vcfs}",
   "GenotypeComplexVariants.complex_resolve_vcfs": "${this.complex_resolve_vcfs}",
   "GenotypeComplexVariants.complex_resolve_vcf_indexes": "${this.complex_resolve_vcf_indexes}",
-  "GenotypeComplexVariants.merged_ped_file": "${workspace.cohort_ped_file}",
+  "GenotypeComplexVariants.ped_file": "${workspace.cohort_ped_file}",
   "GenotypeComplexVariants.bincov_files": "${this.sample_sets.merged_bincov}",
   "GenotypeComplexVariants.depth_gt_rd_sep_files": "${this.sample_sets.trained_genotype_depth_depth_sepcutoff}",
   "GenotypeComplexVariants.median_coverage_files": "${this.sample_sets.median_cov}"

diff --git a/inputs/templates/test/FormatVcfForGatk/FormatVcfForGatk.json.tmpl b/inputs/templates/test/FormatVcfForGatk/FormatVcfForGatk.json.tmpl
@@ -0,0 +1,12 @@
+{
+  "FormatVcfForGatk.vcf": {{ test_batch.clean_vcf | tojson }},
+  "FormatVcfForGatk.prefix": {{ test_batch.name | tojson }},
+  "FormatVcfForGatk.ped_file": {{ test_batch.ped_file | tojson }},
+  "FormatVcfForGatk.formatter_args": {{ test_batch.clean_vcf_gatk_formatter_args | tojson }},
+  "FormatVcfForGatk.contig_list": {{ reference_resources.primary_contigs_list | tojson }},
+  "FormatVcfForGatk.chr_x": {{ reference_resources.chr_x | tojson }},
+  "FormatVcfForGatk.chr_y": {{ reference_resources.chr_y | tojson }},
+  "FormatVcfForGatk.contigs_header": {{ reference_resources.contigs_header | tojson }},
+  "FormatVcfForGatk.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
+  "FormatVcfForGatk.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }}
+}
diff --git a/inputs/templates/test/JoinRawCalls/JoinRawCalls.json.tmpl b/inputs/templates/test/JoinRawCalls/JoinRawCalls.json.tmpl
@@ -1,19 +1,26 @@
 {
-  "JoinRawCalls.gatk_docker":{{ dockers.gatk_docker | tojson }},
+  "JoinRawCalls.gatk_docker": {{ dockers.gatk_docker | tojson }},
   "JoinRawCalls.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
   "JoinRawCalls.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
 
   "JoinRawCalls.clustered_depth_vcfs" : [{{ test_batch.merged_depth_vcf | tojson }}],
+  "JoinRawCalls.clustered_depth_vcf_indexes" : [{{ test_batch.merged_depth_vcf_index | tojson }}],
+
   "JoinRawCalls.clustered_manta_vcfs" : [{{ test_batch.merged_manta_vcf | tojson }}],
+  "JoinRawCalls.clustered_manta_vcf_indexes" : [{{ test_batch.merged_manta_vcf_index | tojson }}],
+
   "JoinRawCalls.clustered_wham_vcfs" : [{{ test_batch.merged_wham_vcf | tojson }}],
+  "JoinRawCalls.clustered_wham_vcf_indexes" : [{{ test_batch.merged_wham_vcf_index | tojson }}],
+
   "JoinRawCalls.clustered_melt_vcfs" : [{{ test_batch.merged_melt_vcf | tojson }}],
+  "JoinRawCalls.clustered_melt_vcf_indexes" : [{{ test_batch.merged_melt_vcf_index | tojson }}],
 
-  "JoinRawCalls.ploidy_table": {{ test_batch.ploidy_table | tojson }},
+  "JoinRawCalls.ped_file": {{ test_batch.ped_file | tojson }},
 
   "JoinRawCalls.contig_list": {{ reference_resources.primary_contigs_list | tojson }},
   "JoinRawCalls.reference_fasta": {{ reference_resources.reference_fasta | tojson }},
   "JoinRawCalls.reference_fasta_fai": {{ reference_resources.reference_index | tojson }},
   "JoinRawCalls.reference_dict": {{ reference_resources.reference_dict | tojson }},
 
-  "JoinRawCalls.cohort": {{ test_batch.name | tojson }}
+  "JoinRawCalls.prefix": {{ test_batch.name | tojson }}
 }
diff --git a/inputs/templates/test/MakeCohortVcf/CleanVcf.json.tmpl b/inputs/templates/test/MakeCohortVcf/CleanVcf.json.tmpl
@@ -20,7 +20,7 @@
   "CleanVcf.sv_base_mini_docker":{{ dockers.sv_base_mini_docker | tojson }},
 
   "CleanVcf.cohort_name": {{ test_batch.name | tojson }},
-  "CleanVcf.merged_ped_file": {{ test_batch.ped_file | tojson }},
+  "CleanVcf.ped_file": {{ test_batch.ped_file | tojson }},
   "CleanVcf.complex_genotype_vcfs": {{ test_batch.complex_genotype_vcfs | tojson }},
   "CleanVcf.complex_resolve_bothside_pass_lists": {{ test_batch.complex_resolve_bothside_pass_lists | tojson }},
   "CleanVcf.complex_resolve_background_fail_lists": {{ test_batch.complex_resolve_background_fail_lists | tojson }}

diff --git a/inputs/templates/test/MakeCohortVcf/GenotypeComplexVariants.json.tmpl b/inputs/templates/test/MakeCohortVcf/GenotypeComplexVariants.json.tmpl
@@ -19,7 +19,7 @@
   ],
   "GenotypeComplexVariants.complex_resolve_vcfs": {{ test_batch.complex_resolve_vcfs | tojson }},
   "GenotypeComplexVariants.complex_resolve_vcf_indexes": {{ test_batch.complex_resolve_vcf_indexes | tojson }},
-  "GenotypeComplexVariants.merged_ped_file": {{ test_batch.ped_file | tojson }},
+  "GenotypeComplexVariants.ped_file": {{ test_batch.ped_file | tojson }},
   "GenotypeComplexVariants.bincov_files": [
     {{ test_batch.merged_coverage_file | tojson }}
   ],

diff --git a/inputs/templates/test/SVConcordance/SVConcordance.json.tmpl b/inputs/templates/test/SVConcordance/SVConcordance.json.tmpl
@@ -1,21 +1,11 @@
 {
-  "SVConcordance.gatk_docker":{{ dockers.gatk_docker_concordance | tojson }},
+  "SVConcordance.gatk_docker": {{ dockers.gatk_docker | tojson }},
   "SVConcordance.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
-  "SVConcordance.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
-  "SVConcordance.sv_utils_docker": {{ dockers.sv_utils_docker | tojson }},
 
-  "SVConcordance.eval_vcf" : {{ test_batch.clean_vcf | tojson }},
+  "SVConcordance.eval_vcf" : {{ test_batch.gatk_formatted_vcf | tojson }},
   "SVConcordance.truth_vcf" : {{ test_batch.joined_raw_calls_vcf | tojson }},
 
-  "SVConcordance.ploidy_table": {{ test_batch.ploidy_table | tojson }},
-  "SVConcordance.cohort": {{ test_batch.name | tojson }},
-
-  "SVConcordance.run_svutils_truth_vcf": "false",
-  "SVConcordance.run_formatter_truth_vcf": "false",
-
-  "SVConcordance.run_svutils_eval_vcf": "true",
-  "SVConcordance.run_formatter_eval_vcf": "true",
-  "SVConcordance.formatter_eval_args": "--only-add-cn-fields --replace-ev-format --filter-unsupported-types",
+  "SVConcordance.output_prefix": {{ test_batch.name | tojson }},
 
   "SVConcordance.contig_list": {{ reference_resources.primary_contigs_list | tojson }},
   "SVConcordance.reference_dict": {{ reference_resources.reference_dict | tojson }}

diff --git a/inputs/templates/test/Vapor/Vapor.json.tmpl b/inputs/templates/test/Vapor/Vapor.json.tmpl
@@ -1,15 +1,15 @@
 {
-    "VaporBatch.sv_base_mini_docker" : {{ dockers.sv_base_mini_docker | tojson }},
-    "VaporBatch.sv_pipeline_docker" : {{ dockers.sv_pipeline_docker | tojson }},
-    "VaporBatch.vapor_docker": {{ dockers.vapor_docker | tojson }},
-    "VaporBatch.contigs": {{ reference_resources.primary_contigs_list | tojson }},
-    "VaporBatch.ref_fasta" : {{ reference_resources.reference_fasta | tojson }},
-    "VaporBatch.ref_fai" : {{ reference_resources.reference_index | tojson }},
-    "VaporBatch.ref_dict": {{ reference_resources.reference_dict | tojson }},
+    "Vapor.sv_base_mini_docker" : {{ dockers.sv_base_mini_docker | tojson }},
+    "Vapor.sv_pipeline_docker" : {{ dockers.sv_pipeline_docker | tojson }},
+    "Vapor.vapor_docker": {{ dockers.vapor_docker | tojson }},
+    "Vapor.contigs": {{ reference_resources.primary_contigs_list | tojson }},
+    "Vapor.ref_fasta" : {{ reference_resources.reference_fasta | tojson }},
+    "Vapor.ref_fai" : {{ reference_resources.reference_index | tojson }},
+    "Vapor.ref_dict": {{ reference_resources.reference_dict | tojson }},
 
-    "VaporBatch.prefix": {{ test_batch.example_pacbio_sample_id | tojson }},
-    "VaporBatch.sample_id": {{ test_batch.example_pacbio_sample_id | tojson }},
-    "VaporBatch.bam_or_cram_file": {{ test_batch.example_pacbio_cram | tojson }},
-    "VaporBatch.bam_or_cram_index": {{ test_batch.example_pacbio_cram_index | tojson }},
-    "VaporBatch.bed_file": {{ test_batch.clean_bed | tojson }}
+    "Vapor.prefix": {{ test_batch.example_pacbio_sample_id | tojson }},
+    "Vapor.sample_id": {{ test_batch.example_pacbio_sample_id | tojson }},
+    "Vapor.bam_or_cram_file": {{ test_batch.example_pacbio_cram | tojson }},
+    "Vapor.bam_or_cram_index": {{ test_batch.example_pacbio_cram_index | tojson }},
+    "Vapor.bed_file": {{ test_batch.clean_bed | tojson }}
 }
diff --git a/inputs/values/dockers.json b/inputs/values/dockers.json
@@ -2,9 +2,8 @@
   "name": "dockers",
   "cnmops_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/cnmops:2023-02-01-v0.26.8-beta-9b25c72d",
   "condense_counts_docker": "us.gcr.io/broad-dsde-methods/tsharpe/gatk:4.2.6.1-57-g9e03432",
-  "gatk_docker": "us.gcr.io/broad-dsde-methods/tsharpe/gatk:4.2.6.1-57-g9e03432",
+  "gatk_docker": "us.gcr.io/broad-dsde-methods/markw/gatk:2023-05-16-4.4.0.0-17-g18edcd3e6-NIGHTLY-SNAPSHOT",
   "gatk_docker_pesr_override": "us.gcr.io/broad-dsde-methods/tsharpe/gatk:4.2.6.1-57-g9e03432",
-  "gatk_docker_concordance": "us.gcr.io/broad-dsde-methods/markw/gatk:mw-sv-concordance-937c81",
   "genomes_in_the_cloud_docker": "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.3.2-1510681135",
   "linux_docker": "marketplace.gcr.io/google/ubuntu1804",
   "manta_docker": "us.gcr.io/broad-dsde-methods/vjalili/manta:5994670",
@@ -33,4 +32,4 @@
   "sv_utils_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/sv-utils:2023-03-16-v0.27-beta-906c6272",
   "gq_recalibrator_docker": "us.gcr.io/broad-dsde-methods/tbrookin/gatk:0a7e1d86f",
   "str": "us.gcr.io/broad-dsde-methods/gatk-sv/str:2023-05-23-v0.27.3-beta-e537bdd6"
-}
+}
diff --git a/inputs/values/dockers_azure.json b/inputs/values/dockers_azure.json
@@ -2,9 +2,8 @@
   "name": "dockers",
   "cnmops_docker": "vahid.azurecr.io/gatk-sv/cnmops:2023-02-01-v0.26.8-beta-9b25c72d",
   "condense_counts_docker": "vahid.azurecr.io/tsharpe/gatk:4.2.6.1-57-g9e03432",
-  "gatk_docker": "vahid.azurecr.io/tsharpe/gatk:4.2.6.1-57-g9e03432",
+  "gatk_docker": "vahid.azurecr.io/markw/gatk:2023-05-16-4.4.0.0-17-g18edcd3e6-NIGHTLY-SNAPSHOT",
   "gatk_docker_pesr_override": "vahid.azurecr.io/tsharpe/gatk:4.2.6.1-57-g9e03432",
-  "gatk_docker_concordance": "vahid.azurecr.io/markw/gatk:mw-sv-concordance-937c81",
   "genomes_in_the_cloud_docker": "vahid.azurecr.io/genomes-in-the-cloud:2.3.2-1510681135",
   "linux_docker": "vahid.azurecr.io/google/ubuntu1804",
   "manta_docker": "vahid.azurecr.io/vjalili/manta:5994670",