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mwalker174mwalker174
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Second round of MakeCohortVcf updates from gnomAD (#288)
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‎dockerfiles/sv-pipeline-base/Dockerfile‎

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@@ -49,7 +49,7 @@ ARG CONDA_DEP_TRANSIENT="make git wget"
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ARG CONDA_DEP="software-properties-common zlib1g-dev libbz2-dev liblzma-dev libcurl4-openssl-dev libssl-dev libblas-dev liblapack-dev libatlas-base-dev g++ gfortran ${CONDA_DEP_TRANSIENT}"
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# versions of bedtools > 2.27.0 seem to have lost the ability to read gzipped files
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# pandas 1.0.0 causes problem with bedtools in aggregate.py
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ARG PYTHON_PKGS="setuptools=52.0.0 wheel=0.34.2 bzip2=1.0.8 cython=0.29.14 numpy=1.18.1 pandas=0.25.3 scikit-learn=0.22.1 scipy=1.4.1 intervaltree=3.0.2 matplotlib=3.1.3 natsort=7.0.1 bedtools=2.27.0 pybedtools=0.8.1 pysam=0.14.1=py36_htslib1.7_0"
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ARG PYTHON_PKGS="pip=21.2.2 setuptools=52.0.0 wheel=0.34.2 bzip2=1.0.8 cython=0.29.14 numpy=1.18.1 pandas=0.25.3 scikit-learn=0.22.1 scipy=1.4.1 intervaltree=3.0.2 matplotlib=3.1.3 natsort=7.0.1 bedtools=2.27.0 pybedtools=0.8.1 pysam=0.14.1=py36_htslib1.7_0"
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ENV LANG=C.UTF-8
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ENV LC_ALL=C.UTF-8
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ARG CONDA_INSTALL_DIR="/opt/conda"

‎dockerfiles/sv-pipeline-hail/Dockerfile‎

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# GATK SV Pipeline Hail dockerfile
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# IMPORTANT: these arguments must be specified at the begining to take advantage of multi-stage build AND runtime specification of base images
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ARG SV_PIPELINE_IMAGE=gatksv/sv-pipeline:latest
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FROM ${SV_PIPELINE_IMAGE}
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# Dependencies for creating a Hail cluster on GCS DataProc
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RUN pip3 --no-cache-dir install hail==0.2.71 && \
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pip3 --no-cache-dir install google-cloud-dataproc \

‎dockerfiles/sv-pipeline/Dockerfile‎

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@@ -48,3 +48,51 @@ RUN apt-get -qqy update --fix-missing && \
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/usr/share/man/?? \
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/usr/share/man/??_*
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ENV PATH="/opt/:${PATH}"
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# Compile StitchFragmentedCNVs Java program
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ENV STITCH_JAR="/opt/sv-pipeline/java/build/StitchFragmentedCNVs.jar"
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RUN cd /opt/sv-pipeline/java && \
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mkdir -p build/classes && \
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javac -d build/classes org/broadinstitute/svpipeline/StitchFragmentedCNVs.java org/broadinstitute/svpipeline/VCFParser.java && \
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jar cfe build/StitchFragmentedCNVs.jar "org.broadinstitute.svpipeline.StitchFragmentedCNVs" -C build/classes . && \
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rm -r build/classes
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# Compile StitchFragmentedCNVs unit tests
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ENV STITCH_UNIT_TEST_JAR="/opt/sv-pipeline/java/build/StitchFragmentedCNVsUnitTest.jar"
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RUN cd /opt/sv-pipeline/java && \
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mkdir -p build/classes && \
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javac -d build/classes org/broadinstitute/svpipeline/StitchFragmentedCNVsUnitTest.java org/broadinstitute/svpipeline/StitchFragmentedCNVs.java org/broadinstitute/svpipeline/VCFParser.java && \
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jar cfe build/StitchFragmentedCNVsUnitTest.jar "org.broadinstitute.svpipeline.StitchFragmentedCNVsUnitTest" -C build/classes . && \
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echo "Running StitchFragmentedCNVsUnitTest..." && \
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java -enableassertions -jar $STITCH_UNIT_TEST_JAR && \
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rm -r build/classes $STITCH_UNIT_TEST_JAR
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# Compile VCFParser unit tests
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ENV VCF_PARSER_UNIT_TEST_JAR="/opt/sv-pipeline/java/build/VCFParserUnitTest.jar"
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RUN cd /opt/sv-pipeline/java && \
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mkdir -p build/classes && \
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javac -d build/classes org/broadinstitute/svpipeline/VCFParserUnitTest.java org/broadinstitute/svpipeline/VCFParser.java && \
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jar cfe build/VCFParserUnitTest.jar "org.broadinstitute.svpipeline.VCFParserUnitTest" -C build/classes . && \
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echo "Running VCFParserUnitTest..." && \
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java -enableassertions -jar $VCF_PARSER_UNIT_TEST_JAR && \
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rm -r build/classes $VCF_PARSER_UNIT_TEST_JAR
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# Compile and test CleanVCFPart1 Java program
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ENV CLEAN_VCF_PART_1_JAR="/opt/sv-pipeline/java/build/CleanVCFPart1.jar"
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RUN cd /opt/sv-pipeline/java && \
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mkdir -p build/classes && \
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javac -d build/classes org/broadinstitute/svpipeline/CleanVCFPart1.java org/broadinstitute/svpipeline/VCFParser.java && \
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jar cfe build/CleanVCFPart1.jar "org.broadinstitute.svpipeline.CleanVCFPart1" -C build/classes . && \
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rm -r build/classes
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# Compile and test CleanVCFPart1 unit tests
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ENV CLEAN_VCF_PART_1_UNIT_TEST_JAR="/opt/sv-pipeline/java/build/CleanVCFPart1UnitTest.jar"
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RUN cd /opt/sv-pipeline/java && \
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mkdir -p build/classes && \
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javac -d build/classes org/broadinstitute/svpipeline/CleanVCFPart1UnitTest.java org/broadinstitute/svpipeline/CleanVCFPart1.java org/broadinstitute/svpipeline/VCFParser.java && \
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jar cfe build/CleanVCFPart1UnitTest.jar "org.broadinstitute.svpipeline.CleanVCFPart1UnitTest" -C build/classes . && \
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echo "Running CleanVCFPart1UnitTest..." && \
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java -enableassertions -jar $CLEAN_VCF_PART_1_UNIT_TEST_JAR && \
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rm -r build/classes $CLEAN_VCF_PART_1_UNIT_TEST_JAR && \
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rm -rf /tmp/* /var/tmp/*
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‎input_templates/GATKSVPipelineBatch.ref_panel_1kg.json.tmpl‎

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"GATKSVPipelineBatch.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }},
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"GATKSVPipelineBatch.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
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"GATKSVPipelineBatch.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
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"GATKSVPipelineBatch.sv_pipeline_hail_docker": {{ dockers.sv_pipeline_hail_docker | tojson }},
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"GATKSVPipelineBatch.sv_pipeline_updates_docker": {{ dockers.sv_pipeline_updates_docker | tojson }},
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"GATKSVPipelineBatch.sv_pipeline_qc_docker": {{ dockers.sv_pipeline_qc_docker | tojson }},
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"GATKSVPipelineBatch.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }},
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"GATKSVPipelineBatch.samtools_cloud_docker": {{ dockers.samtools_cloud_docker | tojson }},
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"GATKSVPipelineBatch.RegenotypeCNVs.n_RdTest_bins": "100000",
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"GATKSVPipelineBatch.RegenotypeCNVs.n_per_split": "5000",
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"GATKSVPipelineBatch.MakeCohortVcf.chr_x": {{ reference_resources.chr_x | tojson }},
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"GATKSVPipelineBatch.MakeCohortVcf.chr_y": {{ reference_resources.chr_y | tojson }},
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"GATKSVPipelineBatch.MakeCohortVcf.bin_exclude": {{ reference_resources.bin_exclude | tojson }},
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"GATKSVPipelineBatch.MakeCohortVcf.empty_file" : {{ reference_resources.empty_file | tojson }},
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"GATKSVPipelineBatch.MakeCohortVcf.cytobands": {{ reference_resources.cytobands | tojson }},
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"GATKSVPipelineBatch.MakeCohortVcf.min_sr_background_fail_batches": 0.5,
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"GATKSVPipelineBatch.MakeCohortVcf.max_shards_per_chrom_clean_vcf_step1": 200,
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"GATKSVPipelineBatch.MakeCohortVcf.min_records_per_shard_clean_vcf_step1": 5000,
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"GATKSVPipelineBatch.MakeCohortVcf.clean_vcf1b_records_per_shard": 10000,
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"GATKSVPipelineBatch.MakeCohortVcf.samples_per_clean_vcf_step2_shard": 100,
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"GATKSVPipelineBatch.MakeCohortVcf.clean_vcf5_records_per_shard": 5000,
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"GATKSVPipelineBatch.MakeCohortVcf.random_seed": 0,
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"GATKSVPipelineBatch.MakeCohortVcf.max_shard_size_resolve": 500,
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‎input_templates/GATKSVPipelineSingleSample.ref_panel_1kg.na12878.json.tmpl‎

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"GATKSVPipelineSingleSample.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }},
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"GATKSVPipelineSingleSample.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
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"GATKSVPipelineSingleSample.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
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"GATKSVPipelineSingleSample.sv_pipeline_hail_docker": {{ dockers.sv_pipeline_hail_docker | tojson }},
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"GATKSVPipelineSingleSample.sv_pipeline_updates_docker": {{ dockers.sv_pipeline_updates_docker | tojson }},
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"GATKSVPipelineSingleSample.sv_pipeline_qc_docker": {{ dockers.sv_pipeline_qc_docker | tojson }},
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"GATKSVPipelineSingleSample.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }},
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"GATKSVPipelineSingleSample.wham_docker": {{ dockers.wham_docker | tojson }},
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"GATKSVPipelineSingleSample.max_shard_size_resolve" : 500,
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"GATKSVPipelineSingleSample.clean_vcf_max_shards_per_chrom_clean_vcf_step1": 200,
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"GATKSVPipelineSingleSample.clean_vcf_min_records_per_shard_clean_vcf_step1": 5000,
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"GATKSVPipelineSingleSample.clean_vcf1b_records_per_shard": 10000,
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"GATKSVPipelineSingleSample.clean_vcf_samples_per_clean_vcf_step2_shard": 100,
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"GATKSVPipelineSingleSample.clean_vcf5_records_per_shard": 5000,
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"GATKSVPipelineSingleSample.clean_vcf_random_seed": 0,
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"GATKSVPipelineSingleSample.run_vcf_qc" : false,
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‎input_templates/GATKSVPipelineSingleSample.ref_panel_1kg.na12878.no_melt.json.tmpl‎

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"GATKSVPipelineSingleSample.sv_pipeline_base_docker": {{ dockers.sv_pipeline_base_docker | tojson }},
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"GATKSVPipelineSingleSample.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
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"GATKSVPipelineSingleSample.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }},
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"GATKSVPipelineSingleSample.sv_pipeline_hail_docker": {{ dockers.sv_pipeline_hail_docker | tojson }},
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"GATKSVPipelineSingleSample.sv_pipeline_updates_docker": {{ dockers.sv_pipeline_updates_docker | tojson }},
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"GATKSVPipelineSingleSample.sv_pipeline_qc_docker": {{ dockers.sv_pipeline_qc_docker | tojson }},
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"GATKSVPipelineSingleSample.sv_pipeline_rdtest_docker": {{ dockers.sv_pipeline_rdtest_docker | tojson }},
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"GATKSVPipelineSingleSample.wham_docker": {{ dockers.wham_docker | tojson }},
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"GATKSVPipelineSingleSample.max_shard_size_resolve" : 500,
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"GATKSVPipelineSingleSample.clean_vcf_max_shards_per_chrom_clean_vcf_step1": 200,
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"GATKSVPipelineSingleSample.clean_vcf_min_records_per_shard_clean_vcf_step1": 5000,
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"GATKSVPipelineSingleSample.clean_vcf1b_records_per_shard": 10000,
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"GATKSVPipelineSingleSample.clean_vcf_samples_per_clean_vcf_step2_shard": 100,
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"GATKSVPipelineSingleSample.clean_vcf_random_seed": 0,
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"GATKSVPipelineSingleSample.clean_vcf5_records_per_shard": 5000,
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"GATKSVPipelineSingleSample.run_vcf_qc" : false,
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"GATKSVPipelineSingleSample.protein_coding_gtf" : {{ reference_resources.protein_coding_gtf | tojson }},

‎input_templates/terra_workspaces/cohort_mode/workflow_configurations/MakeCohortVcf.SingleBatch.json.tmpl‎

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"MakeCohortVcf.min_sr_background_fail_batches": 0.5,
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"MakeCohortVcf.max_shards_per_chrom_clean_vcf_step1": 200,
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"MakeCohortVcf.min_records_per_shard_clean_vcf_step1": 5000,
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"MakeCohortVcf.clean_vcf1b_records_per_shard": 10000,
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"MakeCohortVcf.clean_vcf5_records_per_shard": 5000,
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"MakeCohortVcf.samples_per_clean_vcf_step2_shard": 100,
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"MakeCohortVcf.random_seed": 0,
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"MakeCohortVcf.max_shard_size_resolve": 500,
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"MakeCohortVcf.linux_docker": "${workspace.linux_docker}",
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"MakeCohortVcf.sv_pipeline_docker": "${workspace.sv_pipeline_docker}",
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"MakeCohortVcf.sv_pipeline_hail_docker": "${workspace.sv_pipeline_hail_docker}",
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"MakeCohortVcf.sv_pipeline_updates_docker": "${workspace.sv_pipeline_updates_docker}",
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"MakeCohortVcf.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
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"MakeCohortVcf.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}",
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"MakeCohortVcf.sv_pipeline_qc_docker": "${workspace.sv_pipeline_qc_docker}",
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"MakeCohortVcf.primary_contigs_list": "${workspace.primary_contigs_list}",
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"MakeCohortVcf.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
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"MakeCohortVcf.chr_x": "${workspace.chr_x}",
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"MakeCohortVcf.chr_y": "${workspace.chr_y}",
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"MakeCohortVcf.cohort_name": "${this.sample_set_id}",
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"MakeCohortVcf.batches": "${this.sample_set_id}",
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"MakeCohortVcf.ped_file": "${workspace.cohort_ped_file}",

‎input_templates/terra_workspaces/cohort_mode/workflow_configurations/MakeCohortVcf.json.tmpl‎

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"MakeCohortVcf.min_sr_background_fail_batches": 0.5,
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"MakeCohortVcf.max_shards_per_chrom_clean_vcf_step1": 200,
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"MakeCohortVcf.min_records_per_shard_clean_vcf_step1": 5000,
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"MakeCohortVcf.clean_vcf1b_records_per_shard": 10000,
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"MakeCohortVcf.clean_vcf5_records_per_shard": 5000,
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"MakeCohortVcf.samples_per_clean_vcf_step2_shard": 100,
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"MakeCohortVcf.random_seed": 0,
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"MakeCohortVcf.max_shard_size_resolve": 500,
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"MakeCohortVcf.linux_docker": "${workspace.linux_docker}",
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"MakeCohortVcf.sv_pipeline_docker": "${workspace.sv_pipeline_docker}",
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"MakeCohortVcf.sv_pipeline_hail_docker": "${workspace.sv_pipeline_hail_docker}",
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"MakeCohortVcf.sv_pipeline_updates_docker": "${workspace.sv_pipeline_updates_docker}",
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"MakeCohortVcf.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
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"MakeCohortVcf.sv_pipeline_rdtest_docker": "${workspace.sv_pipeline_rdtest_docker}",
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"MakeCohortVcf.sv_pipeline_qc_docker": "${workspace.sv_pipeline_qc_docker}",
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"MakeCohortVcf.primary_contigs_list": "${workspace.primary_contigs_list}",
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"MakeCohortVcf.sv_pipeline_base_docker": "${workspace.sv_pipeline_base_docker}",
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"MakeCohortVcf.chr_x": "${workspace.chr_x}",
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"MakeCohortVcf.chr_y": "${workspace.chr_y}",
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"MakeCohortVcf.cohort_name": "${this.sample_set_set_id}",
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"MakeCohortVcf.batches": "${this.sample_sets.sample_set_id}",
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"MakeCohortVcf.ped_file": "${workspace.cohort_ped_file}",

‎input_templates/terra_workspaces/cohort_mode/workspace.tsv.tmpl‎

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workspace:cloud_sdk_docker cnmops_docker condense_counts_docker gatk_docker gatk_docker_pesr_override gcnv_gatk_docker genomes_in_the_cloud_docker linux_docker manta_docker samtools_cloud_docker sv_base_docker sv_base_mini_docker sv_pipeline_base_docker sv_pipeline_docker sv_pipeline_qc_docker sv_pipeline_rdtest_docker wham_docker allosome_file autosome_file bin_exclude cnmops_exclude_list cohort_ped_file contig_ploidy_priors copy_number_autosomal_contigs cytobands dbsnp_vcf delly_exclude_intervals_file depth_exclude_list empty_file exclude_intervals_for_gcnv_filter_intervals external_af_ref_bed external_af_ref_bed_prefix genome_file inclusion_bed linc_rna_gtf manta_region_bed mei_bed melt_standard_vcf_header noncoding_bed pesr_exclude_list preprocessed_intervals primary_contigs_fai primary_contigs_list promoter_bed protein_coding_gtf reference_build reference_dict reference_fasta reference_index reference_version rmsk segdups seed_cutoffs unpadded_intervals_file wgd_scoring_mask wham_include_list_bed_file
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{{ dockers.cloud_sdk_docker }} {{ dockers.cnmops_docker }} {{ dockers.condense_counts_docker }} {{ dockers.gatk_docker }} {{ dockers.gatk_docker_pesr_override }} {{ dockers.gatk_docker }} {{ dockers.genomes_in_the_cloud_docker }} {{ dockers.linux_docker }} {{ dockers.manta_docker }} {{ dockers.samtools_cloud_docker }} {{ dockers.sv_base_docker }} {{ dockers.sv_base_mini_docker }} {{ dockers.sv_pipeline_base_docker }} {{ dockers.sv_pipeline_docker }} {{ dockers.sv_pipeline_qc_docker }} {{ dockers.sv_pipeline_rdtest_docker }} {{ dockers.wham_docker }} {{ reference_resources.allosome_file }} {{ reference_resources.autosome_file }} {{ reference_resources.bin_exclude }} {{ reference_resources.cnmops_exclude_list }} gs://broad-dsde-methods-eph/ped_1kgp_all.ped {{ reference_resources.contig_ploidy_priors }} {{ reference_resources.copy_number_autosomal_contigs }} {{ reference_resources.cytobands }} {{ reference_resources.dbsnp_vcf }} {{ reference_resources.delly_exclude_intervals_file }} {{ reference_resources.depth_exclude_list }} {{ reference_resources.empty_file }} {{ reference_resources.exclude_intervals_for_gcnv_filter_intervals }} {{ reference_resources.external_af_ref_bed | tojson }} {{ reference_resources.external_af_ref_bed_prefix | tojson }} {{ reference_resources.genome_file }} {{ reference_resources.inclusion_bed }} {{ reference_resources.linc_rna_gtf | tojson }} {{ reference_resources.manta_region_bed }} {{ reference_resources.mei_bed }} {{ reference_resources.melt_std_vcf_header }} {{ reference_resources.noncoding_bed | tojson }} {{ reference_resources.pesr_exclude_list }} {{ reference_resources.preprocessed_intervals }} {{ reference_resources.primary_contigs_fai }} {{ reference_resources.primary_contigs_list }} {{ reference_resources.promoter_bed | tojson }} {{ reference_resources.protein_coding_gtf | tojson }} {{ reference_resources.reference_build }} {{ reference_resources.reference_dict }} {{ reference_resources.reference_fasta }} {{ reference_resources.reference_index }} {{ reference_resources.reference_version }} {{ reference_resources.rmsk }} {{ reference_resources.segdups }} {{ reference_resources.seed_cutoffs }} {{ reference_resources.unpadded_intervals_file }} {{ reference_resources.wgd_scoring_mask }} {{ reference_resources.wham_include_list_bed_file }}
1+
workspace:cloud_sdk_docker cnmops_docker condense_counts_docker gatk_docker gatk_docker_pesr_override gcnv_gatk_docker genomes_in_the_cloud_docker linux_docker manta_docker samtools_cloud_docker sv_base_docker sv_base_mini_docker sv_pipeline_base_docker sv_pipeline_docker sv_pipeline_hail_docker sv_pipeline_updates_docker sv_pipeline_qc_docker sv_pipeline_rdtest_docker wham_docker allosome_file autosome_file bin_exclude cnmops_exclude_list cohort_ped_file contig_ploidy_priors copy_number_autosomal_contigs cytobands dbsnp_vcf delly_exclude_intervals_file depth_exclude_list empty_file exclude_intervals_for_gcnv_filter_intervals external_af_ref_bed external_af_ref_bed_prefix genome_file inclusion_bed linc_rna_gtf manta_region_bed mei_bed melt_standard_vcf_header noncoding_bed pesr_exclude_list preprocessed_intervals primary_contigs_fai primary_contigs_list promoter_bed protein_coding_gtf reference_build reference_dict reference_fasta reference_index reference_version rmsk segdups seed_cutoffs unpadded_intervals_file wgd_scoring_mask wham_include_list_bed_file chr_x chr_y
2+
{{ dockers.cloud_sdk_docker }} {{ dockers.cnmops_docker }} {{ dockers.condense_counts_docker }} {{ dockers.gatk_docker }} {{ dockers.gatk_docker_pesr_override }} {{ dockers.gatk_docker }} {{ dockers.genomes_in_the_cloud_docker }} {{ dockers.linux_docker }} {{ dockers.manta_docker }} {{ dockers.samtools_cloud_docker }} {{ dockers.sv_base_docker }} {{ dockers.sv_base_mini_docker }} {{ dockers.sv_pipeline_base_docker }} {{ dockers.sv_pipeline_docker }} {{ dockers.sv_pipeline_hail_docker }} {{ dockers.sv_pipeline_updates_docker }} {{ dockers.sv_pipeline_qc_docker }} {{ dockers.sv_pipeline_rdtest_docker }} {{ dockers.wham_docker }} {{ reference_resources.allosome_file }} {{ reference_resources.autosome_file }} {{ reference_resources.bin_exclude }} {{ reference_resources.cnmops_exclude_list }} gs://broad-dsde-methods-eph/ped_1kgp_all.ped {{ reference_resources.contig_ploidy_priors }} {{ reference_resources.copy_number_autosomal_contigs }} {{ reference_resources.cytobands }} {{ reference_resources.dbsnp_vcf }} {{ reference_resources.delly_exclude_intervals_file }} {{ reference_resources.depth_exclude_list }} {{ reference_resources.empty_file }} {{ reference_resources.exclude_intervals_for_gcnv_filter_intervals }} {{ reference_resources.external_af_ref_bed | tojson }} {{ reference_resources.external_af_ref_bed_prefix | tojson }} {{ reference_resources.genome_file }} {{ reference_resources.inclusion_bed }} {{ reference_resources.linc_rna_gtf | tojson }} {{ reference_resources.manta_region_bed }} {{ reference_resources.mei_bed }} {{ reference_resources.melt_std_vcf_header }} {{ reference_resources.noncoding_bed | tojson }} {{ reference_resources.pesr_exclude_list }} {{ reference_resources.preprocessed_intervals }} {{ reference_resources.primary_contigs_fai }} {{ reference_resources.primary_contigs_list }} {{ reference_resources.promoter_bed | tojson }} {{ reference_resources.protein_coding_gtf | tojson }} {{ reference_resources.reference_build }} {{ reference_resources.reference_dict }} {{ reference_resources.reference_fasta }} {{ reference_resources.reference_index }} {{ reference_resources.reference_version }} {{ reference_resources.rmsk }} {{ reference_resources.segdups }} {{ reference_resources.seed_cutoffs }} {{ reference_resources.unpadded_intervals_file }} {{ reference_resources.wgd_scoring_mask }} {{ reference_resources.wham_include_list_bed_file }} {{ reference_resources.chr_x }} {{ reference_resources.chr_y }}

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