Run metrics workflows as part of main module WDLs (#211)

Author: epiercehoffman

input_templates/terra_workspaces/cohort_mode/workflow_configurations/Module00a.json.tmpl

@@ -26,6 +26,9 @@
   "Module00a.gatk_docker_pesr_override": "${workspace.gatk_docker_pesr_override}",
   "Module00a.cloud_sdk_docker": "${workspace.cloud_sdk_docker}",
 
+  "Module00a.primary_contigs_fai": "${workspace.primary_contigs_fai}",
+  "Module00a.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
+
   "Module00a.bam_or_cram_file": "${this.bam_or_cram_file}",
   "Module00a.sample_id": "${this.sample_id}",
 

input_templates/terra_workspaces/cohort_mode/workflow_configurations/Module01.json.tmpl

@@ -13,6 +13,10 @@
   "Module01.depth_exclude_list": "${workspace.depth_exclude_list}",
   "Module01.depth_exclude_list_frac_max": "0.5",
 
+  "Module01.primary_contigs_list": "${workspace.primary_contigs_list}",
+  "Module01.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
+  "Module01.linux_docker": "${workspace.linux_docker}",
+
   "Module01.batch": "${this.sample_set_id}",
   "Module01.del_bed": "${this.merged_dels}",
   "Module01.dup_bed": "${this.merged_dups}",

input_templates/terra_workspaces/cohort_mode/workflow_configurations/Module02.json.tmpl

@@ -17,6 +17,8 @@
   "Module02.segdups": "${workspace.segdups}",
   "Module02.ref_dict": "${workspace.reference_dict}",
 
+  "Module02.primary_contigs_list": "${workspace.primary_contigs_list}",
+
   "Module02.batch": "${this.sample_set_id}",
   "Module02.ped_file": "${workspace.cohort_ped_file}",
 

input_templates/terra_workspaces/cohort_mode/workflow_configurations/Module03.json.tmpl

@@ -5,6 +5,10 @@
 
   "Module03.outlier_cutoff_nIQR": "10000",
 
+  "Module03.primary_contigs_list": "${workspace.primary_contigs_list}",
+  "Module03.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
+  "Module03.ped_file": "${workspace.cohort_ped_file}",
+
   "Module03.batch": "${this.sample_set_id}",
   "Module03.depth_vcf" : "${this.clustered_depth_vcf}",
   "Module03.manta_vcf" : "${this.clustered_manta_vcf}",

input_templates/terra_workspaces/cohort_mode/workflow_configurations/Module04.SingleBatch.json.tmpl

@@ -11,6 +11,9 @@
   "Module04.reference_build": "${workspace.reference_build}",
   "Module04.ref_dict": "${workspace.reference_dict}",
 
+  "Module04.primary_contigs_list": "${workspace.primary_contigs_list}",
+  "Module04.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
+
   "Module04.batch": "${this.sample_set_id}",
   "Module04.rf_cutoffs": "${this.cutoffs}",
   "Module04.batch_depth_vcf": "${this.filtered_depth_vcf}",

input_templates/terra_workspaces/cohort_mode/workflow_configurations/Module04.json.tmpl

@@ -11,6 +11,9 @@
   "Module04.reference_build": "${workspace.reference_build}",
   "Module04.ref_dict": "${workspace.reference_dict}",
 
+  "Module04.primary_contigs_list": "${workspace.primary_contigs_list}",
+  "Module04.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
+
   "Module04.batch": "${this.sample_set_id}",
   "Module04.rf_cutoffs": "${this.cutoffs}",
   "Module04.batch_depth_vcf": "${this.filtered_depth_vcf}",

input_templates/terra_workspaces/cohort_mode/workflow_configurations/Module0506.SingleBatch.json.tmpl

@@ -25,6 +25,9 @@
   "Module0506.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}",
   "Module0506.sv_pipeline_qc_docker": "${workspace.sv_pipeline_qc_docker}",
 
+  "Module0506.primary_contigs_list": "${workspace.primary_contigs_list}",
+  "Module0506.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
+
   "Module0506.cohort_name": "${this.sample_set_id}",
   "Module0506.batches": "${this.sample_set_id}",
   "Module0506.ped_file": "${workspace.cohort_ped_file}",

input_templates/terra_workspaces/cohort_mode/workflow_configurations/Module0506.json.tmpl

@@ -25,6 +25,9 @@
   "Module0506.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}",
   "Module0506.sv_pipeline_qc_docker": "${workspace.sv_pipeline_qc_docker}",
 
+  "Module0506.primary_contigs_list": "${workspace.primary_contigs_list}",
+  "Module0506.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
+
   "Module0506.cohort_name": "${this.sample_set_set_id}",
   "Module0506.batches": "${this.sample_sets.sample_set_id}",
   "Module0506.ped_file": "${workspace.cohort_ped_file}",