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Merged
asmirnov239 merged 1 commit into from
Jun 12, 2017
Merged

Added germline CNV WDL workflows #3071

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10 changes: 7 additions & 3 deletions .travis.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@ env:
- TEST_TYPE=unit TEST_DOCKER=true TEST_VERBOSITY=minimal
- RUN_CNV_SOMATIC_WDL=true
- RUN_M2_WDL=true
- RUN_CNV_GERMLINE_WDL=true
global:
#for genomics db
- LD_LIBRARY_PATH=$TRAVIS_BUILD_DIR/dependencies/libcsv/.libs
Expand Down Expand Up @@ -73,8 +74,8 @@ before_install:
sudo Rscript scripts/docker/gatkbase/install_R_packages.R;
fi
# 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_M2_WDL == true || $RUN_CNV_GERMLINE_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
Expand All @@ -90,7 +91,7 @@ install:
else
./gradlew assemble;
./gradlew installDist;
if [[ $RUN_CNV_SOMATIC_WDL == true || $RUN_M2_WDL == true ]]; then
if [[ $RUN_CNV_SOMATIC_WDL == true || $RUN_M2_WDL == true || $RUN_CNV_GERMLINE_WDL == true ]]; then
echo "building a shadow jar for the wdl";
./gradlew shadowJar;
fi
Expand All @@ -103,6 +104,9 @@ script:
elif [[ $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
echo "Running M2 WDL";
sudo bash scripts/m2_cromwell_tests/run_m2_wdl.sh;
Expand Down
19 changes: 19 additions & 0 deletions scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_calling_workflow_wes.json
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{
"gCNVCohortCallingWorkflow.normal_bams_list": "/home/travis/build/broadinstitute/gatk/scripts/cnv_cromwell_tests/germline/normal_bam_list.tsv",
"gCNVCohortCallingWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/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/src/test/resources/large/cnv_germline_workflows_test_files/inputs/sex_genotypes.tsv",
"gCNVCohortCallingWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.fasta",
"gCNVCohortCallingWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.dict",
"gCNVCohortCallingWorkflow.gatk_jar": "/home/travis/build/broadinstitute/gatk/build/libs/gatk.jar",
"gCNVCohortCallingWorkflow.targets": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/inputs/ice_targets_chr20xy.tsv",
"gCNVCohortCallingWorkflow.contig_ploidy_annotations": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/contig_annots.tsv",
"gCNVCohortCallingWorkflow.transition_prior_table": "/home/travis/build/broadinstitute/gatk/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/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_autosomal.tsv",
"/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XY_X.tsv",
"/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_Y.tsv",
"/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_X.tsv",
"/home/travis/build/broadinstitute/gatk/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/src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/model_final/",
"gCNVCohortCallingWorkflow.output_path": "output"
}
18 changes: 18 additions & 0 deletions scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_calling_workflow_wgs.json
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{
"gCNVCohortCallingWorkflow.normal_bams_list": "/home/travis/build/broadinstitute/gatk/scripts/cnv_cromwell_tests/germline/normal_bam_list.tsv",
"gCNVCohortCallingWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/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/src/test/resources/large/cnv_germline_workflows_test_files/inputs/sex_genotypes.tsv",
"gCNVCohortCallingWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.fasta",
"gCNVCohortCallingWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.dict",
"gCNVCohortCallingWorkflow.gatk_jar": "/home/travis/build/broadinstitute/gatk/build/libs/gatk.jar",
"gCNVCohortCallingWorkflow.contig_ploidy_annotations": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/contig_annots.tsv",
"gCNVCohortCallingWorkflow.transition_prior_table": "/home/travis/build/broadinstitute/gatk/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/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_autosomal.tsv",
"/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XY_X.tsv",
"/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_Y.tsv",
"/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_X.tsv",
"/home/travis/build/broadinstitute/gatk/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/src/test/resources/large/cnv_germline_workflows_test_files/inputs/wgs_pon/model_final/",
"gCNVCohortCallingWorkflow.output_path": "output"
}
18 changes: 18 additions & 0 deletions scripts/cnv_cromwell_tests/germline/cnv_germline_panel_creation_workflow_wes.json
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{
"CNVGermlinePanelWorkflow.gatk_jar": "/home/travis/build/broadinstitute/gatk/build/libs/gatk.jar",
"CNVGermlinePanelWorkflow.sex_genotypes": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/inputs/sex_genotypes.tsv",
"CNVGermlinePanelWorkflow.contig_ploidy_annotations": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/contig_annots.tsv",
"CNVGermlinePanelWorkflow.transition_prior_table": "/home/travis/build/broadinstitute/gatk/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/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_autosomal.tsv",
"/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XY_X.tsv",
"/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_Y.tsv",
"/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_X.tsv",
"/home/travis/build/broadinstitute/gatk/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/src/test/resources/large/cnv_germline_workflows_test_files/inputs/ice_targets_chr20xy.tsv",
"CNVGermlinePanelWorkflow.normal_bams_list": "/home/travis/build/broadinstitute/gatk/scripts/cnv_cromwell_tests/germline/normal_bam_list.tsv",
"CNVGermlinePanelWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/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/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/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.fasta"
}
17 changes: 17 additions & 0 deletions scripts/cnv_cromwell_tests/germline/cnv_germline_panel_creation_workflow_wgs.json
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{
"CNVGermlinePanelWorkflow.gatk_jar": "/home/travis/build/broadinstitute/gatk/build/libs/gatk.jar",
"CNVGermlinePanelWorkflow.sex_genotypes": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/inputs/sex_genotypes.tsv",
"CNVGermlinePanelWorkflow.contig_ploidy_annotations": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/contig_annots.tsv",
"CNVGermlinePanelWorkflow.transition_prior_table": "/home/travis/build/broadinstitute/gatk/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/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_autosomal.tsv",
"/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XY_X.tsv",
"/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_Y.tsv",
"/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_X.tsv",
"/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XY_Y.tsv" ],
"CNVGermlinePanelWorkflow.num_latents": "1",
"CNVGermlinePanelWorkflow.normal_bams_list": "/home/travis/build/broadinstitute/gatk/scripts/cnv_cromwell_tests/germline/normal_bam_list.tsv",
"CNVGermlinePanelWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/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/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/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.fasta"
}
20 changes: 20 additions & 0 deletions scripts/cnv_cromwell_tests/germline/cnv_germline_single_sample_calling_workflow_wes.json
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{
"gCNVSingleSampleWorkflow.normal_bam": "/home/travis/build/broadinstitute/gatk/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/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/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/src/test/resources/large/cnv_germline_workflows_test_files/inputs/sex_genotypes.tsv",
"gCNVSingleSampleWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.fasta",
"gCNVSingleSampleWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.dict",
"gCNVSingleSampleWorkflow.gatk_jar": "/home/travis/build/broadinstitute/gatk/build/libs/gatk.jar",
"gCNVSingleSampleWorkflow.targets": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/inputs/ice_targets_chr20xy.tsv",
"gCNVSingleSampleWorkflow.contig_ploidy_annotations": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/contig_annots.tsv",
"gCNVSingleSampleWorkflow.transition_prior_table": "/home/travis/build/broadinstitute/gatk/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/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_autosomal.tsv",
"/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XY_X.tsv",
"/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_Y.tsv",
"/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_X.tsv",
"/home/travis/build/broadinstitute/gatk/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/src/test/resources/large/cnv_germline_workflows_test_files/inputs/wes_pon/model_final/",
"gCNVSingleSampleWorkflow.output_path": "output"
}
19 changes: 19 additions & 0 deletions scripts/cnv_cromwell_tests/germline/cnv_germline_single_sample_calling_workflow_wgs.json
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{
"gCNVSingleSampleWorkflow.normal_bam": "/home/travis/build/broadinstitute/gatk/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/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/src/test/resources/large/cnv_germline_workflows_test_files/inputs/bams/SM-74NEG_20xy-downsampled.bam.bai",
"gCNVSingleSampleWorkflow.num_latents": "1",
"gCNVSingleSampleWorkflow.sex_genotypes": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/inputs/sex_genotypes.tsv",
"gCNVSingleSampleWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.fasta",
"gCNVSingleSampleWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/Homo_sapiens_assembly19.truncated.dict",
"gCNVSingleSampleWorkflow.gatk_jar": "/home/travis/build/broadinstitute/gatk/build/libs/gatk.jar",
"gCNVSingleSampleWorkflow.contig_ploidy_annotations": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/contig_annots.tsv",
"gCNVSingleSampleWorkflow.transition_prior_table": "/home/travis/build/broadinstitute/gatk/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/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_autosomal.tsv",
"/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XY_X.tsv",
"/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_Y.tsv",
"/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/resources/homo_sapiens_germline_CN_transition_matrix_XX_X.tsv",
"/home/travis/build/broadinstitute/gatk/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/src/test/resources/large/cnv_germline_workflows_test_files/inputs/wgs_pon/model_final/",
"gCNVSingleSampleWorkflow.output_path": "output"
}
3 changes: 3 additions & 0 deletions scripts/cnv_cromwell_tests/germline/normal_bam_list.tsv
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/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/inputs/bams/SM-74NEG_20xy-downsampled.bam /home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/inputs/bams/SM-74NEG_20xy-downsampled.bam.bai
/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/inputs/bams/SM-74P2T_20xy-downsampled.bam /home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/inputs/bams/SM-74P2T_20xy-downsampled.bam.bai
/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/inputs/bams/SM-74P35_20xy-downsampled.bam /home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_germline_workflows_test_files/inputs/bams/SM-74P35_20xy-downsampled.bam.bai
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