Fixed bug issue #1063, Updated cromwell version in travis.yml to v26,…

… added gCNV wdl files, set up travis testing of the gCNV WDL workflows, created gCNV template input files and gCNV resources directory

.travis.yml

@@ -7,10 +7,11 @@ jdk:
 
 env:
   matrix:
-  - RUN_CNV_SOMATIC_WDL=true TEST_DOCKER=false RUN_M2_WDL=false
-  - RUN_CNV_SOMATIC_WDL=false TEST_DOCKER=false RUN_M2_WDL=false
-  - RUN_CNV_SOMATIC_WDL=false TEST_DOCKER=true RUN_M2_WDL=false
-  - RUN_CNV_SOMATIC_WDL=false TEST_DOCKER=false RUN_M2_WDL=true
+  - RUN_CNV_SOMATIC_WDL=true RUN_CNV_GERMLINE_WDL=false TEST_DOCKER=false RUN_M2_WDL=false
+  - RUN_CNV_SOMATIC_WDL=false RUN_CNV_GERMLINE_WDL=false TEST_DOCKER=false RUN_M2_WDL=false
+  - RUN_CNV_SOMATIC_WDL=false RUN_CNV_GERMLINE_WDL=false TEST_DOCKER=true RUN_M2_WDL=false
+  - RUN_CNV_SOMATIC_WDL=false RUN_CNV_GERMLINE_WDL=false TEST_DOCKER=false RUN_M2_WDL=true
+  - RUN_CNV_SOMATIC_WDL=false RUN_CNV_GERMLINE_WDL=true TEST_DOCKER=false RUN_M2_WDL=false
   global:
   #limit gradle jvm memory usage
   - GRADLE_OPTS=-Xmx512m
@@ -30,16 +31,16 @@ before_install:
 # Install git-lfs, and fetch the large test files
 - sudo bash scripts/install_git_lfs.sh
 # Download Cromwell jar
-- if [[ $RUN_CNV_SOMATIC_WDL == true ]] || [[ $RUN_M2_WDL == true ]]; then
-    wget -O ~/cromwell-0.25.jar https://github.com/broadinstitute/cromwell/releases/download/25/cromwell-25.jar;
+- if [[ $RUN_CNV_SOMATIC_WDL == true ]] || [[ $RUN_CNV_GERMLINE_WDL == true ]] || [[ $RUN_M2_WDL == true ]]; then
+    wget -O ~/cromwell-0.26.jar https://github.com/broadinstitute/cromwell/releases/download/26/cromwell-26.jar;
   fi
 # Download Picard jar
 - if [[ $RUN_M2_WDL == true ]]; then
     wget -O ~/picard.jar https://github.com/broadinstitute/picard/releases/download/2.9.0/picard.jar;
   fi
 
 install:
-- if [[ $RUN_CNV_SOMATIC_WDL == true ]]; then 
+- if [[ $RUN_CNV_SOMATIC_WDL == true ]] || [[ $RUN_CNV_GERMLINE_WDL == true ]]; then
     ./gradlew shadowJar;
   elif [[$RUN_M2_WDL == true ]]; then
     ./gradlew shaowJar;
@@ -54,6 +55,9 @@ script:
 - if [[ $RUN_CNV_SOMATIC_WDL == true ]]; then
     echo "Running CNV somatic workflows";
     bash scripts/cnv_cromwell_tests/somatic/run_cnv_somatic_workflows.sh;
+  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_M2_WDL == true ]]; then
     sudo bash scripts/m2_cromwell_tests/run_m2_wdl.sh;
   elif [[ $TEST_DOCKER == true ]]; then
@@ -67,7 +71,7 @@ script:
   fi
 
 after_success:
-- if [[ $RUN_CNV_SOMATIC_WDL == false ]] && [[ $TEST_DOCKER == false ]] && [[ $RUN_M2_WDL == false ]]; then
+- if [[ $RUN_CNV_SOMATIC_WDL == false ]] && [[ $RUN_CNV_GERMLINE_WDL == false ]] && [[ $TEST_DOCKER == false ]] && [[ $RUN_M2_WDL == false ]]; then
     ./gradlew jacocoTestReport coveralls;
   fi
 

scripts/cnv_cromwell_tests/germline/gCNV_cohort_calling_workflow_wes.json

@@ -0,0 +1,19 @@
+{
+  "gCNVCohortCallingWorkflow.normal_bams_list": "/home/travis/build/broadinstitute/gatk-protected/scripts/cnv_cromwell_tests/germline/normal_bam_list.tsv",
+  "gCNVCohortCallingWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.fasta.fai",
+  "gCNVCohortCallingWorkflow.num_latents": "2", 
+  "gCNVCohortCallingWorkflow.sex_genotypes": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/inputs/sex_genotypes.tsv", 
+  "gCNVCohortCallingWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.fasta",
+  "gCNVCohortCallingWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.dict",
+  "gCNVCohortCallingWorkflow.gatk_jar": "/home/travis/build/broadinstitute/gatk-protected/build/libs/gatk-protected.jar",
+  "gCNVCohortCallingWorkflow.targets": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/inputs/ice_targets_chr20xy.tsv",
+  "gCNVCohortCallingWorkflow.contig_ploidy_annotations": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/contig_annots.tsv",
+  "gCNVCohortCallingWorkflow.transition_prior_table": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_priors.tsv",
+  "gCNVCohortCallingWorkflow.copy_number_transition_prior_files": [ "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_autosomal.tsv",
+                                                                    "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XY_X.tsv",
+                                                                    "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_Y.tsv",
+                                                                    "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_X.tsv",
+                                                                    "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XY_Y.tsv" ],
+  "gCNVCohortCallingWorkflow.model_path": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/model_final/",
+  "gCNVCohortCallingWorkflow.output_path": "output"
+}

scripts/cnv_cromwell_tests/germline/gCNV_cohort_calling_workflow_wgs.json

@@ -0,0 +1,18 @@
+{
+  "gCNVCohortCallingWorkflow.normal_bams_list": "/home/travis/build/broadinstitute/gatk-protected/scripts/cnv_cromwell_tests/germline/normal_bam_list.tsv",
+  "gCNVCohortCallingWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.fasta.fai",
+  "gCNVCohortCallingWorkflow.num_latents": "1", 
+  "gCNVCohortCallingWorkflow.sex_genotypes": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/inputs/sex_genotypes.tsv", 
+  "gCNVCohortCallingWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.fasta",
+  "gCNVCohortCallingWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.dict",
+  "gCNVCohortCallingWorkflow.gatk_jar": "/home/travis/build/broadinstitute/gatk-protected/build/libs/gatk-protected.jar",
+  "gCNVCohortCallingWorkflow.contig_ploidy_annotations": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/contig_annots.tsv",
+  "gCNVCohortCallingWorkflow.transition_prior_table": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_priors.tsv",
+  "gCNVCohortCallingWorkflow.copy_number_transition_prior_files": [ "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_autosomal.tsv",
+                                                                    "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XY_X.tsv",
+                                                                    "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_Y.tsv",
+                                                                    "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_X.tsv",
+                                                                    "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XY_Y.tsv" ],
+  "gCNVCohortCallingWorkflow.model_path": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/inputs/wgs_pon/model_final/",
+  "gCNVCohortCallingWorkflow.output_path": "output"
+}

scripts/cnv_cromwell_tests/germline/gCNV_panel_creation_workflow_wes.json

@@ -0,0 +1,19 @@
+{ 
+  "CNVGermlinePanelWorkflow.gatk_jar": "/home/travis/build/broadinstitute/gatk-protected/build/libs/gatk-protected.jar", 
+  "CNVGermlinePanelWorkflow.sex_genotypes": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/inputs/sex_genotypes.tsv",
+  "CNVGermlinePanelWorkflow.contig_ploidy_annotations": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/contig_annots.tsv",
+  "CNVGermlinePanelWorkflow.transition_prior_table": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_priors.tsv",
+  "CNVGermlinePanelWorkflow.copy_number_transition_prior_files": [ "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_autosomal.tsv",
+                                                                    "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XY_X.tsv",
+                                                                    "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_Y.tsv",
+                                                                    "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_X.tsv",
+                                                                    "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XY_Y.tsv" ],
+  "CNVGermlinePanelWorkflow.num_latents": "2", 
+  "CNVGermlinePanelWorkflow.targets": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/inputs/ice_targets_chr20xy.tsv",
+  "CNVGermlinePanelWorkflow.CollectCoverage.disable_all_read_filters": "false", 
+  "CNVGermlinePanelWorkflow.normal_bams_list": "/home/travis/build/broadinstitute/gatk-protected/scripts/cnv_cromwell_tests/germline/normal_bam_list.tsv", 
+  "CNVGermlinePanelWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.fasta.fai",
+  "CNVGermlinePanelWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.dict", 
+  "CNVGermlinePanelWorkflow.pon_output_path": "test_pon",
+  "CNVGermlinePanelWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.fasta"
+}

scripts/cnv_cromwell_tests/germline/gCNV_panel_creation_workflow_wgs.json

@@ -0,0 +1,18 @@
+{ 
+  "CNVGermlinePanelWorkflow.gatk_jar": "/home/travis/build/broadinstitute/gatk-protected/build/libs/gatk-protected.jar", 
+  "CNVGermlinePanelWorkflow.sex_genotypes": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/inputs/sex_genotypes.tsv",
+  "CNVGermlinePanelWorkflow.contig_ploidy_annotations": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/contig_annots.tsv",
+  "CNVGermlinePanelWorkflow.transition_prior_table": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_priors.tsv",
+  "CNVGermlinePanelWorkflow.copy_number_transition_prior_files": [ "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_autosomal.tsv",
+                                                                    "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XY_X.tsv",
+                                                                    "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_Y.tsv",
+                                                                    "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_X.tsv",
+                                                                    "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XY_Y.tsv" ],
+  "CNVGermlinePanelWorkflow.num_latents": "1",
+  "CNVGermlinePanelWorkflow.CollectCoverage.disable_all_read_filters": "false", 
+  "CNVGermlinePanelWorkflow.normal_bams_list": "/home/travis/build/broadinstitute/gatk-protected/scripts/cnv_cromwell_tests/germline/normal_bam_list.tsv", 
+  "CNVGermlinePanelWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.fasta.fai",
+  "CNVGermlinePanelWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.dict", 
+  "CNVGermlinePanelWorkflow.pon_output_path": "test_pon",
+  "CNVGermlinePanelWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.fasta"
+}

scripts/cnv_cromwell_tests/germline/gCNV_single_sample_calling_workflow_wes.json

@@ -0,0 +1,20 @@
+{
+  "gCNVSingleSampleWorkflow.normal_bam": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/inputs/bams/SM-74NEG_20xy-downsampled.bam",
+  "gCNVSingleSampleWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.fasta.fai",
+  "gCNVSingleSampleWorkflow.normal_bam_idx": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/inputs/bams/SM-74NEG_20xy-downsampled.bam.bai",
+  "gCNVSingleSampleWorkflow.num_latents": "2", 
+  "gCNVSingleSampleWorkflow.sex_genotypes": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/inputs/sex_genotypes.tsv", 
+  "gCNVSingleSampleWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.fasta",
+  "gCNVSingleSampleWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.dict",
+  "gCNVSingleSampleWorkflow.gatk_jar": "/home/travis/build/broadinstitute/gatk-protected/build/libs/gatk-protected.jar",
+  "gCNVSingleSampleWorkflow.targets": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/inputs/ice_targets_chr20xy.tsv",
+  "gCNVSingleSampleWorkflow.contig_ploidy_annotations": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/contig_annots.tsv",
+  "gCNVSingleSampleWorkflow.transition_prior_table": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_priors.tsv",
+  "gCNVSingleSampleWorkflow.copy_number_transition_prior_files": [ "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_autosomal.tsv",
+                                                                    "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XY_X.tsv",
+                                                                    "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_Y.tsv",
+                                                                    "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_X.tsv",
+                                                                    "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XY_Y.tsv" ],
+  "gCNVSingleSampleWorkflow.model_path": "/home/travis/build/broadinstitute/gatk-protected/src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/model_final/",
+  "gCNVSingleSampleWorkflow.output_path": "output"
+}