diff --git a/.travis.yml b/.travis.yml
index 3304f74bac2..d4293365916 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -14,7 +14,8 @@ env:
   - TEST_TYPE=unit TEST_DOCKER=true TEST_VERBOSITY=minimal
   - TEST_TYPE=variantcalling TEST_DOCKER=true TEST_VERBOSITY=minimal
   - TEST_TYPE=python TEST_DOCKER=true TEST_VERBOSITY=minimal
-  - RUN_CNV_GERMLINE_WDL=true
+  - RUN_CNV_GERMLINE_COHORT_WDL=true
+  - RUN_CNV_GERMLINE_CASE_WDL=true
   - RUN_CNV_SOMATIC_WDL=true
   - RUN_M2_WDL=true
   - RUN_CNN_WDL=true
@@ -100,7 +101,7 @@ before_install:
    sudo Rscript scripts/docker/gatkbase/install_R_packages.R;
   fi
 # Download Cromwell jar -- if you change the version, please change the CROMWELL_JAR env variable above, too.
-- if [[ $RUN_CNV_GERMLINE_WDL == true || $RUN_CNV_SOMATIC_WDL == true || $RUN_M2_WDL == true || $RUN_CNN_WDL == true ]]; then
+- if [[ $RUN_CNV_GERMLINE_COHORT_WDL == true || $RUN_CNV_GERMLINE_CASE_WDL == true || $RUN_CNV_SOMATIC_WDL == true || $RUN_M2_WDL == true || $RUN_CNN_WDL == true ]]; then
     wget -O $CROMWELL_JAR https://github.com/broadinstitute/cromwell/releases/download/30.2/cromwell-30.2.jar;
   fi
 # Download git lfs files
@@ -116,7 +117,7 @@ install:
   else
     ./gradlew assemble;
     ./gradlew installDist;
-    if [[ $RUN_CNV_GERMLINE_WDL == true || $RUN_CNV_SOMATIC_WDL == true || $RUN_M2_WDL == true || $RUN_CNN_WDL == true ]]; then
+    if [[ $RUN_CNV_GERMLINE_COHORT_WDL == true || $RUN_CNV_GERMLINE_CASE_WDL == true || $RUN_CNV_SOMATIC_WDL == true || $RUN_M2_WDL == true || $RUN_CNN_WDL == true ]]; then
       echo "building a shadow jar for the wdl";
       ./gradlew shadowJar;
     elif [[ $TEST_TYPE == cloud ]]; then
@@ -131,9 +132,12 @@ script:
     echo "Not running any tests for nightly builds";
   elif [[ $TRAVIS_SECURE_ENV_VARS == false && $TEST_TYPE == cloud ]]; then
     echo "Can't run cloud tests without keys so don't run tests";
-  elif [[ $RUN_CNV_GERMLINE_WDL == true ]]; then
-    echo "Running CNV germline workflows";
-    bash scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh;
+  elif [[ $RUN_CNV_GERMLINE_COHORT_WDL == true ]]; then
+    echo "Running CNV germline cohort workflow";
+    travis_wait 60 bash scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh COHORT;
+  elif [[ $RUN_CNV_GERMLINE_CASE_WDL == true ]]; then
+    echo "Running CNV germline case workflow";
+    travis_wait 60 bash scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh CASE;
   elif [[ $RUN_CNV_SOMATIC_WDL == true ]]; then
     echo "Running CNV somatic workflows";
     bash scripts/cnv_cromwell_tests/somatic/run_cnv_somatic_workflows.sh;
diff --git a/scripts/cnv_cromwell_tests/germline/cnv_germline_case_scattered_workflow.json b/scripts/cnv_cromwell_tests/germline/cnv_germline_case_scattered_workflow.json
new file mode 100644
index 00000000000..0b03bf35dd5
--- /dev/null
+++ b/scripts/cnv_cromwell_tests/germline/cnv_germline_case_scattered_workflow.json
@@ -0,0 +1,35 @@
+{
+  "CNVGermlineCaseScatteredWorkflow.normal_bams": [
+    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam",
+    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P2T_20xy-downsampled.bam",
+    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P35_20xy-downsampled.bam"
+    ],
+  "CNVGermlineCaseScatteredWorkflow.normal_bais": [
+    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam.bai",
+    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P2T_20xy-downsampled.bam.bai",
+    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P35_20xy-downsampled.bam.bai"],
+  "CNVGermlineCaseScatteredWorkflow.contig_ploidy_model_tar": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wes-contig-ploidy-model.tar.gz",
+  "CNVGermlineCaseScatteredWorkflow.gatk_docker": "__GATK_DOCKER__",
+  "CNVGermlineCaseScatteredWorkflow.allosomal_contigs": ["X", "Y"],
+  "CNVGermlineCaseScatteredWorkflow.ref_copy_number_autosomal_contigs": 2,
+  "CNVGermlineCaseScatteredWorkflow.gcnv_disable_annealing": true,
+  "CNVGermlineCaseScatteredWorkflow.gcnv_initial_temperature": 1.0,
+  "CNVGermlineCaseScatteredWorkflow.gcnv_max_training_epochs": 1,
+  "CNVGermlineCaseScatteredWorkflow.gcnv_min_training_epochs": 1,
+  "CNVGermlineCaseScatteredWorkflow.gcnv_model_tars": [
+    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wes-do-gc-gcnv-model-0.tar.gz",
+    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wes-do-gc-gcnv-model-1.tar.gz"],
+  "CNVGermlineCaseScatteredWorkflow.gcnv_num_thermal_advi_iters": 1,
+  "CNVGermlineCaseScatteredWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/ice_targets_chr20xy.interval_list",
+  "CNVGermlineCaseScatteredWorkflow.num_intervals_per_scatter": 30,
+  "CNVGermlineCaseScatteredWorkflow.num_samples_per_scatter_block": 2,
+  "CNVGermlineCaseScatteredWorkflow.gcnv_max_advi_iter_first_epoch": 10,
+  "CNVGermlineCaseScatteredWorkflow.gcnv_log_emission_sampling_rounds": 1,
+  "CNVGermlineCaseScatteredWorkflow.gcnv_log_emission_samples_per_round": 1,
+  "CNVGermlineCaseScatteredWorkflow.gcnv_max_advi_iter_subsequent_epochs": 1,
+  "CNVGermlineCaseScatteredWorkflow.gcnv_max_copy_number": 3,
+  "CNVGermlineCaseScatteredWorkflow.gcnv_max_calling_iters": 1,
+  "CNVGermlineCaseScatteredWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.dict",
+  "CNVGermlineCaseScatteredWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta.fai",
+  "CNVGermlineCaseScatteredWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta"
+}
\ No newline at end of file
diff --git a/scripts/cnv_cromwell_tests/germline/cnv_germline_case_wes_do-gc_workflow.json b/scripts/cnv_cromwell_tests/germline/cnv_germline_case_wes_do-gc_workflow.json
deleted file mode 100644
index 9943295d914..00000000000
--- a/scripts/cnv_cromwell_tests/germline/cnv_germline_case_wes_do-gc_workflow.json
+++ /dev/null
@@ -1,21 +0,0 @@
-{
-  "CNVGermlineCaseWorkflow.bam": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam",
-  "CNVGermlineCaseWorkflow.bam_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam.bai",
-  "CNVGermlineCaseWorkflow.contig_ploidy_model_tar": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wes-contig-ploidy-model.tar.gz",
-  "CNVGermlineCaseWorkflow.gatk_docker": "__GATK_DOCKER__",
-  "CNVGermlineCaseWorkflow.allosomal_contigs": ["X", "Y"],
-  "CNVGermlineCaseWorkflow.ref_copy_number_autosomal_contigs": 2,
-  "CNVGermlineCaseWorkflow.gcnv_disable_annealing": true,
-  "CNVGermlineCaseWorkflow.gcnv_initial_temperature": 1.0,
-  "CNVGermlineCaseWorkflow.gcnv_max_training_epochs": 1,
-  "CNVGermlineCaseWorkflow.gcnv_min_training_epochs": 1,
-  "CNVGermlineCaseWorkflow.gcnv_model_tars": [
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wes-do-gc-gcnv-model-0.tar.gz",
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wes-do-gc-gcnv-model-1.tar.gz"],
-  "CNVGermlineCaseWorkflow.gcnv_num_thermal_advi_iters": 1,
-  "CNVGermlineCaseWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/ice_targets_chr20xy.interval_list",
-  "CNVGermlineCaseWorkflow.num_intervals_per_scatter": "100",
-  "CNVGermlineCaseWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.dict",
-  "CNVGermlineCaseWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta.fai",
-  "CNVGermlineCaseWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta"
-}
\ No newline at end of file
diff --git a/scripts/cnv_cromwell_tests/germline/cnv_germline_case_wes_no-gc_workflow.json b/scripts/cnv_cromwell_tests/germline/cnv_germline_case_wes_no-gc_workflow.json
deleted file mode 100644
index d6bd39228c2..00000000000
--- a/scripts/cnv_cromwell_tests/germline/cnv_germline_case_wes_no-gc_workflow.json
+++ /dev/null
@@ -1,21 +0,0 @@
-{
-  "CNVGermlineCaseWorkflow.bam": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam",
-  "CNVGermlineCaseWorkflow.bam_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam.bai",
-  "CNVGermlineCaseWorkflow.contig_ploidy_model_tar": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wes-contig-ploidy-model.tar.gz",
-  "CNVGermlineCaseWorkflow.gatk_docker": "__GATK_DOCKER__",
-  "CNVGermlineCaseWorkflow.allosomal_contigs": ["X", "Y"],
-  "CNVGermlineCaseWorkflow.ref_copy_number_autosomal_contigs": 2,
-  "CNVGermlineCaseWorkflow.gcnv_disable_annealing": true,
-  "CNVGermlineCaseWorkflow.gcnv_initial_temperature": 1.0,
-  "CNVGermlineCaseWorkflow.gcnv_max_training_epochs": 1,
-  "CNVGermlineCaseWorkflow.gcnv_min_training_epochs": 1,
-  "CNVGermlineCaseWorkflow.gcnv_model_tars": [
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wes-no-gc-gcnv-model-0.tar.gz",
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wes-no-gc-gcnv-model-1.tar.gz"],
-  "CNVGermlineCaseWorkflow.gcnv_num_thermal_advi_iters": 1,
-  "CNVGermlineCaseWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/ice_targets_chr20xy.interval_list",
-  "CNVGermlineCaseWorkflow.num_intervals_per_scatter": "100",
-  "CNVGermlineCaseWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.dict",
-  "CNVGermlineCaseWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta.fai",
-  "CNVGermlineCaseWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta"
-}
\ No newline at end of file
diff --git a/scripts/cnv_cromwell_tests/germline/cnv_germline_case_wgs_do-gc_workflow.json b/scripts/cnv_cromwell_tests/germline/cnv_germline_case_wgs_do-gc_workflow.json
deleted file mode 100644
index 674f5941e53..00000000000
--- a/scripts/cnv_cromwell_tests/germline/cnv_germline_case_wgs_do-gc_workflow.json
+++ /dev/null
@@ -1,22 +0,0 @@
-{
-  "CNVGermlineCaseWorkflow.bam": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam",
-  "CNVGermlineCaseWorkflow.bam_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam.bai",
-  "CNVGermlineCaseWorkflow.contig_ploidy_model_tar": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wgs-contig-ploidy-model.tar.gz",
-  "CNVGermlineCaseWorkflow.gatk_docker": "__GATK_DOCKER__",
-  "CNVGermlineCaseWorkflow.allosomal_contigs": ["X", "Y"],
-  "CNVGermlineCaseWorkflow.ref_copy_number_autosomal_contigs": 2,
-  "CNVGermlineCaseWorkflow.gcnv_disable_annealing": true,
-  "CNVGermlineCaseWorkflow.gcnv_initial_temperature": 1.0,
-  "CNVGermlineCaseWorkflow.gcnv_max_training_epochs": 1,
-  "CNVGermlineCaseWorkflow.gcnv_min_training_epochs": 1,
-  "CNVGermlineCaseWorkflow.gcnv_model_tars": [
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wgs-do-gc-gcnv-model-0.tar.gz",
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wgs-do-gc-gcnv-model-1.tar.gz"],
-  "CNVGermlineCaseWorkflow.gcnv_num_thermal_advi_iters": 1,
-  "CNVGermlineCaseWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/chr20xy.interval_list",
-  "CNVGermlineCaseWorkflow.num_intervals_per_scatter": "50",
-  "CNVGermlineCaseWorkflow.bin_length": "20000",
-  "CNVGermlineCaseWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.dict",
-  "CNVGermlineCaseWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta.fai",
-  "CNVGermlineCaseWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta"
-}
\ No newline at end of file
diff --git a/scripts/cnv_cromwell_tests/germline/cnv_germline_case_wgs_no-gc_workflow.json b/scripts/cnv_cromwell_tests/germline/cnv_germline_case_wgs_no-gc_workflow.json
deleted file mode 100644
index c9fdfe17362..00000000000
--- a/scripts/cnv_cromwell_tests/germline/cnv_germline_case_wgs_no-gc_workflow.json
+++ /dev/null
@@ -1,22 +0,0 @@
-{
-  "CNVGermlineCaseWorkflow.bam": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam",
-  "CNVGermlineCaseWorkflow.bam_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam.bai",
-  "CNVGermlineCaseWorkflow.contig_ploidy_model_tar": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wgs-contig-ploidy-model.tar.gz",
-  "CNVGermlineCaseWorkflow.gatk_docker": "__GATK_DOCKER__",
-  "CNVGermlineCaseWorkflow.allosomal_contigs": ["X", "Y"],
-  "CNVGermlineCaseWorkflow.ref_copy_number_autosomal_contigs": 2,
-  "CNVGermlineCaseWorkflow.gcnv_disable_annealing": true,
-  "CNVGermlineCaseWorkflow.gcnv_initial_temperature": 1.0,
-  "CNVGermlineCaseWorkflow.gcnv_max_training_epochs": 1,
-  "CNVGermlineCaseWorkflow.gcnv_min_training_epochs": 1,
-  "CNVGermlineCaseWorkflow.gcnv_model_tars": [
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wgs-no-gc-gcnv-model-0.tar.gz",
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/wgs-no-gc-gcnv-model-1.tar.gz"],
-  "CNVGermlineCaseWorkflow.gcnv_num_thermal_advi_iters": 1,
-  "CNVGermlineCaseWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/chr20xy.interval_list",
-  "CNVGermlineCaseWorkflow.num_intervals_per_scatter": "50",
-  "CNVGermlineCaseWorkflow.bin_length": "20000",
-  "CNVGermlineCaseWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.dict",
-  "CNVGermlineCaseWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta.fai",
-  "CNVGermlineCaseWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta"
-}
\ No newline at end of file
diff --git a/scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_wes_no-gc_workflow.json b/scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_wes_no-gc_workflow.json
deleted file mode 100644
index fdb6a06883b..00000000000
--- a/scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_wes_no-gc_workflow.json
+++ /dev/null
@@ -1,25 +0,0 @@
-{
-  "CNVGermlineCohortWorkflow.cohort_entity_id": "wes-no-gc",
-  "CNVGermlineCohortWorkflow.contig_ploidy_priors": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/contig_ploidy_priors_chr20xy.tsv",
-  "CNVGermlineCohortWorkflow.gatk_docker": "__GATK_DOCKER__",
-  "CNVGermlineCohortWorkflow.allosomal_contigs": ["X", "Y"],
-  "CNVGermlineCohortWorkflow.ref_copy_number_autosomal_contigs": 2,
-  "CNVGermlineCohortWorkflow.gcnv_disable_annealing": true,
-  "CNVGermlineCohortWorkflow.gcnv_initial_temperature": 1.0,
-  "CNVGermlineCohortWorkflow.gcnv_max_training_epochs": 1,
-  "CNVGermlineCohortWorkflow.gcnv_min_training_epochs": 1,
-  "CNVGermlineCohortWorkflow.gcnv_num_thermal_advi_iters": 1,
-  "CNVGermlineCohortWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/ice_targets_chr20xy.interval_list",
-  "CNVGermlineCohortWorkflow.normal_bais": [
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam.bai",
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P2T_20xy-downsampled.bam.bai",
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P35_20xy-downsampled.bam.bai"],
-  "CNVGermlineCohortWorkflow.normal_bams": [
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam",
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P2T_20xy-downsampled.bam",
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P35_20xy-downsampled.bam"],
-  "CNVGermlineCohortWorkflow.num_intervals_per_scatter": "100",
-  "CNVGermlineCohortWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.dict",
-  "CNVGermlineCohortWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta.fai",
-  "CNVGermlineCohortWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta"
-}
\ No newline at end of file
diff --git a/scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_wgs_do-gc_workflow.json b/scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_wgs_do-gc_workflow.json
deleted file mode 100644
index c4fdcabc570..00000000000
--- a/scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_wgs_do-gc_workflow.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
-  "CNVGermlineCohortWorkflow.cohort_entity_id": "wgs-do-gc",
-  "CNVGermlineCohortWorkflow.contig_ploidy_priors": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/contig_ploidy_priors_chr20xy.tsv",
-  "CNVGermlineCohortWorkflow.do_explicit_gc_correction": "true",
-  "CNVGermlineCohortWorkflow.gatk_docker": "__GATK_DOCKER__",
-  "CNVGermlineCohortWorkflow.allosomal_contigs": ["X", "Y"],
-  "CNVGermlineCohortWorkflow.ref_copy_number_autosomal_contigs": 2,
-  "CNVGermlineCohortWorkflow.gcnv_disable_annealing": true,
-  "CNVGermlineCohortWorkflow.gcnv_initial_temperature": 1.0,
-  "CNVGermlineCohortWorkflow.gcnv_max_training_epochs": 1,
-  "CNVGermlineCohortWorkflow.gcnv_min_training_epochs": 1,
-  "CNVGermlineCohortWorkflow.gcnv_num_thermal_advi_iters": 1,
-  "CNVGermlineCohortWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/chr20xy.interval_list",
-  "CNVGermlineCohortWorkflow.normal_bais": [
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam.bai",
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P2T_20xy-downsampled.bam.bai",
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P35_20xy-downsampled.bam.bai"],
-  "CNVGermlineCohortWorkflow.normal_bams": [
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam",
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P2T_20xy-downsampled.bam",
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P35_20xy-downsampled.bam"],
-  "CNVGermlineCohortWorkflow.num_intervals_per_scatter": "50",
-  "CNVGermlineCohortWorkflow.bin_length": "20000",
-  "CNVGermlineCohortWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.dict",
-  "CNVGermlineCohortWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta.fai",
-  "CNVGermlineCohortWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta"
-}
\ No newline at end of file
diff --git a/scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_wgs_no-gc_workflow.json b/scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_wgs_no-gc_workflow.json
deleted file mode 100644
index 625f31766e0..00000000000
--- a/scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_wgs_no-gc_workflow.json
+++ /dev/null
@@ -1,26 +0,0 @@
-{
-  "CNVGermlineCohortWorkflow.cohort_entity_id": "wgs-no-gc",
-  "CNVGermlineCohortWorkflow.contig_ploidy_priors": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/contig_ploidy_priors_chr20xy.tsv",
-  "CNVGermlineCohortWorkflow.gatk_docker": "__GATK_DOCKER__",
-  "CNVGermlineCohortWorkflow.allosomal_contigs": ["X", "Y"],
-  "CNVGermlineCohortWorkflow.ref_copy_number_autosomal_contigs": 2,
-  "CNVGermlineCohortWorkflow.gcnv_disable_annealing": true,
-  "CNVGermlineCohortWorkflow.gcnv_initial_temperature": 1.0,
-  "CNVGermlineCohortWorkflow.gcnv_max_training_epochs": 1,
-  "CNVGermlineCohortWorkflow.gcnv_min_training_epochs": 1,
-  "CNVGermlineCohortWorkflow.gcnv_num_thermal_advi_iters": 1,
-  "CNVGermlineCohortWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/chr20xy.interval_list",
-  "CNVGermlineCohortWorkflow.normal_bais": [
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam.bai",
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P2T_20xy-downsampled.bam.bai",
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P35_20xy-downsampled.bam.bai"],
-  "CNVGermlineCohortWorkflow.normal_bams": [
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam",
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P2T_20xy-downsampled.bam",
-    "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P35_20xy-downsampled.bam"],
-  "CNVGermlineCohortWorkflow.num_intervals_per_scatter": "50",
-  "CNVGermlineCohortWorkflow.bin_length": "20000",
-  "CNVGermlineCohortWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.dict",
-  "CNVGermlineCohortWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta.fai",
-  "CNVGermlineCohortWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta"
-}
\ No newline at end of file
diff --git a/scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_wes_do-gc_workflow.json b/scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_workflow.json
similarity index 95%
rename from scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_wes_do-gc_workflow.json
rename to scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_workflow.json
index e8541cf9952..c1611e2fd63 100644
--- a/scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_wes_do-gc_workflow.json
+++ b/scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_workflow.json
@@ -19,7 +19,8 @@
     "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74NEG_20xy-downsampled.bam",
     "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P2T_20xy-downsampled.bam",
     "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/SM-74P35_20xy-downsampled.bam"],
-  "CNVGermlineCohortWorkflow.num_intervals_per_scatter": "100",
+  "CNVGermlineCohortWorkflow.num_intervals_per_scatter": 30,
+  "CNVGermlineCohortWorkflow.gcnv_max_copy_number": 3,
   "CNVGermlineCohortWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.dict",
   "CNVGermlineCohortWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta.fai",
   "CNVGermlineCohortWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/Homo_sapiens_assembly19.truncated.fasta"
diff --git a/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh b/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh
index 4122c6c349f..e31c712330b 100644
--- a/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh
+++ b/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh
@@ -1,10 +1,20 @@
 #!/bin/bash -l
 set -e
+
+MODE=$1
+# We split up the test into CASE in COHORT to reduce overall travis runtime
+if [[ "$MODE" != "COHORT" ]] && [[ "$MODE" != "CASE" ]]; then
+	echo "First argument to this scripts needs to be COHORT or CASE"
+	exit 1
+fi
+
+
 #cd in the directory of the script in order to use relative paths
 script_path=$( cd "$(dirname "${BASH_SOURCE}")" ; pwd -P )
 cd "$script_path"
 
 ln -fs /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/cnv_common_tasks.wdl
+ln -fs /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl
 
 WORKING_DIR=/home/travis/build/broadinstitute
 
@@ -25,33 +35,16 @@ popd
 
 echo "Inserting docker image into json ========"
 CNV_CROMWELL_TEST_DIR="${WORKING_DIR}/gatk/scripts/cnv_cromwell_tests/germline/"
-sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" ${CNV_CROMWELL_TEST_DIR}/cnv_germline_cohort_wes_no-gc_workflow.json >cnv_germline_cohort_wes_no-gc_workflow_mod.json
-sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" ${CNV_CROMWELL_TEST_DIR}/cnv_germline_cohort_wgs_no-gc_workflow.json >cnv_germline_cohort_wgs_no-gc_workflow_mod.json
-sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" ${CNV_CROMWELL_TEST_DIR}/cnv_germline_cohort_wes_do-gc_workflow.json >cnv_germline_cohort_wes_do-gc_workflow_mod.json
-sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" ${CNV_CROMWELL_TEST_DIR}/cnv_germline_cohort_wgs_do-gc_workflow.json >cnv_germline_cohort_wgs_do-gc_workflow_mod.json
-sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" ${CNV_CROMWELL_TEST_DIR}/cnv_germline_case_wes_no-gc_workflow.json >cnv_germline_case_wes_no-gc_workflow_mod.json
-sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" ${CNV_CROMWELL_TEST_DIR}/cnv_germline_case_wgs_no-gc_workflow.json >cnv_germline_case_wgs_no-gc_workflow_mod.json
-sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" ${CNV_CROMWELL_TEST_DIR}/cnv_germline_case_wes_do-gc_workflow.json >cnv_germline_case_wes_do-gc_workflow_mod.json
-sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" ${CNV_CROMWELL_TEST_DIR}/cnv_germline_case_wgs_do-gc_workflow.json >cnv_germline_case_wgs_do-gc_workflow_mod.json
-
+sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" ${CNV_CROMWELL_TEST_DIR}/cnv_germline_cohort_workflow.json >cnv_germline_cohort_workflow_mod.json
+sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" ${CNV_CROMWELL_TEST_DIR}/cnv_germline_case_scattered_workflow.json >cnv_germline_case_scattered_workflow_mod.json
 echo "Running ========"
 
-# We disable some tests to reduce runtime on Travis
-
-# Cohort WES
-#java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl -i cnv_germline_cohort_wes_no-gc_workflow_mod.json
-# Cohort WGS
-#java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl -i cnv_germline_cohort_wgs_no-gc_workflow_mod.json
 # Cohort WES w/ explicit GC correction
-java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl -i cnv_germline_cohort_wes_do-gc_workflow_mod.json
-# Cohort WGS w/ explicit GC correction
-#java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl -i cnv_germline_cohort_wgs_do-gc_workflow_mod.json
-
-# Case WES
-#java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl -i cnv_germline_case_wes_no-gc_workflow_mod.json
-# Case WGS
-#java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl -i cnv_germline_case_wgs_no-gc_workflow_mod.json
-# Case WES w/ explicit GC correction
-java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl -i cnv_germline_case_wes_do-gc_workflow_mod.json
-# Case WGS w/ explicit GC correction
-#java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl -i cnv_germline_case_wgs_do-gc_workflow_mod.json
\ No newline at end of file
+if [[ "$MODE" == "COHORT" ]]; then
+  java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl -i cnv_germline_cohort_workflow_mod.json
+fi
+
+# Scattered case WES w/ explicit GC correction
+if [[ "$MODE" == "CASE" ]]; then
+  java -jar ${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/germline/cnv_germline_case_scattered_workflow.wdl -i cnv_germline_case_scattered_workflow_mod.json
+fi
\ No newline at end of file
diff --git a/scripts/cnv_wdl/cnv_common_tasks.wdl b/scripts/cnv_wdl/cnv_common_tasks.wdl
old mode 100755
new mode 100644
index 5172dd4251e..bc09133017f
--- a/scripts/cnv_wdl/cnv_common_tasks.wdl
+++ b/scripts/cnv_wdl/cnv_common_tasks.wdl
@@ -242,6 +242,11 @@ 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
@@ -273,12 +278,21 @@ 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
+            mkdir -p CALLS_$index/SAMPLE_${sample_index}
+            tar xzf $gcnv_calls_tar -C CALLS_$index/SAMPLE_${sample_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
 
diff --git a/scripts/cnv_wdl/germline/README.md b/scripts/cnv_wdl/germline/README.md
index 645ed3aebf8..1e036e1a7ff 100644
--- a/scripts/cnv_wdl/germline/README.md
+++ b/scripts/cnv_wdl/germline/README.md
@@ -2,8 +2,9 @@
 
 ### Which WDL should you use?
 
-- Calling a cohort of samples and building a model for denoising further case samples: ``cnv_germline_cohort_workflow.wdl``
-- Calling a case sample using a previously built model for denoising: ``cnv_germline_case_workflow.wdl``
+- Cohort WDL: Calling a cohort of samples and building a model for denoising further case samples: ``cnv_germline_cohort_workflow.wdl``
+- Case WDL: Calling case samples using a previously built model for denoising: ``cnv_germline_case_workflow.wdl``
+- Scattered case WDL (recommended): Functionally equivalent to case WDL, written for reducing cloud compute cost (see below) and wall-clock time ``cnv_germline_case_scattered_workflow.wdl``
 
 #### Setting up parameter json file for a run
 
@@ -38,8 +39,8 @@ Further explanation of other task-level parameters may be found by invoking the
 
 The reference, number of intervals per scatter, and bins (if specified) must be the same between cohort and case samples.
 
-- ``CNVGermlineCaseWorkflow.bam`` -- Path to case BAM file.
-- ``CNVGermlineCaseWorkflow.bam_idx`` -- Path to case BAM file index.
+- ``CNVGermlineCohortWorkflow.normal_bais`` -- List of BAI files.  This list must correspond to `normal_bams`.  For example, `["Sample1.bai", "Sample2.bai"]`.
+- ``CNVGermlineCohortWorkflow.normal_bams`` -- List of BAM files.  This list must correspond to `normal_bais`.  For example, `["Sample1.bam", "Sample2.bam"]`.
 - ``CNVGermlineCaseWorkflow.contig_ploidy_model_tar`` -- Path to tar of the contig-ploidy model directory generated by the DetermineGermlineContigPloidyCohortMode task. 
 - ``CNVGermlineCaseWorkflow.gatk_docker`` -- GATK Docker image (e.g., ``broadinstitute/gatk:latest``).
 - ``CNVGermlineCaseWorkflow.gcnv_model_tars`` -- Array of paths to tars of the contig-ploidy model directories generated by the GermlineCNVCallerCohortMode tasks.
@@ -52,3 +53,18 @@ The reference, number of intervals per scatter, and bins (if specified) must be
 In additional, there are several task-level parameters that may be set by advanced users as above.
 
 Further explanation of these task-level parameters may be found by invoking the ``--help`` documentation available in the gatk.jar for each tool.
+
+#### Required parameters in the scattered germline case workflow
+
+Same required parameters as in the germline case workflow. However, in order to reduce wall-clock time and compute cost, it is recommended to optimize for the following parameters:
+
+- ``CNVGermlineCaseScatteredWorkflow.num_samples_per_scatter_block`` -- (recommended WES value=25) number of samples to process in a single block; blocks of this size will be sent to the germline case workflow and processed in a batch; 
+- ``CNVGermlineCaseScatteredWorkflow.preemptible_attempts`` -- (recommended value=5) this reduces cost by using preemptible instances
+- ``CNVGermlineCaseScatteredWorkflow.mem_gb_for_determine_germline_contig_ploidy`` -- amount of memory allotted for ploidy determination tasks (the lower the cheaper)
+- ``CNVGermlineCaseScatteredWorkflow.cpu_for_determine_germline_contig_ploidy`` -- number of CPU cores allotted for ploidy determination tasks (the lower the cheaper)
+- ``CNVGermlineCaseScatteredWorkflow.disk_for_determine_germline_contig_ploidy`` -- amount of storage allotted for ploidy determination tasks (the lower the cheaper) 
+- ``CNVGermlineCaseScatteredWorkflow.mem_gb_for_germline_cnv_caller`` -- amount of memory allotted for gCNV caller tasks (the lower the cheaper)
+- ``CNVGermlineCaseScatteredWorkflow.cpu_for_germline_cnv_caller`` -- number of CPU cores allotted for gCNV caller tasks (the lower the cheaper)
+- ``CNVGermlineCaseScatteredWorkflow.disk_for_germline_cnv_caller`` -- amount of storage allotted for gCNV caller tasks (the lower the cheaper)
+
+Note that lowering disk and memory too much will eventually lead to the workflow failing. Lowering the number of CPU cores could increase the wall-clock times.
diff --git a/scripts/cnv_wdl/germline/cnv_germline_case_scattered_workflow.wdl b/scripts/cnv_wdl/germline/cnv_germline_case_scattered_workflow.wdl
new file mode 100644
index 00000000000..ce32bead65a
--- /dev/null
+++ b/scripts/cnv_wdl/germline/cnv_germline_case_scattered_workflow.wdl
@@ -0,0 +1,233 @@
+#
+# A wrapper for the gCNV case workflow intended for lowering computing cost by making it feasible to use 
+# preemptible cloud instances with low memory requirements. CPU, memory and disk requirements can be 
+# lowered for GermlineCNVCaller and DetermineGermlineContigPloidy tasks. 
+# 
+#
+# - Example invocation:
+#
+#       java -jar cromwell.jar run cnv_germline_case_scattered_workflow.wdl -i my_parameters.json
+#
+####################
+
+import "cnv_germline_case_workflow.wdl" as GermlineCNVCaseWorkflow
+
+workflow CNVGermlineCaseScatteredWorkflow {
+
+    ##################################
+    #### required basic arguments ####
+    ##################################
+    File intervals
+    Array[String]+ normal_bams
+    Array[String]+ normal_bais
+    File contig_ploidy_model_tar
+    Array[File]+ gcnv_model_tars
+    Int num_intervals_per_scatter
+    File ref_fasta_dict
+    File ref_fasta_fai
+    File ref_fasta
+    String gatk_docker
+    Int num_samples_per_scatter_block
+
+    ##################################
+    #### optional basic arguments ####
+    ##################################
+    File? gatk4_jar_override
+    Int? preemptible_attempts
+
+    ####################################################
+    #### optional arguments for PreprocessIntervals ####
+    ####################################################
+    Int? padding
+    Int? bin_length
+
+    ##############################################
+    #### optional arguments for CollectCounts ####
+    ##############################################
+    String? collect_counts_format
+    Int? mem_gb_for_collect_counts
+
+    ######################################################################
+    #### optional arguments for DetermineGermlineContigPloidyCaseMode ####
+    ######################################################################
+    Float? ploidy_mapping_error_rate
+    Float? ploidy_sample_psi_scale
+    Int? mem_gb_for_determine_germline_contig_ploidy
+    Int? cpu_for_determine_germline_contig_ploidy
+    Int? disk_for_determine_germline_contig_ploidy    
+
+    ##########################################################
+    #### optional arguments for GermlineCNVCallerCaseMode ####
+    ##########################################################
+    Float? gcnv_p_alt
+    Float? gcnv_cnv_coherence_length
+    Int? gcnv_max_copy_number
+    Int? mem_gb_for_germline_cnv_caller
+    Int? cpu_for_germline_cnv_caller
+    Int? disk_for_germline_cnv_caller
+
+    # optional arguments for germline CNV denoising model
+    Float? gcnv_mapping_error_rate
+    Float? gcnv_sample_psi_scale
+    Float? gcnv_depth_correction_tau
+    String? gcnv_copy_number_posterior_expectation_mode
+    Int? gcnv_active_class_padding_hybrid_mode
+
+    # optional arguments for Hybrid ADVI
+    Float? gcnv_learning_rate
+    Float? gcnv_adamax_beta_1
+    Float? gcnv_adamax_beta_2
+    Int? gcnv_log_emission_samples_per_round
+    Float? gcnv_log_emission_sampling_median_rel_error
+    Int? gcnv_log_emission_sampling_rounds
+    Int? gcnv_max_advi_iter_first_epoch
+    Int? gcnv_max_advi_iter_subsequent_epochs
+    Int? gcnv_min_training_epochs
+    Int? gcnv_max_training_epochs
+    Float? gcnv_initial_temperature
+    Int? gcnv_num_thermal_advi_iters
+    Int? gcnv_convergence_snr_averaging_window
+    Float? gcnv_convergence_snr_trigger_threshold
+    Int? gcnv_convergence_snr_countdown_window
+    Int? gcnv_max_calling_iters
+    Float? gcnv_caller_update_convergence_threshold
+    Float? gcnv_caller_internal_admixing_rate
+    Float? gcnv_caller_external_admixing_rate
+    Boolean? gcnv_disable_annealing
+
+    ###################################################
+    #### arguments for PostprocessGermlineCNVCalls ####
+    ###################################################
+    Int ref_copy_number_autosomal_contigs
+    Array[String]? allosomal_contigs
+
+    call SplitInputArray as SplitInputBamsList {
+        input:
+            input_array = normal_bams,
+            num_inputs_in_scatter_block = num_samples_per_scatter_block,
+            gatk_docker = gatk_docker
+    }
+    
+    call SplitInputArray as SplitInputBaisList {
+        input:
+            input_array = normal_bais,
+            num_inputs_in_scatter_block = num_samples_per_scatter_block,
+            gatk_docker = gatk_docker
+    }
+
+    Array[Array[String]] split_bams = SplitInputBamsList.split_array
+    Array[Array[String]] split_bais = SplitInputBaisList.split_array
+
+    scatter (subarray_index in range(length(split_bams))) {
+        call GermlineCNVCaseWorkflow.CNVGermlineCaseWorkflow {
+            input:
+                intervals = intervals,
+                normal_bams = split_bams[subarray_index],
+                normal_bais = split_bais[subarray_index],
+                contig_ploidy_model_tar = contig_ploidy_model_tar,
+                gcnv_model_tars = gcnv_model_tars,
+                num_intervals_per_scatter = num_intervals_per_scatter,
+                ref_fasta_dict = ref_fasta_dict,
+                ref_fasta_fai = ref_fasta_fai,
+                ref_fasta = ref_fasta,
+                gatk_docker = gatk_docker,
+                gatk4_jar_override = gatk4_jar_override,
+                preemptible_attempts = preemptible_attempts,
+                padding = padding,
+                bin_length = bin_length,
+                collect_counts_format = collect_counts_format,
+                mem_gb_for_collect_counts = mem_gb_for_collect_counts,
+                ploidy_mapping_error_rate = ploidy_mapping_error_rate,
+                ploidy_sample_psi_scale = ploidy_sample_psi_scale,
+                mem_gb_for_determine_germline_contig_ploidy = mem_gb_for_determine_germline_contig_ploidy,
+                cpu_for_determine_germline_contig_ploidy = cpu_for_determine_germline_contig_ploidy,
+                disk_for_determine_germline_contig_ploidy = disk_for_determine_germline_contig_ploidy,
+                gcnv_p_alt = gcnv_p_alt,
+                gcnv_cnv_coherence_length = gcnv_cnv_coherence_length,
+                gcnv_max_copy_number = gcnv_max_copy_number,
+                mem_gb_for_germline_cnv_caller = mem_gb_for_germline_cnv_caller,
+                cpu_for_germline_cnv_caller = cpu_for_germline_cnv_caller,
+                disk_for_germline_cnv_caller = disk_for_germline_cnv_caller,
+                gcnv_mapping_error_rate = gcnv_mapping_error_rate,
+                gcnv_sample_psi_scale = gcnv_sample_psi_scale,
+                gcnv_depth_correction_tau = gcnv_depth_correction_tau,
+                gcnv_copy_number_posterior_expectation_mode = gcnv_copy_number_posterior_expectation_mode,
+                gcnv_active_class_padding_hybrid_mode = gcnv_active_class_padding_hybrid_mode,
+                gcnv_learning_rate = gcnv_learning_rate,
+                gcnv_adamax_beta_1 = gcnv_adamax_beta_1,
+                gcnv_adamax_beta_2 = gcnv_adamax_beta_2,
+                gcnv_log_emission_samples_per_round = gcnv_log_emission_samples_per_round,
+                gcnv_log_emission_sampling_median_rel_error = gcnv_log_emission_sampling_median_rel_error,
+                gcnv_log_emission_sampling_rounds = gcnv_log_emission_sampling_rounds,
+                gcnv_max_advi_iter_first_epoch = gcnv_max_advi_iter_first_epoch,
+                gcnv_max_advi_iter_subsequent_epochs = gcnv_max_advi_iter_subsequent_epochs,
+                gcnv_min_training_epochs = gcnv_min_training_epochs,
+                gcnv_max_training_epochs = gcnv_max_training_epochs,
+                gcnv_initial_temperature = gcnv_initial_temperature,
+                gcnv_num_thermal_advi_iters = gcnv_num_thermal_advi_iters,
+                gcnv_convergence_snr_averaging_window = gcnv_convergence_snr_averaging_window,
+                gcnv_convergence_snr_trigger_threshold = gcnv_convergence_snr_trigger_threshold,
+                gcnv_convergence_snr_countdown_window = gcnv_convergence_snr_countdown_window,
+                gcnv_max_calling_iters = gcnv_max_calling_iters,
+                gcnv_caller_update_convergence_threshold = gcnv_caller_update_convergence_threshold,
+                gcnv_caller_internal_admixing_rate = gcnv_caller_internal_admixing_rate,
+                gcnv_caller_external_admixing_rate = gcnv_caller_external_admixing_rate,
+                gcnv_disable_annealing = gcnv_disable_annealing,
+                ref_copy_number_autosomal_contigs = ref_copy_number_autosomal_contigs,
+                allosomal_contigs = allosomal_contigs 
+        }
+    }
+
+    output {
+        Array[File] contig_ploidy_calls_tars = CNVGermlineCaseWorkflow.contig_ploidy_calls_tar
+        Array[Array[Array[File]]] gcnv_calls_tars = CNVGermlineCaseWorkflow.gcnv_calls_tars
+        Array[Array[File]] gcnv_tracking_tars = CNVGermlineCaseWorkflow.gcnv_tracking_tars
+        Array[Array[File]] genotyped_intervals_vcf = CNVGermlineCaseWorkflow.genotyped_intervals_vcf
+        Array[Array[File]] genotyped_segments_vcf = CNVGermlineCaseWorkflow.genotyped_segments_vcf
+    }
+}
+
+task SplitInputArray {
+    Array[String] input_array
+    Int num_inputs_in_scatter_block
+    String gatk_docker
+
+    Int machine_mem_mb = 4000
+    Int disk_space_gb = 20
+    Int cpu = 1
+    Int? preemptible_attempts
+    Boolean use_ssd = false
+
+    File input_array_file = write_lines(input_array)
+
+    # This tasks takes as input an array of strings and number of columns (num_inputs_in_scatter_block)
+    # and outputs a 2-dimensional reshaped array with same contents and with width equal to num_inputs_in_scatter_block
+    # (with last row potentially having a smaller length than others)
+    command <<<
+        python <<CODE
+        import math
+        with open("${input_array_file}", "r") as input_array_file:
+            input_array = input_array_file.read().splitlines()
+        num = ${num_inputs_in_scatter_block}
+        values_to_write = [input_array[num*i:num*i+min(num, len(input_array)-num*i)] for i in range(int(math.ceil(len(input_array)/num)))]
+        with open('input_array_split.tsv', 'w') as outfile:
+            for i in range(len(values_to_write)):
+                current_sub_array = values_to_write[i]
+                for j in range(len(current_sub_array)):
+                    outfile.write(current_sub_array[j] + "\t")
+                outfile.write("\n")
+        CODE
+    >>>
+
+    runtime {
+        docker: "${gatk_docker}"
+        memory: machine_mem_mb + " MB"
+        disks: "local-disk " + select_first([disk_space_gb, 150]) + if use_ssd then " SSD" else " HDD"
+        cpu: select_first([cpu, 8])
+        preemptible: select_first([preemptible_attempts, 5])
+    }
+
+    output {
+        Array[Array[String]] split_array = read_tsv("input_array_split.tsv")
+    }
+}
diff --git a/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl b/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl
index 945fad8a173..9300adf1282 100644
--- a/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl
+++ b/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl
@@ -1,4 +1,5 @@
-# Workflow for running GATK GermlineCNVCaller on a single case sample. Supports both WGS and WES.
+# Workflow for running GATK GermlineCNVCaller on multiple case samples using a trained model (obtained from running 
+# GATK GermlineCNVCaller in the cohort mode). Supports both WGS and WES.
 #
 # Notes:
 #
@@ -29,8 +30,8 @@ workflow CNVGermlineCaseWorkflow {
     ##################################
     File intervals
     File? blacklist_intervals
-    File bam
-    File bam_idx
+    Array[String]+ normal_bams
+    Array[String]+ normal_bais
     File contig_ploidy_model_tar
     Array[File]+ gcnv_model_tars
     Int num_intervals_per_scatter
@@ -51,6 +52,12 @@ workflow CNVGermlineCaseWorkflow {
     Int? padding
     Int? bin_length
 
+    ##############################################
+    #### optional arguments for CollectCounts ####
+    ##############################################
+    String? collect_counts_format
+    Int? mem_gb_for_collect_counts
+
     ######################################################################
     #### optional arguments for DetermineGermlineContigPloidyCaseMode ####
     ######################################################################
@@ -58,6 +65,7 @@ workflow CNVGermlineCaseWorkflow {
     Float? ploidy_sample_psi_scale
     Int? mem_gb_for_determine_germline_contig_ploidy
     Int? cpu_for_determine_germline_contig_ploidy
+    Int? disk_for_determine_germline_contig_ploidy
 
     ##########################################################
     #### optional arguments for GermlineCNVCallerCaseMode ####
@@ -67,6 +75,7 @@ workflow CNVGermlineCaseWorkflow {
     Int? gcnv_max_copy_number
     Int? mem_gb_for_germline_cnv_caller
     Int? cpu_for_germline_cnv_caller
+    Int? disk_for_germline_cnv_caller
 
     # optional arguments for germline CNV denoising model
     Float? gcnv_mapping_error_rate
@@ -103,6 +112,8 @@ workflow CNVGermlineCaseWorkflow {
     Int ref_copy_number_autosomal_contigs
     Array[String]? allosomal_contigs
 
+    Array[Pair[String, String]] normal_bams_and_bais = zip(normal_bams, normal_bais)
+
     call CNVTasks.PreprocessIntervals {
         input:
             intervals = intervals,
@@ -117,17 +128,21 @@ workflow CNVGermlineCaseWorkflow {
             preemptible_attempts = preemptible_attempts
     }
 
-    call CNVTasks.CollectCounts {
-        input:
-            intervals = PreprocessIntervals.preprocessed_intervals,
-            bam = bam,
-            bam_idx = bam_idx,
-            ref_fasta = ref_fasta,
-            ref_fasta_fai = ref_fasta_fai,
-            ref_fasta_dict = ref_fasta_dict,
-            gatk4_jar_override = gatk4_jar_override,
-            gatk_docker = gatk_docker,
-            preemptible_attempts = preemptible_attempts
+    scatter (normal_bam_and_bai in normal_bams_and_bais) {
+        call CNVTasks.CollectCounts {
+            input:
+                intervals = PreprocessIntervals.preprocessed_intervals,
+                bam = normal_bam_and_bai.left,
+                bam_idx = normal_bam_and_bai.right,
+                ref_fasta = ref_fasta,
+                ref_fasta_fai = ref_fasta_fai,
+                ref_fasta_dict = ref_fasta_dict,
+                format = collect_counts_format,
+                gatk4_jar_override = gatk4_jar_override,
+                gatk_docker = gatk_docker,
+                mem_gb = mem_gb_for_collect_counts,
+                preemptible_attempts = preemptible_attempts
+        }
     }
 
     call DetermineGermlineContigPloidyCaseMode {
@@ -138,6 +153,7 @@ workflow CNVGermlineCaseWorkflow {
             gatk_docker = gatk_docker,
             mem_gb = mem_gb_for_determine_germline_contig_ploidy,
             cpu = cpu_for_determine_germline_contig_ploidy,
+            disk_space_gb = disk_for_determine_germline_contig_ploidy,
             mapping_error_rate = ploidy_mapping_error_rate,
             sample_psi_scale = ploidy_sample_psi_scale,
             preemptible_attempts = preemptible_attempts
@@ -195,29 +211,37 @@ workflow CNVGermlineCaseWorkflow {
         }
     }
 
-    call CNVTasks.PostprocessGermlineCNVCalls {
-        input:
-            entity_id = CollectCounts.entity_id,
-            gcnv_calls_tars = GermlineCNVCallerCaseMode.gcnv_calls_tar,
-            gcnv_model_tars = gcnv_model_tars,
-            allosomal_contigs = allosomal_contigs,
-            ref_copy_number_autosomal_contigs = ref_copy_number_autosomal_contigs,
-            contig_ploidy_calls_tar = DetermineGermlineContigPloidyCaseMode.contig_ploidy_calls_tar,
-            sample_index = 0,
-            gatk4_jar_override = gatk4_jar_override,
-            gatk_docker = gatk_docker,
-            preemptible_attempts = preemptible_attempts
+    Array[Array[File]] call_tars_sample_by_shard = transpose(GermlineCNVCallerCaseMode.gcnv_call_tars)
+
+    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 = call_tars_sample_by_shard[sample_index],
+                gcnv_model_tars = gcnv_model_tars,
+                allosomal_contigs = allosomal_contigs,
+                ref_copy_number_autosomal_contigs = ref_copy_number_autosomal_contigs,
+                contig_ploidy_calls_tar = DetermineGermlineContigPloidyCaseMode.contig_ploidy_calls_tar,
+                sample_index = sample_index,
+                gatk4_jar_override = gatk4_jar_override,
+                gatk_docker = gatk_docker,
+                preemptible_attempts = preemptible_attempts
+        }
     }
 
     output {
         File preprocessed_intervals = PreprocessIntervals.preprocessed_intervals
-        File read_counts_entity_id = CollectCounts.entity_id
-        File read_counts = CollectCounts.counts
+        Array[File] read_counts_entity_id = CollectCounts.entity_id
+        Array[File] read_counts = CollectCounts.counts
         File contig_ploidy_calls_tar = DetermineGermlineContigPloidyCaseMode.contig_ploidy_calls_tar
-        Array[File] gcnv_calls_tars = GermlineCNVCallerCaseMode.gcnv_calls_tar
+        Array[Array[File]] gcnv_calls_tars = GermlineCNVCallerCaseMode.gcnv_call_tars
         Array[File] gcnv_tracking_tars = GermlineCNVCallerCaseMode.gcnv_tracking_tar
-        File genotyped_intervals_vcf = PostprocessGermlineCNVCalls.genotyped_intervals_vcf
-        File genotyped_segments_vcf = PostprocessGermlineCNVCalls.genotyped_segments_vcf
+        Array[File] genotyped_intervals_vcf = PostprocessGermlineCNVCalls.genotyped_intervals_vcf
+        Array[File] genotyped_segments_vcf = PostprocessGermlineCNVCalls.genotyped_segments_vcf
     }
 }
 
@@ -274,7 +298,7 @@ task DetermineGermlineContigPloidyCaseMode {
         memory: machine_mem_mb + " MB"
         disks: "local-disk " + select_first([disk_space_gb, 150]) + if use_ssd then " SSD" else " HDD"
         cpu: select_first([cpu, 8])
-        preemptible: select_first([preemptible_attempts, 2])
+        preemptible: select_first([preemptible_attempts, 5])
     }
 
     output {
@@ -340,6 +364,7 @@ task GermlineCNVCallerCaseMode {
     # If optional output_dir not specified, use "out"
     String output_dir_ = select_first([output_dir, "out"])
 
+    Int num_samples = length(read_count_files)
     command <<<
         set -e
         mkdir ${output_dir_}
@@ -390,7 +415,11 @@ task GermlineCNVCallerCaseMode {
             --caller-external-admixing-rate ${default="1.00" caller_external_admixing_rate} \
             --disable-annealing ${default="false" disable_annealing}
 
-        tar czf case-gcnv-calls-${scatter_index}.tar.gz -C ${output_dir_}/case-calls .
+        CURRENT_SAMPLE=0
+        while [ $CURRENT_SAMPLE -lt ${num_samples} ]; do
+            tar czf case-gcnv-shard-${scatter_index}-sample-$CURRENT_SAMPLE-gcnv-calls.tar.gz -C ${output_dir_}/case-calls/SAMPLE_$CURRENT_SAMPLE .
+            let CURRENT_SAMPLE=CURRENT_SAMPLE+1
+        done
         tar czf case-gcnv-tracking-${scatter_index}.tar.gz -C ${output_dir_}/case-tracking .
     >>>
 
@@ -399,11 +428,15 @@ task GermlineCNVCallerCaseMode {
         memory: machine_mem_mb + " MB"
         disks: "local-disk " + select_first([disk_space_gb, 150]) + if use_ssd then " SSD" else " HDD"
         cpu: select_first([cpu, 8])
-        preemptible: select_first([preemptible_attempts, 2])
+        preemptible: select_first([preemptible_attempts, 5])
     }
 
     output {
-        File gcnv_calls_tar = "case-gcnv-calls-${scatter_index}.tar.gz"
+        File calling_config_json = "${output_dir_}/case-calls/calling_config.json"
+        File denoising_config_json = "${output_dir_}/case-calls/denoising_config.json"
+        File gcnvkernel_version_json = "${output_dir_}/case-calls/gcnvkernel_version.json"
+        File sharded_interval_list = "${output_dir_}/case-calls/interval_list.tsv"
+        Array[File] gcnv_call_tars = glob("*-gcnv-calls.tar.gz")
         File gcnv_tracking_tar = "case-gcnv-tracking-${scatter_index}.tar.gz"
     }
 }
diff --git a/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl b/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl
index 8be52144d5c..e35b7c5fe44 100644
--- a/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl
+++ b/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl
@@ -29,8 +29,8 @@ workflow CNVGermlineCohortWorkflow {
     ##################################
     File intervals
     File? blacklist_intervals
-    Array[String] normal_bams
-    Array[String] normal_bais
+    Array[String]+ normal_bams
+    Array[String]+ normal_bais
     String cohort_entity_id
     File contig_ploidy_priors
     Int num_intervals_per_scatter
@@ -65,7 +65,7 @@ workflow CNVGermlineCohortWorkflow {
     ##############################################
     #### optional arguments for CollectCounts ####
     ##############################################
-    String? format
+    String? collect_counts_format
     Int? mem_gb_for_collect_counts
 
     ########################################################################
@@ -173,7 +173,7 @@ workflow CNVGermlineCohortWorkflow {
                 ref_fasta = ref_fasta,
                 ref_fasta_fai = ref_fasta_fai,
                 ref_fasta_dict = ref_fasta_dict,
-                format = format,
+                format = collect_counts_format,
                 gatk4_jar_override = gatk4_jar_override,
                 gatk_docker = gatk_docker,
                 mem_gb = mem_gb_for_collect_counts,
@@ -259,11 +259,17 @@ workflow CNVGermlineCohortWorkflow {
         }
     }
 
+    Array[Array[File]] call_tars_sample_by_shard = transpose(GermlineCNVCallerCohortMode.gcnv_call_tars)
+
     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_calls_tars = call_tars_sample_by_shard[sample_index],
                 gcnv_model_tars = GermlineCNVCallerCohortMode.gcnv_model_tar,
                 contig_ploidy_calls_tar = DetermineGermlineContigPloidyCohortMode.contig_ploidy_calls_tar,
                 allosomal_contigs = allosomal_contigs,
@@ -282,7 +288,7 @@ workflow CNVGermlineCohortWorkflow {
         File contig_ploidy_model_tar = DetermineGermlineContigPloidyCohortMode.contig_ploidy_model_tar
         File contig_ploidy_calls_tar = DetermineGermlineContigPloidyCohortMode.contig_ploidy_calls_tar
         Array[File] gcnv_model_tars = GermlineCNVCallerCohortMode.gcnv_model_tar
-        Array[File] gcnv_calls_tars = GermlineCNVCallerCohortMode.gcnv_calls_tar
+        Array[Array[File]] gcnv_calls_tars = GermlineCNVCallerCohortMode.gcnv_call_tars
         Array[File] gcnv_tracking_tars = GermlineCNVCallerCohortMode.gcnv_tracking_tar
         Array[File] genotyped_intervals_vcfs = PostprocessGermlineCNVCalls.genotyped_intervals_vcf
         Array[File] genotyped_segments_vcfs = PostprocessGermlineCNVCalls.genotyped_segments_vcf
@@ -420,6 +426,7 @@ task GermlineCNVCallerCohortMode {
 
     # If optional output_dir not specified, use "out"
     String output_dir_ = select_first([output_dir, "out"])
+    Int num_samples = length(read_count_files)
 
     command <<<
         set -e
@@ -480,7 +487,11 @@ task GermlineCNVCallerCohortMode {
             --disable-annealing ${default="false" disable_annealing}
 
         tar czf ${cohort_entity_id}-gcnv-model-${scatter_index}.tar.gz -C ${output_dir_}/${cohort_entity_id}-model .
-        tar czf ${cohort_entity_id}-gcnv-calls-${scatter_index}.tar.gz -C ${output_dir_}/${cohort_entity_id}-calls .
+        CURRENT_SAMPLE=0
+        while [ $CURRENT_SAMPLE -lt ${num_samples} ]; do
+            tar czf ${cohort_entity_id}-shard-${scatter_index}-sample-$CURRENT_SAMPLE-gcnv-calls.tar.gz -C ${output_dir_}/${cohort_entity_id}-calls/SAMPLE_$CURRENT_SAMPLE .
+            let CURRENT_SAMPLE=CURRENT_SAMPLE+1
+        done
         tar czf ${cohort_entity_id}-gcnv-tracking-${scatter_index}.tar.gz -C ${output_dir_}/${cohort_entity_id}-tracking .
     >>>
 
@@ -494,7 +505,11 @@ task GermlineCNVCallerCohortMode {
 
     output {
         File gcnv_model_tar = "${cohort_entity_id}-gcnv-model-${scatter_index}.tar.gz"
-        File gcnv_calls_tar = "${cohort_entity_id}-gcnv-calls-${scatter_index}.tar.gz"
+        File calling_config_json = "${output_dir_}/${cohort_entity_id}-calls/calling_config.json"
+        File denoising_config_json = "${output_dir_}/${cohort_entity_id}-calls/denoising_config.json"
+        File gcnvkernel_version_json = "${output_dir_}/${cohort_entity_id}-calls/gcnvkernel_version.json"
+        File sharded_interval_list = "${output_dir_}/${cohort_entity_id}-calls/interval_list.tsv"
+        Array[File] gcnv_call_tars = glob("*-gcnv-calls.tar.gz")
         File gcnv_tracking_tar = "${cohort_entity_id}-gcnv-tracking-${scatter_index}.tar.gz"
     }
 }
diff --git a/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl b/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl
index 1c837b006b6..73c2be6f8a3 100644
--- a/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl
+++ b/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl
@@ -66,7 +66,7 @@ workflow CNVSomaticPairWorkflow {
     ##############################################
     #### optional arguments for CollectCounts ####
     ##############################################
-    String? format
+    String? collect_counts_format
     Int? mem_gb_for_collect_counts
 
     #####################################################
@@ -165,7 +165,7 @@ workflow CNVSomaticPairWorkflow {
             ref_fasta = ref_fasta,
             ref_fasta_fai = ref_fasta_fai,
             ref_fasta_dict = ref_fasta_dict,
-            format = format,
+            format = collect_counts_format,
             gatk4_jar_override = gatk4_jar_override,
             gatk_docker = gatk_docker,
             mem_gb = mem_gb_for_collect_counts,
@@ -295,7 +295,7 @@ workflow CNVSomaticPairWorkflow {
                 ref_fasta = ref_fasta,
                 ref_fasta_fai = ref_fasta_fai,
                 ref_fasta_dict = ref_fasta_dict,
-                format = format,
+                format = collect_counts_format,
                 gatk4_jar_override = gatk4_jar_override,
                 gatk_docker = gatk_docker,
                 mem_gb = mem_gb_for_collect_counts,
diff --git a/scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl b/scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl
index 0163477110a..8048808d79a 100644
--- a/scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl
+++ b/scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl
@@ -66,7 +66,7 @@ workflow CNVSomaticPanelWorkflow {
     ##############################################
     #### optional arguments for CollectCounts ####
     ##############################################
-    String? format
+    String? collect_counts_format
     Int? mem_gb_for_collect_counts
 
     ##############################################################
@@ -125,7 +125,7 @@ workflow CNVSomaticPanelWorkflow {
                 ref_fasta = ref_fasta,
                 ref_fasta_fai = ref_fasta_fai,
                 ref_fasta_dict = ref_fasta_dict,
-                format = format,
+                format = collect_counts_format,
                 gatk4_jar_override = gatk4_jar_override,
                 gatk_docker = gatk_docker,
                 mem_gb = mem_gb_for_collect_counts,
diff --git a/src/main/python/org/broadinstitute/hellbender/gcnvkernel/postprocess/viterbi_segmentation.py b/src/main/python/org/broadinstitute/hellbender/gcnvkernel/postprocess/viterbi_segmentation.py
index 6660f6ef4df..e00c6cd04e9 100644
--- a/src/main/python/org/broadinstitute/hellbender/gcnvkernel/postprocess/viterbi_segmentation.py
+++ b/src/main/python/org/broadinstitute/hellbender/gcnvkernel/postprocess/viterbi_segmentation.py
@@ -21,11 +21,8 @@
 
 
 class ViterbiSegmentationEngine:
-    """This class runs the forward-backward and Viterbi algorithm on gCNV model/calls shards, obtains
-    constant copy-number segments, calculates various quality metrics, and saves the result to disk.
-
-    Note:
-        This class is callable. Upon calling, all samples in the call-set will be processed sequentially.
+    """This class runs the forward-backward and Viterbi algorithm on gCNV model/calls shards for a single sample,
+     obtains constant copy-number segments, calculates various quality metrics, and saves the result to disk.
 
     Note:
         It is assumed that the model and calls shards are provided in order according to the SAM sequence dictionary.
@@ -35,20 +32,23 @@ def __init__(self,
                  model_shards_paths: List[str],
                  calls_shards_paths: List[str],
                  sample_metadata_collection: SampleMetadataCollection,
+                 sample_index: int,
                  output_path: str):
         """Initializer.
         
         Args:
             model_shards_paths: list of paths to model shards
             calls_shards_paths: list of paths to calls shards
-            sample_metadata_collection: sample metadata collection (must contain all samples)
+            sample_metadata_collection: sample metadata collection (must contain sample being analyzed)
+            sample_index: index of the sample in the callset
             output_path: output path for writing segmentation results
         """
         try:
-            self._validate_args(model_shards_paths, calls_shards_paths, sample_metadata_collection)
+            self._validate_args(model_shards_paths, calls_shards_paths, sample_metadata_collection, sample_index)
         except AssertionError as ex:
             raise Exception("Inconsistency detected in the provided model and calls shards.") from ex
 
+        self.sample_index = sample_index
         self.output_path = output_path
         self.calls_shards_paths = calls_shards_paths
         self.sample_metadata_collection = sample_metadata_collection
@@ -69,8 +69,7 @@ def __init__(self,
             os.path.join(model_shards_paths[0], io_consts.default_interval_list_filename))
 
         # sample names
-        self.sample_names = self._get_sample_names_from_calls_shard(calls_shards_paths[0])
-        self.num_samples = len(self.sample_names)
+        self.sample_name = self._get_sample_name_from_calls_shard(calls_shards_paths[0], sample_index)
 
         # interval list metadata
         interval_list_metadata: IntervalListMetadata = IntervalListMetadata(self.interval_list)
@@ -107,50 +106,23 @@ def __init__(self,
         self.get_copy_number_hmm_specs = HHMMClassAndCopyNumberBasicCaller\
             .get_compiled_copy_number_hmm_specs_theano_func()
 
-    def __call__(self):
-        """Perform Viterbi segmentation for all samples, calculates segment qualities and writes the results
-        to disk.
-        """
-        io_commons.assert_output_path_writable(self.output_path)
-
-        # write configs and gcnvkernel version to output path
-        shutil.copy(os.path.join(self.calls_shards_paths[0], io_consts.default_denoising_config_json_filename),
-                    self.output_path)
-        shutil.copy(os.path.join(self.calls_shards_paths[0], io_consts.default_calling_config_json_filename),
-                    self.output_path)
-        io_commons.write_gcnvkernel_version(self.output_path)
-
-        # write concatenated interval list to output path
-        io_intervals_and_counts.write_interval_list_to_tsv_file(
-            os.path.join(self.output_path, io_consts.default_interval_list_filename),
-            self.interval_list,
-            self.interval_list_sam_header_lines)
-
-        for si in range(self.num_samples):
-            self.write_copy_number_segments_for_single_sample(si)
-
-    def _viterbi_segments_generator_for_single_sample(self, sample_index: int)\
-            -> Generator[IntegerCopyNumberSegment, None, None]:
+    def _viterbi_segments_generator(self) -> Generator[IntegerCopyNumberSegment, None, None]:
         """Performs Viterbi segmentation and segment quality calculation for a single sample in
         the call-set and returns a generator for segments.
 
-        Args:
-            sample_index: index of the sample in the collection
-
         Returns:
             a generator for segments
         """
-        assert 0 <= sample_index < self.num_samples, "Sample index is out of range."
 
         # load copy number log emission for the sample
         copy_number_log_emission_tc_shards = ()
         for calls_path in self.calls_shards_paths:
             copy_number_log_emission_tc_shards += (self._get_log_copy_number_emission_tc_from_calls_shard(
-                calls_path, sample_index),)
+                calls_path, self.sample_index),)
         copy_number_log_emission_tc = np.concatenate(copy_number_log_emission_tc_shards, axis=0)
 
         # iterate over contigs and perform segmentation
-        sample_name = self.sample_names[sample_index]
+        sample_name = self.sample_name
         for contig_index, contig in enumerate(self.ordered_contig_list):
             _logger.info("Segmenting contig ({0}/{1}) (contig name: {2})...".format(
                 contig_index + 1, len(self.ordered_contig_list), contig))
@@ -228,17 +200,14 @@ def _viterbi_segments_generator_for_single_sample(self, sample_index: int)\
 
                 yield segment
 
-    def write_copy_number_segments_for_single_sample(self, sample_index: int):
+    def write_copy_number_segments(self):
         """Performs Viterbi segmentation and segment quality calculation for a single sample in
         the call-set and saves the results to disk.
 
-        Args:
-            sample_index: sample index in the call-set
         """
-        assert 0 <= sample_index < self.num_samples, "Sample index is out of range."
-        sample_name = self.sample_names[sample_index]
-        _logger.info("Processing sample index: {0}, sample name: {1}...".format(sample_index, sample_name))
-        sample_output_path = os.path.join(self.output_path, io_consts.sample_folder_prefix + repr(sample_index))
+        sample_name = self.sample_name
+        _logger.info("Processing sample index: {0}, sample name: {1}...".format(self.sample_index, sample_name))
+        sample_output_path = os.path.join(self.output_path, io_consts.sample_folder_prefix + repr(self.sample_index))
         io_commons.assert_output_path_writable(sample_output_path, try_creating_output_path=True)
 
         # write configs, gcnvkernel version and sample name to output path
@@ -262,19 +231,21 @@ def write_copy_number_segments_for_single_sample(self, sample_index: int):
             of.write(IntegerCopyNumberSegment.get_header_column_string() + '\n')
 
             # add segments
-            for segment in self._viterbi_segments_generator_for_single_sample(sample_index):
+            for segment in self._viterbi_segments_generator():
                 of.write(repr(segment) + '\n')
 
     @staticmethod
     def _validate_args(model_shards_paths: List[str],
                        calls_shards_paths: List[str],
-                       sample_metadata_collection: SampleMetadataCollection):
+                       sample_metadata_collection: SampleMetadataCollection,
+                       sample_index: int):
         assert len(model_shards_paths) > 0, "At least one model shard must be provided."
         assert len(calls_shards_paths) == len(model_shards_paths),\
             "The number of model shards ({0}) and calls shards ({1}) must match.".format(
                 len(model_shards_paths), len(calls_shards_paths))
+        assert sample_index >= 0, "Sample index must be an integer non-negative number"
 
-        scattered_sample_names: List[Tuple[str]] = []
+        scattered_sample_names: List[str] = []
         for model_path, calls_path in zip(model_shards_paths, calls_shards_paths):
             # assert interval lists are identical
             model_interval_list_file = os.path.join(model_path, io_consts.default_interval_list_filename)
@@ -308,7 +279,8 @@ def _validate_args(model_shards_paths: List[str],
                                 "proceeding at your own risk!")
 
             # extract and store sample names for the current shard
-            scattered_sample_names.append(ViterbiSegmentationEngine._get_sample_names_from_calls_shard(calls_path))
+            scattered_sample_names.append(
+                ViterbiSegmentationEngine._get_sample_name_from_calls_shard(calls_path, sample_index))
 
         # all scattered calls have the same set of samples and in the same order
         assert len(set(scattered_sample_names)) == 1,\
@@ -319,19 +291,13 @@ def _validate_args(model_shards_paths: List[str],
         sample_metadata_collection.all_samples_have_ploidy_metadata(sample_names)
 
     @staticmethod
-    def _get_sample_names_from_calls_shard(calls_path: str) -> Tuple[str]:
-        sample_names: Tuple[str] = ()
-        sample_index = 0
-        while True:
-            sample_posteriors_path = io_denoising_calling.get_sample_posterior_path(calls_path, sample_index)
-            if not os.path.isdir(sample_posteriors_path):
-                break
-            sample_names += (io_commons.get_sample_name_from_txt_file(sample_posteriors_path),)
-            sample_index += 1
-        if len(sample_names) == 0:
-            raise Exception("Could not find any sample posterior calls in {0}.".format(calls_path))
-        else:
-            return tuple(sample_names)
+    def _get_sample_name_from_calls_shard(calls_path: str, sample_index: int) -> str:
+        sample_posteriors_path = io_denoising_calling.get_sample_posterior_path(calls_path, sample_index)
+        if not os.path.isdir(sample_posteriors_path):
+            raise Exception("Could not find any sample posterior calls in {0} for sample with index {1}.".
+                            format(calls_path, sample_index))
+        sample_name = io_commons.get_sample_name_from_txt_file(sample_posteriors_path)
+        return sample_name
 
     @staticmethod
     def _get_denoising_config(input_path: str) -> DenoisingModelConfig:
diff --git a/src/main/resources/org/broadinstitute/hellbender/tools/copynumber/segment_gcnv_calls.py b/src/main/resources/org/broadinstitute/hellbender/tools/copynumber/segment_gcnv_calls.py
index 49db66f4076..f38631a7c9f 100644
--- a/src/main/resources/org/broadinstitute/hellbender/tools/copynumber/segment_gcnv_calls.py
+++ b/src/main/resources/org/broadinstitute/hellbender/tools/copynumber/segment_gcnv_calls.py
@@ -69,5 +69,5 @@
     logger.debug("Calls shards path(s): {0}".format(repr(args.model_shards)))
 
     viterbi_engine = gcnvkernel.ViterbiSegmentationEngine(
-        args.model_shards, args.calls_shards, sample_metadata_collection, args.output_path)
-    viterbi_engine.write_copy_number_segments_for_single_sample(args.sample_index)
+        args.model_shards, args.calls_shards, sample_metadata_collection, args.sample_index, args.output_path)
+    viterbi_engine.write_copy_number_segments()
diff --git a/src/test/resources/large/cnv_germline_workflows_test_files/ice_targets_chr20xy.interval_list b/src/test/resources/large/cnv_germline_workflows_test_files/ice_targets_chr20xy.interval_list
index 99384de09ae..ceefea343a4 100755
--- a/src/test/resources/large/cnv_germline_workflows_test_files/ice_targets_chr20xy.interval_list
+++ b/src/test/resources/large/cnv_germline_workflows_test_files/ice_targets_chr20xy.interval_list
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:28cf6de883c0ce48de84df15e2cb65758658fcb801ddd1a705562b481563bd69
-size 8916
+oid sha256:19dbffe91b7662dc8210f74568a6ea3e44bb40f3902b00f35af6b089522fdb16
+size 2120
diff --git a/src/test/resources/large/cnv_germline_workflows_test_files/wes-contig-ploidy-model.tar.gz b/src/test/resources/large/cnv_germline_workflows_test_files/wes-contig-ploidy-model.tar.gz
index 51c3e7373b8..866bd3914f3 100644
--- a/src/test/resources/large/cnv_germline_workflows_test_files/wes-contig-ploidy-model.tar.gz
+++ b/src/test/resources/large/cnv_germline_workflows_test_files/wes-contig-ploidy-model.tar.gz
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:b18af3fa8aeed18c517c9aec2fac5cba80f948f8a50f1c50172621bdb7ff1c8f
-size 2187
+oid sha256:78190124c8d8e344d92d4530846641664f556eacd48584f29f8e3722a6833622
+size 1244
diff --git a/src/test/resources/large/cnv_germline_workflows_test_files/wes-do-gc-gcnv-model-0.tar.gz b/src/test/resources/large/cnv_germline_workflows_test_files/wes-do-gc-gcnv-model-0.tar.gz
index 211ef2f000d..df120d29127 100644
--- a/src/test/resources/large/cnv_germline_workflows_test_files/wes-do-gc-gcnv-model-0.tar.gz
+++ b/src/test/resources/large/cnv_germline_workflows_test_files/wes-do-gc-gcnv-model-0.tar.gz
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:d0c811739714898a6a3e848cd32a07a3688ef9c03f7414095daa6b45ab75ead1
-size 19238
+oid sha256:b258ab287c70c063a0bfc28bd18210e44b7551269b09a525656e97cd5c6530e4
+size 6771
diff --git a/src/test/resources/large/cnv_germline_workflows_test_files/wes-do-gc-gcnv-model-1.tar.gz b/src/test/resources/large/cnv_germline_workflows_test_files/wes-do-gc-gcnv-model-1.tar.gz
index 84899b69eea..9d7204b1e22 100644
--- a/src/test/resources/large/cnv_germline_workflows_test_files/wes-do-gc-gcnv-model-1.tar.gz
+++ b/src/test/resources/large/cnv_germline_workflows_test_files/wes-do-gc-gcnv-model-1.tar.gz
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:9c8396faea3e3852e820f580d9e9e14ad3c4ee91711f215f090def5addaf1696
-size 11727
+oid sha256:26169b480ec60ff7ac4ad5d0f8fe2c396a4eb20a6e06dff71ac96a5c678a12b0
+size 3336