Addressed PR comments.

Author: samuelklee

scripts/cnv_wdl/cnv_common_tasks.wdl

@@ -242,11 +242,6 @@ task ScatterIntervals {
 }
 
 task PostprocessGermlineCNVCalls {
-    Array[File] calling_configs
-    Array[File] denoising_configs
-    Array[File] gcnvkernel_version
-    Array[File] sharded_interval_lists
-
     String entity_id
     Array[File] gcnv_calls_tars
     Array[File] gcnv_model_tars
@@ -278,21 +273,12 @@ task PostprocessGermlineCNVCalls {
         export GATK_LOCAL_JAR=${default="/root/gatk.jar" gatk4_jar_override}
 
         # untar calls to CALLS_0, CALLS_1, etc directories and build the command line
-        # also copy over shard config and interval files
         gcnv_calls_tar_array=(${sep=" " gcnv_calls_tars})
-        calling_configs_array=(${sep=" " calling_configs})
-        denoising_configs_array=(${sep=" " denoising_configs})
-        gcnvkernel_version_array=(${sep=" " gcnvkernel_version})
-        sharded_interval_lists_array=(${sep=" " sharded_interval_lists})
         calls_args=""
         for index in ${dollar}{!gcnv_calls_tar_array[@]}; do
             gcnv_calls_tar=${dollar}{gcnv_calls_tar_array[$index]}
             mkdir CALLS_$index
             tar xzf $gcnv_calls_tar -C CALLS_$index
-            cp ${dollar}{calling_configs_array[$index]} CALLS_$index/
-            cp ${dollar}{denoising_configs_array[$index]} CALLS_$index/
-            cp ${dollar}{gcnvkernel_version_array[$index]} CALLS_$index/
-            cp ${dollar}{sharded_interval_lists_array[$index]} CALLS_$index/
             calls_args="$calls_args --calls-shard-path CALLS_$index"
         done
 

scripts/cnv_wdl/germline/cnv_germline_case_scattered_workflow.wdl

@@ -179,6 +179,9 @@ workflow CNVGermlineCaseScatteredWorkflow {
     }
 
     output {
+        Array[File] preprocessed_intervals = CNVGermlineCaseWorkflow.preprocessed_intervals
+        Array[Array[File]] read_counts_entity_id = CNVGermlineCaseWorkflow.read_counts_entity_id
+        Array[Array[File]] read_counts = CNVGermlineCaseWorkflow.read_counts
         Array[File] contig_ploidy_calls_tars = CNVGermlineCaseWorkflow.contig_ploidy_calls_tar
         Array[Array[File]] gcnv_calls_tars = CNVGermlineCaseWorkflow.gcnv_calls_tars
         Array[Array[File]] gcnv_tracking_tars = CNVGermlineCaseWorkflow.gcnv_tracking_tars

scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl

@@ -214,10 +214,6 @@ workflow CNVGermlineCaseWorkflow {
     scatter (sample_index in range(length(normal_bams))) {
         call CNVTasks.PostprocessGermlineCNVCalls {
             input:
-                calling_configs = GermlineCNVCallerCaseMode.calling_config_json,
-                denoising_configs = GermlineCNVCallerCaseMode.denoising_config_json,
-                gcnvkernel_version = GermlineCNVCallerCaseMode.gcnvkernel_version_json,
-                sharded_interval_lists = GermlineCNVCallerCaseMode.sharded_interval_list,
                 entity_id = CollectCounts.entity_id[sample_index],
                 gcnv_calls_tars = GermlineCNVCallerCaseMode.gcnv_calls_tar,
                 gcnv_model_tars = gcnv_model_tars,

scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl

@@ -262,10 +262,6 @@ workflow CNVGermlineCohortWorkflow {
     scatter (sample_index in range(length(CollectCounts.entity_id))) {
         call CNVTasks.PostprocessGermlineCNVCalls {
             input:
-                calling_configs = GermlineCNVCallerCohortMode.calling_config_json,
-                denoising_configs = GermlineCNVCallerCohortMode.denoising_config_json,
-                gcnvkernel_version = GermlineCNVCallerCohortMode.gcnvkernel_version_json,
-                sharded_interval_lists = GermlineCNVCallerCohortMode.sharded_interval_list,
                 entity_id = CollectCounts.entity_id[sample_index],
                 gcnv_calls_tars = GermlineCNVCallerCohortMode.gcnv_calls_tar,
                 gcnv_model_tars = GermlineCNVCallerCohortMode.gcnv_model_tar,