-Enforced ViterbiSegmentationEngine to analyze single samples only

-Added multi-sample functionality to gCNV case mode WDL, and added a wrapper for gCNV case mode WDL to help optimize cloud computation cost. Also optimized how data is sent to postprocessing task in gCNV WDLs.

.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;

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"
+}